Diff of the two buildlogs: -- --- b1/build.log 2025-08-02 19:30:42.133176729 +0000 +++ b2/build.log 2025-08-02 19:31:29.301234105 +0000 @@ -1,6 +1,7 @@ +W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Fri Sep 4 13:51:56 -12 2026 -I: pbuilder-time-stamp: 1788573116 +I: Current time: Sun Aug 3 09:30:44 +14 2025 +I: pbuilder-time-stamp: 1754163044 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -32,52 +33,83 @@ dpkg-source: info: applying gcc-15.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/844946/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1152006/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Aug 2 19:30 /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/1152006/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1152006/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + 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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='49eca4d7d6824c7ba854e4b7cd195753' - 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='844946' - 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=1152006 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.3HrnxrTZ/pbuilderrc_pEW8 --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3HrnxrTZ/b1 --logfile b1/build.log aegean_0.16.0+dfsg-5~exp0.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.3HrnxrTZ/pbuilderrc_AXm5 --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3HrnxrTZ/b2 --logfile b2/build.log aegean_0.16.0+dfsg-5~exp0.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 codethink03-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/844946/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1152006/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -249,7 +281,7 @@ Get: 128 http://deb.debian.org/debian unstable/main arm64 lua-md5 arm64 1.2+git+1+8d87fee-2+b2 [13.7 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libgenometools0t64 arm64 1.6.5+ds-2.2 [1210 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libgenometools0-dev arm64 1.6.5+ds-2.2 [95.2 kB] -Fetched 38.9 MB in 1s (47.2 MB/s) +Fetched 38.9 MB in 1s (71.5 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19964 files and directories currently installed.) @@ -683,8 +715,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Sep 5 01:53:00 UTC 2026. -Universal Time is now: Sat Sep 5 01:53:00 UTC 2026. +Local time is now: Sat Aug 2 19:31:07 UTC 2025. +Universal Time is now: Sat Aug 2 19:31:07 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libsysprof-capture-4-dev:arm64 (48.0-2) ... @@ -800,7 +832,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/aegean-0.16.0+dfsg/ && 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 > ../aegean_0.16.0+dfsg-5~exp0_source.changes +I: user script /srv/workspace/pbuilder/1152006/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/1152006/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/aegean-0.16.0+dfsg/ && 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 > ../aegean_0.16.0+dfsg-5~exp0_source.changes dpkg-buildpackage: info: source package aegean dpkg-buildpackage: info: source version 0.16.0+dfsg-5~exp0 dpkg-buildpackage: info: source distribution experimental @@ -842,10 +878,6 @@ [compile AgnFilterStream] [compile AgnGaevalVisitor] [compile AgnGeneStream] -[compile AgnInferCDSVisitor] -[compile AgnInferExonsVisitor] -[compile AgnInferParentStream] -[compile AgnLocus] src/core/AgnCompareReportText.c: In function ‘compare_report_text_comp_class_summary’: src/core/AgnCompareReportText.c:287:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 287 | strncpy(header + 4, label, strlen(label)); @@ -853,7 +885,8 @@ src/core/AgnCompareReportText.c:287:3: note: length computed here 287 | strncpy(header + 4, label, strlen(label)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[compile AgnLocusFilterStream] +[compile AgnInferCDSVisitor] +[compile AgnInferExonsVisitor] src/core/AgnCompareReportText.c: In function ‘compare_report_text_summary_struc’: src/core/AgnCompareReportText.c:589:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 589 | strncpy(buffer + 14, units, strlen(units)); @@ -861,12 +894,15 @@ src/core/AgnCompareReportText.c:589:3: note: length computed here 589 | strncpy(buffer + 14, units, strlen(units)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[compile AgnInferParentStream] src/core/AgnCompareReportText.c:599:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 599 | strncpy(buffer + 15, units, strlen(units)); | ^ src/core/AgnCompareReportText.c:599:3: note: length computed here 599 | strncpy(buffer + 15, units, strlen(units)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[compile AgnLocus] +[compile AgnLocusFilterStream] [compile AgnLocusMapVisitor] [compile AgnLocusRefineStream] [compile AgnLocusStream] @@ -884,8 +920,8 @@ [compile Xtractore] [compile bin/pmrna] [compile bin/tidygff3] -[compile unit tests] [create libaegean] +[compile unit tests] ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libaegean.a make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' @@ -1123,8 +1159,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'aegean' in '../aegean_0.16.0+dfsg-5~exp0_arm64.deb'. dpkg-deb: building package 'aegean-dbgsym' in '../aegean-dbgsym_0.16.0+dfsg-5~exp0_arm64.deb'. +dpkg-deb: building package 'aegean' in '../aegean_0.16.0+dfsg-5~exp0_arm64.deb'. dpkg-genbuildinfo --build=binary -O../aegean_0.16.0+dfsg-5~exp0_arm64.buildinfo dpkg-genchanges --build=binary -O../aegean_0.16.0+dfsg-5~exp0_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1132,12 +1168,14 @@ 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/1152006/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1152006/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/844946 and its subdirectories -I: Current time: Fri Sep 4 13:53:40 -12 2026 -I: pbuilder-time-stamp: 1788573220 +I: removing directory /srv/workspace/pbuilder/1152006 and its subdirectories +I: Current time: Sun Aug 3 09:31:28 +14 2025 +I: pbuilder-time-stamp: 1754163088