Running as unit: rb-build-amd64_37-38639.service ==================================================================================== Mon Nov 25 09:35:41 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_37) on jenkins, called using "infom01-amd64 infom02-amd64" as arguments. Mon Nov 25 09:35:42 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-2PmTC01m" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 25 09:35:42 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Nov 25 09:35:42 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Q8B1fi' Mon Nov 25 09:35:42 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Nov 25 09:35:42 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-9m8KZ8' ok, let's check if snap-aligner is building anywhere yet… ok, snap-aligner is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of snap-aligner in trixie on amd64 on jenkins now. 1st build will be done on infom01-amd64.debian.net. 2nd build will be done on infom02-amd64.debian.net. ============================================================================= Mon Nov 25 09:36:01 UTC 2024 I: starting to build snap-aligner/trixie/amd64 on jenkins on '2024-11-25 09:35' Mon Nov 25 09:36:01 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_37/38639/console.log 1732527361 amd64 trixie snap-aligner Mon Nov 25 09:36:01 UTC 2024 I: Downloading source for trixie/snap-aligner=2.0.3+dfsg-2 --2024-11-25 09:36:01-- http://deb.debian.org/debian/pool/main/s/snap-aligner/snap-aligner_2.0.3%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2281 (2.2K) [text/prs.lines.tag] Saving to: ‘snap-aligner_2.0.3+dfsg-2.dsc’ 0K .. 100% 247M=0s 2024-11-25 09:36:01 (247 MB/s) - ‘snap-aligner_2.0.3+dfsg-2.dsc’ saved [2281/2281] --2024-11-25 09:36:01-- http://deb.debian.org/debian/pool/main/s/snap-aligner/snap-aligner_2.0.3%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2281 (2.2K) [text/prs.lines.tag] Saving to: ‘snap-aligner_2.0.3+dfsg-2.dsc’ 0K .. 100% 247M=0s 2024-11-25 09:36:01 (247 MB/s) - ‘snap-aligner_2.0.3+dfsg-2.dsc’ saved [2281/2281] Mon Nov 25 09:36:01 UTC 2024 I: snap-aligner_2.0.3+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: snap-aligner Binary: snap-aligner Architecture: amd64 arm64 mips64el ppc64el s390x alpha kfreebsd-amd64 ppc64 riscv64 sparc64 loong64 Version: 2.0.3+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Pranav Ballaney Homepage: https://snap.cs.berkeley.edu/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/snap-aligner Vcs-Git: https://salsa.debian.org/med-team/snap-aligner.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), help2man, zlib1g-dev, libsimde-dev Package-List: snap-aligner deb science optional arch=amd64,arm64,mips64el,ppc64el,s390x,alpha,kfreebsd-amd64,ppc64,riscv64,sparc64,loong64 Checksums-Sha1: 9e63e397151ab04ea3a2c42f486fb1d25afb2c41 2023128 snap-aligner_2.0.3+dfsg.orig.tar.xz 631671bcd8f50d0e5e4447797c341b34a0f228f6 7788 snap-aligner_2.0.3+dfsg-2.debian.tar.xz Checksums-Sha256: f340590a4cff3e1f27bfa081123e4dacf61b1514855ae3dc9393b179756faff0 2023128 snap-aligner_2.0.3+dfsg.orig.tar.xz e20be3f8a3bc7204ea5ee293462dc2903eaf649eacb723ec4e27d71d405a266e 7788 snap-aligner_2.0.3+dfsg-2.debian.tar.xz Files: 0f41c32b741a1a0d43dfd09256ca2d12 2023128 snap-aligner_2.0.3+dfsg.orig.tar.xz fde1efc44134a040d2b715f1ef6623f9 7788 snap-aligner_2.0.3+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCgAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWgVLgOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtESZw//TeqeTPoJrTCr0gs5Pwej4NR6xZe4KkAQV3YJ aOE62pXAu0LsfRodNsI4edQEy7Hfjwp7IZOxe9FYmUYeE5j48MKpcM/itikisXDX F6i02De5qryMbij96y/xbqXu3YhTApl810+tY91HcIFrcbyxzcoL+7vcT5bbUL5V qEthVLebUkJDDLcMVUEbOTr1sW7R9RxVKqd8916GqpJOSLnfru0potS57QmdinBb cCbHHu/yvytlWCggbWaWzzibiSiW0Z9UmJYm7o9uK6KBq3+GqCL/luXFoOWeizjF j1hLftvyQAZZiZMGOMAPB0n4PYWZoZSdfpRmMVdo1YNqrv8BxTlxAF9rP1ufDfyL cqi4YpPAAF0AVdv4Fuqlrm78g+I/6AOqxC3yS4/6rcErmxY07dwhnEtHXyGxOuhW xC9/BoWC11uxcIuozA0DB7VgMyEGeIEg9EjZfNDIcx3074RCy6lZ6+3X39288Rrm 9I8fxixYusxpFPQTitMY+EarnR3rc4Yhr3NeAlXgNPg+t6jT6Mg4UWcE3VcMXjhB 4tmqkD+xFL2kYKtl7/kmwqVUDyXEyZAi8CL6i4T5wjUGA0s/Y8zHn4r0DOMIaCEN T4lJUjpf2Uhu7TcDCxvlGyA3zYJsYdfrdZM1+8Fzxc8r7jTHPy7O1e6PEnc6w1QP 6hJWAhg= =bnq5 -----END PGP SIGNATURE----- Mon Nov 25 09:36:01 UTC 2024 I: Checking whether the package is not for us Mon Nov 25 09:36:01 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Mon Nov 25 09:36:01 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Mon Nov 25 09:36:01 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Mon Nov 25 09:36:01 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-FuHg6V' ==================================================================================== Mon Nov 25 09:36:02 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "1 snap-aligner trixie /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx 2.0.3+dfsg-2" as arguments. Mon Nov 25 09:36:02 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-bIYSb5Bl" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Nov 25 09:36:03 UTC 2024 I: Downloading source for trixie/snap-aligner=2.0.3+dfsg-2 Reading package lists... NOTICE: 'snap-aligner' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snap-aligner.git Please use: git clone https://salsa.debian.org/med-team/snap-aligner.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2033 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (dsc) [2281 B] Get:2 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (tar) [2023 kB] Get:3 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (diff) [7788 B] Fetched 2033 kB in 0s (11.9 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'snap-aligner' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snap-aligner.git Please use: git clone https://salsa.debian.org/med-team/snap-aligner.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2033 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (dsc) [2281 B] Get:2 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (tar) [2023 kB] Get:3 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (diff) [7788 B] Fetched 2033 kB in 0s (11.9 MB/s) Download complete and in download only mode ============================================================================= Building snap-aligner in trixie on amd64 on infom01-amd64 now. Date: Mon Nov 25 09:36:03 UTC 2024 Date UTC: Mon Nov 25 09:36:03 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 24 21:36:03 -12 2024 I: pbuilder-time-stamp: 1732527363 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [snap-aligner_2.0.3+dfsg-2.dsc] I: copying [./snap-aligner_2.0.3+dfsg.orig.tar.xz] I: copying [./snap-aligner_2.0.3+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 11 20:51:04 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snap-aligner_2.0.3+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting snap-aligner in snap-aligner-2.0.3+dfsg dpkg-source: info: unpacking snap-aligner_2.0.3+dfsg.orig.tar.xz dpkg-source: info: unpacking snap-aligner_2.0.3+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying non-x86-and-kfreebsd dpkg-source: info: applying drop-msse dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2984219/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='eb77c74ecbdd485cbefd7bfe120609f2' 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='2984219' 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.Sz4RWHvx/pbuilderrc_52Fz --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b1 --logfile b1/build.log snap-aligner_2.0.3+dfsg-2.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' I: uname -a Linux infom01-amd64 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2984219/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: amd64 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), help2man, zlib1g-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 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. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev 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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{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, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 21.4 MB of archives. After unpacking 86.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 21.4 MB in 0s (77.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19969 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/snap-aligner-2.0.3+dfsg/ && 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 > ../snap-aligner_2.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 2.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' rm -f SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' rm -f debian/*.1 rm -f */*.d */*/*.d make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentAdjuster.