Diff of the two buildlogs: -- --- b1/build.log 2023-04-22 09:16:03.869047388 +0000 +++ b2/build.log 2023-04-22 09:17:00.958514510 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 21 21:14:50 -12 2023 -I: pbuilder-time-stamp: 1682154890 +I: Current time: Sat May 25 05:39:07 +14 2024 +I: pbuilder-time-stamp: 1716565147 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./allelecount_4.3.0.orig.tar.gz] I: copying [./allelecount_4.3.0-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Sep 29 23:15:52 2022 -12 +gpgv: Signature made Sat Oct 1 01:15:52 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -28,52 +28,84 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/27841/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/8989/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-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 25 05:39 /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/8989/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/8989/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='27841' - PS1='# ' - PS2='> ' + 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=8989 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.h9q1U68t/pbuilderrc_ACcm --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.h9q1U68t/b1 --logfile b1/build.log allelecount_4.3.0-2.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.h9q1U68t/pbuilderrc_GcYR --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.h9q1U68t/b2 --logfile b2/build.log --extrapackages usrmerge allelecount_4.3.0-2.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink12-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 20 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/27841/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 24 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/8989/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -200,7 +232,7 @@ Get: 67 http://deb.debian.org/debian bookworm/main arm64 libpod-coverage-perl all 0.23-2 [22.1 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libtest-fatal-perl all 0.017-1 [13.2 kB] -Fetched 24.2 MB in 1s (37.1 MB/s) +Fetched 24.2 MB in 1s (45.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19616 files and directories currently installed.) @@ -492,8 +524,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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_4.3.0-2_source.changes +I: user script /srv/workspace/pbuilder/8989/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/8989/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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_4.3.0-2_source.changes dpkg-buildpackage: info: source package allelecount dpkg-buildpackage: info: source version 4.3.0-2 dpkg-buildpackage: info: source distribution unstable @@ -503,21 +544,21 @@ debian/rules clean dh clean debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/allelecount-4.3.0' +make[1]: Map '/build/allelecount-4.3.0' wordt binnengegaan dh_auto_clean --sourcedirectory=c cd c && make -j8 clean -make[2]: Entering directory '/build/allelecount-4.3.0/c' +make[2]: Map '/build/allelecount-4.3.0/c' wordt binnengegaan 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/allelecount-4.3.0/c' +make[2]: Map '/build/allelecount-4.3.0/c' wordt verlaten dh_auto_clean --sourcedirectory=perl -make[1]: Leaving directory '/build/allelecount-4.3.0' +make[1]: Map '/build/allelecount-4.3.0' wordt verlaten dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/allelecount-4.3.0' +make[1]: Map '/build/allelecount-4.3.0' wordt binnengegaan dh_auto_configure --sourcedirectory=c dh_auto_configure --sourcedirectory=perl cd perl && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -ffile-prefix-map=/build/allelecount-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/allelecount-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now" @@ -526,12 +567,12 @@ Generating a Unix-style Makefile Writing Makefile for alleleCount Writing MYMETA.yml and MYMETA.json -make[1]: Leaving directory '/build/allelecount-4.3.0' +make[1]: Map '/build/allelecount-4.3.0' wordt verlaten debian/rules override_dh_auto_build -make[1]: Entering directory '/build/allelecount-4.3.0' +make[1]: Map '/build/allelecount-4.3.0' wordt binnengegaan dh_auto_build --sourcedirectory=c cd c && make -j8 "INSTALL=install --strip-program=true" -make[2]: Entering directory '/build/allelecount-4.3.0/c' +make[2]: Map '/build/allelecount-4.3.0/c' wordt binnengegaan 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 mkdir -p ./bin mkdir -p ./htslib_tmp @@ -563,26 +604,26 @@ remove tmp hts location rm -rf ./htslib_tmp Binaries have been compiled. -make[2]: Leaving directory '/build/allelecount-4.3.0/c' +make[2]: Map '/build/allelecount-4.3.0/c' wordt verlaten dh_auto_build --sourcedirectory=perl cd perl && make -j8 -make[2]: Entering directory '/build/allelecount-4.3.0/perl' -cp lib/Sanger/CGP/AlleleCount/ToJson.pm blib/lib/Sanger/CGP/AlleleCount/ToJson.pm +make[2]: Map '/build/allelecount-4.3.0/perl' wordt binnengegaan 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 lib/Sanger/CGP/AlleleCount/ToJson.pm blib/lib/Sanger/CGP/AlleleCount/ToJson.