Diff of the two buildlogs: -- --- b1/build.log 2024-05-10 13:13:35.524070000 +0000 +++ b2/build.log 2024-05-10 13:22:21.905646687 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 10 01:08:50 -12 2024 -I: pbuilder-time-stamp: 1715346530 +I: Current time: Fri Jun 13 09:36:38 +14 2025 +I: pbuilder-time-stamp: 1749756998 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying spellings.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1874524/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2689631/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 12 19:36 /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/2689631/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2689631/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='3bb132b4349f4f21b80821c051f06012' - 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='1874524' - PS1='# ' - PS2='> ' + INVOCATION_ID=6d91393620f040bda4b8786e12a33cea + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2689631 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.iBHVE8y7/pbuilderrc_ts4O --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.iBHVE8y7/b1 --logfile b1/build.log art-nextgen-simulation-tools_20160605+dfsg-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.iBHVE8y7/pbuilderrc_8Y2d --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.iBHVE8y7/b2 --logfile b2/build.log art-nextgen-simulation-tools_20160605+dfsg-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 8 11:23 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1874524/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 10 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2689631/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +178,7 @@ Get: 31 http://deb.debian.org/debian trixie/main arm64 libgslcblas0 arm64 2.7.1+dfsg-6+b1 [72.7 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libgsl27 arm64 2.7.1+dfsg-6+b1 [822 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libgsl-dev arm64 2.7.1+dfsg-6+b1 [1039 kB] -Fetched 20.6 MB in 0s (142 MB/s) +Fetched 20.6 MB in 0s (76.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19744 files and directories currently installed.) @@ -293,7 +325,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/art-nextgen-simulation-tools-20160605+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 > ../art-nextgen-simulation-tools_20160605+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/2689631/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2689631/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/art-nextgen-simulation-tools-20160605+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 > ../art-nextgen-simulation-tools_20160605+dfsg-5_source.changes dpkg-buildpackage: info: source package art-nextgen-simulation-tools dpkg-buildpackage: info: source version 20160605+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -405,9 +441,9 @@ Single-end simulation -Total CPU time used: 0.037373 +Total CPU time used: 0.031819 -The random seed for the run: 1715346563 +The random seed for the run: 1749757065 Parameters Settings number of flow cycles: 100 @@ -438,9 +474,9 @@ Paired-end simulation -Total CPU time used: 0.031832 +Total CPU time used: 0.024527 -The random seed for the run: 1715346563 +The random seed for the run: 1749757066 Parameters Settings number of flow cycles: 100 @@ -476,9 +512,9 @@ Paired-end simulation -Total CPU time used: 0.037545 +Total CPU time used: 0.027247 -The random seed for the run: 1715346563 +The random seed for the run: 1749757066 Parameters Settings number of flow cycles: 200 @@ -514,9 +550,9 @@ Amplicon 5'-end sequencing with single-end reads -Total CPU time used: 4.6252 +Total CPU time used: 4.77926 -The random seed for the run: 1715346564 +The random seed for the run: 1749757066 Parameters Settings number of flow cycles: 100 @@ -547,9 +583,9 @@ Amplicon two-end sequencing with paired-end reads -Total CPU time used: 3.41614 +Total CPU time used: 3.49035 -The random seed for the run: 1715346568 +The random seed for the run: 1749757075 Parameters Settings number of flow cycles: 100 @@ -582,7 +618,7 @@ Single-end simulation -Total CPU time used: 0.032378 +Total CPU time used: 0.031858 The random seed for the run: 777 @@ -615,7 +651,7 @@ Single-end simulation -Total CPU time used: 0.031228 +Total CPU time used: 0.032675 The random seed for the run: 777 @@ -649,9 +685,9 @@ Single-end simulation -Total CPU time used: 0.045275 +Total CPU time used: 0.045333 -The random seed for the run: 1715346572 +The random seed for the run: 1749757081 Parameters Settings fold of read coverage: 10X @@ -681,9 +717,9 @@ Single-end simulation -Total CPU time used: 0.063358 +Total CPU time used: 0.06362 -The random seed for the run: 1715346572 +The random seed for the run: 1749757081 Parameters Settings fold of read coverage: 20X @@ -711,9 +747,9 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.076533 +Total CPU time used: 0.077688 -The random seed for the run: 1715346572 +The random seed for the run: 1749757081 Parameters Settings fold of read coverage: 20X @@ -751,7 +787,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.036907 +Total CPU time used: 0.037152 The random seed for the run: 777 @@ -789,7 +825,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.036766 +Total CPU time used: 0.0371 The random seed for the run: 777 @@ -832,9 +868,9 @@ Paired-end (F3-F5) simulation -Total CPU time used: 0.123002 +Total CPU time used: 0.126689 -The random seed for the run: 1715346573 +The random seed for the run: 1749757081 Parameters Settings fold of read coverage: 50X @@ -868,9 +904,9 @@ Amplicon single-end sequencing simulation -Total CPU time used: 