Diff of the two buildlogs: -- --- b1/build.log 2025-11-02 01:14:41.296376418 +0000 +++ b2/build.log 2025-11-02 01:16:46.428485009 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Nov 1 13:13:18 -12 2025 -I: pbuilder-time-stamp: 1762045998 +I: Current time: Sat Dec 5 21:37:43 +14 2026 +I: pbuilder-time-stamp: 1796456263 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -24,52 +24,84 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1158924/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/802889/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-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 Dec 5 07:37 /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/802889/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/802889/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=12 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=16 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='c0487d3a8ea143cfb275761484ac94a7' - 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='1158924' - PS1='# ' - PS2='> ' + INVOCATION_ID=5d76a3faa8014093a4ffa31089e8989b + 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=802889 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.JD0tkDif/pbuilderrc_6gCf --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JD0tkDif/b1 --logfile b1/build.log allelecount_4.3.0-3.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.JD0tkDif/pbuilderrc_2eXC --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JD0tkDif/b2 --logfile b2/build.log allelecount_4.3.0-3.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.48+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1158924/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/802889/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -82,7 +114,7 @@ Depends: debhelper-compat (= 13), libhts-dev, libbz2-dev, libconst-fast-perl, libdevel-cover-perl, libfile-slurp-perl, libfile-which-perl, libipc-system-simple-perl, libjson-perl, libpod-coverage-perl, libtest-fatal-perl, libtry-tiny-perl, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19869 files and directories currently installed.) +(Reading database ... 19862 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -239,10 +271,10 @@ Get: 110 http://deb.debian.org/debian forky/main amd64 libpod-coverage-perl all 0.23-2 [22.1 kB] Get: 111 http://deb.debian.org/debian forky/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 libtest-fatal-perl all 0.017-2 [12.9 kB] -Fetched 32.1 MB in 1s (43.7 MB/s) +Fetched 32.1 MB in 1s (40.8 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. -(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 ... 19869 files and directories currently installed.) +(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 ... 19862 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. @@ -704,7 +736,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/allelecount-4.3.0/ && 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 > ../allelecount_4.3.0-3_source.changes +I: user script /srv/workspace/pbuilder/802889/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/802889/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/allelecount-4.3.0/ && 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 > ../allelecount_4.3.0-3_source.changes dpkg-buildpackage: info: source package allelecount dpkg-buildpackage: info: source version 4.3.0-3 dpkg-buildpackage: info: source distribution unstable @@ -716,7 +752,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0' dh_auto_clean --sourcedirectory=c - cd c && make -j12 clean + cd c && make -j16 clean make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/c' rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/c' @@ -769,11 +805,11 @@ Binaries have been compiled. make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/c' dh_auto_build --sourcedirectory=perl - cd perl && make -j12 + cd perl && make -j16 make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/perl' +cp lib/Sanger/CGP/AlleleCount.pm blib/lib/Sanger/CGP/AlleleCount.pm cp lib/Sanger/CGP/AlleleCount/ToJson.pm blib/lib/Sanger/CGP/AlleleCount/ToJson.pm cp lib/Sanger/CGP/AlleleCount/Genotype.pm blib/lib/Sanger/CGP/AlleleCount/Genotype.pm -cp lib/Sanger/CGP/AlleleCount.pm blib/lib/Sanger/CGP/AlleleCount.pm cp bin/alleleCounter.pl blib/script/alleleCounter.pl cp bin/alleleCounterToJson.pl blib/script/alleleCounterToJson.pl "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/alleleCounter.pl @@ -782,87 +818,13 @@ Manifying 2 pod documents make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/perl' make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0' - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0' -dh_auto_test --sourcedirectory=c - cd c && make -j12 test -make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/c' -sh ./tests/runtests.sh -Running unit tests: ----- -RUNNING: ./tests/bam_access_tests -Performing pileup of 11250 reads at 1 198661939 -ALL TESTS PASSED -Tests run: 1 -tests/bam_access_tests PASS - -make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/c' -dh_auto_test --sourcedirectory=perl - cd perl && make -j12 test TEST_VERBOSE=1 -make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/perl' -PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t -t/1_pm_compile.t .. -ok 1 - use Sanger::CGP::AlleleCount; -ok 2 - use Sanger::CGP::AlleleCount::Genotype; -ok 3 - use Sanger::CGP::AlleleCount::ToJson; -ok 4 - Check version inheritance exists (Sanger::CGP::AlleleCount) -ok 5 - Check version inheritance exists (Sanger::CGP::AlleleCount::Genotype) -ok 6 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype' -ok 7 - Check version inheritance exists (Sanger::CGP::AlleleCount::ToJson) -ok 8 - An object of class 'Sanger::CGP::AlleleCount::ToJson' isa 'Sanger::CGP::AlleleCount::ToJson' -1..8 -ok -t/2_pl_compile.t .. -ok 1 - Compilation check: /build/reproducible-path/allelecount-4.3.0/perl/t/../bin/alleleCounterToJson.pl -ok 2 - Compilation check: /build/reproducible-path/allelecount-4.3.0/perl/t/../bin/alleleCounter.pl -1..2 -ok -t/genotype.t ...... -ok 1 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype' -ok 2 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype' -ok 3 - Check execution of loci profile (BAM) -ok 4 - Expected result for defaults (BAM) -ok 5 - Check execution of loci profile (BAM, pbq=20) -ok 6 - Expected result for defaults (BAM, pbq=20) -ok 7 - Check execution of loci profile (BAM, mapq=1) -ok 8 - Expected result for defaults (BAM, mapq=1) -ok 9 - Check execution of snp6 loci profile (BAM) -ok 10 - Expected result for defaults (BAM) -ok 11 - Check execution of snp6 loci profile (BAM, pbq=20) -ok 12 - Expected result for defaults (BAM, pbq=20) -ok 13 - Check execution of snp6 loci profile (BAM, mapq=1) -ok 14 - Expected result for defaults (BAM, mapq>0) -ok 15 - Check execution of loci profile (CRAM) -ok 16 - Expected result for defaults (CRAM) -ok 17 - Check execution of loci profile (CRAM, pbq=20) -ok 18 - Expected result for defaults (CRAM, pbq=20) -ok 19 - Check execution of loci profile (CRAM, mapq=1) -ok 20 - Expected result for defaults (CRAM, mapq=1) -ok 21 - Check execution of snp6 loci profile (CRAM) -ok 22 - Expected result for defaults (CRAM) -ok 23 - Check execution of snp6 loci profile (CRAM, pbq=20) -ok 24 - Expected result for defaults (CRAM, pbq=20) -ok 25 - Check execution of snp6 loci profile (CRAM, mapq=1) -ok 26 - Expected result for defaults (CRAM, mapq=1) -1..26 -ok -t/tojson.t ........ -ok 1 - An object of class 'Sanger::CGP::AlleleCount::ToJson' isa 'Sanger::CGP::AlleleCount::ToJson' -ok 2 - Check conversion to JSON -1..2 -ok -All tests successful. -Files=4, Tests=38, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.45 cusr 0.14 csys = 0.62 CPU) -Result: PASS -make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/perl' -make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0' dh_auto_install --sourcedirectory=c dh_auto_install --sourcedirectory=perl - cd perl && make -j12 install DESTDIR=/build/reproducible-path/allelecount-4.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr + cd perl && make -j16 install DESTDIR=/build/reproducible-path/allelecount-4.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/perl' Manifying 2 pod documents Manifying 2 pod documents @@ -871,10 +833,10 @@ Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/ToJson.pm Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounterToJson.pl.1p Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounter.pl.1p -Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::ToJson.3pm Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::Genotype.3pm -Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounterToJson.pl +Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::ToJson.3pm Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounter.pl +Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounterToJson.pl make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/perl' make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0' dh_install @@ -906,12 +868,14 @@ 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/802889/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/802889/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/1158924 and its subdirectories -I: Current time: Sat Nov 1 13:14:40 -12 2025 -I: pbuilder-time-stamp: 1762046080 +I: removing directory /srv/workspace/pbuilder/802889 and its subdirectories +I: Current time: Sat Dec 5 21:39:46 +14 2026 +I: pbuilder-time-stamp: 1796456386