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp SNAPLib/DataReader.cpp: In static member function 'static bool DecompressDataReader::decompress(z_stream*, ThreadHeap*, char*, _int64, _int64*, char*, _int64, _int64*, DecompressMode)': SNAPLib/DataReader.cpp:2052:53: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2052 | fprintf(stderr, "\n0x%llx\t", offset); | ~~~^ ~~~~~~ | | | | | _int64 {aka long int} | long long unsigned int | %lx SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)': SNAPLib/DataReader.cpp:2105:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2105 | sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp:2109:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2109 | sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp:2113:43: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2113 | sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)': SNAPLib/DataReader.cpp:2261:174: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/DataReader.cpp:2261:198: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | ~~~^ ~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/DataReader.cpp:2265:74: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2265 | fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] 96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); | ~~~^ ~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HitDepth.o SNAPLib/HitDepth.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)': SNAPLib/GenomeIndex.cpp:952:36: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:952:61: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:952:103: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:1007:36: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | ~~~^ | | | long long int | %ld 1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | _uint64 {aka long unsigned int} SNAPLib/GenomeIndex.cpp:1007:50: warning: format '%lld' expects argument of type 'long long int', but argument 10 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | ~~~^ | | | long long int | %ld 1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | ~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} SNAPLib/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)': SNAPLib/GenomeIndex.cpp:1879:57: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] 1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/GenomeIndex.cpp:1879:71: warning: format '%lld' expects argument of type 'long long int*', but argument 10 has type 'size_t*' {aka 'long unsigned int*'} [-Wformat=] 1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | ~~~^ | | | long long int* | %ld 1880 | &hashTableKeySize, &hashTablesFileSize, &smallHashTable, &locationSize))) { | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': SNAPLib/Genome.cpp:216:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] 216 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, GENOME_FLAG_ALT_CONTIGS_MARKED); | ~~~^ ~~~~~~ | | | | | long int | long long int | %ld SNAPLib/Genome.cpp:226:31: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/Genome.cpp:226:42: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_int64' {aka 'long int'} [-Wformat=] 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': SNAPLib/Genome.cpp:356:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { | ~~~^ ~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/Genome.cpp:356:58: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { | ~~~^ ~~~~~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)': SNAPLib/Genome.cpp:497:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] 497 | if (NULL == retval || 3 != sscanf(linebuf,"%lld %d %d\n", nBases, nContigs, &flags)) { | ~~~^ ~~~~~~ | | | | | GenomeDistance* {aka long int*} | long long int* | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp In file included from SNAPLib/PairedAligner.cpp:47: SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/PairedAligner.cpp: In member function 'void PairedAlignerContext::runIterationThreadImpl(Read**)': SNAPLib/PairedAligner.cpp:673:72: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 673 | fprintf(stderr, "reporter:counter:SNAP,readsAligned,%llu\n", stats->totalReads - readsWhenLastReported); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] 44 | } | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': SNAPLib/SAM.cpp:1292:116: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'long int' [-Wformat=] 1292 | bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%llu%s\n", contig->name, contig->length - context.genome->getChromosomePadding(), contig->isALT ? "\tAH:*":""); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long int | %lu SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writePairs(const ReaderContext&, LandauVishkinWithCigar*, AffineGapVectorizedWithCigar*, bool, char*, size_t, size_t*, size_t*, Read**, GenomeLocation*, PairedAlignmentResult*, bool, bool, char*, bool, int*, int*, bool*, bool*) const': SNAPLib/SAM.cpp:1854:77: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 1858 | positionInContig[whichRead], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:1854:95: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 1862 | matePositionInContig[whichRead], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, LandauVishkinWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': SNAPLib/SAM.cpp:2076:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2080 | positionInContig, | ~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2076:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2084 | matePositionInContig, | ~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2076:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long int | %ld ...... 2085 | templateLength, | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, AffineGapVectorizedWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': SNAPLib/SAM.cpp:2312:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2316 | positionInContig, | ~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2312:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2320 | matePositionInContig, | ~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2312:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long int | %ld ...... 2321 | templateLength, | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2650:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp:2654:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2745:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp:2749:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp: In static member function 'static void SAMFormat::printRead(const Genome*, Read*, GenomeLocation)': SNAPLib/SAM.cpp:2820:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'GenomeLocation' {aka 'long int'} [-Wformat=] 2820 | printf("Aligned location %s:%llu\n", | ~~~^ | | | long long unsigned int | %lu 2821 | genome->getContigAtLocation(location)->name, 2822 | location - genome->getContigAtLocation(location)->beginningLocation); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeLocation {aka long int} g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThreadImpl(Read*&)': SNAPLib/SingleAligner.cpp:207:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 207 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': SNAPLib/Util.cpp:167:49: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 167 | sprintf(tempBuf, ",%03lld", x % 1000); | ~~~~~^ ~~~~~~~~ | | | | | _uint64 {aka long unsigned int} | long long int | %03ld SNAPLib/Util.cpp:170:46: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 170 | sprintf(tempBuf, "%lld", x); | ~~~^ ~ | | | | | _uint64 {aka long unsigned int} | long long int | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2650:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~ SNAPLib/SAM.cpp:2650:54: note: directive argument in the range [1, 9223372036854775807] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/fstream:43, from SNAPLib/stdafx.h:14, from SNAPLib/SAM.cpp:19: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2650:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2654:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~ SNAPLib/SAM.cpp:2654:52: note: directive argument in the range [1, 9223372036854775807] 2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2654:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2745:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~ SNAPLib/SAM.cpp:2745:54: note: directive argument in the range [1, 9223372036854775807] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2745:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2749:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~ SNAPLib/SAM.cpp:2749:52: note: directive argument in the range [1, 9223372036854775807] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2749:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o snap-aligner -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz g++ -o unit_tests -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o g++ -o SNAPCommand -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' help2man --no-discard-stderr --no-info --version-string="2.0.3" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./snap-aligner > debian/snap-aligner.1 for option in index single paired; do help2man \ --no-discard-stderr --no-info --version-string="2.0.3" \ --include=debian/snap-aligner-${option}-man-include \ --help-option=" " "./snap-aligner ${option}" > \ debian/snap-aligner-${option}.1; done help2man --no-discard-stderr --no-info --version-string="2.0.3" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./SNAPCommand > debian/SNAPCommand.1 make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_test ./unit_tests AffineGapTest: - synthetic: [OK] AffineGapVectorizedTest: - equal strings: [OK] - one deletion: [OK] - long deletion: [OK] - long insertion: [OK] - synthetic: [OK] EventTest: - many waiters: [OK] - single waiters: [OK] LandauVishkinTest: - equal strings: [OK] - prefixes: [OK] - non-equal strings: [OK] - overly distant strings: [OK] - CIGAR strings: [OK] ProbabilityDistanceTest: - basic probabilities: [OK] - indels: [OK] 15 / 15 tests passed. make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/snap-aligner/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'snap-aligner' in '../snap-aligner_2.0.3+dfsg-2_amd64.deb'. dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.