105.883 +Total CPU time used: 107.556 -The random seed for the run: 1715346573 +The random seed for the run: 1749757082 Parameters Settings # reads per amplion: 100 @@ -900,9 +936,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 66.0757 +Total CPU time used: 66.6754 -The random seed for the run: 1715346679 +The random seed for the run: 1749757304 Parameters Settings # read pairs per amplion: 80 @@ -933,9 +969,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 41.9424 +Total CPU time used: 42.672 -The random seed for the run: 1715346751 +The random seed for the run: 1749757423 Parameters Settings # read pairs per amplion: 50 @@ -967,9 +1003,9 @@ Single-end Simulation -Total CPU time used: 0.069861 +Total CPU time used: 0.03055 -The random seed for the run: 1715346794 +The random seed for the run: 1749757492 Parameters used during run Read Length: 35 @@ -1001,9 +1037,9 @@ Single-end Simulation -Total CPU time used: 0.056502 +Total CPU time used: 0.023604 -The random seed for the run: 1715346794 +The random seed for the run: 1749757492 Parameters used during run Read Length: 50 @@ -1035,9 +1071,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.048161 +Total CPU time used: 0.01781 -The random seed for the run: 1715346794 +The random seed for the run: 1749757492 Parameters used during run Read Length: 150 @@ -1074,9 +1110,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.074215 +Total CPU time used: 0.031627 -The random seed for the run: 1715346794 +The random seed for the run: 1749757492 Parameters used during run Read Length: 100 @@ -1113,9 +1149,9 @@ Matepair-end sequencing simulation -Total CPU time used: 0.050729 +Total CPU time used: 0.02067 -The random seed for the run: 1715346794 +The random seed for the run: 1749757492 Parameters used during run Read Length: 100 @@ -1152,9 +1188,9 @@ Amplicon 5'-end sequencing simulation -Total CPU time used: 0.228629 +Total CPU time used: 0.18819 -The random seed for the run: 1715346794 +The random seed for the run: 1749757492 Parameters used during run Read Length: 100 @@ -1186,9 +1222,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 0.223172 +Total CPU time used: 0.218627 -The random seed for the run: 1715346795 +The random seed for the run: 1749757493 Parameters used during run Read Length: 100 @@ -1223,9 +1259,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 0.344314 +Total CPU time used: 0.309472 -The random seed for the run: 1715346795 +The random seed for the run: 1749757493 Parameters used during run Read Length: 100 @@ -1260,7 +1296,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.041835 +Total CPU time used: 0.019319 The random seed for the run: 777 @@ -1299,7 +1335,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.050778 +Total CPU time used: 0.019325 The random seed for the run: 777 @@ -1338,9 +1374,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.056559 +Total CPU time used: 0.022473 -The random seed for the run: 1715346796 +The random seed for the run: 1749757494 Parameters used during run Read Length: 100 @@ -1379,9 +1415,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.053237 +Total CPU time used: 0.019775 -The random seed for the run: 1715346796 +The random seed for the run: 1749757494 Parameters used during run Read Length: 75 @@ -1417,11 +1453,11 @@ make -j12 install DESTDIR=/build/reproducible-path/art-nextgen-simulation-tools-20160605\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[2]: Entering directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' -make[2]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' /usr/bin/mkdir -p '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' - /usr/bin/install -c art_illumina art_454 art_SOLiD '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' +make[2]: Nothing to be done for 'install-data-am'. /usr/bin/install -c aln2bed.pl map2bed.pl ART_profiler_454/art_profiler_454 ART_profiler_illumina/combinedAvg.pl ART_profiler_illumina/fastqReadAvg.pl ART_profiler_illumina/art_profiler_illumina ART_profiler_illumina/empDist.pl ART_profiler_illumina/summation.pl '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' + /usr/bin/install -c art_illumina art_454 art_SOLiD '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg/debian/tmp/usr/bin' make[2]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' make[1]: Leaving directory '/build/reproducible-path/art-nextgen-simulation-tools-20160605+dfsg' debian/rules override_dh_install-arch @@ -1469,14 +1505,14 @@ dh_shlibdeps -a dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools-profiles: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined +dpkg-gencontrol: warning: package art-nextgen-simulation-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb +dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools' in '../art-nextgen-simulation-tools_20160605+dfsg-5_arm64.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-5_arm64.deb'. -dpkg-deb: building package 'art-nextgen-simulation-tools-profiles' in '../art-nextgen-simulation-tools-profiles_20160605+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_arm64.buildinfo dpkg-genchanges --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1484,12 +1520,14 @@ 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/2689631/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2689631/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/1874524 and its subdirectories -I: Current time: Fri May 10 01:13:34 -12 2024 -I: pbuilder-time-stamp: 1715346814 +I: removing directory /srv/workspace/pbuilder/2689631 and its subdirectories +I: Current time: Fri Jun 13 09:45:20 +14 2025 +I: pbuilder-time-stamp: 1749757520