Diff of the two buildlogs: -- --- b1/build.log 2025-02-05 16:13:30.185320021 +0000 +++ b2/build.log 2025-02-05 16:17:25.538707575 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 5 04:10:41 -12 2025 -I: pbuilder-time-stamp: 1738771841 +I: Current time: Thu Feb 6 06:13:40 +14 2025 +I: pbuilder-time-stamp: 1738772020 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ 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/16131/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/18060/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +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 Feb 5 16:13 /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/18060/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/18060/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='unstable' - 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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='88781650d32946b8b893a817b2b1804d' - 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='16131' - PS1='# ' - PS2='> ' + INVOCATION_ID=9057169ae60141f49ca71a35d6a1d6fd + 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=18060 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.Fj7GNUoM/pbuilderrc_9kHg --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.Fj7GNUoM/b1 --logfile b1/build.log spoa_4.1.4-2.dsc' - SUDO_GID='110' - SUDO_UID='103' - 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.Fj7GNUoM/pbuilderrc_aSs2 --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.Fj7GNUoM/b2 --logfile b2/build.log spoa_4.1.4-2.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 virt64z 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) 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/16131/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/18060/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -84,7 +116,7 @@ Depends: debhelper-compat (= 13), cmake, d-shlibs, libbioparser-dev, libcereal-dev, libgtest-dev, zlib1g-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19531 files and directories currently installed.) +(Reading database ... 19565 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: @@ -189,10 +221,10 @@ Get: 66 http://deb.debian.org/debian unstable/main armhf libcereal-dev armhf 1.3.2+dfsg-5 [221 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libgtest-dev armhf 1.15.2-1 [246 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libsimde-dev all 0.8.2-2 [467 kB] -Fetched 35.8 MB in 4s (9777 kB/s) +Fetched 35.8 MB in 1s (51.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0: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 ... 19531 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 ... 19565 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-7_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.4-7) ... Selecting previously unselected package procps. @@ -476,7 +508,11 @@ 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/18060/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/18060/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 @@ -527,7 +563,7 @@ CMakeLists.txt:53 (FetchContent_Populate) --- Configuring done (1.0s) +-- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -633,47 +669,47 @@ [----------] 19 tests from SpoaTest [ RUN ] SpoaTest.Clear -[ OK ] SpoaTest.Clear (1862 ms) +[ OK ] SpoaTest.Clear (2894 ms) [ RUN ] SpoaTest.Local -[ OK ] SpoaTest.Local (935 ms) +[ OK ] SpoaTest.Local (1445 ms) [ RUN ] SpoaTest.LocalAffine -[ OK ] SpoaTest.LocalAffine (1269 ms) +[ OK ] SpoaTest.LocalAffine (1914 ms) [ RUN ] SpoaTest.LocalConvex -[ OK ] SpoaTest.LocalConvex (2210 ms) +[ OK ] SpoaTest.LocalConvex (3246 ms) [ RUN ] SpoaTest.LocalWithQualities -[ OK ] SpoaTest.LocalWithQualities (947 ms) +[ OK ] SpoaTest.LocalWithQualities (1454 ms) [ RUN ] SpoaTest.LocalAffineWithQualities -[ OK ] SpoaTest.LocalAffineWithQualities (1276 ms) +[ OK ] SpoaTest.LocalAffineWithQualities (1913 ms) [ RUN ] SpoaTest.LocalConvexWithQualities -[ OK ] SpoaTest.LocalConvexWithQualities (2205 ms) +[ OK ] SpoaTest.LocalConvexWithQualities (3538 ms) [ RUN ] SpoaTest.Global -[ OK ] SpoaTest.Global (874 ms) +[ OK ] SpoaTest.Global (1324 ms) [ RUN ] SpoaTest.GlobalAffine -[ OK ] SpoaTest.GlobalAffine (1197 ms) +[ OK ] SpoaTest.GlobalAffine (1811 ms) [ RUN ] SpoaTest.GlobalConvex -[ OK ] SpoaTest.GlobalConvex (2105 ms) +[ OK ] SpoaTest.GlobalConvex (3107 ms) [ RUN ] SpoaTest.GlobalWithQualities -[ OK ] SpoaTest.GlobalWithQualities (872 ms) +[ OK ] SpoaTest.GlobalWithQualities (1359 ms) [ RUN ] SpoaTest.GlobalAffineWithQualities -[ OK ] SpoaTest.GlobalAffineWithQualities (1197 ms) +[ OK ] SpoaTest.GlobalAffineWithQualities (1803 ms) [ RUN ] SpoaTest.GlobalConvexWithQualities -[ OK ] SpoaTest.GlobalConvexWithQualities (2102 ms) +[ OK ] SpoaTest.GlobalConvexWithQualities (3177 ms) [ RUN ] SpoaTest.SemiGlobal -[ OK ] SpoaTest.SemiGlobal (864 ms) +[ OK ] SpoaTest.SemiGlobal (1325 ms) [ RUN ] SpoaTest.SemiGlobalAffine -[ OK ] SpoaTest.SemiGlobalAffine (1189 ms) +[ OK ] SpoaTest.SemiGlobalAffine (1789 ms) [ RUN ] SpoaTest.SemiGlobalConvex -[ OK ] SpoaTest.SemiGlobalConvex (2103 ms) +[ OK ] SpoaTest.SemiGlobalConvex (3105 ms) [ RUN ] SpoaTest.SemiGlobalWithQualities -[ OK ] SpoaTest.SemiGlobalWithQualities (931 ms) +[ OK ] SpoaTest.SemiGlobalWithQualities (1315 ms) [ RUN ] SpoaTest.SemiGlobalAffineWithQualities -[ OK ] SpoaTest.SemiGlobalAffineWithQualities (1189 ms) +[ OK ] SpoaTest.SemiGlobalAffineWithQualities (1787 ms) [ RUN ] SpoaTest.SemiGlobalConvexWithQualities -[ OK ] SpoaTest.SemiGlobalConvexWithQualities (2101 ms) -[----------] 19 tests from SpoaTest (27441 ms total) +[ OK ] SpoaTest.SemiGlobalConvexWithQualities (3121 ms) +[----------] 19 tests from SpoaTest (41443 ms total) [----------] Global test environment tear-down -[==========] 22 tests from 2 test suites ran. (27442 ms total) +[==========] 22 tests from 2 test suites ran. (41444 ms total) [ PASSED ] 22 tests. `find . -name spoa | grep bin` test/data/sample.fastq.gz >Consensus LN:i:495 @@ -698,9 +734,9 @@ -- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/lib/arm-linux-gnueabihf/libspoa_static.a -- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/include/spoa -- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/include/spoa/version.hpp +-- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/include/spoa/alignment_engine.hpp -- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/include/spoa/graph.hpp -- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/include/spoa/spoa.hpp --- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/include/spoa/alignment_engine.hpp -- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/spoa/spoaTargets.cmake -- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/spoa/spoaTargets-release.cmake -- Installing: /build/reproducible-path/spoa-4.1.4/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/spoa/spoaConfig.cmake @@ -761,8 +797,8 @@ dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'spoa' in '../spoa_4.1.4-2_armhf.deb'. -dpkg-deb: building package 'libspoa7.0.0' in '../libspoa7.0.0_4.1.4-2_armhf.deb'. dpkg-deb: building package 'libspoa-dev' in '../libspoa-dev_4.1.4-2_armhf.deb'. +dpkg-deb: building package 'libspoa7.0.0' in '../libspoa7.0.0_4.1.4-2_armhf.deb'. dpkg-deb: building package 'spoa-dbgsym' in '../spoa-dbgsym_4.1.4-2_armhf.deb'. dpkg-deb: building package 'libspoa7.0.0-dbgsym' in '../libspoa7.0.0-dbgsym_4.1.4-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../spoa_4.1.4-2_armhf.buildinfo @@ -772,12 +808,14 @@ 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/18060/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/18060/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/16131 and its subdirectories -I: Current time: Wed Feb 5 04:13:26 -12 2025 -I: pbuilder-time-stamp: 1738772006 +I: removing directory /srv/workspace/pbuilder/18060 and its subdirectories +I: Current time: Thu Feb 6 06:17:21 +14 2025 +I: pbuilder-time-stamp: 1738772241