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/2984219 and its subdirectories I: Current time: Sun Nov 24 21:37:40 -12 2024 I: pbuilder-time-stamp: 1732527460 Mon Nov 25 09:37:40 UTC 2024 I: Signing ./b1/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo as snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc Mon Nov 25 09:37:40 UTC 2024 I: Signed ./b1/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo as ./b1/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc Mon Nov 25 09:37:40 UTC 2024 - build #1 for snap-aligner/trixie/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Mon Nov 25 09:37:40 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-bIYSb5Bl, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 09:37 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 09:36 b2 -rw------- 1 jenkins jenkins 3441 Nov 25 09:36 rbuildlog.5Q2jOJH -rw-r--r-- 1 jenkins jenkins 2281 Jan 11 2024 snap-aligner_2.0.3+dfsg-2.dsc /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b1: total 3740 -rw-r--r-- 1 jenkins jenkins 94897 Nov 25 09:37 build.log -rw-r--r-- 1 jenkins jenkins 2858108 Nov 25 09:37 snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 7788 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2281 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5177 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6059 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1511 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 831912 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1364 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b2: total 0 Mon Nov 25 09:37:41 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 24 21:36:03 -12 2024 I: pbuilder-time-stamp: 1732527363 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [snap-aligner_2.0.3+dfsg-2.dsc] I: copying [./snap-aligner_2.0.3+dfsg.orig.tar.xz] I: copying [./snap-aligner_2.0.3+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 11 20:51:04 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snap-aligner_2.0.3+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting snap-aligner in snap-aligner-2.0.3+dfsg dpkg-source: info: unpacking snap-aligner_2.0.3+dfsg.orig.tar.xz dpkg-source: info: unpacking snap-aligner_2.0.3+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying non-x86-and-kfreebsd dpkg-source: info: applying drop-msse dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2984219/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='eb77c74ecbdd485cbefd7bfe120609f2' 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='2984219' 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.Sz4RWHvx/pbuilderrc_52Fz --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b1 --logfile b1/build.log snap-aligner_2.0.3+dfsg-2.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' I: uname -a Linux infom01-amd64 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2984219/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: amd64 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), help2man, zlib1g-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 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. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev 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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{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, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 21.4 MB of archives. After unpacking 86.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 21.4 MB in 0s (77.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19969 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/snap-aligner-2.0.3+dfsg/ && 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 > ../snap-aligner_2.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 2.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' rm -f SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' rm -f debian/*.1 rm -f */*.d */*/*.d make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentAdjuster.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp SNAPLib/DataReader.cpp: In static member function 'static bool DecompressDataReader::decompress(z_stream*, ThreadHeap*, char*, _int64, _int64*, char*, _int64, _int64*, DecompressMode)': SNAPLib/DataReader.cpp:2052:53: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2052 | fprintf(stderr, "\n0x%llx\t", offset); | ~~~^ ~~~~~~ | | | | | _int64 {aka long int} | long long unsigned int | %lx SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)': SNAPLib/DataReader.cpp:2105:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2105 | sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp:2109:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2109 | sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp:2113:43: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2113 | sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)': SNAPLib/DataReader.cpp:2261:174: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/DataReader.cpp:2261:198: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | ~~~^ ~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/DataReader.cpp:2265:74: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2265 | fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] 96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); | ~~~^ ~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HitDepth.o SNAPLib/HitDepth.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)': SNAPLib/GenomeIndex.cpp:952:36: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:952:61: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:952:103: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:1007:36: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | ~~~^ | | | long long int | %ld 1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | _uint64 {aka long unsigned int} SNAPLib/GenomeIndex.cpp:1007:50: warning: format '%lld' expects argument of type 'long long int', but argument 10 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | ~~~^ | | | long long int | %ld 1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | ~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} SNAPLib/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)': SNAPLib/GenomeIndex.cpp:1879:57: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] 1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/GenomeIndex.cpp:1879:71: warning: format '%lld' expects argument of type 'long long int*', but argument 10 has type 'size_t*' {aka 'long unsigned int*'} [-Wformat=] 1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | ~~~^ | | | long long int* | %ld 1880 | &hashTableKeySize, &hashTablesFileSize, &smallHashTable, &locationSize))) { | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': SNAPLib/Genome.cpp:216:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] 216 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, GENOME_FLAG_ALT_CONTIGS_MARKED); | ~~~^ ~~~~~~ | | | | | long int | long long int | %ld SNAPLib/Genome.cpp:226:31: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/Genome.cpp:226:42: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_int64' {aka 'long int'} [-Wformat=] 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': SNAPLib/Genome.cpp:356:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { | ~~~^ ~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/Genome.cpp:356:58: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { | ~~~^ ~~~~~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)': SNAPLib/Genome.cpp:497:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] 497 | if (NULL == retval || 3 != sscanf(linebuf,"%lld %d %d\n", nBases, nContigs, &flags)) { | ~~~^ ~~~~~~ | | | | | GenomeDistance* {aka long int*} | long long int* | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp In file included from SNAPLib/PairedAligner.cpp:47: SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/PairedAligner.cpp: In member function 'void PairedAlignerContext::runIterationThreadImpl(Read**)': SNAPLib/PairedAligner.cpp:673:72: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 673 | fprintf(stderr, "reporter:counter:SNAP,readsAligned,%llu\n", stats->totalReads - readsWhenLastReported); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] 44 | } | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': SNAPLib/SAM.cpp:1292:116: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'long int' [-Wformat=] 1292 | bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%llu%s\n", contig->name, contig->length - context.genome->getChromosomePadding(), contig->isALT ? "\tAH:*":""); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long int | %lu SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writePairs(const ReaderContext&, LandauVishkinWithCigar*, AffineGapVectorizedWithCigar*, bool, char*, size_t, size_t*, size_t*, Read**, GenomeLocation*, PairedAlignmentResult*, bool, bool, char*, bool, int*, int*, bool*, bool*) const': SNAPLib/SAM.cpp:1854:77: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 1858 | positionInContig[whichRead], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:1854:95: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 1862 | matePositionInContig[whichRead], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, LandauVishkinWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': SNAPLib/SAM.cpp:2076:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2080 | positionInContig, | ~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2076:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2084 | matePositionInContig, | ~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2076:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long int | %ld ...... 