Diff of the two buildlogs: -- --- b1/build.log 2024-10-24 12:11:34.629783929 +0000 +++ b2/build.log 2024-10-24 12:15:47.108812339 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Oct 24 00:09:03 -12 2024 -I: pbuilder-time-stamp: 1729771743 +I: Current time: Thu Nov 27 08:34:37 +14 2025 +I: pbuilder-time-stamp: 1764182077 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,51 +31,83 @@ dpkg-source: info: applying relax-cython-dep.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3474472/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/300713/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 Nov 26 18:34 /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/300713/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/300713/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='65ab74cfd1de4fefa9cf2ef394fa18be' - 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='3474472' - PS1='# ' - PS2='> ' + INVOCATION_ID=dd202bfab3794949a84157bee7f3c0e5 + 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=300713 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.qEv0LxX1/pbuilderrc_llUL --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.qEv0LxX1/b1 --logfile b1/build.log abpoa_1.5.3-1.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.qEv0LxX1/pbuilderrc_Ad87 --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.qEv0LxX1/b2 --logfile b2/build.log abpoa_1.5.3-1.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 6.1.0-26-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) 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/3474472/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/300713/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -274,7 +306,7 @@ Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.12.6-1 [1068 B] Get: 146 http://deb.debian.org/debian trixie/main amd64 python3-wheel all 0.44.0-2 [53.4 kB] -Fetched 61.3 MB in 2s (38.1 MB/s) +Fetched 61.3 MB in 1s (74.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 21880 files and directories currently installed.) @@ -765,8 +797,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Oct 24 12:09:52 UTC 2024. -Universal Time is now: Thu Oct 24 12:09:52 UTC 2024. +Local time is now: Wed Nov 26 18:36:31 UTC 2025. +Universal Time is now: Wed Nov 26 18:36:31 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -891,7 +923,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/abpoa-1.5.3/ && 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 > ../abpoa_1.5.3-1_source.changes +I: user script /srv/workspace/pbuilder/300713/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/300713/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/abpoa-1.5.3/ && 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 > ../abpoa_1.5.3-1_source.changes dpkg-buildpackage: info: source package abpoa dpkg-buildpackage: info: source version 1.5.3-1 dpkg-buildpackage: info: source distribution unstable @@ -1415,36 +1451,36 @@ # Tests from the README.md document ./bin/abpoa ./test_data/seq.fa > cons.fa [main] CMD: ./bin/abpoa.avx2 ./test_data/seq.fa -[abpoa_main] Real time: 0.000 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. +[abpoa_main] Real time: 0.001 sec; CPU: 0.006 sec; Peak RSS: 0.003 GB. ./bin/abpoa ./test_data/heter.fa > 2cons.fa [main] CMD: ./bin/abpoa.avx2 ./test_data/heter.fa -[abpoa_main] Real time: 0.005 sec; CPU: 0.007 sec; Peak RSS: 0.009 GB. +[abpoa_main] Real time: 0.010 sec; CPU: 0.014 sec; Peak RSS: 0.009 GB. ./bin/abpoa -r1 ./test_data/seq.fa > out.msa [main] CMD: ./bin/abpoa.avx2 -r1 ./test_data/seq.fa -[abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. +[abpoa_main] Real time: 0.001 sec; CPU: 0.005 sec; Peak RSS: 0.003 GB. ./bin/abpoa -r2 ./test_data/seq.fa > out_cons.msa [main] CMD: ./bin/abpoa.avx2 -r2 ./test_data/seq.fa -[abpoa_main] Real time: 0.000 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. +[abpoa_main] Real time: 0.001 sec; CPU: 0.004 sec; Peak RSS: 0.003 GB. ./bin/abpoa -r3 ./test_data/seq.fa > out.gfa [main] CMD: ./bin/abpoa.avx2 -r3 ./test_data/seq.fa -[abpoa_main] Real time: 0.000 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. +[abpoa_main] Real time: 0.002 sec; CPU: 0.005 sec; Peak RSS: 0.003 GB. ./bin/abpoa -r4 ./test_data/seq.fa > out4.gfa [main] CMD: ./bin/abpoa.avx2 -r4 ./test_data/seq.fa -[abpoa_main] Real time: 0.000 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB. +[abpoa_main] Real time: 0.001 sec; CPU: 0.004 sec; Peak RSS: 0.003 GB. cp out.gfa in.gfa cp out.msa in.msa ./bin/abpoa -i in.gfa ./test_data/seq.fa -r3 > out.gfa [main] CMD: ./bin/abpoa.avx2 -i in.gfa -r3 ./test_data/seq.fa -[abpoa_main] Real time: 0.001 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. +[abpoa_main] Real time: 0.001 sec; CPU: 0.004 sec; Peak RSS: 0.003 GB. ./bin/abpoa -i in.msa ./test_data/seq.fa -r1 > out.msa [main] CMD: ./bin/abpoa.avx2 -i in.msa -r1 ./test_data/seq.fa -[abpoa_main] Real time: 0.000 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. +[abpoa_main] Real time: 0.001 sec; CPU: 0.004 sec; Peak RSS: 0.003 GB. ./bin/abpoa ./test_data/seq.fa -g poa.png > cons.fa [main] CMD: ./bin/abpoa.avx2 -g poa.png ./test_data/seq.fa -[abpoa_main] Real time: 0.322 sec; CPU: 0.002 sec; Peak RSS: 0.003 GB. +[abpoa_main] Real time: 0.512 sec; CPU: 0.004 sec; Peak RSS: 0.003 GB. ./bin/abpoa ./test_data/heter.fa -d2 [main] CMD: ./bin/abpoa.avx2 -d2 ./test_data/heter.fa -[abpoa_main] Real time: 0.008 sec; CPU: 0.010 sec; Peak RSS: 0.010 GB. +[abpoa_main] Real time: 0.008 sec; CPU: 0.011 sec; Peak RSS: 0.009 GB. >Consensus_sequence_1 0,2,3,4,10,13,14 CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC >Consensus_sequence_2 1,5,6,7,8,9,11,12 @@ -1527,8 +1563,8 @@ make[1]: Leaving directory '/build/reproducible-path/abpoa-1.5.3' dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'abpoa' in '../abpoa_1.5.3-1_amd64.deb'. dpkg-deb: building package 'abpoa-dbgsym' in '../abpoa-dbgsym_1.5.3-1_amd64.deb'. +dpkg-deb: building package 'abpoa' in '../abpoa_1.5.3-1_amd64.deb'. dpkg-deb: building package 'python3-pyabpoa' in '../python3-pyabpoa_1.5.3-1_amd64.deb'. dpkg-deb: building package 'python3-pyabpoa-dbgsym' in '../python3-pyabpoa-dbgsym_1.5.3-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../abpoa_1.5.3-1_amd64.buildinfo @@ -1538,12 +1574,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/300713/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/300713/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/3474472 and its subdirectories -I: Current time: Thu Oct 24 00:11:33 -12 2024 -I: pbuilder-time-stamp: 1729771893 +I: removing directory /srv/workspace/pbuilder/300713 and its subdirectories +I: Current time: Thu Nov 27 08:38:46 +14 2025 +I: pbuilder-time-stamp: 1764182326