Running as unit: rb-build-arm64_8-80494.service ==================================================================================== Fri Aug 1 00:58:26 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_8) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Fri Aug 1 00:58:26 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-gDBDduAF" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Aug 1 00:58:26 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Aug 1 00:58:26 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-qvjmUB' Fri Aug 1 00:58:27 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Aug 1 00:58:27 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-8SoJml' ok, let's check if wham-align is building anywhere yet… ok, wham-align is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of wham-align in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Fri Aug 1 00:58:29 UTC 2025 I: starting to build wham-align/unstable/arm64 on jenkins on '2025-08-01 00:58' Fri Aug 1 00:58:29 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/80494/console.log 1754009909 arm64 unstable wham-align Fri Aug 1 00:58:29 UTC 2025 I: Downloading source for unstable/wham-align=0.1.5-8 --2025-08-01 00:58:29-- http://deb.debian.org/debian/pool/main/w/wham-align/wham-align_0.1.5-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1987 (1.9K) [text/prs.lines.tag] Saving to: ‘wham-align_0.1.5-8.dsc’ 0K . 100% 249M=0s 2025-08-01 00:58:29 (249 MB/s) - ‘wham-align_0.1.5-8.dsc’ saved [1987/1987] --2025-08-01 00:58:29-- http://deb.debian.org/debian/pool/main/w/wham-align/wham-align_0.1.5-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1987 (1.9K) [text/prs.lines.tag] Saving to: ‘wham-align_0.1.5-8.dsc’ 0K . 100% 249M=0s 2025-08-01 00:58:29 (249 MB/s) - ‘wham-align_0.1.5-8.dsc’ saved [1987/1987] Fri Aug 1 00:58:29 UTC 2025 I: wham-align_0.1.5-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: wham-align Binary: wham-align Architecture: any Version: 0.1.5-8 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: http://research.cs.wisc.edu/wham Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/wham-align Vcs-Git: https://salsa.debian.org/med-team/wham-align.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: wham-align deb science optional arch=any Checksums-Sha1: e1ecc46d4ab3af47518fbdee4b8efab2c7a89bb9 120296 wham-align_0.1.5.orig.tar.gz 773e0fe0987dacc59f7eeb4a11b66e8b400a74e8 7760 wham-align_0.1.5-8.debian.tar.xz Checksums-Sha256: c020b999c0d4a3a8e29b32e91dba559b6d6ce3a221081212689c9662828d7b02 120296 wham-align_0.1.5.orig.tar.gz 414f05ebb057aad00779ec62fa010f9df2ac81f9d031851df88402ec72ccd4c3 7760 wham-align_0.1.5-8.debian.tar.xz Files: 56e14e483b0fed5ae5faa4d1621ee3d7 120296 wham-align_0.1.5.orig.tar.gz 5d5a8e7882d16a4347f47248d1b377f7 7760 wham-align_0.1.5-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmAvZR4UHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafH2gA//fckzTQTiwUZf+XYyH1wB8Khwg4aM qqcCFWQwcmOuLjzEAUGL26lHaKFm/LUU4GOfeiIICDIqwZ5JKXk+gtokc1yEicnm RN+hitekv0pBWrygGsc+vFhN6gC5arEGqvBJ7MUzelqFeWGXVdPPcoX6klcqzrj6 Tbac4SUJW4JC70/19v8xi+zMeVIMNVsnNMHVR9uwx0WSwTYZt3ZjC2OM98djorq+ yuv4aMkY5jL3zpgHCom7Icz5PvKqA5mbk/W5ju25ps/fOYlFJ2N2DW5vw9ZjbwJV 7sSQUQNV2lXbDpZ7tH2U0ZP537SmIF9O3ZwkKZnUPKlZ8FEK0wJrV7xSQPJQoB6w XdG97OgGo5c4cWTnUQEVaWK+8Ya3vzVXEiyr67rqRXizsLkRzhB9AD/Nwnoz+Srq /E5gcVKWX1gSvj7VGOaYkzttJzvoXunwQinY9KCktiOe8Nyp/keiudRrl02xENNj Uhg+ptkOT98rdTr038I7R2VPpZY51tH5xFgzHaDRtBSjFIvOMalE7EARs65asQJK ljzu0Zi3DFc4E1OfxPufWiVlSf5xYRbPLBlPG2ZCqqNqkbo6il3F4Wp+juIvqpOy onOqu0tFOLm1nbedZgCTu0UKWGC8x3VgKOhBSyJRAbjEr9eDg3NGqk5pjRv39FCg ub8XgN1tkdDDVhE= =2pK9 -----END PGP SIGNATURE----- Fri Aug 1 00:58:29 UTC 2025 I: Checking whether the package is not for us Fri Aug 1 00:58:29 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Fri Aug 1 00:58:29 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Fri Aug 1 00:58:29 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Aug 1 00:58:29 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-nFYuqX' ==================================================================================== Fri Aug 1 00:58:30 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 wham-align unstable /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk 0.1.5-8" as arguments. Fri Aug 1 00:58:30 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-mSKqkSl0" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Aug 1 00:58:30 UTC 2025 I: Downloading source for unstable/wham-align=0.1.5-8 Reading package lists... NOTICE: 'wham-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/wham-align.git Please use: git clone https://salsa.debian.org/med-team/wham-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 130 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (dsc) [1987 B] Get:2 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (tar) [120 kB] Get:3 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (diff) [7760 B] Fetched 130 kB in 0s (2055 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'wham-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/wham-align.git Please use: git clone https://salsa.debian.org/med-team/wham-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 130 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (dsc) [1987 B] Get:2 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (tar) [120 kB] Get:3 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (diff) [7760 B] Fetched 130 kB in 0s (2055 kB/s) Download complete and in download only mode ============================================================================= Building wham-align in unstable on arm64 on codethink04-arm64 now. Date: Fri Aug 1 01:58:31 BST 2025 Date UTC: Fri Aug 1 00:58:31 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 31 12:58:31 -12 2025 I: pbuilder-time-stamp: 1754009911 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [wham-align_0.1.5-8.dsc] I: copying [./wham-align_0.1.5.orig.tar.gz] I: copying [./wham-align_0.1.5-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./wham-align_0.1.5-8.dsc: no acceptable signature found dpkg-source: info: extracting wham-align in wham-align-0.1.5 dpkg-source: info: unpacking wham-align_0.1.5.orig.tar.gz dpkg-source: info: unpacking wham-align_0.1.5-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile.patch dpkg-source: info: applying non-x86.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying cross-build.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/343008/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='7f8c17cfd97a456aa773f7c1d84f4c19' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='343008' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/pbuilderrc_25AF --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/343008/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After unpacking 44.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Fetched 11.0 MB in 0s (103 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_arm64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5' rm -f wham wham-build *.o make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/wham-align.substvars debian/files rm -fr -- debian/wham-align/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hash.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings embedhash.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings main.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hitset.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp error.cpp: In function 'void elog(int, char*, ...)': error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable] 31 | char *filename = __FILE__; | ^~~~~~~~ error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] 32 | int lineno = __LINE__; | ^~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp short.cpp: In member function 'int ShortRead::preProcess(int)': short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 212 | while (len = readLine(file, str, 256)) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 483 | if (szPartition <= nRead - curRead) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)': model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable] 76 | unsigned int nIndex, nLookup, nBucket; | ^~~~~~ model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()': model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 166 | fscanf(file, "MemTotal: %d kB\n", &memTotal); | ~^ ~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 167 | fscanf(file, "MemFree: %d kB\n", &memFree); | ~^ ~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 168 | fscanf(file, "Buffers: %d kB\n", &memBuffer); | ~^ ~~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 169 | fscanf(file, "Cached: %d kB\n", &memCache); | ~^ ~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] 198 | double nSpace, p0, p1, p2; | ^~ In file included from hitset.h:31, from writer.h:26, from writer.cpp:21: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] 148 | uint32 sid = 0, soffset = 0; | ^~~ writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] 148 | uint32 sid = 0, soffset = 0; | ^~~~~~~ writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^~~~~~~~ writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] 272 | int64 code1, code2; | ^~~~~ writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] 272 | int64 code1, code2; | ^~~~~ writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] 278 | double p, sump; | ^ writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] 278 | double p, sump; | ^~~~ writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] 279 | char qseq[128], rseq[128], tag[128]; | ^~~ writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] 281 | char shortread[256]; | ^~~~~~~~~ writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { | ~~^~~~~~~~~~~~~~~ writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { | ~~^~~~~~~~~~~~~~~ writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { | ~~~~~^~~~~~~ In file included from hitset.h:31, from hitset.cpp:1: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] 90 | bool pairMatch = false; | ^~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from hash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from aligner.cpp:25: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from embedhash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 67 | for (int i = 0; i < numLevel - 1; i++) { | ~~^~~~~~~~~~~~~~ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ interval.cpp: In member function 'int IntervalTree::save(char*)': interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 304 | if (ret != numLEntry) { | ~~~~^~~~~~~~~~~~ interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 310 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ interval.cpp: In member function 'int IntervalTree::load(char*)': interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 359 | if (ret != numLEntry) { | ~~~~^~~~~~~~~~~~ interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 370 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] 61 | int i; | ^ edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] 181 | char tmp_trace = traceback[i][j]; | ^~~~~~~~~ edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] 132 | int k = 0, x = 0, y = 0; | ^ edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] 132 | int k = 0, x = 0, y = 0; | ^ edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] 178 | int kk = 0; | ^~ short.cpp: In member function 'int ShortRead::load(int)': short.cpp:424:28: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] 424 | forward_word = (forward_word << BITS_PER_BASE) | code; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp:310:38: note: 'code' was declared here 310 | int64 forward_word, backward_word, code; | ^~~~ short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ^~ short.cpp:503:42: note: directive argument in the range [0, 2147483646] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ^~~~~~~~ short.cpp:503:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ^~ short.cpp:510:42: note: directive argument in the range [0, 2147483646] 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ^~~~~~~~ short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from builder.cpp:31: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from sequence.cpp:30: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] 97 | char * str; | ^~~ sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 238 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 309 | ( i = 0; i < nSeq; i++) | ~~^~~~~~ sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 324 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 344 | for (j = 0; j < numError + 1; j++) { | ~~^~~~~~~~~~~~~~ sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 410 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 429 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~ sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~~~~~ sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 599 | if (lenSegmentN > nError + 1) | ~~~~~~~~~~~~^~~~~~~~~~~~ sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] 520 | unsigned int step, nextstep; | ^~~~ sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] 520 | unsigned int step, nextstep; | ^~~~~~~~ sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~~ sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~~ sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~ sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~ sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~ sequence.cpp: In member function 'int CompactSequence::save(char*)': sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 738 | if (ret != size) { | ~~~~^~~~~~~ sequence.cpp: In member function 'int CompactSequence::load(char*)': sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 804 | if (ret != size) { | ~~~~^~~~~~~ hash.cpp: In member function 'int HashTable::preProcessEnd()': hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] 236 | if (h >= nHistogram) | ~~^~~~~~~~~~~~~ hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] 285 | if (useEmbedTables() && tmp > embedShreshold) { | ~~~~^~~~~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::setScanThreshold(double)': hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 343 | for (int i = 0; i < nHistogram - 1; i++) { | ~~^~~~~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 460 | overflowPool[curOverflowEntry] = hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] 411 | uint32 seqOffset; | ^~~~~~~~~ hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] 413 | uint32 counter = 0; | ^~~~~~~ hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 414 | int64 * seqVector; | ^~~~~~~~~ hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] 416 | int64 * target = &tspace[8]; | ^~~~~~ hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] 417 | bool isBloomFilter; | ^~~~~~~~~~~~~ hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] 418 | uint32 * bloomFilter; | ^~~~~~~~~~~ hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 419 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ hash.cpp: In member function 'int HashTable::buildEmbedTable()': hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], | ^~~~ hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], | ^~~~~ hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; | ^~~~~ hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; | ^~~~~~~~~ hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 472 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)': hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable] 587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] 746 | int num; | ^~~ hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~ hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] 973 | int64 * seqVector = sequence->getSequence(); | ^~~~~~~~~ hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] 1052 | int num; | ^~~ hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable] 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable] 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~~~ hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 1057 | int64 * seqVector; | ^~~~~~~~~ hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~ hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~~~~~ hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)': hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++) hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++) hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1247 | for (int j = 0; j < strlen(set[i].str); j++) | ~~^~~~~~~~~~~~~~~~~~~~ hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1254 | for (int j = 0; j < strlen(set[i].str); j++) | ~~^~~~~~~~~~~~~~~~~~~~ hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp: In member function 'int HashTable::sortList()': hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable] 1430 | uint32 * pool; | ^~~~ hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1321 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ aligner.cpp: In member function 'int Aligner::initLookupArray()': aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 365 | if ((indexBits[i] >> j) & 0x1 == 1) { | ~~~~^~~~ aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 371 | if ((indexBits[i] >> j) & 0x1 == 1) { | ~~~~^~~~ hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1673 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ aligner.cpp: In member function 'int Aligner::preProcessHashTables()': aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 712 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp: In member function 'int Aligner::build(char*)': aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] 724 | unsigned int i, j; | ^ aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] 724 | unsigned int i, j; | ^ aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 807 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 983 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1006 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] 137 | const double ln2 = log(2); | ^~~ embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)': embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable] 253 | int64 sum = 0; | ^~~ embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] 255 | int64 top = total - total * r; | ^~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] 1035 | uint32 offset; | ^~~~~~ embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)': embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 369 | overflowPool[curOverflowEntry] = embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable] 328 | uint32 seqOffset; | ^~~~~~~~~ aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] 1039 | int nHit = 0; | ^~~~ embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable] 330 | uint32 counter = 0; | ^~~~~~~ embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 331 | int64 * seqVector; | ^~~~~~~~~ embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable] 333 | int64 * target = &tspace[8]; | ^~~~~~ embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] 334 | bool isBloomFilter; | ^~~~~~~~~~~~~ embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable] 335 | uint32 * bloomFilter; | ^~~~~~~~~~~ embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 336 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable] 385 | int num; | ^~~ embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 387 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1119 | uint32 offset; | ^~~~~~ aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] 1123 | int nHit = 0; | ^~~~ embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable] 389 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~ embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~~~~~ aligner.cpp: In member function 'int Aligner::check(int)': aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1436 | for (i = 0; i < num; i++) { | ~~^~~~~ aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1452 | for (j = 0; j < nError; j++) { | ~~^~~~~~~~ aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] 1426 | int ret; | ^~~ aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)': aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1541 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1547 | for (i = 0; i < res.nRead; i++) { | ~~^~~~~~~~~~~ aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1629 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~ aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~~~ aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~~~ aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] 1505 | int strand; | ^~~~~~ aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] 1508 | float ratio; | ^~~~~ aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] 1514 | bool sorted = info->sorted, strata = info->strata; | ^~~~~~ aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1685 | for (i = 0; i < res.nRead; i++) { | ~~^~~~~~~~~~~ aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1754 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] 1637 | bool success; | ^~~~~~~ aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] 1638 | unsigned int nSuccessRead = 0; | ^~~~~~~~~~~~ aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] 1639 | FILE * file = NULL; | ^~~~ aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] 1646 | char mateFilename[256]; | ^~~~~~~~~~~~ aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] 1652 | bool sorted = info->sorted, strata = info->strata; | ^~~~~~ aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1851 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] 1775 | int i, ret; | ^~~ aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1989 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from main.cpp:34: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] 1049 | } | ^ builder.cpp: In function 'int getArguVal(char*)': builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 115 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ In file included from embedhash.cpp:32: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ builder.cpp: In function 'int main(int, char**)': builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] 159 | int build_mode = BUILD_MODE_ALL; | ^~~~~~~~~~ builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] 277 | int nChar = sequence->getNum(); | ^~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.cpp:31: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] 32 | return tick; | ^~~~ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ In file included from pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] 32 | return tick; | ^~~~ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ main.cpp: In function 'int getArguVal(char*)': main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 159 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] 350 | int i, j, ret; | ^ main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] 350 | int i, j, ret; | ^ In file included from builder.cpp:34: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ main.cpp: In function 'int main(int, char**)': main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] 523 | int numKeys; | ^~~~~~~ main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] 526 | int nSeq = 1; | ^~~~ main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] 532 | CompactSequence * sequence; | ^~~~~~~~ main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] 534 | pthread_t * threadpool; | ^~~~~~~~~~ main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] 536 | int * threadid; | ^~~~~~~~ In file included from main.cpp:38: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': sequence.cpp:430:27: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized] 430 | offsetInOrgSeq++; | ~~~~~~~~~~~~~~^~ sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; | ^~~~~~~~~~~~~~ main.cpp: In function 'void mergeFiles(std::string)': main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 269 | sprintf(buf, ".t%d ", i); | ^~ main.cpp:269:18: note: directive argument in the range [0, 2147483646] 269 | sprintf(buf, ".t%d ", i); | ^~~~~~~ main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 269 | sprintf(buf, ".t%d ", i); | ~~~~~~~^~~~~~~~~~~~~~~~~ main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 276 | sprintf(buf, ".t%d", i); | ^~ main.cpp:276:18: note: directive argument in the range [0, 2147483646] 276 | sprintf(buf, ".t%d", i); | ^~~~~~ main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 276 | sprintf(buf, ".t%d", i); | ~~~~~~~^~~~~~~~~~~~~~~~ sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': sequence.cpp:676:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] 676 | forward_word = (forward_word << BITS_PER_BASE) | code; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cpp:630:23: note: 'code' was declared here 630 | int64 forward_word, code; | ^~~~ In member function 'void HashTable::setLookupInfo(int, int*)', inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] 353 | widthKeySpan = keySpan; | ~~~~~~~~~~~~~^~~~~~~~~ aligner.cpp: In member function 'int Aligner::initLookupArray()': aligner.cpp:360:7: note: 'keySpan' was declared here 360 | int keySpan; | ^~~~~~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1097:3: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized] 1097 | if (ret == MSG_HITSETFULL) | ^~ aligner.cpp:1040:7: note: 'ret' was declared here 1040 | int ret; | ^~~ g++ -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5' dh_auto_test rm -fr -- /tmp/dh-xdg-rundir-YemjULBL create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars rm -fr -- debian/.debhelper/generated/wham-align/ debian/wham-align/ debian/tmp/ dh_auto_install --destdir=debian/wham-align/ install -m0755 -d /build/reproducible-path/wham-align-0.1.5/debian/wham-align dh_install install -m0755 -d debian/wham-align/usr/bin cp --reflink=auto -a ./wham ./wham-build debian/wham-align/usr/bin/ dh_installdocs install -m0755 -d debian/wham-align/usr/share/doc/wham-align install -m0755 -d debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./MANUAL debian/wham-align/usr/share/doc/wham-align cd './reads/..' && find 'reads' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align cd './sequences/..' && find 'sequences' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./debian/README.test debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./debian/tests/ref/README.test_data debian/wham-align/usr/share/doc/wham-align chmod -R u\+rw,go=rX debian/wham-align/usr/share/doc install -p -m0644 debian/copyright debian/wham-align/usr/share/doc/wham-align/copyright install -m0755 -d debian/wham-align/usr/share/doc-base/ install -p -m0644 debian/wham-align.doc-base debian/wham-align/usr/share/doc-base/wham-align.wham dh_installchangelogs install -m0755 -d debian/wham-align/usr/share/doc/wham-align install -p -m0644 debian/.debhelper/generated/wham-align/dh_installchangelogs.dch.trimmed debian/wham-align/usr/share/doc/wham-align/changelog.Debian dh_installexamples install -m0755 -d debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./reads debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./sequences debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./debian/tests/ref debian/wham-align/usr/share/doc/wham-align/examples dh_installman install -m0755 -d debian/wham-align/usr/share/man/man1/ install -p -m0644 ./debian/wham-build.1 debian/wham-align/usr/share/man/man1/wham-build.1 install -m0755 -d debian/wham-align/usr/share/man/man1/ install -p -m0644 ./debian/wham.1 debian/wham-align/usr/share/man/man1/wham.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham-build.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1 mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1 mv debian/wham-align/usr/share/man/man1/wham.1.dh-new debian/wham-align/usr/share/man/man1/wham.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/wham-align chmod a-x usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1 gzip -9nf usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1 cd '/build/reproducible-path/wham-align-0.1.5' dh_fixperms find debian/wham-align ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wham-align/usr/share/doc -type f -a -true -a ! -regex 'debian/wham-align/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wham-align/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a install -m0755 -d debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug -- debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build objcopy --compress-debug-sections debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug chmod 0644 -- debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug dh_strip -a install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85 objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85/f6c93474de12fa9fbe490e3c5f204e05d1449f.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85/f6c93474de12fa9fbe490e3c5f204e05d1449f.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85/f6c93474de12fa9fbe490e3c5f204e05d1449f.debug debian/wham-align/usr/bin/wham install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22 objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham-build debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22/483addbb7deee9a03b20ff6b4dde41ece16f7c.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22/483addbb7deee9a03b20ff6b4dde41ece16f7c.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham-build objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22/483addbb7deee9a03b20ff6b4dde41ece16f7c.debug debian/wham-align/usr/bin/wham-build install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wham-align/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/wham-align/usr/lib/debug install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/share/doc ln -s wham-align debian/.debhelper/wham-align/dbgsym-root/usr/share/doc/wham-align-dbgsym install -m0755 -d debian/.debhelper/wham-align dh_makeshlibs -a rm -f debian/wham-align/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/wham-align/DEBIAN dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb install -m0755 -d debian/wham-align/DEBIAN dh_gencontrol install -m0755 -d debian/wham-align/DEBIAN echo misc:Depends= >> debian/wham-align.substvars echo misc:Pre-Depends= >> debian/wham-align.substvars install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -cdebian/control -Pdebian/.debhelper/wham-align/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wham-align-dbgsym "-DDepends=wham-align (= \${binary:Version})" "-DDescription=debug symbols for wham-align" "-DBuild-Ids=22483addbb7deee9a03b20ff6b4dde41ece16f7c 85f6c93474de12fa9fbe490e3c5f204e05d1449f" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/control dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -cdebian/control -Pdebian/wham-align chmod 0644 -- debian/wham-align/DEBIAN/control dh_md5sums install -m0755 -d debian/wham-align/DEBIAN cd debian/wham-align >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/wham-align/DEBIAN/md5sums install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN cd debian/.debhelper/wham-align/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/wham-align .. dpkg-deb --root-owner-group --build debian/.debhelper/wham-align/dbgsym-root .. dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_arm64.deb'. dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../wham-align_0.1.5-8_arm64.buildinfo dpkg-genchanges --build=binary -O../wham-align_0.1.5-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/343008 and its subdirectories I: Current time: Thu Jul 31 12:58:56 -12 2025 I: pbuilder-time-stamp: 1754009936 Fri Aug 1 00:58:56 UTC 2025 I: Signing ./b1/wham-align_0.1.5-8_arm64.buildinfo as wham-align_0.1.5-8_arm64.buildinfo.asc Fri Aug 1 00:58:56 UTC 2025 I: Signed ./b1/wham-align_0.1.5-8_arm64.buildinfo as ./b1/wham-align_0.1.5-8_arm64.buildinfo.asc Fri Aug 1 00:58:56 UTC 2025 - build #1 for wham-align/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Fri Aug 1 00:58:56 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-mSKqkSl0, removing. /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Aug 1 00:58 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 1 00:58 b2 -rw------- 1 jenkins jenkins 3117 Aug 1 00:58 rbuildlog.jrPCAOm -rw-r--r-- 1 jenkins jenkins 1987 Feb 19 2021 wham-align_0.1.5-8.dsc /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b1: total 792 -rw-r--r-- 1 jenkins jenkins 100819 Aug 1 00:58 build.log -rw-r--r-- 1 jenkins jenkins 514056 Aug 1 00:58 wham-align-dbgsym_0.1.5-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 7760 Aug 1 00:58 wham-align_0.1.5-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1987 Aug 1 00:58 wham-align_0.1.5-8.dsc -rw-r--r-- 1 jenkins jenkins 4873 Aug 1 00:58 wham-align_0.1.5-8_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5755 Aug 1 00:58 wham-align_0.1.5-8_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1394 Aug 1 00:58 wham-align_0.1.5-8_arm64.changes -rw-r--r-- 1 jenkins jenkins 155040 Aug 1 00:58 wham-align_0.1.5-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 1249 Aug 1 00:58 wham-align_0.1.5-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b2: total 0 Fri Aug 1 00:58:57 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 31 12:58:31 -12 2025 I: pbuilder-time-stamp: 1754009911 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [wham-align_0.1.5-8.dsc] I: copying [./wham-align_0.1.5.orig.tar.gz] I: copying [./wham-align_0.1.5-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./wham-align_0.1.5-8.dsc: no acceptable signature found dpkg-source: info: extracting wham-align in wham-align-0.1.5 dpkg-source: info: unpacking wham-align_0.1.5.orig.tar.gz dpkg-source: info: unpacking wham-align_0.1.5-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile.patch dpkg-source: info: applying non-x86.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying cross-build.