2085 | templateLength, | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, AffineGapVectorizedWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': SNAPLib/SAM.cpp:2312:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2316 | positionInContig, | ~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2312:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2320 | matePositionInContig, | ~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2312:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long int | %ld ...... 2321 | templateLength, | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2650:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp:2654:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2745:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp:2749:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp: In static member function 'static void SAMFormat::printRead(const Genome*, Read*, GenomeLocation)': SNAPLib/SAM.cpp:2820:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'GenomeLocation' {aka 'long int'} [-Wformat=] 2820 | printf("Aligned location %s:%llu\n", | ~~~^ | | | long long unsigned int | %lu 2821 | genome->getContigAtLocation(location)->name, 2822 | location - genome->getContigAtLocation(location)->beginningLocation); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeLocation {aka long int} g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThreadImpl(Read*&)': SNAPLib/SingleAligner.cpp:207:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 207 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': SNAPLib/Util.cpp:167:49: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 167 | sprintf(tempBuf, ",%03lld", x % 1000); | ~~~~~^ ~~~~~~~~ | | | | | _uint64 {aka long unsigned int} | long long int | %03ld SNAPLib/Util.cpp:170:46: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 170 | sprintf(tempBuf, "%lld", x); | ~~~^ ~ | | | | | _uint64 {aka long unsigned int} | long long int | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2650:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~ SNAPLib/SAM.cpp:2650:54: note: directive argument in the range [1, 9223372036854775807] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/fstream:43, from SNAPLib/stdafx.h:14, from SNAPLib/SAM.cpp:19: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2650:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2654:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~ SNAPLib/SAM.cpp:2654:52: note: directive argument in the range [1, 9223372036854775807] 2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2654:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2745:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~ SNAPLib/SAM.cpp:2745:54: note: directive argument in the range [1, 9223372036854775807] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2745:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2749:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~ SNAPLib/SAM.cpp:2749:52: note: directive argument in the range [1, 9223372036854775807] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2749:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o snap-aligner -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz g++ -o unit_tests -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o g++ -o SNAPCommand -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' help2man --no-discard-stderr --no-info --version-string="2.0.3" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./snap-aligner > debian/snap-aligner.1 for option in index single paired; do help2man \ --no-discard-stderr --no-info --version-string="2.0.3" \ --include=debian/snap-aligner-${option}-man-include \ --help-option=" " "./snap-aligner ${option}" > \ debian/snap-aligner-${option}.1; done help2man --no-discard-stderr --no-info --version-string="2.0.3" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./SNAPCommand > debian/SNAPCommand.1 make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_test ./unit_tests AffineGapTest: - synthetic: [OK] AffineGapVectorizedTest: - equal strings: [OK] - one deletion: [OK] - long deletion: [OK] - long insertion: [OK] - synthetic: [OK] EventTest: - many waiters: [OK] - single waiters: [OK] LandauVishkinTest: - equal strings: [OK] - prefixes: [OK] - non-equal strings: [OK] - overly distant strings: [OK] - CIGAR strings: [OK] ProbabilityDistanceTest: - basic probabilities: [OK] - indels: [OK] 15 / 15 tests passed. make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/snap-aligner/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'snap-aligner' in '../snap-aligner_2.0.3+dfsg-2_amd64.deb'. dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.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/2984219 and its subdirectories I: Current time: Sun Nov 24 21:37:40 -12 2024 I: pbuilder-time-stamp: 1732527460 Mon Nov 25 09:37:42 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Mon Nov 25 09:37:42 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Mon Nov 25 09:37:42 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Mon Nov 25 09:37:42 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-JqDdT6' ==================================================================================== Sun Dec 28 16:00:43 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "2 snap-aligner trixie /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx 2.0.3+dfsg-2" as arguments. Sun Dec 28 16:00:43 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-wF5iDbDh" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Dec 28 16:00:43 UTC 2025 I: Downloading source for trixie/snap-aligner=2.0.3+dfsg-2 Reading package lists... NOTICE: 'snap-aligner' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snap-aligner.git Please use: git clone https://salsa.debian.org/med-team/snap-aligner.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2033 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (dsc) [2281 B] Get:2 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (tar) [2023 kB] Get:3 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (diff) [7788 B] Fetched 2033 kB in 0s (18.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'snap-aligner' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/snap-aligner.git Please use: git clone https://salsa.debian.org/med-team/snap-aligner.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2033 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (dsc) [2281 B] Get:2 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (tar) [2023 kB] Get:3 http://deb.debian.org/debian trixie/main snap-aligner 2.0.3+dfsg-2 (diff) [7788 B] Fetched 2033 kB in 0s (18.0 MB/s) Download complete and in download only mode ============================================================================= Re-Building snap-aligner in trixie on amd64 on infom02-amd64 now. Date: Sun Dec 28 16:00:43 UTC 2025 Date UTC: Sun Dec 28 16:00:43 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/pbuilderrc_ij0J + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' snap-aligner = debian-installer -o snap-aligner = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' snap-aligner = u-boot ']' + case "${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.Sz4RWHvx/pbuilderrc_ij0J --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b2 --logfile b2/build.log snap-aligner_2.0.3+dfsg-2.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: Mon Dec 29 06:00:44 +14 2025 I: pbuilder-time-stamp: 1766937644 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [snap-aligner_2.0.3+dfsg-2.dsc] I: copying [./snap-aligner_2.0.3+dfsg.orig.tar.xz] I: copying [./snap-aligner_2.0.3+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 11 20:51:04 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./snap-aligner_2.0.3+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting snap-aligner in snap-aligner-2.0.3+dfsg dpkg-source: info: unpacking snap-aligner_2.0.3+dfsg.orig.tar.xz dpkg-source: info: unpacking snap-aligner_2.0.3+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying non-x86-and-kfreebsd dpkg-source: info: applying drop-msse dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3017260/tmp/hooks/D01_modify_environment starting debug: Running on infom02-amd64. 