Diff of the two buildlogs: -- --- b1/build.log 2025-02-14 00:58:54.450229677 +0000 +++ b2/build.log 2025-02-14 01:00:04.527077229 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Mar 18 19:19:46 -12 2026 -I: pbuilder-time-stamp: 1773904786 +I: Current time: Fri Feb 14 14:58:57 +14 2025 +I: pbuilder-time-stamp: 1739494737 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -24,52 +24,84 @@ dpkg-source: info: applying adapt_doc.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2870959/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3634650/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Feb 14 00:59 /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/3634650/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3634650/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='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='d693700d62b049b9be7a4f7f6f90660c' - 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='2870959' - PS1='# ' - PS2='> ' + INVOCATION_ID=ee8dc9f03d604dc8af0d775277d41006 + 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=3634650 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.8jpsSAcY/pbuilderrc_8C71 --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.8jpsSAcY/b1 --logfile b1/build.log artfastqgenerator_0.0.20150519-5.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.8jpsSAcY/pbuilderrc_ry3C --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.8jpsSAcY/b2 --logfile b2/build.log artfastqgenerator_0.0.20150519-5.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 codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2870959/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3634650/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -362,7 +394,7 @@ Get: 251 http://deb.debian.org/debian trixie/main arm64 fastjar arm64 2:0.98-7+b1 [74.9 kB] Get: 252 http://deb.debian.org/debian trixie/main arm64 jarwrapper all 0.80 [9692 B] Get: 253 http://deb.debian.org/debian trixie/main arm64 javahelper all 0.80 [80.4 kB] -Fetched 235 MB in 2s (151 MB/s) +Fetched 235 MB in 1s (286 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared: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 ... 19922 files and directories currently installed.) @@ -1210,8 +1242,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Mar 19 07:20:51 UTC 2026. -Universal Time is now: Thu Mar 19 07:20:51 UTC 2026. +Local time is now: Fri Feb 14 00:59:29 UTC 2025. +Universal Time is now: Fri Feb 14 00:59:29 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -1625,7 +1657,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/artfastqgenerator-0.0.20150519/ && 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 > ../artfastqgenerator_0.0.20150519-5_source.changes +I: user script /srv/workspace/pbuilder/3634650/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3634650/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/artfastqgenerator-0.0.20150519/ && 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 > ../artfastqgenerator_0.0.20150519-5_source.changes dpkg-buildpackage: info: source package artfastqgenerator dpkg-buildpackage: info: source version 0.0.20150519-5 dpkg-buildpackage: info: source distribution unstable @@ -1635,7 +1671,7 @@ debian/rules clean dh clean --with javahelper jh_clean -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" dh_clean debian/rules binary dh binary --with javahelper @@ -1665,66 +1701,66 @@ You should have received a copy of the GNU General Public License along with this program; if not, see . -Mar 18, 2026 7:21:40 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +Feb 14, 2025 2:59:55 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Found the start sequence ID str >1 in >1 dna:chromosome chromosome:GRCh37:1:1:249250621:1 -Mar 18, 2026 7:21:40 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +Feb 14, 2025 2:59:55 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Read generation begun. -Mar 18, 2026 7:21:40 PM artificialFastqGenerator.CoverageStatisticsCalculator logCoverageStatsHeader +Feb 14, 2025 2:59:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logCoverageStatsHeader INFO: ALL_SO_FAR_NUM,ALL_AV_COV,ALL_MIN_COV,ALL_MAX_COV,ACGT_NUM,ACGT_AV_COV,ACGT_MIN_COV,ACGT_MAX_COV -Mar 18, 2026 7:21:41 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 10000,29.1883,1,49,9880,29.358502024291496,7,49 -Mar 18, 2026 7:21:41 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 20000,30.2802,7,48,10000,30.2802,7,48 -Mar 18, 2026 7:21:41 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 30000,33.0462,16,51,10000,33.0462,16,51 -Mar 18, 2026 7:21:42 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 40000,32.0785,14,49,10000,32.0785,14,49 -Mar 18, 2026 7:21:42 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 50000,32.6453,13,58,10000,32.6453,13,58 -Mar 18, 2026 7:21:42 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 60000,29.6733,2,55,10000,29.6733,2,55 -Mar 18, 