Diff of the two buildlogs: -- --- b1/build.log 2024-05-28 18:39:57.513419661 +0000 +++ b2/build.log 2024-05-28 18:46:48.379945927 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 28 06:33:03 -12 2024 -I: pbuilder-time-stamp: 1716921183 +I: Current time: Tue Jul 1 15:03:00 +14 2025 +I: pbuilder-time-stamp: 1751331780 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,51 +30,83 @@ dpkg-source: info: applying spellings.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2857149/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4165173/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 Jul 1 01:03 /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/4165173/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4165173/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]="21" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d46b43ca55184c8aa065ec1e977a2594' - 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='2857149' - PS1='# ' - PS2='> ' + INVOCATION_ID=f50a927708b1400aa231446de12b7b44 + 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=4165173 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.94P4HfbR/pbuilderrc_xQ77 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.94P4HfbR/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' + 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.94P4HfbR/pbuilderrc_6UTT --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.94P4HfbR/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' I: uname -a - Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 28 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2857149/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 30 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4165173/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 30 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.7.1+dfsg-6+b1 [1146 kB] -Fetched 21.2 MB in 1s (16.5 MB/s) +Fetched 21.2 MB in 0s (64.5 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 ... 19717 files and directories currently installed.) @@ -287,7 +319,11 @@ 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/4165173/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/4165173/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 @@ -399,9 +435,9 @@ Single-end simulation -Total CPU time used: 0.0468 +Total CPU time used: 0.049132 -The random seed for the run: 1716921233 +The random seed for the run: 1751331822 Parameters Settings number of flow cycles: 100 @@ -432,9 +468,9 @@ Paired-end simulation -Total CPU time used: 0.036157 +Total CPU time used: 0.036924 -The random seed for the run: 1716921233 +The random seed for the run: 1751331822 Parameters Settings number of flow cycles: 100 @@ -470,9 +506,9 @@ Paired-end simulation -Total CPU time used: 0.040298 +Total CPU time used: 0.040382 -The random seed for the run: 1716921233 +The random seed for the run: 1751331822 Parameters Settings number of flow cycles: 200 @@ -508,9 +544,9 @@ Amplicon 5'-end sequencing with single-end reads -Total CPU time used: 8.19927 +Total CPU time used: 6.75797 -The random seed for the run: 1716921233 +The random seed for the run: 1751331822 Parameters Settings number of flow cycles: 100 @@ -541,9 +577,9 @@ Amplicon two-end sequencing with paired-end reads -Total CPU time used: 6.58458 +Total CPU time used: 5.72195 -The random seed for the run: 1716921242 +The random seed for the run: 1751331829 Parameters Settings number of flow cycles: 100 @@ -576,7 +612,7 @@ Single-end simulation -Total CPU time used: 0.047575 +Total CPU time used: 0.04868 The random seed for the run: 777 @@ -609,7 +645,7 @@ Single-end simulation -Total CPU time used: 0.051071 +Total CPU time used: 0.049772 The random seed for the run: 777 @@ -643,9 +679,9 @@ Single-end simulation -Total CPU time used: 0.073771 +Total CPU time used: 0.092275 -The random seed for the run: 1716921249 +The random seed for the run: 1751331835 Parameters Settings fold of read coverage: 10X @@ -675,9 +711,9 @@ Single-end simulation -Total CPU time used: 0.095003 +Total CPU time used: 0.093648 -The random seed for the run: 1716921249 +The random seed for the run: 1751331835 Parameters Settings fold of read coverage: 20X @@ -705,9 +741,9 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.127859 +Total CPU time used: 0.130194 -The random seed for the run: 1716921249 +The random seed for the run: 1751331835 Parameters Settings fold of read coverage: 20X @@ -745,7 +781,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.056922 +Total CPU time used: 0.05832 The random seed for the run: 777 @@ -783,7 +819,7 @@ Mate-Pair (F3-R3) simulation -Total CPU time used: 0.056658 +Total CPU time used: 0.060868 The random seed for the run: 777 @@ -826,9 +862,9 @@ Paired-end (F3-F5) simulation -Total CPU time used: 0.203858 +Total CPU time used: 0.202138 -The random seed for the run: 1716921249 +The random seed for the run: 1751331835 Parameters Settings fold of read coverage: 50X @@ -862,9 +898,9 @@ Amplicon single-end sequencing simulation -Total CPU time used: 169.818 +Total CPU time used: 162.559 -The random seed for the run: 1716921250 +The random seed for the run: 1751331835 Parameters Settings # reads per amplion: 100 @@ -894,9 +930,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 92.4989 +Total CPU time used: 97.4182 -The random seed for the run: 1716921420 +The random seed for the run: 1751332001 Parameters Settings # read pairs per amplion: 80 @@ -927,9 +963,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 62.0838 +Total CPU time used: 68.7986 -The random seed for the run: 1716921513 +The random seed for the run: 1751332102 Parameters Settings # read pairs per amplion: 50 @@ -961,9 +997,9 @@ Single-end Simulation -Total CPU time used: 0.051187 +Total CPU time used: 0.052225 -The random seed for the run: 1716921577 +The random seed for the run: 1751332172 Parameters used during run Read Length: 35 @@ -995,9 +1031,9 @@ Single-end Simulation -Total CPU time used: 0.038369 +Total CPU time used: 0.039385 -The random seed for the run: 1716921577 +The random seed for the run: 1751332172 Parameters used during run Read Length: 50 @@ -1029,9 +1065,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.021822 +Total CPU time used: 0.023834 -The random seed for the run: 1716921577 +The random seed for the run: 1751332172 Parameters used during run Read Length: 150 @@ -1068,9 +1104,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.039329 +Total CPU time used: 0.041491 -The random seed for the run: 1716921577 +The random seed for the run: 1751332172 Parameters used during run Read Length: 100 @@ -1107,9 +1143,9 @@ Matepair-end sequencing simulation -Total CPU time used: 0.026223 +Total CPU time used: 0.027992 -The random seed for the run: 1716921577 +The random seed for the run: 1751332172 Parameters used during run Read Length: 100 @@ -1146,9 +1182,9 @@ Amplicon 5'-end sequencing simulation -Total CPU time used: 0.323336 +Total CPU time used: 0.254901 -The random seed for the run: 1716921578 +The random seed for the run: 1751332172 Parameters used during run Read Length: 100 @@ -1180,9 +1216,9 @@ Amplicon paired-end sequencing simulation -Total CPU time used: 0.297131 +Total CPU time used: 0.301063 -The random seed for the run: 1716921578 +The random seed for the run: 1751332173 Parameters used during run Read Length: 100 @@ -1217,9 +1253,9 @@ Amplicon matepair sequencing simulation -Total CPU time used: 0.399578 +Total CPU time used: 0.48009 -The random seed for the run: 1716921578 +The random seed for the run: 1751332173 Parameters used during run Read Length: 100 @@ -1254,7 +1290,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.023381 +Total CPU time used: 0.02674 The random seed for the run: 777 @@ -1293,7 +1329,7 @@ Paired-end sequencing simulation -Total CPU time used: 0.02322 +Total CPU time used: 0.025744 The random seed for the run: 777 @@ -1332,9 +1368,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.033728 +Total CPU time used: 0.032067 -The random seed for the run: 1716921579 +The random seed for the run: 1751332174 Parameters used during run Read Length: 100 @@ -1373,9 +1409,9 @@ Paired-end sequencing simulation -Total CPU time used: 0.026905 +Total CPU time used: 0.029754 -The random seed for the run: 1716921579 +The random seed for the run: 1751332174 Parameters used during run Read Length: 75 @@ -1414,8 +1450,8 @@ 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 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' + /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' 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 @@ -1468,9 +1504,9 @@ 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' in '../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.deb'. dpkg-deb: building package 'art-nextgen-simulation-tools-dbgsym' in '../art-nextgen-simulation-tools-dbgsym_20160605+dfsg-5_amd64.deb'. 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_amd64.deb'. dpkg-genbuildinfo --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../art-nextgen-simulation-tools_20160605+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1478,12 +1514,14 @@ 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/4165173/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4165173/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/2857149 and its subdirectories -I: Current time: Tue May 28 06:39:56 -12 2024 -I: pbuilder-time-stamp: 1716921596 +I: removing directory /srv/workspace/pbuilder/4165173 and its subdirectories +I: Current time: Tue Jul 1 15:09:47 +14 2025 +I: pbuilder-time-stamp: 1751332187