Diff of the two buildlogs: -- --- b1/build.log 2024-05-08 01:21:03.720198794 +0000 +++ b2/build.log 2024-05-08 01:23:26.666123113 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 9 19:43:06 -12 2025 -I: pbuilder-time-stamp: 1749541386 +I: Current time: Wed May 8 15:21:06 +14 2024 +I: pbuilder-time-stamp: 1715131266 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ 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/2793576/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1195398/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 May 8 01:21 /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/1195398/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1195398/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='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='f6b8998cc6544c2d81e2f44aef068277' - 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='2793576' - PS1='# ' - PS2='> ' + INVOCATION_ID=250cf87141844112a551994df05f6453 + 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=1195398 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.FlR9KO86/pbuilderrc_20NH --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.FlR9KO86/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.FlR9KO86/pbuilderrc_6ddG --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.FlR9KO86/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 6.1.0-21-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 Jun 9 14:06 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2793576/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 7 07:42 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1195398/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -333,7 +365,7 @@ Get: 218 http://deb.debian.org/debian unstable/main arm64 fastjar arm64 2:0.98-7 [75.5 kB] Get: 219 http://deb.debian.org/debian unstable/main arm64 jarwrapper all 0.79 [10.1 kB] Get: 220 http://deb.debian.org/debian unstable/main arm64 javahelper all 0.79 [84.6 kB] -Fetched 209 MB in 1s (261 MB/s) +Fetched 209 MB in 1s (141 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19744 files and directories currently installed.) @@ -1058,8 +1090,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jun 10 07:43:35 UTC 2025. -Universal Time is now: Tue Jun 10 07:43:35 UTC 2025. +Local time is now: Wed May 8 01:22:12 UTC 2024. +Universal Time is now: Wed May 8 01:22:12 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.11-1) ... @@ -1434,7 +1466,11 @@ 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/1195398/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1195398/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 @@ -1470,66 +1506,66 @@ You should have received a copy of the GNU General Public License along with this program; if not, see . -Jun 09, 2025 7:43:54 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +May 08, 2024 3:23:12 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Found the start sequence ID str >1 in >1 dna:chromosome chromosome:GRCh37:1:1:249250621:1 -Jun 09, 2025 7:43:54 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +May 08, 2024 3:23:12 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Read generation begun. -Jun 09, 2025 7:43:54 PM artificialFastqGenerator.CoverageStatisticsCalculator logCoverageStatsHeader +May 08, 2024 3:23:12 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 -Jun 09, 2025 7:43:54 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 10000,28.198,1,48,9880,28.380364372469636,5,48 -Jun 09, 2025 7:43:54 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 20000,29.1503,7,54,10000,29.1503,7,54 -Jun 09, 2025 7:43:54 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 30000,32.6518,17,51,10000,32.6518,17,51 -Jun 09, 2025 7:43:54 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 40000,31.3592,10,48,10000,31.3592,10,48 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 50000,32.1943,11,51,10000,32.1943,11,51 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 60000,29.4095,3,65,10000,29.4095,3,65 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 70000,31.7374,9,47,10000,31.7374,9,47 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 80000,30.661,9,53,10000,30.661,9,53 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 90000,32.0634,11,54,10000,32.0634,11,54 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +May 08, 2024 3:23:13 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 10000,27.0955,1,59,9880,27.328441295546558,3,59 +May 08, 2024 3:23:13 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 20000,31.2689,7,60,10000,31.2689,7,60 +May 08, 2024 3:23:13 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 30000,33.7656,11,52,10000,33.7656,11,52 +May 08, 2024 3:23:13 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 40000,30.8709,8,54,10000,30.8709,8,54 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 50000,30.9579,10,51,10000,30.9579,10,51 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 60000,28.5134,2,46,10000,28.5134,2,46 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 70000,31.7526,11,52,10000,31.7526,11,52 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 80000,29.6768,11,56,10000,29.6768,11,56 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 90000,32.3598,13,54,10000,32.3598,13,54 +May 08, 2024 3:23:14 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Found the end sequence identifier > in >2 dna:chromosome chromosome:GRCh37:2:1:243199373:1 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +May 08, 2024 3:23:14 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Further reads generated only for nucleobases already in memory. -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 100000,34.2356,7,53,9960,34.33624497991968,7,53 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 100080,5.7375,0,10,0,0.0,0,0 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 100000,31.9294,4,50,9960,32.03473895582329,4,50 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 100080,2.45,0,6,0,0.0,0,0 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: OVERALL STATISTICS: -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: # nucleobases processed=100080 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: Average coverage=31.14572342126299 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: Average coverage=30.79640287769784 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: Minimum coverage=0 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: Maximum coverage=65 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: Maximum coverage=60 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: # ACGTs processed=99840 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: ACGT average coverage=31.19647435897436 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: ACGT minimum coverage=3 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: ACGT maximum coverage=65 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # reads=41014 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # nucleobase calls=3117064 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # ACGT nucleobase calls=3114656 -Jun 09, 2025 7:43:55 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # ACGT call errors=182226 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: ACGT average coverage=30.856670673076923 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: ACGT minimum coverage=2 +May 08, 2024 3:23:14 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: ACGT maximum coverage=60 +May 08, 2024 3:23:14 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # reads=40554 +May 08, 2024 3:23:14 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # nucleobase calls=3082104 +May 08, 2024 3:23:14 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # ACGT nucleobase calls=3080730 +May 08, 2024 3:23:14 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # ACGT call errors=178225 rm C1.1.fastq C1.2.fastq make[1]: Leaving directory '/build/reproducible-path/artfastqgenerator-0.0.20150519' create-stamp debian/debhelper-build-stamp @@ -1554,8 +1590,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'artfastqgenerator' in '../artfastqgenerator_0.0.20150519-5_all.deb'. dpkg-deb: building package 'artfastqgenerator-doc' in '../artfastqgenerator-doc_0.0.20150519-5_all.deb'. +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-genbuildinfo --build=binary -O../artfastqgenerator_0.0.20150519-5_arm64.buildinfo dpkg-genchanges --build=binary -O../artfastqgenerator_0.0.20150519-5_arm64.changes @@ -1564,12 +1600,14 @@ 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/1195398/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1195398/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/2793576 and its subdirectories -I: Current time: Mon Jun 9 19:44:02 -12 2025 -I: pbuilder-time-stamp: 1749541442 +I: removing directory /srv/workspace/pbuilder/1195398 and its subdirectories +I: Current time: Wed May 8 15:23:25 +14 2024 +I: pbuilder-time-stamp: 1715131405