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/343008/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='7f8c17cfd97a456aa773f7c1d84f4c19' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='343008' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/pbuilderrc_25AF --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/343008/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After unpacking 44.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Fetched 11.0 MB in 0s (103 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5' rm -f wham wham-build *.o make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/wham-align.substvars debian/files rm -fr -- debian/wham-align/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hash.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings embedhash.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings main.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hitset.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp error.cpp: In function 'void elog(int, char*, ...)': error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable] 31 | char *filename = __FILE__; | ^~~~~~~~ error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] 32 | int lineno = __LINE__; | ^~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp short.cpp: In member function 'int ShortRead::preProcess(int)': short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 212 | while (len = readLine(file, str, 256)) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 483 | if (szPartition <= nRead - curRead) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)': model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable] 76 | unsigned int nIndex, nLookup, nBucket; | ^~~~~~ model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()': model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 166 | fscanf(file, "MemTotal: %d kB\n", &memTotal); | ~^ ~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 167 | fscanf(file, "MemFree: %d kB\n", &memFree); | ~^ ~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 168 | fscanf(file, "Buffers: %d kB\n", &memBuffer); | ~^ ~~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 169 | fscanf(file, "Cached: %d kB\n", &memCache); | ~^ ~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] 198 | double nSpace, p0, p1, p2; | ^~ In file included from hitset.h:31, from writer.h:26, from writer.cpp:21: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] 148 | uint32 sid = 0, soffset = 0; | ^~~ writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] 148 | uint32 sid = 0, soffset = 0; | ^~~~~~~ writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^~~~~~~~ writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] 272 | int64 code1, code2; | ^~~~~ writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] 272 | int64 code1, code2; | ^~~~~ writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] 278 | double p, sump; | ^ writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] 278 | double p, sump; | ^~~~ writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] 279 | char qseq[128], rseq[128], tag[128]; | ^~~ writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] 281 | char shortread[256]; | ^~~~~~~~~ writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { | ~~^~~~~~~~~~~~~~~ writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { | ~~^~~~~~~~~~~~~~~ writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { | ~~~~~^~~~~~~ In file included from hitset.h:31, from hitset.cpp:1: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] 90 | bool pairMatch = false; | ^~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from hash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from aligner.cpp:25: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from embedhash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 67 | for (int i = 0; i < numLevel - 1; i++) { | ~~^~~~~~~~~~~~~~ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ interval.cpp: In member function 'int IntervalTree::save(char*)': interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 304 | if (ret != numLEntry) { | ~~~~^~~~~~~~~~~~ interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 310 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ interval.cpp: In member function 'int IntervalTree::load(char*)': interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 359 | if (ret != numLEntry) { | ~~~~^~~~~~~~~~~~ interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 370 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] 61 | int i; | ^ edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] 181 | char tmp_trace = traceback[i][j]; | ^~~~~~~~~ edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] 132 | int k = 0, x = 0, y = 0; | ^ edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] 132 | int k = 0, x = 0, y = 0; | ^ edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] 178 | int kk = 0; | ^~ short.cpp: In member function 'int ShortRead::load(int)': short.cpp:424:28: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] 424 | forward_word = (forward_word << BITS_PER_BASE) | code; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp:310:38: note: 'code' was declared here 310 | int64 forward_word, backward_word, code; | ^~~~ short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ^~ short.cpp:503:42: note: directive argument in the range [0, 2147483646] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ^~~~~~~~ short.cpp:503:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ^~ short.cpp:510:42: note: directive argument in the range [0, 2147483646] 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ^~~~~~~~ short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from builder.cpp:31: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from sequence.cpp:30: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] 97 | char * str; | ^~~ sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 238 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 309 | ( i = 0; i < nSeq; i++) | ~~^~~~~~ sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 324 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 344 | for (j = 0; j < numError + 1; j++) { | ~~^~~~~~~~~~~~~~ sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 410 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 429 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~ sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~~~~~ sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 599 | if (lenSegmentN > nError + 1) | ~~~~~~~~~~~~^~~~~~~~~~~~ sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] 520 | unsigned int step, nextstep; | ^~~~ sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] 520 | unsigned int step, nextstep; | ^~~~~~~~ sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~~ sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~~ sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~ sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~ sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~ sequence.cpp: In member function 'int CompactSequence::save(char*)': sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 738 | if (ret != size) { | ~~~~^~~~~~~ sequence.cpp: In member function 'int CompactSequence::load(char*)': sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 804 | if (ret != size) { | ~~~~^~~~~~~ hash.cpp: In member function 'int HashTable::preProcessEnd()': hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] 236 | if (h >= nHistogram) | ~~^~~~~~~~~~~~~ hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] 285 | if (useEmbedTables() && tmp > embedShreshold) { | ~~~~^~~~~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::setScanThreshold(double)': hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 343 | for (int i = 0; i < nHistogram - 1; i++) { | ~~^~~~~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 460 | overflowPool[curOverflowEntry] = hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] 411 | uint32 seqOffset; | ^~~~~~~~~ hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] 413 | uint32 counter = 0; | ^~~~~~~ hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 414 | int64 * seqVector; | ^~~~~~~~~ hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] 416 | int64 * target = &tspace[8]; | ^~~~~~ hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] 417 | bool isBloomFilter; | ^~~~~~~~~~~~~ hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] 418 | uint32 * bloomFilter; | ^~~~~~~~~~~ hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 419 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ hash.cpp: In member function 'int HashTable::buildEmbedTable()': hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], | ^~~~ hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], | ^~~~~ hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; | ^~~~~ hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; | ^~~~~~~~~ hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 472 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)': hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable] 587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] 746 | int num; | ^~~ hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~ hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] 973 | int64 * seqVector = sequence->getSequence(); | ^~~~~~~~~ hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] 1052 | int num; | ^~~ hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable] 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable] 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~~~ hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 1057 | int64 * seqVector; | ^~~~~~~~~ hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~ hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~~~~~ hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)': hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++) hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++) hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1247 | for (int j = 0; j < strlen(set[i].str); j++) | ~~^~~~~~~~~~~~~~~~~~~~ hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1254 | for (int j = 0; j < strlen(set[i].str); j++) | ~~^~~~~~~~~~~~~~~~~~~~ hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp: In member function 'int HashTable::sortList()': hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable] 1430 | uint32 * pool; | ^~~~ hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1321 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ aligner.cpp: In member function 'int Aligner::initLookupArray()': aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 365 | if ((indexBits[i] >> j) & 0x1 == 1) { | ~~~~^~~~ aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 371 | if ((indexBits[i] >> j) & 0x1 == 1) { | ~~~~^~~~ hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1673 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ aligner.cpp: In member function 'int Aligner::preProcessHashTables()': aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 712 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp: In member function 'int Aligner::build(char*)': aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] 724 | unsigned int i, j; | ^ aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] 724 | unsigned int i, j; | ^ aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 807 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 983 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1006 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] 137 | const double ln2 = log(2); | ^~~ embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)': embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable] 253 | int64 sum = 0; | ^~~ embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] 255 | int64 top = total - total * r; | ^~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] 1035 | uint32 offset; | ^~~~~~ embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)': embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 369 | overflowPool[curOverflowEntry] = embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable] 328 | uint32 seqOffset; | ^~~~~~~~~ aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] 1039 | int nHit = 0; | ^~~~ embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable] 330 | uint32 counter = 0; | ^~~~~~~ embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 331 | int64 * seqVector; | ^~~~~~~~~ embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable] 333 | int64 * target = &tspace[8]; | ^~~~~~ embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] 334 | bool isBloomFilter; | ^~~~~~~~~~~~~ embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable] 335 | uint32 * bloomFilter; | ^~~~~~~~~~~ embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 336 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable] 385 | int num; | ^~~ embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 387 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1119 | uint32 offset; | ^~~~~~ aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] 1123 | int nHit = 0; | ^~~~ embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable] 389 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~ embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~~~~~ aligner.cpp: In member function 'int Aligner::check(int)': aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1436 | for (i = 0; i < num; i++) { | ~~^~~~~ aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1452 | for (j = 0; j < nError; j++) { | ~~^~~~~~~~ aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] 1426 | int ret; | ^~~ aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)': aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1541 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1547 | for (i = 0; i < res.nRead; i++) { | ~~^~~~~~~~~~~ aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1629 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~ aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~~~ aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~~~ aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] 1505 | int strand; | ^~~~~~ aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] 1508 | float ratio; | ^~~~~ aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] 1514 | bool sorted = info->sorted, strata = info->strata; | ^~~~~~ aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1685 | for (i = 0; i < res.nRead; i++) { | ~~^~~~~~~~~~~ aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1754 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] 1637 | bool success; | ^~~~~~~ aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] 1638 | unsigned int nSuccessRead = 0; | ^~~~~~~~~~~~ aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] 1639 | FILE * file = NULL; | ^~~~ aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] 1646 | char mateFilename[256]; | ^~~~~~~~~~~~ aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] 1652 | bool sorted = info->sorted, strata = info->strata; | ^~~~~~ aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1851 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] 1775 | int i, ret; | ^~~ aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1989 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from main.cpp:34: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] 1049 | } | ^ builder.cpp: In function 'int getArguVal(char*)': builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 115 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ In file included from embedhash.cpp:32: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ builder.cpp: In function 'int main(int, char**)': builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] 159 | int build_mode = BUILD_MODE_ALL; | ^~~~~~~~~~ builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] 277 | int nChar = sequence->getNum(); | ^~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ In file included from hash.cpp:31: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] 32 | return tick; | ^~~~ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ In file included from pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] 32 | return tick; | ^~~~ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ main.cpp: In function 'int getArguVal(char*)': main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 159 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] 350 | int i, j, ret; | ^ main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] 350 | int i, j, ret; | ^ In file included from builder.cpp:34: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ main.cpp: In function 'int main(int, char**)': main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] 523 | int numKeys; | ^~~~~~~ main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] 526 | int nSeq = 1; | ^~~~ main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] 532 | CompactSequence * sequence; | ^~~~~~~~ main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] 534 | pthread_t * threadpool; | ^~~~~~~~~~ main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] 536 | int * threadid; | ^~~~~~~~ In file included from main.cpp:38: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': sequence.cpp:430:27: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized] 430 | offsetInOrgSeq++; | ~~~~~~~~~~~~~~^~ sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; | ^~~~~~~~~~~~~~ main.cpp: In function 'void mergeFiles(std::string)': main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 269 | sprintf(buf, ".t%d ", i); | ^~ main.cpp:269:18: note: directive argument in the range [0, 2147483646] 269 | sprintf(buf, ".t%d ", i); | ^~~~~~~ main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 269 | sprintf(buf, ".t%d ", i); | ~~~~~~~^~~~~~~~~~~~~~~~~ main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 276 | sprintf(buf, ".t%d", i); | ^~ main.cpp:276:18: note: directive argument in the range [0, 2147483646] 276 | sprintf(buf, ".t%d", i); | ^~~~~~ main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 276 | sprintf(buf, ".t%d", i); | ~~~~~~~^~~~~~~~~~~~~~~~ sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': sequence.cpp:676:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] 676 | forward_word = (forward_word << BITS_PER_BASE) | code; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cpp:630:23: note: 'code' was declared here 630 | int64 forward_word, code; | ^~~~ In member function 'void HashTable::setLookupInfo(int, int*)', inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] 353 | widthKeySpan = keySpan; | ~~~~~~~~~~~~~^~~~~~~~~ aligner.cpp: In member function 'int Aligner::initLookupArray()': aligner.cpp:360:7: note: 'keySpan' was declared here 360 | int keySpan; | ^~~~~~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1097:3: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized] 1097 | if (ret == MSG_HITSETFULL) | ^~ aligner.cpp:1040:7: note: 'ret' was declared here 1040 | int ret; | ^~~ g++ -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5' dh_auto_test rm -fr -- /tmp/dh-xdg-rundir-YemjULBL create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars rm -fr -- debian/.debhelper/generated/wham-align/ debian/wham-align/ debian/tmp/ dh_auto_install --destdir=debian/wham-align/ install -m0755 -d /build/reproducible-path/wham-align-0.1.5/debian/wham-align dh_install install -m0755 -d debian/wham-align/usr/bin cp --reflink=auto -a ./wham ./wham-build debian/wham-align/usr/bin/ dh_installdocs install -m0755 -d debian/wham-align/usr/share/doc/wham-align install -m0755 -d debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./MANUAL debian/wham-align/usr/share/doc/wham-align cd './reads/..' && find 'reads' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align cd './sequences/..' && find 'sequences' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./debian/README.test debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./debian/tests/ref/README.test_data debian/wham-align/usr/share/doc/wham-align chmod -R u\+rw,go=rX debian/wham-align/usr/share/doc install -p -m0644 debian/copyright debian/wham-align/usr/share/doc/wham-align/copyright install -m0755 -d debian/wham-align/usr/share/doc-base/ install -p -m0644 debian/wham-align.doc-base debian/wham-align/usr/share/doc-base/wham-align.wham dh_installchangelogs install -m0755 -d debian/wham-align/usr/share/doc/wham-align install -p -m0644 debian/.debhelper/generated/wham-align/dh_installchangelogs.dch.trimmed debian/wham-align/usr/share/doc/wham-align/changelog.Debian dh_installexamples install -m0755 -d debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./reads debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./sequences debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./debian/tests/ref debian/wham-align/usr/share/doc/wham-align/examples dh_installman install -m0755 -d debian/wham-align/usr/share/man/man1/ install -p -m0644 ./debian/wham-build.1 debian/wham-align/usr/share/man/man1/wham-build.1 install -m0755 -d debian/wham-align/usr/share/man/man1/ install -p -m0644 ./debian/wham.1 debian/wham-align/usr/share/man/man1/wham.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham-build.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1 mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1 mv debian/wham-align/usr/share/man/man1/wham.1.dh-new debian/wham-align/usr/share/man/man1/wham.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/wham-align chmod a-x usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1 gzip -9nf usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1 cd '/build/reproducible-path/wham-align-0.1.5' dh_fixperms find debian/wham-align ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wham-align/usr/share/doc -type f -a -true -a ! -regex 'debian/wham-align/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wham-align/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a install -m0755 -d debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug -- debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build objcopy --compress-debug-sections debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug chmod 0644 -- debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug dh_strip -a install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85 objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85/f6c93474de12fa9fbe490e3c5f204e05d1449f.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85/f6c93474de12fa9fbe490e3c5f204e05d1449f.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85/f6c93474de12fa9fbe490e3c5f204e05d1449f.debug debian/wham-align/usr/bin/wham install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22 objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham-build debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22/483addbb7deee9a03b20ff6b4dde41ece16f7c.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22/483addbb7deee9a03b20ff6b4dde41ece16f7c.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham-build objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22/483addbb7deee9a03b20ff6b4dde41ece16f7c.debug debian/wham-align/usr/bin/wham-build install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wham-align/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/wham-align/usr/lib/debug install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/share/doc ln -s wham-align debian/.debhelper/wham-align/dbgsym-root/usr/share/doc/wham-align-dbgsym install -m0755 -d debian/.debhelper/wham-align dh_makeshlibs -a rm -f debian/wham-align/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/wham-align/DEBIAN dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb install -m0755 -d debian/wham-align/DEBIAN dh_gencontrol install -m0755 -d debian/wham-align/DEBIAN echo misc:Depends= >> debian/wham-align.substvars echo misc:Pre-Depends= >> debian/wham-align.substvars install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -cdebian/control -Pdebian/.debhelper/wham-align/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wham-align-dbgsym "-DDepends=wham-align (= \${binary:Version})" "-DDescription=debug symbols for wham-align" "-DBuild-Ids=22483addbb7deee9a03b20ff6b4dde41ece16f7c 85f6c93474de12fa9fbe490e3c5f204e05d1449f" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/control dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -cdebian/control -Pdebian/wham-align chmod 0644 -- debian/wham-align/DEBIAN/control dh_md5sums install -m0755 -d debian/wham-align/DEBIAN cd debian/wham-align >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/wham-align/DEBIAN/md5sums install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN cd debian/.debhelper/wham-align/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/wham-align .. dpkg-deb --root-owner-group --build debian/.debhelper/wham-align/dbgsym-root .. dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_arm64.deb'. dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../wham-align_0.1.5-8_arm64.buildinfo dpkg-genchanges --build=binary -O../wham-align_0.1.5-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/343008 and its subdirectories I: Current time: Thu Jul 31 12:58:56 -12 2025 I: pbuilder-time-stamp: 1754009936 Fri Aug 1 00:58:58 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Fri Aug 1 00:58:58 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Fri Aug 1 00:58:58 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Aug 1 00:58:58 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-xetp7l' ==================================================================================== Thu Sep 3 07:21:59 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 wham-align unstable /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk 0.1.5-8" as arguments. Thu Sep 3 07:21:59 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-f6Cnfijh" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 3 07:21:59 UTC 2026 I: Downloading source for unstable/wham-align=0.1.5-8 Reading package lists... NOTICE: 'wham-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/wham-align.git Please use: git clone https://salsa.debian.org/med-team/wham-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 130 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (dsc) [1987 B] Get:2 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (tar) [120 kB] Get:3 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (diff) [7760 B] Fetched 130 kB in 0s (6862 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'wham-align' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/wham-align.git Please use: git clone https://salsa.debian.org/med-team/wham-align.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 130 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (dsc) [1987 B] Get:2 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (tar) [120 kB] Get:3 http://deb.debian.org/debian unstable/main wham-align 0.1.5-8 (diff) [7760 B] Fetched 130 kB in 0s (6862 kB/s) Download complete and in download only mode ============================================================================= Re-Building wham-align in unstable on arm64 on codethink03-arm64 now. Date: Thu Sep 3 08:21:59 BST 2026 Date UTC: Thu Sep 3 07:21:59 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/pbuilderrc_Enk8 + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' wham-align = debian-installer -o wham-align = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' wham-align = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/pbuilderrc_Enk8 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 3 21:21:59 +14 2026 I: pbuilder-time-stamp: 1788420119 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [wham-align_0.1.5-8.dsc] I: copying [./wham-align_0.1.5.orig.tar.gz] I: copying [./wham-align_0.1.5-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./wham-align_0.1.5-8.dsc: no acceptable signature found dpkg-source: info: extracting wham-align in wham-align-0.1.5 dpkg-source: info: unpacking wham-align_0.1.5.orig.tar.gz dpkg-source: info: unpacking wham-align_0.1.5-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile.patch dpkg-source: info: applying non-x86.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying cross-build.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/650689/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 3 07:22 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/650689/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/650689/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=89f9b3d315294d5baa4bfe043155ff74 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=650689 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/pbuilderrc_Enk8 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/650689/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After unpacking 44.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-2.1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Fetched 11.0 MB in 0s (77.5 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_arm64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_arm64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-2.1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2_arm64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Processing triggers for libc-bin (2.41-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/650689/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/650689/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5' rm -f wham wham-build *.o make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/wham-align.substvars debian/files rm -fr -- debian/wham-align/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hash.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings embedhash.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings main.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hitset.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp error.cpp: In function 'void elog(int, char*, ...)': error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable] 31 | char *filename = __FILE__; | ^~~~~~~~ error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] 32 | int lineno = __LINE__; | ^~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp short.cpp: In member function 'int ShortRead::preProcess(int)': short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 212 | while (len = readLine(file, str, 256)) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 67 | for (int i = 0; i < numLevel - 1; i++) { | ~~^~~~~~~~~~~~~~ short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 483 | if (szPartition <= nRead - curRead) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hitset.h:31, from hitset.cpp:1: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ interval.cpp: In member function 'int IntervalTree::save(char*)': interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 304 | if (ret != numLEntry) { | ~~~~^~~~~~~~~~~~ interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 310 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)': model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable] 76 | unsigned int nIndex, nLookup, nBucket; | ^~~~~~ interval.cpp: In member function 'int IntervalTree::load(char*)': interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 359 | if (ret != numLEntry) { | ~~~~^~~~~~~~~~~~ interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 370 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()': model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 166 | fscanf(file, "MemTotal: %d kB\n", &memTotal); | ~^ ~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 167 | fscanf(file, "MemFree: %d kB\n", &memFree); | ~^ ~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 168 | fscanf(file, "Buffers: %d kB\n", &memBuffer); | ~^ ~~~~~~~~~~ | | | | int* unsigned int* | %d model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 169 | fscanf(file, "Cached: %d kB\n", &memCache); | ~^ ~~~~~~~~~ | | | | int* unsigned int* | %d pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] 198 | double nSpace, p0, p1, p2; | ^~ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] 90 | bool pairMatch = false; | ^~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from aligner.cpp:25: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ In file included from hitset.h:31, from hash.h:29, from hash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] 61 | int i; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] 181 | char tmp_trace = traceback[i][j]; | ^~~~~~~~~ edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] 132 | int k = 0, x = 0, y = 0; | ^ edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] 132 | int k = 0, x = 0, y = 0; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] 178 | int kk = 0; | ^~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ In file included from hitset.h:31, from hash.h:29, from embedhash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ short.cpp: In member function 'int ShortRead::load(int)': short.cpp:424:28: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] 424 | forward_word = (forward_word << BITS_PER_BASE) | code; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp:310:38: note: 'code' was declared here 310 | int64 forward_word, backward_word, code; | ^~~~ In file included from hitset.h:31, from writer.h:26, from writer.cpp:21: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] 148 | uint32 sid = 0, soffset = 0; | ^~~ writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] 148 | uint32 sid = 0, soffset = 0; | ^~~~~~~ writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^ writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] 271 | int i, j, k, h, lastDiff; | ^~~~~~~~ writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] 272 | int64 code1, code2; | ^~~~~ writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] 272 | int64 code1, code2; | ^~~~~ writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] 278 | double p, sump; | ^ writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] 278 | double p, sump; | ^~~~ writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] 