Diff of the two buildlogs: -- --- b1/build.log 2025-01-30 19:15:34.120788412 +0000 +++ b2/build.log 2025-01-30 19:17:39.527134514 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 30 07:13:37 -12 2025 -I: pbuilder-time-stamp: 1738264417 +I: Current time: Thu Mar 5 15:38:37 +14 2026 +I: pbuilder-time-stamp: 1772674717 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -44,52 +44,84 @@ dpkg-source: info: applying update-blastdbcmd-error-output.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/334474/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3191/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 5 01:38 /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/3191/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3191/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='7272960abea841acbbd6e5ae0d439fc3' - 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='334474' - PS1='# ' - PS2='> ' + INVOCATION_ID=0aa2cfef5df343cd9f55f325220a90c1 + 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=3191 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.ubP3A6KZ/pbuilderrc_aOE2 --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.ubP3A6KZ/b1 --logfile b1/build.log bioperl-run_1.7.3-13.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.ubP3A6KZ/pbuilderrc_zKVp --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.ubP3A6KZ/b2 --logfile b2/build.log bioperl-run_1.7.3-13.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 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/334474/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3191/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -463,7 +495,7 @@ Get: 262 http://deb.debian.org/debian unstable/main arm64 tigr-glimmer arm64 3.02b-6+b2 [274 kB] Get: 263 http://deb.debian.org/debian unstable/main arm64 wise-data all 2.4.1-25 [76.1 kB] Get: 264 http://deb.debian.org/debian unstable/main arm64 wise arm64 2.4.1-25 [1007 kB] -Fetched 215 MB in 5s (45.3 MB/s) +Fetched 215 MB in 1s (214 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19956 files and directories currently installed.) @@ -1335,8 +1367,8 @@ Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jan 30 19:14:23 UTC 2025. -Universal Time is now: Thu Jan 30 19:14:23 UTC 2025. +Local time is now: Thu Mar 5 01:39:16 UTC 2026. +Universal Time is now: Thu Mar 5 01:39:16 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up mariadb-common (1:11.4.4-3) ... @@ -1569,7 +1601,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bioperl-run-1.7.3/ && 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 > ../bioperl-run_1.7.3-13_source.changes +I: user script /srv/workspace/pbuilder/3191/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3191/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bioperl-run-1.7.3/ && 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 > ../bioperl-run_1.7.3-13_source.changes dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-13 dpkg-buildpackage: info: source distribution unstable @@ -1635,7 +1671,7 @@ gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } -Loading sequence file: /tmp/FYpAxdJ0b_ +Loading sequence file: /tmp/2HF3VzcxCm Computing posterior matrices Building DAG Starting the sequence annealing process @@ -2713,15 +2749,15 @@ Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 -[2025-01-30 07:14:55] : LOG : Detected protein sequences. -[2025-01-30 07:14:55] : LOG : Read 7 sequences from standard input. -[2025-01-30 07:14:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2025-01-30 07:14:55] : LOG : Calculating pairwise distances -[2025-01-30 07:14:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2025-01-30 07:14:55] : LOG : Building guide tree. -[2025-01-30 07:14:55] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -[2025-01-30 07:14:55] : LOG : Aligning -[2025-01-30 07:14:55] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +[2026-03-05 15:39:54] : LOG : Detected protein sequences. +[2026-03-05 15:39:54] : LOG : Read 7 sequences from standard input. +[2026-03-05 15:39:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2026-03-05 15:39:54] : LOG : Calculating pairwise distances +[2026-03-05 15:39:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2026-03-05 15:39:54] : LOG : Building guide tree. +[2026-03-05 15:39:54] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +[2026-03-05 15:39:54] : LOG : Aligning +[2026-03-05 15:39:54] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 ok 5 ok 6 @@ -2740,15 +2776,15 @@ Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 -[2025-01-30 07:14:55] : LOG : Detected protein sequences. -[2025-01-30 07:14:55] : LOG : Read 7 sequences from standard input. -[2025-01-30 07:14:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2025-01-30 07:14:55] : LOG : Calculating pairwise distances -[2025-01-30 07:14:55] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -[2025-01-30 07:14:55] : LOG : Building guide tree. -[2025-01-30 07:14:55] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2025-01-30 07:14:55] : LOG : Aligning -[2025-01-30 07:14:55] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +[2026-03-05 15:39:54] : LOG : Detected protein sequences. +[2026-03-05 15:39:54] : LOG : Read 7 sequences from standard input. +[2026-03-05 15:39:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2026-03-05 15:39:54] : LOG : Calculating pairwise distances +[2026-03-05 15:39:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2026-03-05 15:39:54] : LOG : Building guide tree. +[2026-03-05 15:39:54] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +[2026-03-05 15:39:54] : LOG : Aligning +[2026-03-05 15:39:54] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 ok 7 ok # Required executable for Bio::Tools::Run::Phylo::LVB is not present @@ -3208,7 +3244,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/CNpginiUev +Loading sequence file: /tmp/RNrSEX3rHr Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -3221,7 +3257,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/djFdXVeM6d +Loading sequence file: /tmp/x3sNtsZK2V Computing posterior matrix: (1) CYS1_DICDI vs. (2) ALEU_HORVU -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (4) CATH_RAT -- done. @@ -3257,7 +3293,7 @@ gapOpen[] = { 0.01386308484 0.01386308484 0.006556345616 0.006556345616 } gapExtend[] = { 0.3603379726 0.3603379726 0.7831884027 0.7831884027 } -Loading sequence file: /tmp/XaVng4KkmV +Loading sequence file: /tmp/WlFL4vBteD Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -3710,7 +3746,7 @@ ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not present ok All tests successful. -Files=60, Tests=1652, 53 wallclock secs ( 0.35 usr 0.19 sys + 47.83 cusr 5.52 csys = 53.89 CPU) +Files=60, Tests=1652, 58 wallclock secs ( 0.42 usr 0.17 sys + 52.04 cusr 6.21 csys = 58.84 CPU) Result: PASS mv t.skip/* t rm -rf t.skip @@ -3920,11 +3956,11 @@ Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl -Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_papplmaker.pl +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl +Installing /build/reproducible-path/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl dh_install dh_installdocs dh_installchangelogs @@ -3940,8 +3976,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'bioperl-run' in '../bioperl-run_1.7.3-13_all.deb'. dpkg-deb: building package 'libbio-perl-run-perl' in '../libbio-perl-run-perl_1.7.3-13_all.deb'. +dpkg-deb: building package 'bioperl-run' in '../bioperl-run_1.7.3-13_all.deb'. dpkg-genbuildinfo --build=binary -O../bioperl-run_1.7.3-13_arm64.buildinfo dpkg-genchanges --build=binary -O../bioperl-run_1.7.3-13_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3949,12 +3985,14 @@ 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/3191/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3191/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/334474 and its subdirectories -I: Current time: Thu Jan 30 07:15:33 -12 2025 -I: pbuilder-time-stamp: 1738264533 +I: removing directory /srv/workspace/pbuilder/3191 and its subdirectories +I: Current time: Thu Mar 5 15:40:38 +14 2026 +I: pbuilder-time-stamp: 1772674838