Diff of the two buildlogs: -- --- b1/build.log 2024-12-21 04:06:26.783727181 +0000 +++ b2/build.log 2024-12-21 04:14:30.405652785 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Dec 20 16:03:10 -12 2024 -I: pbuilder-time-stamp: 1734753790 +I: Current time: Sat Dec 21 18:06:37 +14 2024 +I: pbuilder-time-stamp: 1734753997 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/11873/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/24720/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4a. +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 Dec 21 04:07 /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/24720/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/24720/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='bbe4fe3851894f738cb4bb03ee0ea9fb' - 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='11873' - PS1='# ' - PS2='> ' + INVOCATION_ID=9f4d25c5c2a94a558a44dfd5df358507 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=24720 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.JlMhLzD6/pbuilderrc_WzAj --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.JlMhLzD6/b1 --logfile b1/build.log artfastqgenerator_0.0.20150519-5.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.JlMhLzD6/pbuilderrc_PcSx --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.JlMhLzD6/b2 --logfile b2/build.log artfastqgenerator_0.0.20150519-5.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-23-armmp #1 SMP Debian 6.1.99-1 (2024-07-15) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/11873/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/24720/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -360,7 +392,7 @@ Get: 245 http://deb.debian.org/debian trixie/main armhf fastjar armhf 2:0.98-7 [43.9 kB] Get: 246 http://deb.debian.org/debian trixie/main armhf jarwrapper all 0.80 [9692 B] Get: 247 http://deb.debian.org/debian trixie/main armhf javahelper all 0.80 [80.4 kB] -Fetched 220 MB in 4s (49.0 MB/s) +Fetched 220 MB in 24s (9350 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:armhf. (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 ... 19674 files and directories currently installed.) @@ -1192,8 +1224,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Dec 21 04:04:50 UTC 2024. -Universal Time is now: Sat Dec 21 04:04:50 UTC 2024. +Local time is now: Sat Dec 21 04:10:16 UTC 2024. +Universal Time is now: Sat Dec 21 04:10:16 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:armhf (1.17.0-2+b1) ... @@ -1593,7 +1625,11 @@ 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/24720/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/24720/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 @@ -1603,7 +1639,7 @@ debian/rules clean dh clean --with javahelper jh_clean -Duplicate specification "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" dh_clean debian/rules binary dh binary --with javahelper @@ -1633,66 +1669,66 @@ You should have received a copy of the GNU General Public License along with this program; if not, see . -Dec 20, 2024 4:05:53 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +Dec 21, 2024 6:12:54 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Found the start sequence ID str >1 in >1 dna:chromosome chromosome:GRCh37:1:1:249250621:1 -Dec 20, 2024 4:05:53 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +Dec 21, 2024 6:12:54 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Read generation begun. -Dec 20, 2024 4:05:53 PM artificialFastqGenerator.CoverageStatisticsCalculator logCoverageStatsHeader +Dec 21, 2024 6:12:54 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 -Dec 20, 2024 4:05:54 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 10000,26.6478,1,53,9880,26.851923076923075,5,53 -Dec 20, 2024 4:05:55 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 20000,30.0644,7,53,10000,30.0644,7,53 -Dec 20, 2024 4:05:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 30000,31.0919,10,50,10000,31.0919,10,50 -Dec 20, 2024 4:05:56 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 40000,29.9159,9,50,10000,29.9159,9,50 -Dec 20, 2024 4:05:57 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 50000,30.9618,14,48,10000,30.9618,14,48 -Dec 20, 2024 4:05:57 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 60000,28.1754,2,50,10000,28.1754,2,50 -Dec 20, 2024 4:05:58 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 70000,31.9329,10,51,10000,31.9329,10,51 -Dec 20, 2024 4:05:58 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 80000,30.9848,9,47,10000,30.9848,9,47 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 90000,33.7366,15,53,10000,33.7366,15,53 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +Dec 21, 2024 6:13:01 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 10000,27.391,1,48,9880,27.592914979757087,4,48 +Dec 21, 2024 6:13:06 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 20000,29.3781,4,53,10000,29.3781,4,53 +Dec 21, 2024 6:13:09 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 30000,33.5918,13,48,10000,33.5918,13,48 +Dec 21, 2024 6:13:11 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 40000,30.6313,11,50,10000,30.6313,11,50 +Dec 21, 2024 6:13:13 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 50000,32.1799,11,57,10000,32.1799,11,57 +Dec 21, 2024 6:13:16 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 60000,29.1573,2,50,10000,29.1573,2,50 +Dec 21, 2024 6:13:18 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 70000,31.4766,13,50,10000,31.4766,13,50 +Dec 21, 2024 6:13:19 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 80000,29.586,10,61,10000,29.586,10,61 +Dec 21, 2024 6:13:21 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 90000,32.3344,11,49,10000,32.3344,11,49 +Dec 21, 2024 6:13:22 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Found the end sequence identifier > in >2 dna:chromosome chromosome:GRCh37:2:1:243199373:1 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs +Dec 21, 2024 6:13:22 PM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs INFO: Further reads generated only for nucleobases already in memory. -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 100000,32.2691,7,49,9960,32.36355421686747,7,49 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats -INFO: 100080,5.425,1,10,0,0.0,0,0 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Dec 21, 2024 6:13:23 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 100000,33.8233,7,54,9960,33.92409638554217,8,54 +Dec 21, 2024 6:13:23 PM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats +INFO: 100080,5.4875,1,10,0,0.0,0,0 +Dec 21, 2024 6:13:23 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Dec 21, 2024 6:13:23 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: OVERALL STATISTICS: -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Dec 21, 2024 6:13:23 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: # nucleobases processed=100080 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: Average coverage=30.55795363709033 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Dec 21, 2024 6:13:23 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: Average coverage=30.934612310151877 +Dec 21, 2024 6:13:23 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: Minimum coverage=1 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: Maximum coverage=53 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Dec 21, 2024 6:13:23 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: Maximum coverage=61 +Dec 21, 2024 6:13:24 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: # ACGTs processed=99840 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: ACGT average coverage=30.611728766025642 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +Dec 21, 2024 6:13:24 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: ACGT average coverage=30.988141025641024 +Dec 21, 2024 6:13:24 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats INFO: ACGT minimum coverage=2 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats -INFO: ACGT maximum coverage=53 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # reads=40240 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # nucleobase calls=3058240 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # ACGT nucleobase calls=3056275 -Dec 20, 2024 4:05:59 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats -INFO: # ACGT call errors=175881 +Dec 21, 2024 6:13:24 PM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats +INFO: ACGT maximum coverage=61 +Dec 21, 2024 6:13:24 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # reads=40736 +Dec 21, 2024 6:13:24 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # nucleobase calls=3095936 +Dec 21, 2024 6:13:24 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # ACGT nucleobase calls=3093856 +Dec 21, 2024 6:13:24 PM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats +INFO: # ACGT call errors=178992 rm C1.1.fastq C1.2.fastq make[1]: Leaving directory '/build/reproducible-path/artfastqgenerator-0.0.20150519' create-stamp debian/debhelper-build-stamp @@ -1727,12 +1763,14 @@ 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/24720/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/24720/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/11873 and its subdirectories -I: Current time: Fri Dec 20 16:06:16 -12 2024 -I: pbuilder-time-stamp: 1734753976 +I: removing directory /srv/workspace/pbuilder/24720 and its subdirectories +I: Current time: Sat Dec 21 18:14:24 +14 2024 +I: pbuilder-time-stamp: 1734754464