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 Dec 28 16:00 /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/3017260/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3017260/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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=ac7a0dd3b6db4b6bba9bc073fdc8d5bb LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=3017260 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.Sz4RWHvx/pbuilderrc_ij0J --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b2 --logfile b2/build.log snap-aligner_2.0.3+dfsg-2.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' I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3017260/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: amd64 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), help2man, zlib1g-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 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. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev 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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsimde-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{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, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 21.4 MB of archives. After unpacking 86.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 21.4 MB in 0s (81.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19969 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. 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Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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/3017260/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3017260/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/snap-aligner-2.0.3+dfsg/ && 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 > ../snap-aligner_2.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 2.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' rm -f SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' rm -f debian/*.1 rm -f */*.d */*/*.d make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGap.o SNAPLib/AffineGap.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AffineGapVectorized.o SNAPLib/AffineGapVectorized.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentAdjuster.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp SNAPLib/DataReader.cpp: In static member function 'static bool DecompressDataReader::decompress(z_stream*, ThreadHeap*, char*, _int64, _int64*, char*, _int64, _int64*, DecompressMode)': SNAPLib/DataReader.cpp:2052:53: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2052 | fprintf(stderr, "\n0x%llx\t", offset); | ~~~^ ~~~~~~ | | | | | _int64 {aka long int} | long long unsigned int | %lx SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)': SNAPLib/DataReader.cpp:2105:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2105 | sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp:2109:50: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2109 | sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp:2113:43: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 2113 | sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int long int | %ld SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)': SNAPLib/DataReader.cpp:2261:174: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/DataReader.cpp:2261:198: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] 2261 | fprintf(stderr, "Bug in DecompressDataReader::decompressThread(); don't have enough decompress buffer when we thought we'd assured it. Existing size %lld, needed (at least) %lld, entry @0x%p\n", entry->decompressedSize, output, entry); | ~~~^ ~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/DataReader.cpp:2265:74: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 2265 | fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset()); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': SNAPLib/Error.cpp:96:49: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] 96 | fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); | ~~~^ ~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HitDepth.o SNAPLib/HitDepth.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': SNAPLib/Genome.cpp:216:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] 216 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, GENOME_FLAG_ALT_CONTIGS_MARKED); | ~~~^ ~~~~~~ | | | | | long int | long long int | %ld SNAPLib/Genome.cpp:226:31: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/Genome.cpp:226:42: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_int64' {aka 'long int'} [-Wformat=] 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _int64 {aka long int} | %ld SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': SNAPLib/Genome.cpp:356:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { | ~~~^ ~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/Genome.cpp:356:58: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { | ~~~^ ~~~~~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)': SNAPLib/Genome.cpp:497:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] 497 | if (NULL == retval || 3 != sscanf(linebuf,"%lld %d %d\n", nBases, nContigs, &flags)) { | ~~~^ ~~~~~~ | | | | | GenomeDistance* {aka long int*} | long long int* | %ld SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)': SNAPLib/GenomeIndex.cpp:952:36: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:952:61: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:952:103: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); | ~~~^ ~~~~~~~~~~~ | | | | long long int _uint64 {aka long unsigned int} | %ld SNAPLib/GenomeIndex.cpp:1007:36: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | ~~~^ | | | long long int | %ld 1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | _uint64 {aka long unsigned int} SNAPLib/GenomeIndex.cpp:1007:50: warning: format '%lld' expects argument of type 'long long int', but argument 10 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1007 | fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, | ~~~^ | | | long long int | %ld 1008 | index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); | ~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} SNAPLib/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)': SNAPLib/GenomeIndex.cpp:1879:57: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] 1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | long long int* _int64* {aka long int*} | %ld SNAPLib/GenomeIndex.cpp:1879:71: warning: format '%lld' expects argument of type 'long long int*', but argument 10 has type 'size_t*' {aka 'long unsigned int*'} [-Wformat=] 1879 | if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, | ~~~^ | | | long long int* | %ld 1880 | &hashTableKeySize, &hashTablesFileSize, &smallHashTable, &locationSize))) { | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp In file included from SNAPLib/PairedAligner.cpp:47: SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ SNAPLib/PairedAligner.cpp: In member function 'void PairedAlignerContext::runIterationThreadImpl(Read**)': SNAPLib/PairedAligner.cpp:673:72: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 673 | fprintf(stderr, "reporter:counter:SNAP,readsAligned,%llu\n", stats->totalReads - readsWhenLastReported); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] 44 | } | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': SNAPLib/SAM.cpp:1292:116: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'long int' [-Wformat=] 1292 | bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%llu%s\n", contig->name, contig->length - context.genome->getChromosomePadding(), contig->isALT ? "\tAH:*":""); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long int | %lu SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writePairs(const ReaderContext&, LandauVishkinWithCigar*, AffineGapVectorizedWithCigar*, bool, char*, size_t, size_t*, size_t*, Read**, GenomeLocation*, PairedAlignmentResult*, bool, bool, char*, bool, int*, int*, bool*, bool*) const': SNAPLib/SAM.cpp:1854:77: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 1858 | positionInContig[whichRead], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:1854:95: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 1854 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%d\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 1862 | matePositionInContig[whichRead], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, LandauVishkinWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': SNAPLib/SAM.cpp:2076:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2080 | positionInContig, | ~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2076:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2084 | matePositionInContig, | ~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2076:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] 2076 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long int | %ld ...... 