Diff of the two buildlogs: -- --- b1/build.log 2024-11-17 15:23:50.960828118 +0000 +++ b2/build.log 2024-11-17 15:24:58.997748910 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Dec 20 09:45:47 -12 2025 -I: pbuilder-time-stamp: 1766267147 +I: Current time: Sun Dec 21 11:46:53 +14 2025 +I: pbuilder-time-stamp: 1766267213 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying shared_and_static.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1193442/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3620623/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Dec 20 21:46 /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/3620623/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3620623/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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(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='882303db6379468cac723775b280ee86' - 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='1193442' - PS1='# ' - PS2='> ' + INVOCATION_ID=84b88bcdc3d64254895e98815d876b3b + 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=3620623 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.rVgZixZM/pbuilderrc_t0eD --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.rVgZixZM/b1 --logfile b1/build.log spoa_4.1.4-2.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.rVgZixZM/pbuilderrc_3gqO --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.rVgZixZM/b2 --logfile b2/build.log spoa_4.1.4-2.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 codethink01-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1193442/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/3620623/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -187,7 +219,7 @@ Get: 60 http://deb.debian.org/debian unstable/main arm64 libcereal-dev arm64 1.3.2+dfsg-5 [221 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libgtest-dev arm64 1.15.2-1 [245 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-1 [465 kB] -Fetched 37.6 MB in 0s (125 MB/s) +Fetched 37.6 MB in 0s (154 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 20084 files and directories currently installed.) @@ -450,7 +482,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/spoa-4.1.4/ && 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 > ../spoa_4.1.4-2_source.changes +I: user script /srv/workspace/pbuilder/3620623/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3620623/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/spoa-4.1.4/ && 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 > ../spoa_4.1.4-2_source.changes dpkg-buildpackage: info: source package spoa dpkg-buildpackage: info: source version 4.1.4-2 dpkg-buildpackage: info: source distribution unstable @@ -501,7 +537,7 @@ CMakeLists.txt:53 (FetchContent_Populate) --- Configuring done (0.8s) +-- Configuring done (0.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -607,21 +643,21 @@ [----------] 19 tests from SpoaTest [ RUN ] SpoaTest.Clear -[ OK ] SpoaTest.Clear (154 ms) +[ OK ] SpoaTest.Clear (179 ms) [ RUN ] SpoaTest.Local -[ OK ] SpoaTest.Local (62 ms) +[ OK ] SpoaTest.Local (63 ms) [ RUN ] SpoaTest.LocalAffine -[ OK ] SpoaTest.LocalAffine (80 ms) +[ OK ] SpoaTest.LocalAffine (81 ms) [ RUN ] SpoaTest.LocalConvex -[ OK ] SpoaTest.LocalConvex (101 ms) +[ OK ] SpoaTest.LocalConvex (102 ms) [ RUN ] SpoaTest.LocalWithQualities -[ OK ] SpoaTest.LocalWithQualities (62 ms) +[ OK ] SpoaTest.LocalWithQualities (63 ms) [ RUN ] SpoaTest.LocalAffineWithQualities [ OK ] SpoaTest.LocalAffineWithQualities (81 ms) [ RUN ] SpoaTest.LocalConvexWithQualities [ OK ] SpoaTest.LocalConvexWithQualities (102 ms) [ RUN ] SpoaTest.Global -[ OK ] SpoaTest.Global (61 ms) +[ OK ] SpoaTest.Global (62 ms) [ RUN ] SpoaTest.GlobalAffine [ OK ] SpoaTest.GlobalAffine (80 ms) [ RUN ] SpoaTest.GlobalConvex @@ -629,25 +665,25 @@ [ RUN ] SpoaTest.GlobalWithQualities [ OK ] SpoaTest.GlobalWithQualities (62 ms) [ RUN ] SpoaTest.GlobalAffineWithQualities -[ OK ] SpoaTest.GlobalAffineWithQualities (80 ms) +[ OK ] SpoaTest.GlobalAffineWithQualities (81 ms) [ RUN ] SpoaTest.GlobalConvexWithQualities -[ OK ] SpoaTest.GlobalConvexWithQualities (98 ms) +[ OK ] SpoaTest.GlobalConvexWithQualities (101 ms) [ RUN ] SpoaTest.SemiGlobal -[ OK ] SpoaTest.SemiGlobal (61 ms) +[ OK ] SpoaTest.SemiGlobal (62 ms) [ RUN ] SpoaTest.SemiGlobalAffine -[ OK ] SpoaTest.SemiGlobalAffine (79 ms) +[ OK ] SpoaTest.SemiGlobalAffine (81 ms) [ RUN ] SpoaTest.SemiGlobalConvex -[ OK ] SpoaTest.SemiGlobalConvex (99 ms) +[ OK ] SpoaTest.SemiGlobalConvex (101 ms) [ RUN ] SpoaTest.SemiGlobalWithQualities -[ OK ] SpoaTest.SemiGlobalWithQualities (61 ms) +[ OK ] SpoaTest.SemiGlobalWithQualities (62 ms) [ RUN ] SpoaTest.SemiGlobalAffineWithQualities -[ OK ] SpoaTest.SemiGlobalAffineWithQualities (79 ms) +[ OK ] SpoaTest.SemiGlobalAffineWithQualities (80 ms) [ RUN ] SpoaTest.SemiGlobalConvexWithQualities -[ OK ] SpoaTest.SemiGlobalConvexWithQualities (99 ms) -[----------] 19 tests from SpoaTest (1611 ms total) +[ OK ] SpoaTest.SemiGlobalConvexWithQualities (100 ms) +[----------] 19 tests from SpoaTest (1652 ms total) [----------] Global test environment tear-down -[==========] 22 tests from 2 test suites ran. (1611 ms total) +[==========] 22 tests from 2 test suites ran. (1653 ms total) [ PASSED ] 22 tests. `find . -name spoa | grep bin` test/data/sample.fastq.gz >Consensus LN:i:495 @@ -734,11 +770,11 @@ dpkg-gencontrol: warning: Depends field of package libspoa-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel -dpkg-deb: building package 'spoa' in '../spoa_4.1.4-2_arm64.deb'. -dpkg-deb: building package 'spoa-dbgsym' in '../spoa-dbgsym_4.1.4-2_arm64.deb'. dpkg-deb: building package 'libspoa7.0.0' in '../libspoa7.0.0_4.1.4-2_arm64.deb'. dpkg-deb: building package 'libspoa7.0.0-dbgsym' in '../libspoa7.0.0-dbgsym_4.1.4-2_arm64.deb'. +dpkg-deb: building package 'spoa-dbgsym' in '../spoa-dbgsym_4.1.4-2_arm64.deb'. dpkg-deb: building package 'libspoa-dev' in '../libspoa-dev_4.1.4-2_arm64.deb'. +dpkg-deb: building package 'spoa' in '../spoa_4.1.4-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../spoa_4.1.4-2_arm64.buildinfo dpkg-genchanges --build=binary -O../spoa_4.1.4-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -746,12 +782,14 @@ 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/3620623/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3620623/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/1193442 and its subdirectories -I: Current time: Sat Dec 20 09:46:49 -12 2025 -I: pbuilder-time-stamp: 1766267209 +I: removing directory /srv/workspace/pbuilder/3620623 and its subdirectories +I: Current time: Sun Dec 21 11:47:57 +14 2025 +I: pbuilder-time-stamp: 1766267277