Diff of the two buildlogs: -- --- b1/build.log 2024-05-09 23:22:18.012557111 +0000 +++ b2/build.log 2024-05-09 23:29:23.822409674 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 9 11:15:39 -12 2024 -I: pbuilder-time-stamp: 1715296539 +I: Current time: Thu Jun 12 19:45:21 +14 2025 +I: pbuilder-time-stamp: 1749707121 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying prefixes.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1573513/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/420469/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Jun 12 05:45 /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/420469/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/420469/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='095313ee17bd437b8144a9bf2725d2f3' - 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='1573513' - PS1='# ' - PS2='> ' + INVOCATION_ID=c0c623ddbfcd4a72add65c38ba40180e + 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=420469 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.bNX9eLIJ/pbuilderrc_8JY5 --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.bNX9eLIJ/b1 --logfile b1/build.log mcaller_1.0.3+git20210624.b415090-3.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.bNX9eLIJ/pbuilderrc_Blab --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.bNX9eLIJ/b2 --logfile b2/build.log mcaller_1.0.3+git20210624.b415090-3.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 8 11:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1573513/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 11 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/420469/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -279,7 +311,7 @@ Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 python3-sklearn-lib amd64 1.4.2+dfsg-1 [6606 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-sklearn all 1.4.2+dfsg-1 [2247 kB] -Fetched 141 MB in 7s (20.7 MB/s) +Fetched 141 MB in 5s (30.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19699 files and directories currently installed.) @@ -784,8 +816,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu May 9 23:17:21 UTC 2024. -Universal Time is now: Thu May 9 23:17:21 UTC 2024. +Local time is now: Thu Jun 12 05:46:47 UTC 2025. +Universal Time is now: Thu Jun 12 05:46:47 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -929,7 +961,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mcaller-1.0.3+git20210624.b415090/ && 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 > ../mcaller_1.0.3+git20210624.b415090-3_source.changes +I: user script /srv/workspace/pbuilder/420469/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/420469/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mcaller-1.0.3+git20210624.b415090/ && 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 > ../mcaller_1.0.3+git20210624.b415090-3_source.changes dpkg-buildpackage: info: source package mcaller dpkg-buildpackage: info: source version 1.0.3+git20210624.b415090-3 dpkg-buildpackage: info: source distribution unstable @@ -980,12 +1016,6 @@ 1 contigs 4 threads thread finished processing...: -28 observations -28 positions -0 regions with multiple methylated bases -0 observations with skips included -6 observations with too many skips -thread finished processing...: 44 observations 44 positions 1 regions with multiple methylated bases @@ -997,6 +1027,12 @@ 0 regions with multiple methylated bases 0 observations with skips included 4 observations with too many skips +thread finished processing...: +28 observations +28 positions +0 regions with multiple methylated bases +0 observations with skips included +6 observations with too many skips Error: could not find sequence for reference contig li thread finished processing...: 16 observations @@ -1008,10 +1044,10 @@ Merging files... Training... ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'] -[[-1.44, -5.03, 1.4449999999999998, 0.4000000000000001, -0.588, -0.55, 7.055265349382997], [-1.4433333333333334, -0.020000000000000018, -0.0366666666666667, -0.5499999999999999, 0.64, -2.71, 7.055265349382997], [-1.23, -1.635, -0.24, 1.1033333333333333, -2.215, -2.93, 7.055265349382997], [-0.21, 0.07500000000000001, -1.3083333333333333, 4.15, -0.3, -0.21500000000000002, 7.055265349382997], [-1.355, -0.34, -1.8633333333333333, -1.87, -1.2650000000000001, -1.22, 7.055265349382997], [-5.64, -3.6, -5.13, -0.255, 0.4, 0.73, 7.055265349382997], [-1.1400000000000001, 0.94, -4.55, 2.0, -0.34, -2.71, 7.055265349382997], [1.02, -2.38, 0.915, 0.05, 1.75, 0.8875000000000001, 7.055265349382997], [-0.56, -3.505, 1.02, -1.55, -0.7139999999999999, -0.4825, 7.055265349382997], [3.49, 1.3, -1.4949999999999999, -2.3, -1.2, -0.62, 7.055265349382997]] -['AAATGMGATTT', 'AGTAGMTTGAT', 'ACTTAMCCGGT', 'AGCATMTTTAT', 'GTTATMTGCAA', 'GGTAAMAATTT', 'GTGACMGTTTT', 'GGCTTMTTTTA', 'GGATGMAAGAA', 'ATATTMTGCAT'] -NN general model scores: 1.0,0.875,1.0,0.5,0.5 -Cross validation accuracy: 0.78 (+/- 0.46) +[[1.1, -0.23666666666666666, 0.28, 1.17, -0.02, 0.6699999999999999, 7.055265349382997], [-0.53, -2.56, -0.45999999999999996, -2.09, -5.4, 1.05, 7.055265349382997], [0.06, -1.5999999999999999, -3.48, 1.365, 1.06, 3.94, 7.055265349382997], [2.98, 1.47, -2.14, 5.63, 1.07, 5.135, 7.055265349382997], [-0.68, -0.74, -0.585, -0.48, -0.815, -1.08, 7.055265349382997], [4.0249999999999995, -0.11499999999999999, -1.02, -0.48, 0.17333333333333337, 1.19, 7.055265349382997], [-1.3733333333333333, 0.17999999999999994, -0.6133333333333334, -1.43, -0.0050000000000000044, -4.32, 7.055265349382997], [-0.1, 2.23, -2.058, 2.78, -0.68, 0.51, 7.055265349382997], [-2.7199999999999998, -1.03, -0.14, 2.625, 1.0375, -1.075, 7.055265349382997], [-2.38, -1.03, -2.8833333333333333, -0.59, -4.31, -4.94, 7.055265349382997]] +['CATTAMCAATC', 'GCCCGMTATAT', 'TTTTGMGMTCC', 'TCGTGMATGCA', 'TAAAAMAGAGA', 'ATCAAMCCGAG', 'GCTTTMGCAAA', 'TGCGTMTTCAA', 'CTTCCMGCCAC', 'AGATAMTAAAT'] +NN general model scores: 0.875,0.375,0.25,0.875,0.625 +Cross validation accuracy: 0.60 (+/- 0.51) Finished training rm -rf testdata mv testdata_save testdata @@ -1044,12 +1080,14 @@ 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/420469/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/420469/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/1573513 and its subdirectories -I: Current time: Thu May 9 11:22:17 -12 2024 -I: pbuilder-time-stamp: 1715296937 +I: removing directory /srv/workspace/pbuilder/420469 and its subdirectories +I: Current time: Thu Jun 12 19:52:23 +14 2025 +I: pbuilder-time-stamp: 1749707543