2085 | templateLength, | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, AffineGapVectorizedWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, bool, int*, int, int, bool, char*, bool, _int64, int, int, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool, int, int) const': SNAPLib/SAM.cpp:2312:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2316 | positionInContig, | ~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2312:91: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long unsigned int | %lu ...... 2320 | matePositionInContig, | ~~~~~~~~~~~~~~~~~~~~ | | | GenomeDistance {aka long int} SNAPLib/SAM.cpp:2312:97: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] 2312 | int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%llu\t%d\t%s\t%s\t%llu\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s%s%s%s%.*s\n", | ~~~^ | | | long long int | %ld ...... 2321 | templateLength, | ~~~~~~~~~~~~~~ | | | _int64 {aka long int} SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2650:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp:2654:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2745:58: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp:2749:56: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int GenomeDistance {aka long int} | %lu SNAPLib/SAM.cpp: In static member function 'static void SAMFormat::printRead(const Genome*, Read*, GenomeLocation)': SNAPLib/SAM.cpp:2820:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'GenomeLocation' {aka 'long int'} [-Wformat=] 2820 | printf("Aligned location %s:%llu\n", | ~~~^ | | | long long unsigned int | %lu 2821 | genome->getContigAtLocation(location)->name, 2822 | location - genome->getContigAtLocation(location)->beginningLocation); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | GenomeLocation {aka long int} g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp SNAPLib/SingleAligner.cpp: In member function 'virtual void SingleAlignerContext::runIterationThreadImpl(Read*&)': SNAPLib/SingleAligner.cpp:207:67: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 207 | fprintf(stderr,"reporter:counter:SNAP,readsAligned,%llu\n",stats->totalReads - readsWhenLastReported); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': SNAPLib/Util.cpp:167:49: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 167 | sprintf(tempBuf, ",%03lld", x % 1000); | ~~~~~^ ~~~~~~~~ | | | | | _uint64 {aka long unsigned int} | long long int | %03ld SNAPLib/Util.cpp:170:46: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 170 | sprintf(tempBuf, "%lld", x); | ~~~^ ~ | | | | | _uint64 {aka long unsigned int} | long long int | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2650:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~ SNAPLib/SAM.cpp:2650:54: note: directive argument in the range [1, 9223372036854775807] 2650 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/fstream:43, from SNAPLib/stdafx.h:14, from SNAPLib/SAM.cpp:19: In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2650:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2654:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~ SNAPLib/SAM.cpp:2654:52: note: directive argument in the range [1, 9223372036854775807] 2654 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2654:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2745:55: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~ SNAPLib/SAM.cpp:2745:54: note: directive argument in the range [1, 9223372036854775807] 2745 | snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2745:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)': SNAPLib/SAM.cpp:2749:53: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~ SNAPLib/SAM.cpp:2749:52: note: directive argument in the range [1, 9223372036854775807] 2749 | snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', inlined from 'static const char* SAMFormat::computeCigarString(const Genome*, AffineGapVectorizedWithCigar*, char*, int, char*, int, const char*, const char*, GenomeDistance, int, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*, int*)' at SNAPLib/SAM.cpp:2749:21: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -o snap-aligner -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz g++ -o unit_tests -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o tests/AffineGapTest.o tests/AffineGapVectorizedTest.o tests/EventTest.o tests/LandauVishkinTest.o tests/ProbabilityDistanceTest.o tests/TestLib.o tests/main.o -lrt -lz echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o g++ -o SNAPCommand -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/AffineGap.o SNAPLib/AffineGapVectorized.o SNAPLib/AlignerContext.o SNAPLib/AlignerOptions.o SNAPLib/AlignerStats.o SNAPLib/AlignmentAdjuster.o SNAPLib/AlignmentResult.o SNAPLib/ApproximateCounter.o SNAPLib/Bam.o SNAPLib/BaseAligner.o SNAPLib/BigAlloc.o SNAPLib/BufferedAsync.o SNAPLib/ChimericPairedEndAligner.o SNAPLib/CommandProcessor.o SNAPLib/Compat.o SNAPLib/DataReader.o SNAPLib/DataWriter.o SNAPLib/Error.o SNAPLib/FASTA.o SNAPLib/FASTQ.o SNAPLib/GenericFile.o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_stdio.o SNAPLib/Genome.o SNAPLib/GenomeIndex.o SNAPLib/GzipDataWriter.o SNAPLib/HashTable.o SNAPLib/Histogram.o SNAPLib/HitDepth.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/LandauVishkin.o SNAPLib/MultiInputReadSupplier.o SNAPLib/PairedAligner.o SNAPLib/PairedReadMatcher.o SNAPLib/ParallelTask.o SNAPLib/ProbabilityDistance.o SNAPLib/RangeSplitter.o SNAPLib/Read.o SNAPLib/ReadReader.o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadWriter.o SNAPLib/SAM.o SNAPLib/Seed.o SNAPLib/SeedSequencer.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/Tables.o SNAPLib/Util.o SNAPLib/exit.o SNAPLib/mapq.o SNAPLib/stdafx.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz make[2]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' help2man --no-discard-stderr --no-info --version-string="2.0.3" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./snap-aligner > debian/snap-aligner.1 for option in index single paired; do help2man \ --no-discard-stderr --no-info --version-string="2.0.3" \ --include=debian/snap-aligner-${option}-man-include \ --help-option=" " "./snap-aligner ${option}" > \ debian/snap-aligner-${option}.1; done help2man --no-discard-stderr --no-info --version-string="2.0.3" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./SNAPCommand > debian/SNAPCommand.1 make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' dh_auto_test ./unit_tests AffineGapTest: - synthetic: [OK] AffineGapVectorizedTest: - equal strings: [OK] - one deletion: [OK] - long deletion: [OK] - long insertion: [OK] - synthetic: [OK] EventTest: - many waiters: [OK] - single waiters: [OK] LandauVishkinTest: - equal strings: [OK] - prefixes: [OK] - non-equal strings: [OK] - overly distant strings: [OK] - CIGAR strings: [OK] ProbabilityDistanceTest: - basic probabilities: [OK] - indels: [OK] 15 / 15 tests passed. make[1]: Leaving directory '/build/reproducible-path/snap-aligner-2.0.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/snap-aligner/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb'. dpkg-deb: building package 'snap-aligner' in '../snap-aligner_2.0.3+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.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/3017260/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3017260/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/3017260 and its subdirectories I: Current time: Mon Dec 29 06:02:49 +14 2025 I: pbuilder-time-stamp: 1766937769 + false + set +x Sun Dec 28 16:02:49 UTC 2025 I: Signing ./b2/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo as snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc Sun Dec 28 16:02:49 UTC 2025 I: Signed ./b2/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo as ./b2/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc Sun Dec 28 16:02:49 UTC 2025 - build #2 for snap-aligner/trixie/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Sun Dec 28 16:02:49 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-wF5iDbDh, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx: total 116 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 09:37 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 25 09:39 b2 -rw------- 1 jenkins jenkins 98627 Nov 25 09:37 rbuildlog.5Q2jOJH -rw-r--r-- 1 jenkins jenkins 2281 Jan 11 2024 snap-aligner_2.0.3+dfsg-2.dsc /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b1: total 3752 -rw-r--r-- 1 jenkins jenkins 94897 Nov 25 09:37 build.log -rw-r--r-- 1 jenkins jenkins 2858108 Nov 25 09:37 snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 7788 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2281 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5177 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6059 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1511 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 831912 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1364 Nov 25 09:37 snap-aligner_2.0.3+dfsg-2_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b2: total 3740 -rw-r--r-- 1 jenkins jenkins 96832 Nov 25 09:39 build.log -rw-r--r-- 1 jenkins jenkins 2858108 Nov 25 09:39 snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 7788 Nov 25 09:39 snap-aligner_2.0.3+dfsg-2.