279 | char qseq[128], rseq[128], tag[128]; | ^~~ writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] 281 | char shortread[256]; | ^~~~~~~~~ short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ^~ writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { | ~~^~~~~~~~~~~~~~~ short.cpp:503:42: note: directive argument in the range [0, 2147483646] 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ^~~~~~~~ short.cpp:503:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ^~ short.cpp:510:42: note: directive argument in the range [0, 2147483646] 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ^~~~~~~~ short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { | ~~^~~~~~~~~~~~~~~ writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { | ~~~~~^~~~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from builder.cpp:31: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from main.cpp:34: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, from sequence.cpp:30: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~~ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~ pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] 755 | int i, p, num, base, Cscore; | ^~~~ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ aligner.cpp: In member function 'int Aligner::initLookupArray()': aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 365 | if ((indexBits[i] >> j) & 0x1 == 1) { | ~~~~^~~~ aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 371 | if ((indexBits[i] >> j) & 0x1 == 1) { | ~~~~^~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ aligner.cpp: In member function 'int Aligner::preProcessHashTables()': aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 712 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp: In member function 'int Aligner::build(char*)': aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] 724 | unsigned int i, j; | ^ aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] 724 | unsigned int i, j; | ^ aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 807 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 983 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1006 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ hash.cpp: In member function 'int HashTable::preProcessEnd()': hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] 236 | if (h >= nHistogram) | ~~^~~~~~~~~~~~~ hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] 285 | if (useEmbedTables() && tmp > embedShreshold) { | ~~~~^~~~~~~~~~~~~~~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] 1035 | uint32 offset; | ^~~~~~ aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] 1039 | int nHit = 0; | ^~~~ sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] 97 | char * str; | ^~~ sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 238 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ hash.cpp: In member function 'void HashTable::setScanThreshold(double)': hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 343 | for (int i = 0; i < nHistogram - 1; i++) { | ~~^~~~~~~~~~~~~~~~ aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1119 | uint32 offset; | ^~~~~~ aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] 1123 | int nHit = 0; | ^~~~ sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 309 | ( i = 0; i < nSeq; i++) | ~~^~~~~~ sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 324 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 344 | for (j = 0; j < numError + 1; j++) { | ~~^~~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 460 | overflowPool[curOverflowEntry] = hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] 411 | uint32 seqOffset; | ^~~~~~~~~ hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] 413 | uint32 counter = 0; | ^~~~~~~ hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 414 | int64 * seqVector; | ^~~~~~~~~ hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] 416 | int64 * target = &tspace[8]; | ^~~~~~ hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] 417 | bool isBloomFilter; | ^~~~~~~~~~~~~ hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] 418 | uint32 * bloomFilter; | ^~~~~~~~~~~ aligner.cpp: In member function 'int Aligner::check(int)': aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1436 | for (i = 0; i < num; i++) { | ~~^~~~~ hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 419 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1452 | for (j = 0; j < nError; j++) { | ~~^~~~~~~~ sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 410 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] 1426 | int ret; | ^~~ sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 429 | if (lenSegmentN > numError + 1) { | ~~~~~~~~~~~~^~~~~~~~~~~~~~ sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~ sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] 223 | unsigned int step, nextstep; | ^~~~~~~~ aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)': aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1541 | for (i = 0; i < nHashTable; i++) { | ~~^~~~~~~~~~~~ aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1547 | for (i = 0; i < res.nRead; i++) { | ~~^~~~~~~~~~~ hash.cpp: In member function 'int HashTable::buildEmbedTable()': hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], | ^~~~ hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], | ^~~~~ hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; | ^~~~~ hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; | ^~~~~~~~~ hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 472 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1629 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~ aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~~~ aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; | ^~~~~~ aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] 1505 | int strand; | ^~~~~~ aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] 1508 | float ratio; | ^~~~~ aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] 1514 | bool sorted = info->sorted, strata = info->strata; | ^~~~~~ sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 534 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 599 | if (lenSegmentN > nError + 1) | ~~~~~~~~~~~~^~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)': hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable] 587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] 520 | unsigned int step, nextstep; | ^~~~ sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] 520 | unsigned int step, nextstep; | ^~~~~~~~ sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~~ sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~~ sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~~ sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~ sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; | ^~~~~~~~~ aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1685 | for (i = 0; i < res.nRead; i++) { | ~~^~~~~~~~~~~ aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1754 | delete writer; | ^~~~~~~~~~~~~ aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] 1637 | bool success; | ^~~~~~~ aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] 1638 | unsigned int nSuccessRead = 0; | ^~~~~~~~~~~~ aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] 1639 | FILE * file = NULL; | ^~~~ aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] 1646 | char mateFilename[256]; | ^~~~~~~~~~~~ aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] 1652 | bool sorted = info->sorted, strata = info->strata; | ^~~~~~ hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ sequence.cpp: In member function 'int CompactSequence::save(char*)': sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 738 | if (ret != size) { | ~~~~^~~~~~~ aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1851 | delete writer; | ^~~~~~~~~~~~~ sequence.cpp: In member function 'int CompactSequence::load(char*)': sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 804 | if (ret != size) { | ~~~~^~~~~~~ aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] 1775 | int i, ret; | ^~~ hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] 746 | int num; | ^~~ hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~ hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~~~~~ aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] 1989 | delete writer; | ^~~~~~~~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; | ^~~~~~~~~ hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] 973 | int64 * seqVector = sequence->getSequence(); | ^~~~~~~~~ hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] 1052 | int num; | ^~~ hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable] 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable] 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~~~ hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 1057 | int64 * seqVector; | ^~~~~~~~~ hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~ hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] 1059 | uint32 sid, soffset; | ^~~~~~~ hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)': hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++) hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++) hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1247 | for (int j = 0; j < strlen(set[i].str); j++) | ~~^~~~~~~~~~~~~~~~~~~~ hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1254 | for (int j = 0; j < strlen(set[i].str); j++) | ~~^~~~~~~~~~~~~~~~~~~~ hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ hash.cpp: In member function 'int HashTable::sortList()': hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable] 1430 | uint32 * pool; | ^~~~ hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1321 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1673 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] 137 | const double ln2 = log(2); | ^~~ embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)': embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable] 253 | int64 sum = 0; | ^~~ embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] 255 | int64 top = total - total * r; | ^~~ embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)': embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 369 | overflowPool[curOverflowEntry] = embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable] 328 | uint32 seqOffset; | ^~~~~~~~~ embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable] 330 | uint32 counter = 0; | ^~~~~~~ embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] 331 | int64 * seqVector; | ^~~~~~~~~ embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable] 333 | int64 * target = &tspace[8]; | ^~~~~~ embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] 334 | bool isBloomFilter; | ^~~~~~~~~~~~~ embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable] 335 | uint32 * bloomFilter; | ^~~~~~~~~~~ embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 336 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable] 385 | int num; | ^~~ embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 387 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable] 389 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~ embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~~~~~ main.cpp: In function 'int getArguVal(char*)': main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 159 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] 350 | int i, j, ret; | ^ main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] 350 | int i, j, ret; | ^ main.cpp: In function 'int main(int, char**)': main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] 523 | int numKeys; | ^~~~~~~ main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] 526 | int nSeq = 1; | ^~~~ main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] 532 | CompactSequence * sequence; | ^~~~~~~~ main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] 534 | pthread_t * threadpool; | ^~~~~~~~~~ main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] 536 | int * threadid; | ^~~~~~~~ In file included from embedhash.cpp:32: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] 1049 | } | ^ In file included from hash.cpp:31: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ In file included from pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] 32 | return tick; | ^~~~ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ In file included from pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] 32 | return tick; | ^~~~ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ builder.cpp: In function 'int getArguVal(char*)': builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 115 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ builder.cpp: In function 'int main(int, char**)': builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] 159 | int build_mode = BUILD_MODE_ALL; | ^~~~~~~~~~ builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] 277 | int nChar = sequence->getNum(); | ^~~~~ In file included from main.cpp:38: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ In file included from builder.cpp:34: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ main.cpp: In function 'void mergeFiles(std::string)': main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 269 | sprintf(buf, ".t%d ", i); | ^~ main.cpp:269:18: note: directive argument in the range [0, 2147483646] 269 | sprintf(buf, ".t%d ", i); | ^~~~~~~ main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 269 | sprintf(buf, ".t%d ", i); | ~~~~~~~^~~~~~~~~~~~~~~~~ main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 276 | sprintf(buf, ".t%d", i); | ^~ main.cpp:276:18: note: directive argument in the range [0, 2147483646] 276 | sprintf(buf, ".t%d", i); | ^~~~~~ main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 276 | sprintf(buf, ".t%d", i); | ~~~~~~~^~~~~~~~~~~~~~~~ sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': sequence.cpp:430:27: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized] 430 | offsetInOrgSeq++; | ~~~~~~~~~~~~~~^~ sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; | ^~~~~~~~~~~~~~ In member function 'void HashTable::setLookupInfo(int, int*)', inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] 353 | widthKeySpan = keySpan; | ~~~~~~~~~~~~~^~~~~~~~~ aligner.cpp: In member function 'int Aligner::initLookupArray()': aligner.cpp:360:7: note: 'keySpan' was declared here 360 | int keySpan; | ^~~~~~~ sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': sequence.cpp:676:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] 676 | forward_word = (forward_word << BITS_PER_BASE) | code; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cpp:630:23: note: 'code' was declared here 630 | int64 forward_word, code; | ^~~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1097:3: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized] 1097 | if (ret == MSG_HITSETFULL) | ^~ aligner.cpp:1040:7: note: 'ret' was declared here 1040 | int ret; | ^~~ g++ -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5' dh_auto_test rm -fr -- /tmp/dh-xdg-rundir-zVdUpRYy create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars rm -fr -- debian/.debhelper/generated/wham-align/ debian/wham-align/ debian/tmp/ dh_auto_install --destdir=debian/wham-align/ install -m0755 -d /build/reproducible-path/wham-align-0.1.5/debian/wham-align dh_install install -m0755 -d debian/wham-align/usr/bin cp --reflink=auto -a ./wham ./wham-build debian/wham-align/usr/bin/ dh_installdocs install -m0755 -d debian/wham-align/usr/share/doc/wham-align install -m0755 -d debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./MANUAL debian/wham-align/usr/share/doc/wham-align cd './reads/..' && find 'reads' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align cd './sequences/..' && find 'sequences' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wham-align-0.1.5/debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./debian/README.test debian/wham-align/usr/share/doc/wham-align cp --reflink=auto -a ./debian/tests/ref/README.test_data debian/wham-align/usr/share/doc/wham-align chmod -R u\+rw,go=rX debian/wham-align/usr/share/doc install -p -m0644 debian/copyright debian/wham-align/usr/share/doc/wham-align/copyright install -m0755 -d debian/wham-align/usr/share/doc-base/ install -p -m0644 debian/wham-align.doc-base debian/wham-align/usr/share/doc-base/wham-align.wham dh_installchangelogs install -m0755 -d debian/wham-align/usr/share/doc/wham-align install -p -m0644 debian/.debhelper/generated/wham-align/dh_installchangelogs.dch.trimmed debian/wham-align/usr/share/doc/wham-align/changelog.Debian dh_installexamples install -m0755 -d debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./reads debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./sequences debian/wham-align/usr/share/doc/wham-align/examples cp --reflink=auto -a ./debian/tests/ref debian/wham-align/usr/share/doc/wham-align/examples dh_installman install -m0755 -d debian/wham-align/usr/share/man/man1/ install -p -m0644 ./debian/wham-build.1 debian/wham-align/usr/share/man/man1/wham-build.1 install -m0755 -d debian/wham-align/usr/share/man/man1/ install -p -m0644 ./debian/wham.1 debian/wham-align/usr/share/man/man1/wham.