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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/alleleCounterToJson.pl +"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/alleleCounter.pl Manifying 2 pod documents Manifying 2 pod documents -make[2]: Leaving directory '/build/allelecount-4.3.0/perl' -make[1]: Leaving directory '/build/allelecount-4.3.0' +make[2]: Map '/build/allelecount-4.3.0/perl' wordt verlaten +make[1]: Map '/build/allelecount-4.3.0' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/allelecount-4.3.0' +make[1]: Map '/build/allelecount-4.3.0' wordt binnengegaan dh_auto_test --sourcedirectory=c cd c && make -j8 test -make[2]: Entering directory '/build/allelecount-4.3.0/c' +make[2]: Map '/build/allelecount-4.3.0/c' wordt binnengegaan sh ./tests/runtests.sh Running unit tests: ---- @@ -592,10 +633,10 @@ Tests run: 1 tests/bam_access_tests PASS -make[2]: Leaving directory '/build/allelecount-4.3.0/c' +make[2]: Map '/build/allelecount-4.3.0/c' wordt verlaten dh_auto_test --sourcedirectory=perl cd perl && make -j8 test TEST_VERBOSE=1 -make[2]: Entering directory '/build/allelecount-4.3.0/perl' +make[2]: Map '/build/allelecount-4.3.0/perl' wordt binnengegaan 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; @@ -648,31 +689,31 @@ 1..2 ok All tests successful. -Files=4, Tests=38, 3 wallclock secs ( 0.07 usr 0.02 sys + 2.22 cusr 0.33 csys = 2.64 CPU) +Files=4, Tests=38, 2 wallclock secs ( 0.07 usr 0.01 sys + 1.65 cusr 0.27 csys = 2.00 CPU) Result: PASS -make[2]: Leaving directory '/build/allelecount-4.3.0/perl' -make[1]: Leaving directory '/build/allelecount-4.3.0' +make[2]: Map '/build/allelecount-4.3.0/perl' wordt verlaten +make[1]: Map '/build/allelecount-4.3.0' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install -make[1]: Entering directory '/build/allelecount-4.3.0' +make[1]: Map '/build/allelecount-4.3.0' wordt binnengegaan dh_auto_install --sourcedirectory=c dh_auto_install --sourcedirectory=perl cd perl && make -j8 install DESTDIR=/build/allelecount-4.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr -make[2]: Entering directory '/build/allelecount-4.3.0/perl' +make[2]: Map '/build/allelecount-4.3.0/perl' wordt binnengegaan Manifying 2 pod documents Manifying 2 pod documents Installing /build/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount.pm -Installing /build/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/Genotype.pm Installing /build/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/ToJson.pm +Installing /build/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/Genotype.pm Installing /build/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounterToJson.pl.1p Installing /build/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounter.pl.1p Installing /build/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::ToJson.3pm Installing /build/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::Genotype.3pm Installing /build/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounterToJson.pl Installing /build/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounter.pl -make[2]: Leaving directory '/build/allelecount-4.3.0/perl' -make[1]: Leaving directory '/build/allelecount-4.3.0' +make[2]: Map '/build/allelecount-4.3.0/perl' wordt verlaten +make[1]: Map '/build/allelecount-4.3.0' wordt verlaten dh_install dh_installdocs dh_installchangelogs @@ -692,9 +733,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'liballelecount-perl' in '../liballelecount-perl_4.3.0-2_all.deb'. -dpkg-deb: building package 'allelecount-dbgsym' in '../allelecount-dbgsym_4.3.0-2_arm64.deb'. -dpkg-deb: building package 'allelecount' in '../allelecount_4.3.0-2_arm64.deb'. +dpkg-deb: pakket 'allelecount' wordt gebouwd in '../allelecount_4.3.0-2_arm64.deb'. +dpkg-deb: pakket 'allelecount-dbgsym' wordt gebouwd in '../allelecount-dbgsym_4.3.0-2_arm64.deb'. +dpkg-deb: pakket 'liballelecount-perl' wordt gebouwd in '../liballelecount-perl_4.3.0-2_all.deb'. dpkg-genbuildinfo --build=binary -O../allelecount_4.3.0-2_arm64.buildinfo dpkg-genchanges --build=binary -O../allelecount_4.3.0-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -702,12 +743,14 @@ 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/8989/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/8989/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/27841 and its subdirectories -I: Current time: Fri Apr 21 21:16:02 -12 2023 -I: pbuilder-time-stamp: 1682154962 +I: removing directory /srv/workspace/pbuilder/8989 and its subdirectories +I: Current time: Sat May 25 05:40:00 +14 2024 +I: pbuilder-time-stamp: 1716565200