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2281 Nov 25 09:39 snap-aligner_2.0.3+dfsg-2.dsc -rw-r--r-- 1 jenkins jenkins 5180 Nov 25 09:39 snap-aligner_2.0.3+dfsg-2_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6062 Nov 25 09:39 snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1511 Nov 25 09:39 snap-aligner_2.0.3+dfsg-2_amd64.changes -rw-r--r-- 1 jenkins jenkins 831912 Nov 25 09:39 snap-aligner_2.0.3+dfsg-2_amd64.deb -rw-r--r-- 1 jenkins jenkins 1364 Nov 25 09:39 snap-aligner_2.0.3+dfsg-2_source.changes Mon Nov 25 09:39:50 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Mon Nov 25 09:39:51 UTC 2024 I: snap-aligner_2.0.3+dfsg-2_amd64.changes: Format: 1.8 Date: Thu, 11 Jan 2024 21:49:06 +0100 Source: snap-aligner Binary: snap-aligner snap-aligner-dbgsym Architecture: amd64 Version: 2.0.3+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: snap-aligner - Scalable Nucleotide Alignment Program Closes: 1050330 1059989 Changes: snap-aligner (2.0.3+dfsg-2) unstable; urgency=medium . * Team upload. * Add loong64 to list of architectures Closes: #1050330, #1059989 Checksums-Sha1: f7ca4f09cced386ccaac54a456109dc23e588461 2858108 snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb 1d6a558b1eada118cc8c4327c0d9591c7e884e7b 5177 snap-aligner_2.0.3+dfsg-2_amd64.buildinfo 2cfa4a3750effd9b10884a31750ff2195813cf2c 831912 snap-aligner_2.0.3+dfsg-2_amd64.deb Checksums-Sha256: 66d816c219b7de29304739aa10abca269e524c2635579c3c9e6f4f99cbd4324a 2858108 snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb 72753d959e903f10234088bb87d989a1bed463bbdb6d7e794ba5ef04cc10af4c 5177 snap-aligner_2.0.3+dfsg-2_amd64.buildinfo 652dc15fe2f514681cea4d33b46016424d1af30d56f588e1b810e87bf2bb57c6 831912 snap-aligner_2.0.3+dfsg-2_amd64.deb Files: d8bd4bc402e7831966b9d4230b1294dc 2858108 debug optional snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb 14de1a7eccbd359e03ac5f8fb746ee70 5177 science optional snap-aligner_2.0.3+dfsg-2_amd64.buildinfo c005d2d75ea9fa872f4a2b07f9e28d24 831912 science optional snap-aligner_2.0.3+dfsg-2_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snap-aligner_2.0.3+dfsg-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snap-aligner_2.0.3+dfsg-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/snap-aligner_2.0.3+dfsg-2.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/snap-aligner_2.0.3+dfsg-2.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snap-aligner_2.0.3+dfsg-2.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-25 09:37:41.404199727 +0000 +++ b2/build.log 2024-11-25 09:39:50.482394635 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Nov 24 21:36:03 -12 2024 -I: pbuilder-time-stamp: 1732527363 +I: Current time: Mon Dec 29 06:00:44 +14 2025 +I: pbuilder-time-stamp: 1766937644 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,51 +30,83 @@ dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2984219/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3017260/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +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 Dec 28 16:00 /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/3017260/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3017260/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='amd64' - 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='eb77c74ecbdd485cbefd7bfe120609f2' - 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='2984219' - PS1='# ' - PS2='> ' + INVOCATION_ID=ac7a0dd3b6db4b6bba9bc073fdc8d5bb + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=3017260 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.Sz4RWHvx/pbuilderrc_52Fz --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b1 --logfile b1/build.log snap-aligner_2.0.3+dfsg-2.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' + 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.Sz4RWHvx/pbuilderrc_ij0J --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b2 --logfile b2/build.log snap-aligner_2.0.3+dfsg-2.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' I: uname -a - Linux infom01-amd64 6.1.0-28-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2984219/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3017260/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -149,7 +181,7 @@ Get: 31 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 21.4 MB in 0s (77.9 MB/s) +Fetched 21.4 MB in 0s (81.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19969 files and directories currently installed.) @@ -296,7 +328,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snap-aligner-2.0.3+dfsg/ && 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 > ../snap-aligner_2.0.3+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/3017260/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3017260/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snap-aligner-2.0.3+dfsg/ && 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 > ../snap-aligner_2.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 2.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -412,6 +448,47 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HitDepth.o SNAPLib/HitDepth.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp +SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': +SNAPLib/Genome.cpp:216:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] + 216 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, GENOME_FLAG_ALT_CONTIGS_MARKED); + | ~~~^ ~~~~~~ + | | | + | | long int + | long long int + | %ld +SNAPLib/Genome.cpp:226:31: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] + 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +SNAPLib/Genome.cpp:226:42: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_int64' {aka 'long int'} [-Wformat=] + 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), + | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long long int _int64 {aka long int} + | %ld +SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': +SNAPLib/Genome.cpp:356:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] + 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { + | ~~~^ ~~~~~~~~~~~~ + | | | + | long long int* _int64* {aka long int*} + | %ld +SNAPLib/Genome.cpp:356:58: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] + 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { + | ~~~^ ~~~~~~~~~~~~~~~~ + | | | + | long long int* _int64* {aka long int*} + | %ld +SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)': +SNAPLib/Genome.cpp:497:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] + 497 | if (NULL == retval || 3 != sscanf(linebuf,"%lld %d %d\n", nBases, nContigs, &flags)) { + | ~~~^ ~~~~~~ + | | | + | | GenomeDistance* {aka long int*} + | long long int* + | %ld SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)': SNAPLib/GenomeIndex.cpp:952:36: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 952 | fprintf(histogramFile, "%lld larger than %d with %lld total genome locations, largest seed %lld\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); @@ -468,51 +545,8 @@ | ~~~~~~~~~~~~~~~~~~~ | | | size_t* {aka long unsigned int*} -SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': -SNAPLib/Genome.cpp:216:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'long int' [-Wformat=] - 216 | fprintf(saveFile,"%lld %d %d\n",nBases, nContigs, GENOME_FLAG_ALT_CONTIGS_MARKED); - | ~~~^ ~~~~~~ - | | | - | | long int - | long long int - | %ld -SNAPLib/Genome.cpp:226:31: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] - 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -SNAPLib/Genome.cpp:226:42: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_int64' {aka 'long int'} [-Wformat=] - 226 | fprintf(saveFile, "%lld %x %d %lld %x %d %d %s %s\n", GenomeLocationAsInt64(contigs[i].beginningLocation), (contigs[i].isALT ? GENOME_FLAG_CONTIG_IS_ALT : 0), OriginalContigNumToInt(contigs[i].originalContigNumber), GenomeLocationAsInt64(contigs[i].projBeginningLocation), - | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long long int _int64 {aka long int} - | %ld -SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': -SNAPLib/Genome.cpp:356:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] - 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { - | ~~~^ ~~~~~~~~~~~~ - | | | - | long long int* _int64* {aka long int*} - | %ld -SNAPLib/Genome.cpp:356:58: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] - 356 | if (7 != sscanf(contigNameBuffer, "%lld %x %d %lld %x %d %d", &contigStart, &flags, &originalContigNumber, &projContigStart, &altProjRC, &contigNameSize, &cigarLength)) { - | ~~~^ ~~~~~~~~~~~~~~~~ - | | | - | long long int* _int64* {aka long int*} - | %ld -SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)': -SNAPLib/Genome.cpp:497:51: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] - 497 | if (NULL == retval || 3 != sscanf(linebuf,"%lld %d %d\n", nBases, nContigs, &flags)) { - | ~~~^ ~~~~~~ - | | | - | | GenomeDistance* {aka long int*} - | long long int* - | %ld g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp In file included from SNAPLib/IntersectingPairedEndAligner.cpp:24: SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; @@ -520,7 +554,8 @@ SNAPLib/IntersectingPairedEndAligner.h:767:104: warning: extended initializer lists only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp In file included from SNAPLib/PairedAligner.cpp:47: SNAPLib/IntersectingPairedEndAligner.h:767:71: warning: non-static data member initializers only available with '-std=c++11' or '-std=gnu++11' [-Wc++11-extensions] 767 | Direction setPairDirection[NUM_SET_PAIRS][NUM_READS_PER_PAIR] = { {FORWARD, RC}, {RC, FORWARD} }; @@ -535,6 +570,7 @@ | | | | long long unsigned int long unsigned int | %lu +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp @@ -697,6 +733,9 @@ | long long unsigned int long unsigned int | %lu g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t, size_t)': SNAPLib/Util.cpp:167:49: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] 167 | sprintf(tempBuf, ",%03lld", x % 1000); @@ -712,9 +751,6 @@ | | _uint64 {aka long unsigned int} | long long int | %ld -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapTest.o tests/AffineGapTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/AffineGapVectorizedTest.o tests/AffineGapVectorizedTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/snap-aligner-2.