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham-build.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1 mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1 mv debian/wham-align/usr/share/man/man1/wham.1.dh-new debian/wham-align/usr/share/man/man1/wham.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/wham-align chmod a-x usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1 gzip -9nf usr/share/doc/wham-align/MANUAL usr/share/doc/wham-align/changelog.Debian usr/share/doc/wham-align/sequences/chr1_100k.fa usr/share/man/man1/wham-build.1 usr/share/man/man1/wham.1 cd '/build/reproducible-path/wham-align-0.1.5' dh_fixperms find debian/wham-align ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wham-align/usr/share/doc -type f -a -true -a ! -regex 'debian/wham-align/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wham-align/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wham-align/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a install -m0755 -d debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug -- debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build objcopy --compress-debug-sections debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug chmod 0644 -- debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu/wham-align.debug dh_strip -a install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85 objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85/f6c93474de12fa9fbe490e3c5f204e05d1449f.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85/f6c93474de12fa9fbe490e3c5f204e05d1449f.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/85/f6c93474de12fa9fbe490e3c5f204e05d1449f.debug debian/wham-align/usr/bin/wham install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22 objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham-build debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22/483addbb7deee9a03b20ff6b4dde41ece16f7c.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22/483addbb7deee9a03b20ff6b4dde41ece16f7c.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham-build objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/22/483addbb7deee9a03b20ff6b4dde41ece16f7c.debug debian/wham-align/usr/bin/wham-build install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wham-align/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wham-align/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/wham-align/usr/lib/debug install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/share/doc ln -s wham-align debian/.debhelper/wham-align/dbgsym-root/usr/share/doc/wham-align-dbgsym install -m0755 -d debian/.debhelper/wham-align dh_makeshlibs -a rm -f debian/wham-align/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/wham-align/DEBIAN dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb install -m0755 -d debian/wham-align/DEBIAN dh_gencontrol install -m0755 -d debian/wham-align/DEBIAN echo misc:Depends= >> debian/wham-align.substvars echo misc:Pre-Depends= >> debian/wham-align.substvars install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -cdebian/control -Pdebian/.debhelper/wham-align/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wham-align-dbgsym "-DDepends=wham-align (= \${binary:Version})" "-DDescription=debug symbols for wham-align" "-DBuild-Ids=22483addbb7deee9a03b20ff6b4dde41ece16f7c 85f6c93474de12fa9fbe490e3c5f204e05d1449f" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/control dpkg-gencontrol -pwham-align -ldebian/changelog -Tdebian/wham-align.substvars -cdebian/control -Pdebian/wham-align chmod 0644 -- debian/wham-align/DEBIAN/control dh_md5sums install -m0755 -d debian/wham-align/DEBIAN cd debian/wham-align >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/wham-align/DEBIAN/md5sums install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/DEBIAN cd debian/.debhelper/wham-align/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/wham-align .. dpkg-deb --root-owner-group --build debian/.debhelper/wham-align/dbgsym-root .. dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_arm64.deb'. dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../wham-align_0.1.5-8_arm64.buildinfo dpkg-genchanges --build=binary -O../wham-align_0.1.5-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/650689/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/650689/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/650689 and its subdirectories I: Current time: Thu Sep 3 21:22:28 +14 2026 I: pbuilder-time-stamp: 1788420148 + false + set +x Thu Sep 3 07:22:28 UTC 2026 I: Signing ./b2/wham-align_0.1.5-8_arm64.buildinfo as wham-align_0.1.5-8_arm64.buildinfo.asc Thu Sep 3 07:22:28 UTC 2026 I: Signed ./b2/wham-align_0.1.5-8_arm64.buildinfo as ./b2/wham-align_0.1.5-8_arm64.buildinfo.asc Thu Sep 3 07:22:28 UTC 2026 - build #2 for wham-align/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Thu Sep 3 07:22:28 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-f6Cnfijh, removing. /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk: total 120 drwxr-xr-x 2 jenkins jenkins 4096 Aug 1 00:58 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 1 00:59 b2 -rw------- 1 jenkins jenkins 104237 Aug 1 00:58 rbuildlog.jrPCAOm -rw-r--r-- 1 jenkins jenkins 1987 Feb 19 2021 wham-align_0.1.5-8.dsc /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b1: total 804 -rw-r--r-- 1 jenkins jenkins 100819 Aug 1 00:58 build.log -rw-r--r-- 1 jenkins jenkins 514056 Aug 1 00:58 wham-align-dbgsym_0.1.5-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 7760 Aug 1 00:58 wham-align_0.1.5-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1987 Aug 1 00:58 wham-align_0.1.5-8.dsc -rw-r--r-- 1 jenkins jenkins 4873 Aug 1 00:58 wham-align_0.1.5-8_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5755 Aug 1 00:58 wham-align_0.1.5-8_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1394 Aug 1 00:58 wham-align_0.1.5-8_arm64.changes -rw-r--r-- 1 jenkins jenkins 155040 Aug 1 00:58 wham-align_0.1.5-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 1249 Aug 1 00:58 wham-align_0.1.5-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b2: total 796 -rw-r--r-- 1 jenkins jenkins 102759 Aug 1 00:59 build.log -rw-r--r-- 1 jenkins jenkins 514056 Aug 1 00:59 wham-align-dbgsym_0.1.5-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 7760 Aug 1 00:59 wham-align_0.1.5-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1987 Aug 1 00:59 wham-align_0.1.5-8.dsc -rw-r--r-- 1 jenkins jenkins 4873 Aug 1 00:59 wham-align_0.1.5-8_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5755 Aug 1 00:59 wham-align_0.1.5-8_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1394 Aug 1 00:59 wham-align_0.1.5-8_arm64.changes -rw-r--r-- 1 jenkins jenkins 155040 Aug 1 00:59 wham-align_0.1.5-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 1249 Aug 1 00:59 wham-align_0.1.5-8_source.changes Fri Aug 1 00:59:29 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Fri Aug 1 00:59:30 UTC 2025 I: wham-align_0.1.5-8_arm64.changes: Format: 1.8 Date: Fri, 19 Feb 2021 12:34:48 +0530 Source: wham-align Binary: wham-align wham-align-dbgsym Architecture: arm64 Version: 0.1.5-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: wham-align - Wisconsin's High-Throughput Alignment Method Changes: wham-align (0.1.5-8) unstable; urgency=medium . * Team Upload. * Append -fsignedchar in CXXFLAFS for autopkgtests fix Checksums-Sha1: 313605a9db12653aa4d55dae00ab35cc76174d81 514056 wham-align-dbgsym_0.1.5-8_arm64.deb 8c1e978f612e981ece8775130de75da43abf7723 4873 wham-align_0.1.5-8_arm64.buildinfo f38ac7fd78565ccd681d0c5d8d9fb1b730017aed 155040 wham-align_0.1.5-8_arm64.deb Checksums-Sha256: 5eebd5b47a2963a09ed773872070f853b95f3e5bc84d8853d61e353c0dd83a64 514056 wham-align-dbgsym_0.1.5-8_arm64.deb 2e43a2c4920ec147fd8fa65f446a31b6a4f0e2b45a5e3aa70949c935fac98a0e 4873 wham-align_0.1.5-8_arm64.buildinfo f89d7dbaade6c5ed53d55cf2f0379955fb78317de60982f1c771166d898dd675 155040 wham-align_0.1.5-8_arm64.deb Files: 06267089f464cbfddcb79af4304f3a8a 514056 debug optional wham-align-dbgsym_0.1.5-8_arm64.deb 448c5b7d5ccabb62a598257c25ed229c 4873 science optional wham-align_0.1.5-8_arm64.buildinfo 7efc5baa6eae69284a141ae39f74b7fc 155040 science optional wham-align_0.1.5-8_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/wham-align_0.1.5-8.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/wham-align_0.1.5-8.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/wham-align_0.1.5-8.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/wham-align_0.1.5-8.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/wham-align_0.1.5-8_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/wham-align_0.1.5-8.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-08-01 00:58:57.426276239 +0000 +++ b2/build.log 2025-08-01 00:59:29.698317694 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 31 12:58:31 -12 2025 -I: pbuilder-time-stamp: 1754009911 +I: Current time: Thu Sep 3 21:21:59 +14 2026 +I: pbuilder-time-stamp: 1788420119 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying cross-build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/343008/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/650689/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 3 07:22 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/650689/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/650689/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='7f8c17cfd97a456aa773f7c1d84f4c19' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='343008' - PS1='# ' - PS2='> ' + INVOCATION_ID=89f9b3d315294d5baa4bfe043155ff74 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=650689 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/pbuilderrc_25AF --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/pbuilderrc_Enk8 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/343008/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/650689/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -137,7 +169,7 @@ Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] -Fetched 11.0 MB in 0s (103 MB/s) +Fetched 11.0 MB in 0s (77.5 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) @@ -268,7 +300,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes +I: user script /srv/workspace/pbuilder/650689/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/650689/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/wham-align-0.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../wham-align_0.1.5-8_source.changes dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable @@ -328,14 +364,42 @@ short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 212 | while (len = readLine(file, str, 256)) { | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': +interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 67 | for (int i = 0; i < numLevel - 1; i++) { + | ~~^~~~~~~~~~~~~~ short.cpp: In member function 'ShortRead** ShortRead::split(int)': short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 483 | if (szPartition <= nRead - curRead) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +In file included from hitset.h:31, + from hitset.cpp:1: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ +interval.cpp: In member function 'int IntervalTree::save(char*)': +interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 304 | if (ret != numLEntry) { + | ~~~~^~~~~~~~~~~~ +interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 310 | if (ret != numIEntry) { + | ~~~~^~~~~~~~~~~~ model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)': model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable] 76 | unsigned int nIndex, nLookup, nBucket; | ^~~~~~ +interval.cpp: In member function 'int IntervalTree::load(char*)': +interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 359 | if (ret != numLEntry) { + | ~~~~^~~~~~~~~~~~ +interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 370 | if (ret != numIEntry) { + | ~~~~^~~~~~~~~~~~ +pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': +pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] + 602 | int i, j, offset, min, tmp; + | ^~~~~~ model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()': model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] 166 | fscanf(file, "MemTotal: %d kB\n", &memTotal); @@ -361,21 +425,6 @@ | | | | int* unsigned int* | %d -model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': -model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] - 198 | double nSpace, p0, p1, p2; - | ^~ -In file included from hitset.h:31, - from writer.h:26, - from writer.cpp:21: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ -pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': -pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] - 602 | int i, j, offset, min, tmp; - | ^~~~~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; @@ -392,6 +441,10 @@ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ +model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': +model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] + 198 | double nSpace, p0, p1, p2; + | ^~ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ @@ -419,60 +472,21 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': -writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] - 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; -writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] - 148 | uint32 sid = 0, soffset = 0; - | ^~~ -writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] - 148 | uint32 sid = 0, soffset = 0; - | ^~~~~~~ -writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': -writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^ -writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^ -writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^ -writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^~~~~~~~ -writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] - 272 | int64 code1, code2; - | ^~~~~ -writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] - 272 | int64 code1, code2; - | ^~~~~ -writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] - 278 | double p, sump; - | ^ -writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] - 278 | double p, sump; - | ^~~~ -writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] - 279 | char qseq[128], rseq[128], tag[128]; - | ^~~ -writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] - 281 | char shortread[256]; +hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': +hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] + 90 | bool pairMatch = false; | ^~~~~~~~~ -writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': -writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { - | ~~^~~~~~~~~~~~~~~ -writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': -writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { - | ~~^~~~~~~~~~~~~~~ -writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': -writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] - 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { - | ~~~~~^~~~~~~ In file included from hitset.h:31, - from hitset.cpp:1: + from hash.h:29, + from aligner.h:25, + from aligner.cpp:25: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ +In file included from hitset.h:31, + from hash.h:29, + from hash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { @@ -497,6 +511,10 @@ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ +edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': +edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] + 61 | int i; + | ^ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ @@ -506,6 +524,16 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ +edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': +edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] + 181 | char tmp_trace = traceback[i][j]; + | ^~~~~~~~~ +edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] + 132 | int k = 0, x = 0, y = 0; + | ^ +edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] + 132 | int k = 0, x = 0, y = 0; + | ^ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; @@ -516,25 +544,75 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ +edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] + 178 | int kk = 0; + | ^~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ +pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': +pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] + 602 | int i, j, offset, min, tmp; + | ^~~~~~ +pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': +pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': -hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] - 90 | bool pairMatch = false; - | ^~~~~~~~~ +pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ In file included from hitset.h:31, from hash.h:29, - from hash.cpp:27: + from embedhash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ +pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~ +pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] + 685 | int a; + | ^ +pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': +pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~ +pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] + 756 | int a; + | ^ +pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': +pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] + 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); + | ~~~~~~~^~~~~~~~~~ +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ +hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': +hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] + 86 | int size; + | ^~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -574,6 +652,10 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); @@ -586,10 +668,16 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ +short.cpp: In member function 'int ShortRead::load(int)': +short.cpp:424:28: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] + 424 | forward_word = (forward_word << BITS_PER_BASE) | code; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +short.cpp:310:38: note: 'code' was declared here + 310 | int64 forward_word, backward_word, code; + | ^~~~ In file included from hitset.h:31, - from hash.h:29, - from aligner.h:25, - from aligner.cpp:25: + from writer.h:26, + from writer.cpp:21: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { @@ -637,17 +725,89 @@ pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ +hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': +hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] + 86 | int size; + | ^~~~ +writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': +writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] + 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; +writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] + 148 | uint32 sid = 0, soffset = 0; + | ^~~ +writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] + 148 | uint32 sid = 0, soffset = 0; + | ^~~~~~~ +writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': +writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^ +writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^ +writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^ +writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^~~~~~~~ +writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] + 272 | int64 code1, code2; + | ^~~~~ +writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] + 272 | int64 code1, code2; + | ^~~~~ +writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] + 278 | double p, sump; + | ^ +writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] + 278 | double p, sump; + | ^~~~ +writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] + 279 | char qseq[128], rseq[128], tag[128]; + | ^~~ +writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] + 281 | char shortread[256]; + | ^~~~~~~~~ +short.cpp: In member function 'ShortRead** ShortRead::split(int)': +short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] + 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); + | ^~ +writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': +writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { + | ~~^~~~~~~~~~~~~~~ +short.cpp:503:42: note: directive argument in the range [0, 2147483646] + 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); + | ^~~~~~~~ +short.cpp:503:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 + 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] + 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); + | ^~ +short.cpp:510:42: note: directive argument in the range [0, 2147483646] + 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); + | ^~~~~~~~ +short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 + 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': +writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { + | ~~^~~~~~~~~~~~~~~ +writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': +writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] + 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { + | ~~~~~^~~~~~~ In file included from hitset.h:31, from hash.h:29, - from embedhash.cpp:27: + from aligner.h:25, + from builder.cpp:31: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { | ~~~~^~~~~~~~ -hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': -hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] - 86 | int size; - | ^~~~ pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; @@ -668,10 +828,6 @@ pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 682 | register unsigned long long P, M, X, U, Y; | ^ -interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': -interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 67 | for (int i = 0; i < numLevel - 1; i++) { - | ~~^~~~~~~~~~~~~~ pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] 684 | int i, p, num, base, Cscore; | ^~~ @@ -681,10 +837,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] 755 | int i, p, num, base, Cscore; @@ -695,24 +847,10 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ -interval.cpp: In member function 'int IntervalTree::save(char*)': -interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 304 | if (ret != numLEntry) { - | ~~~~^~~~~~~~~~~~ -interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 310 | if (ret != numIEntry) { - | ~~~~^~~~~~~~~~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ -interval.cpp: In member function 'int IntervalTree::load(char*)': -interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 359 | if (ret != numLEntry) { - | ~~~~^~~~~~~~~~~~ -interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 370 | if (ret != numIEntry) { - | ~~~~^~~~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; @@ -721,53 +859,10 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ -edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': -edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] - 61 | int i; - | ^ -edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': -edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] - 181 | char tmp_trace = traceback[i][j]; - | ^~~~~~~~~ -edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] - 132 | int k = 0, x = 0, y = 0; - | ^ -edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] - 132 | int k = 0, x = 0, y = 0; - | ^ -edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] - 178 | int kk = 0; - | ^~ -short.cpp: In member function 'int ShortRead::load(int)': -short.cpp:424:28: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] - 424 | forward_word = (forward_word << BITS_PER_BASE) | code; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -short.cpp:310:38: note: 'code' was declared here - 310 | int64 forward_word, backward_word, code; - | ^~~~ -short.cpp: In member function 'ShortRead** ShortRead::split(int)': -short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] - 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); - | ^~ -short.cpp:503:42: note: directive argument in the range [0, 2147483646] - 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); - | ^~~~~~~~ -short.cpp:503:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 - 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] - 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); - | ^~ -short.cpp:510:42: note: directive argument in the range [0, 2147483646] - 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); - | ^~~~~~~~ -short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 - 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, - from builder.cpp:31: + from main.cpp:34: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { @@ -870,18 +965,108 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ +aligner.cpp: In member function 'int Aligner::initLookupArray()': +aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] + 365 | if ((indexBits[i] >> j) & 0x1 == 1) { + | ~~~~^~~~ +aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] + 371 | if ((indexBits[i] >> j) & 0x1 == 1) { + | ~~~~^~~~ pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); | ~~~~~~~^~~~~~~~~~ +aligner.cpp: In member function 'int Aligner::preProcessHashTables()': +aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 534 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ +aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 712 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp: In member function 'int Aligner::build(char*)': +aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] + 724 | unsigned int i, j; + | ^ +aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] + 724 | unsigned int i, j; + | ^ +aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': +aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 807 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ +aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 983 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1006 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +hash.cpp: In member function 'int HashTable::preProcessEnd()': +hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] + 236 | if (h >= nHistogram) + | ~~^~~~~~~~~~~~~ +hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 285 | if (useEmbedTables() && tmp > embedShreshold) { + | ~~~~^~~~~~~~~~~~~~~~ +aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': +aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] + 1035 | uint32 offset; + | ^~~~~~ +aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] + 1039 | int nHit = 0; + | ^~~~ sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] 97 | char * str; @@ -890,6 +1075,17 @@ sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 238 | for (i = 0; i < numFile; i++) { | ~~^~~~~~~~~ +hash.cpp: In member function 'void HashTable::setScanThreshold(double)': +hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 343 | for (int i = 0; i < nHistogram - 1; i++) { + | ~~^~~~~~~~~~~~~~~~ +aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': +aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] + 1119 | uint32 offset; + | ^~~~~~ +aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] + 1123 | int nHit = 0; + | ^~~~ sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 309 | ( i = 0; i < nSeq; i++) | ~~^~~~~~ @@ -899,65 +1095,6 @@ sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 344 | for (j = 0; j < numError + 1; j++) { | ~~^~~~~~~~~~~~~~ -sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 410 | if (lenSegmentN > numError + 1) { - | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 429 | if (lenSegmentN > numError + 1) { - | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] - 223 | unsigned int step, nextstep; - | ^~~~ -sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] - 223 | unsigned int step, nextstep; - | ^~~~~~~~ -sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': -sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 534 | for (i = 0; i < numFile; i++) { - | ~~^~~~~~~~~ -sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 599 | if (lenSegmentN > nError + 1) - | ~~~~~~~~~~~~^~~~~~~~~~~~ -sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] - 520 | unsigned int step, nextstep; - | ^~~~ -sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] - 520 | unsigned int step, nextstep; - | ^~~~~~~~ -sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~~~ -sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~~~ -sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~~ -sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~ -sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~ -sequence.cpp: In member function 'int CompactSequence::save(char*)': -sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 738 | if (ret != size) { - | ~~~~^~~~~~~ -sequence.cpp: In member function 'int CompactSequence::load(char*)': -sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 804 | if (ret != size) { - | ~~~~^~~~~~~ -hash.cpp: In member function 'int HashTable::preProcessEnd()': -hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] - 236 | if (h >= nHistogram) - | ~~^~~~~~~~~~~~~ -hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 285 | if (useEmbedTables() && tmp > embedShreshold) { - | ~~~~^~~~~~~~~~~~~~~~ -hash.cpp: In member function 'void HashTable::setScanThreshold(double)': -hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 343 | for (int i = 0; i < nHistogram - 1; i++) { - | ~~^~~~~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 460 | overflowPool[curOverflowEntry] = @@ -979,9 +1116,38 @@ hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] 418 | uint32 * bloomFilter; | ^~~~~~~~~~~ +aligner.cpp: In member function 'int Aligner::check(int)': +aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1436 | for (i = 0; i < num; i++) { + | ~~^~~~~ hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] 419 | uint32 bloomFilterNum; | ^~~~~~~~~~~~~~ +aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1452 | for (j = 0; j < nError; j++) { + | ~~^~~~~~~~ +sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 410 | if (lenSegmentN > numError + 1) { + | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] + 1426 | int ret; + | ^~~ +sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 429 | if (lenSegmentN > numError + 1) { + | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] + 223 | unsigned int step, nextstep; + | ^~~~ +sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] + 223 | unsigned int step, nextstep; + | ^~~~~~~~ +aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)': +aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1541 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1547 | for (i = 0; i < res.nRead; i++) { + | ~~^~~~~~~~~~~ hash.cpp: In member function 'int HashTable::buildEmbedTable()': hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], @@ -998,6 +1164,34 @@ hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 472 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ +aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1629 | delete writer; + | ^~~~~~~~~~~~~ +aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] + 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; + | ^~~~ +aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] + 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; + | ^~~~~~ +aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] + 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; + | ^~~~~~ +aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] + 1505 | int strand; + | ^~~~~~ +aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] + 1508 | float ratio; + | ^~~~~ +aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] + 1514 | bool sorted = info->sorted, strata = info->strata; + | ^~~~~~ +sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': +sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 534 | for (i = 0; i < numFile; i++) { + | ~~^~~~~~~~~ +sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 599 | if (lenSegmentN > nError + 1) + | ~~~~~~~~~~~~^~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)': hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable] 587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; @@ -1008,6 +1202,49 @@ hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ +sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] + 520 | unsigned int step, nextstep; + | ^~~~ +sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] + 520 | unsigned int step, nextstep; + | ^~~~~~~~ +sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~~~ +sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~~~ +sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~~ +sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~ +sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~ +aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': +aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1685 | for (i = 0; i < res.nRead; i++) { + | ~~^~~~~~~~~~~ +aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1754 | delete writer; + | ^~~~~~~~~~~~~ +aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] + 1637 | bool success; + | ^~~~~~~ +aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] + 1638 | unsigned int nSuccessRead = 0; + | ^~~~~~~~~~~~ +aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] + 1639 | FILE * file = NULL; + | ^~~~ +aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] + 1646 | char mateFilename[256]; + | ^~~~~~~~~~~~ +aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] + 1652 | bool sorted = info->sorted, strata = info->strata; + | ^~~~~~ hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; @@ -1018,6 +1255,21 @@ hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ +sequence.cpp: In member function 'int CompactSequence::save(char*)': +sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 738 | if (ret != size) { + | ~~~~^~~~~~~ +aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': +aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1851 | delete writer; + | ^~~~~~~~~~~~~ +sequence.cpp: In member function 'int CompactSequence::load(char*)': +sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 804 | if (ret != size) { + | ~~~~^~~~~~~ +aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] + 1775 | int i, ret; + | ^~~ hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] 746 | int num; @@ -1031,6 +1283,10 @@ hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] 753 | uint32 sid, soffset; | ^~~~~~~ +aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': +aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1989 | delete writer; + | ^~~~~~~~~~~~~ hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; @@ -1038,6 +1294,9 @@ hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ +aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] + 1874 | int i, ret; + | ^~~ hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable] 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; | ^~~~~~~ @@ -1084,13 +1343,6 @@ hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1321 | uint32 entryOffset, seqOffset, offset; | ^~~~~~ -aligner.cpp: In member function 'int Aligner::initLookupArray()': -aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] - 365 | if ((indexBits[i] >> j) & 0x1 == 1) { - | ~~~~^~~~ -aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] - 371 | if ((indexBits[i] >> j) & 0x1 == 1) { - | ~~~~^~~~ hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 1673 | uint32 entryOffset, seqOffset, offset; @@ -1098,75 +1350,6 @@ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ -aligner.cpp: In member function 'int Aligner::preProcessHashTables()': -aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 534 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 712 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp: In member function 'int Aligner::build(char*)': -aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] - 724 | unsigned int i, j; - | ^ -aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] - 724 | unsigned int i, j; - | ^ -aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': -aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 807 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 983 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1006 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] 137 | const double ln2 = log(2); @@ -1178,19 +1361,12 @@ embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] 255 | int64 top = total - total * r; | ^~~ -aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': -aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] - 1035 | uint32 offset; - | ^~~~~~ embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)': embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] 369 | overflowPool[curOverflowEntry] = embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable] 328 | uint32 seqOffset; | ^~~~~~~~~ -aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] - 1039 | int nHit = 0; - | ^~~~ embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable] 330 | uint32 counter = 0; | ^~~~~~~ @@ -1216,13 +1392,6 @@ embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 387 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ -aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': -aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] - 1119 | uint32 offset; - | ^~~~~~ -aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] - 1123 | int nHit = 0; - | ^~~~ embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable] 389 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ @@ -1232,164 +1401,47 @@ embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~~~~~ -aligner.cpp: In member function 'int Aligner::check(int)': -aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1436 | for (i = 0; i < num; i++) { - | ~~^~~~~ -aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1452 | for (j = 0; j < nError; j++) { - | ~~^~~~~~~~ -aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] - 1426 | int ret; - | ^~~ -aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)': -aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1541 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1547 | for (i = 0; i < res.nRead; i++) { - | ~~^~~~~~~~~~~ -aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1629 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] - 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; - | ^~~~ -aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] - 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; - | ^~~~~~ -aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] - 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; - | ^~~~~~ -aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] - 1505 | int strand; - | ^~~~~~ -aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] - 1508 | float ratio; - | ^~~~~ -aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] - 1514 | bool sorted = info->sorted, strata = info->strata; - | ^~~~~~ -aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': -aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1685 | for (i = 0; i < res.nRead; i++) { - | ~~^~~~~~~~~~~ -aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1754 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] - 1637 | bool success; - | ^~~~~~~ -aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] - 1638 | unsigned int nSuccessRead = 0; - | ^~~~~~~~~~~~ -aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] - 1639 | FILE * file = NULL; - | ^~~~ -aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] - 1646 | char mateFilename[256]; - | ^~~~~~~~~~~~ -aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] - 1652 | bool sorted = info->sorted, strata = info->strata; - | ^~~~~~ -aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': -aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1851 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] - 1775 | int i, ret; - | ^~~ -aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': -aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1989 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] - 1874 | int i, ret; - | ^~~ -In file included from hitset.h:31, - from hash.h:29, - from aligner.h:25, - from main.cpp:34: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ -hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': -hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] - 1049 | } - | ^ -builder.cpp: In function 'int getArguVal(char*)': -builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 115 | else if (*c = 'g' || *c == 'G') +main.cpp: In function 'int getArguVal(char*)': +main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 159 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ -pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': -pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] - 602 | int i, j, offset, min, tmp; - | ^~~~~~ -pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': -pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~ +main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': +main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] + 350 | int i, j, ret; + | ^ +main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] + 350 | int i, j, ret; + | ^ +main.cpp: In function 'int main(int, char**)': +main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] + 523 | int numKeys; + | ^~~~~~~ +main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] + 526 | int nSeq = 1; + | ^~~~ +main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] + 532 | CompactSequence * sequence; + | ^~~~~~~~ +main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] + 534 | pthread_t * threadpool; + | ^~~~~~~~~~ +main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] + 536 | int * threadid; + | ^~~~~~~~ In file included from embedhash.cpp:32: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ -pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~~ -pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] - 685 | int a; - | ^ -builder.cpp: In function 'int main(int, char**)': -builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] - 159 | int build_mode = BUILD_MODE_ALL; - | ^~~~~~~~~~ -builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] - 277 | int nChar = sequence->getNum(); - | ^~~~~ -pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': -pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~ -pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~~ -pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] - 756 | int a; - | ^ -pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': -pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] - 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); - | ~~~~~~~^~~~~~~~~~ +hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': +hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] + 1049 | } + | ^ In file included from hash.cpp:31: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ -hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': -hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] - 86 | int size; - | ^~~~ -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ In file included from pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] @@ -1406,50 +1458,27 @@ rdtsc.h:20:22: note: 'tick' was declared here 20 | unsigned long long tick; | ^~~~ -main.cpp: In function 'int getArguVal(char*)': -main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 159 | else if (*c = 'g' || *c == 'G') +builder.cpp: In function 'int getArguVal(char*)': +builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 115 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ -main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': -main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] - 350 | int i, j, ret; - | ^ -main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] - 350 | int i, j, ret; - | ^ -In file included from builder.cpp:34: +builder.cpp: In function 'int main(int, char**)': +builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] + 159 | int build_mode = BUILD_MODE_ALL; + | ^~~~~~~~~~ +builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] + 277 | int nChar = sequence->getNum(); + | ^~~~~ +In file included from main.cpp:38: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ -main.cpp: In function 'int main(int, char**)': -main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] - 523 | int numKeys; - | ^~~~~~~ -main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] - 526 | int nSeq = 1; - | ^~~~ -main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] - 532 | CompactSequence * sequence; - | ^~~~~~~~ -main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] - 534 | pthread_t * threadpool; - | ^~~~~~~~~~ -main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] - 536 | int * threadid; - | ^~~~~~~~ -In file included from main.cpp:38: +In file included from builder.cpp:34: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ -sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': -sequence.cpp:430:27: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized] - 430 | offsetInOrgSeq++; - | ~~~~~~~~~~~~~~^~ -sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here - 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; - | ^~~~~~~~~~~~~~ main.cpp: In function 'void mergeFiles(std::string)': main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] 269 | sprintf(buf, ".t%d ", i); @@ -1469,13 +1498,13 @@ main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 276 | sprintf(buf, ".t%d", i); | ~~~~~~~^~~~~~~~~~~~~~~~ -sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': -sequence.cpp:676:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] - 676 | forward_word = (forward_word << BITS_PER_BASE) | code; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence.cpp:630:23: note: 'code' was declared here - 630 | int64 forward_word, code; - | ^~~~ +sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': +sequence.cpp:430:27: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized] + 430 | offsetInOrgSeq++; + | ~~~~~~~~~~~~~~^~ +sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here + 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; + | ^~~~~~~~~~~~~~ In member function 'void HashTable::setLookupInfo(int, int*)', inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] @@ -1485,6 +1514,13 @@ aligner.cpp:360:7: note: 'keySpan' was declared here 360 | int keySpan; | ^~~~~~~ +sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': +sequence.cpp:676:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] + 676 | forward_word = (forward_word << BITS_PER_BASE) | code; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence.cpp:630:23: note: 'code' was declared here + 630 | int64 forward_word, code; + | ^~~~ aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': aligner.cpp:1097:3: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized] 1097 | if (ret == MSG_HITSETFULL) @@ -1496,7 +1532,7 @@ g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5' dh_auto_test - rm -fr -- /tmp/dh-xdg-rundir-YemjULBL + rm -fr -- /tmp/dh-xdg-rundir-zVdUpRYy create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1615,12 +1651,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/650689/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/650689/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/343008 and its subdirectories -I: Current time: Thu Jul 31 12:58:56 -12 2025 -I: pbuilder-time-stamp: 1754009936 +I: removing directory /srv/workspace/pbuilder/650689 and its subdirectories +I: Current time: Thu Sep 3 21:22:28 +14 2026 +I: pbuilder-time-stamp: 1788420148 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/wham-align_0.1.5-8.diff: 85.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/wham-align_0.1.5-8.diff.gz b2/build.log: 85.5% -- replaced with stdout Compressing the 1st log... b1/build.log: 86.0% -- replaced with stdout Fri Aug 1 00:59:31 UTC 2025 I: diffoscope 302 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_wham-align_unstable_arm64_1754009971 + touch /var/log/reproducible-builds/diffoscope_stamp_wham-align_unstable_arm64_1754009971 + RESULT=0 + systemd-run '--description=diffoscope on wham-align/0.1.5-8 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_8-80494 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk --run-session -c jenkins-reproducible-unstable-diffoscope-e048ddf7-374a-496d-a256-f99d2e45c63e -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/dbd-tmp-fJplFDe ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/wham-align_0.1.5-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/wham-align_0.1.5-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/wham-align_0.1.5-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b1/wham-align_0.1.5-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b2/wham-align_0.1.5-8_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_8-80494.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/wham-align_0.1.5-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/wham-align_0.1.5-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/wham-align_0.1.5-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b1/wham-align_0.1.5-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.3r4sbfsk/b2/wham-align_0.1.5-8_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 161ms CPU time consumed: 163ms _ _ _ __ _| |__ __ _ _ __ ___ __ _| (_) __ _ _ __ \ \ /\ / / '_ \ / _` | '_ ` _ \ _____ / _` | | |/ _` | '_ \ \ V V /| | | | (_| | | | | | |_____| (_| | | | (_| | | | | \_/\_/ |_| |_|\__,_|_| |_| |_| \__,_|_|_|\__, |_| |_| |___/ Fri Aug 1 00:59:31 UTC 2025 I: diffoscope 302 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 1 00:59:31 UTC 2025 I: wham-align from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-08-01 00:59:31] INFO: Starting at 2025-08-01 00:59:31.946285 [2025-08-01 00:59:31] INFO: Generating the pages of 1 package(s) [2025-08-01 00:59:32] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/wham-align didn't produce a buildlog, even though it has been built. [2025-08-01 00:59:32] INFO: Finished at 2025-08-01 00:59:32.130499, took: 0:00:00.184217 Fri Aug 1 00:59:32 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/wham-align.html Fri Aug 1 00:59:32 UTC 2025 I: Removing signed wham-align_0.1.5-8_arm64.buildinfo.asc files: removed './b1/wham-align_0.1.5-8_arm64.buildinfo.asc' removed './b2/wham-align_0.1.5-8_arm64.buildinfo.asc' 1754009972 arm64 unstable wham-align Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/wham-align_0.1.5-8.rbuild.log: 84.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/wham-align_0.1.5-8.rbuild.log.gz [2025-08-01 00:59:32] INFO: Starting at 2025-08-01 00:59:32.384381 [2025-08-01 00:59:32] INFO: Generating the pages of 1 package(s) [2025-08-01 00:59:32] INFO: Finished at 2025-08-01 00:59:32.566775, took: 0:00:00.182398 All cleanup done. Fri Aug 1 00:59:32 UTC 2025 - total duration: 0h 1m 5s. Fri Aug 1 00:59:32 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-gDBDduAF, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1min 6.100s CPU time consumed: 4.395s