2026 7:21:42 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 70000,30.3434,8,51,10000,30.3434,8,51 -Mar 18, 2026 7:21:42 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 80000,30.8038,12,61,10000,30.8038,12,61 -Mar 18, 2026 7:21:42 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 90000,32.9527,11,55,10000,32.9527,11,55 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +Feb 14, 2025 2:59:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 10000,27.3664,1,47,9880,27.60172064777328,5,47 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 20000,29.7218,9,57,10000,29.7218,9,57 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 30000,34.0675,14,57,10000,34.0675,14,57 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 40000,32.3101,9,56,10000,32.3101,9,56 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 50000,31.4971,11,52,10000,31.4971,11,52 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 60000,29.6154,3,57,10000,29.6154,3,57 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 70000,30.636,12,53,10000,30.636,12,53 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 80000,29.4737,10,49,10000,29.4737,10,49 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 90000,32.5973,9,54,10000,32.5973,9,54 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Found the end sequence identifier > in >2 dna:chromosome chromosome:GRCh37:2:1:243199373:1 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Further reads generated only for nucleobases already in memory. -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 100000,33.5745,5,59,9960,33.68363453815261,7,59 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 100080,2.925,0,6,0,0.0,0,0 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 100000,32.8496,6,56,9960,32.94598393574297,6,56 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 100080,4.5375,0,10,0,0.0,0,0 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: OVERALL STATISTICS: -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: # nucleobases processed=100080 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: Average coverage=31.435811350919266 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: Average coverage=30.99232613908873 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: Minimum coverage=0 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: Maximum coverage=61 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: Maximum coverage=57 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: # ACGTs processed=99840 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: ACGT average coverage=31.488231169871796 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: ACGT minimum coverage=2 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: ACGT maximum coverage=61 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # reads=41396 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # nucleobase calls=3146096 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # ACGT nucleobase calls=3143785 -Mar 18, 2026 7:21:43 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # ACGT call errors=183996 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: ACGT average coverage=31.050040064102564 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: ACGT minimum coverage=3 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: ACGT maximum coverage=57 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # reads=40812 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # nucleobase calls=3101712 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # ACGT nucleobase calls=3100036 +Feb 14, 2025 2:59:56 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # ACGT call errors=179979 rm C1.1.fastq C1.2.fastq make[1]: Leaving directory '/build/reproducible-path/artfastqgenerator-0.0.20150519' create-stamp debian/debhelper-build-stamp @@ -1749,8 +1785,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'artfastqgenerator' in '../artfastqgenerator_0.0.20150519-5_all.deb'. dpkg-deb: building package 'artfastqgenerator-examples' in '../artfastqgenerator-examples_0.0.20150519-5_all.deb'. +dpkg-deb: building package 'artfastqgenerator' in '../artfastqgenerator_0.0.20150519-5_all.deb'. dpkg-deb: building package 'artfastqgenerator-doc' in '../artfastqgenerator-doc_0.0.20150519-5_all.deb'. dpkg-genbuildinfo --build=binary -O../artfastqgenerator_0.0.20150519-5_arm64.buildinfo dpkg-genchanges --build=binary -O../artfastqgenerator_0.0.20150519-5_arm64.changes @@ -1759,12 +1795,14 @@ 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/3634650/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3634650/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/2870959 and its subdirectories -I: Current time: Wed Mar 18 19:21:53 -12 2026 -I: pbuilder-time-stamp: 1773904913 +I: removing directory /srv/workspace/pbuilder/3634650 and its subdirectories +I: Current time: Fri Feb 14 15:00:03 +14 2025 +I: pbuilder-time-stamp: 1739494803