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++98 -O3 -fopenmp-simd -DSIMDE_ENABLE_OPENMP -MMD -ISNAPLib -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp @@ -865,8 +901,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'snap-aligner' in '../snap-aligner_2.0.3+dfsg-2_amd64.deb'. dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_2.0.3+dfsg-2_amd64.deb'. +dpkg-deb: building package 'snap-aligner' in '../snap-aligner_2.0.3+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../snap-aligner_2.0.3+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -874,12 +910,14 @@ 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/3017260/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3017260/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/2984219 and its subdirectories -I: Current time: Sun Nov 24 21:37:40 -12 2024 -I: pbuilder-time-stamp: 1732527460 +I: removing directory /srv/workspace/pbuilder/3017260 and its subdirectories +I: Current time: Mon Dec 29 06:02:49 +14 2025 +I: pbuilder-time-stamp: 1766937769 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snap-aligner_2.0.3+dfsg-2.diff: 83.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/snap-aligner_2.0.3+dfsg-2.diff.gz b2/build.log: 87.2% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.7% -- replaced with stdout Mon Nov 25 09:39:52 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_snap-aligner_trixie_amd64_1732527592 + touch /var/log/reproducible-builds/diffoscope_stamp_snap-aligner_trixie_amd64_1732527592 + RESULT=0 + systemd-run '--description=diffoscope on snap-aligner/2.0.3+dfsg-2 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_37-38639 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx --run-session -c jenkins-reproducible-trixie-diffoscope-9507897d-1bf2-4ecd-b190-bbf5ff8ab4ff -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/dbd-tmp-cYCxttZ ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/snap-aligner_2.0.3+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/snap-aligner_2.0.3+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/snap-aligner_2.0.3+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b1/snap-aligner_2.0.3+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b2/snap-aligner_2.0.3+dfsg-2_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_37-38639.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/snap-aligner_2.0.3+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/snap-aligner_2.0.3+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/snap-aligner_2.0.3+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b1/snap-aligner_2.0.3+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Sz4RWHvx/b2/snap-aligner_2.0.3+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.436s) 0.436s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.062s) 0.062s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 773ms CPU time consumed: 774ms _ _ ___ _ __ __ _ _ __ __ _| (_) __ _ _ __ ___ _ __ / __| '_ \ / _` | '_ \ _____ / _` | | |/ _` | '_ \ / _ \ '__| \__ \ | | | (_| | |_) |_____| (_| | | | (_| | | | | __/ | |___/_| |_|\__,_| .__/ \__,_|_|_|\__, |_| |_|\___|_| |_| |___/ Mon Nov 25 09:39:53 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Mon Nov 25 09:39:53 UTC 2024 I: snap-aligner from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-25 09:39:54] INFO: Starting at 2024-11-25 09:39:54.107265 [2024-11-25 09:39:54] INFO: Generating the pages of 1 package(s) [2024-11-25 09:39:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/snap-aligner_2.0.3+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/snap-aligner_2.0.3+dfsg-2.diff.gz is missing [2024-11-25 09:39:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/snap-aligner_2.0.3+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/snap-aligner_2.0.3+dfsg-2.diff.gz is missing [2024-11-25 09:39:54] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/snap-aligner didn't produce a buildlog, even though it has been built. [2024-11-25 09:39:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/snap-aligner_2.0.3+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/snap-aligner_2.0.3+dfsg-2.diff.gz is missing [2024-11-25 09:39:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/snap-aligner_2.0.3+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/snap-aligner_2.0.3+dfsg-2.diff.gz is missing [2024-11-25 09:39:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/snap-aligner_2.0.2+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/snap-aligner_2.0.2+dfsg-1.diff.gz is missing [2024-11-25 09:39:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/snap-aligner_2.0.2+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/snap-aligner_2.0.2+dfsg-1.diff.gz is missing [2024-11-25 09:39:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/snap-aligner_1.0.0+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/snap-aligner_1.0.0+dfsg-2.diff.gz is missing [2024-11-25 09:39:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/snap-aligner_1.0.0+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/snap-aligner_1.0.0+dfsg-2.diff.gz is missing [2024-11-25 09:39:54] INFO: Finished at 2024-11-25 09:39:54.601121, took: 0:00:00.493865 Mon Nov 25 09:39:54 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/snap-aligner.html Mon Nov 25 09:39:54 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Nov 25 09:39:54 UTC 2024 I: Submitting 8.0K b1/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc https://buildinfo.debian.net/1d6a558b1eada118cc8c4327c0d9591c7e884e7b/snap-aligner_2.0.3+dfsg-2_amd64 Mon Nov 25 09:39:55 UTC 2024 I: Submitting 8.0K b2/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc https://buildinfo.debian.net/c8f923e5a7c8c48ecf1c12bef709f6c3471667e2/snap-aligner_2.0.3+dfsg-2_amd64 Mon Nov 25 09:39:56 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Nov 25 09:39:56 UTC 2024 I: Done submitting .buildinfo files. Mon Nov 25 09:39:56 UTC 2024 I: Removing signed snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc files: removed './b1/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc' removed './b2/snap-aligner_2.0.3+dfsg-2_amd64.buildinfo.asc' 1732527596 amd64 trixie snap-aligner Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snap-aligner_2.0.3+dfsg-2.rbuild.log: 85.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/snap-aligner_2.0.3+dfsg-2.rbuild.log.gz [2024-11-25 09:39:56] INFO: Starting at 2024-11-25 09:39:56.560974 [2024-11-25 09:39:56] INFO: Generating the pages of 1 package(s) [2024-11-25 09:39:56] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/snap-aligner_2.0.3+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/snap-aligner_2.0.3+dfsg-2.diff.gz is missing [2024-11-25 09:39:56] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/snap-aligner_2.0.3+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/snap-aligner_2.0.3+dfsg-2.diff.gz is missing [2024-11-25 09:39:56] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/snap-aligner_2.0.3+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/snap-aligner_2.0.3+dfsg-2.diff.gz is missing [2024-11-25 09:39:56] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/snap-aligner_2.0.3+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/snap-aligner_2.0.3+dfsg-2.diff.gz is missing [2024-11-25 09:39:56] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/snap-aligner_2.0.2+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/snap-aligner_2.0.2+dfsg-1.diff.gz is missing [2024-11-25 09:39:56] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/snap-aligner_2.0.2+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/snap-aligner_2.0.2+dfsg-1.diff.gz is missing [2024-11-25 09:39:56] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/snap-aligner_1.0.0+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/snap-aligner_1.0.0+dfsg-2.diff.gz is missing [2024-11-25 09:39:56] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/i386/snap-aligner_1.0.0+dfsg-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/i386/snap-aligner_1.0.0+dfsg-2.diff.gz is missing [2024-11-25 09:39:56] INFO: Finished at 2024-11-25 09:39:56.988289, took: 0:00:00.427319 All cleanup done. Mon Nov 25 09:39:57 UTC 2024 - total duration: 0h 4m 11s. Mon Nov 25 09:39:57 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-2PmTC01m, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 4min 15.116s CPU time consumed: 7.594s