Diff of the two buildlogs: -- --- b1/build.log 2025-11-01 13:12:25.329506105 +0000 +++ b2/build.log 2025-11-01 13:15:23.281682237 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Nov 1 01:09:37 -12 2025 -I: pbuilder-time-stamp: 1762002577 +I: Current time: Sat Dec 5 09:35:26 +14 2026 +I: pbuilder-time-stamp: 1796412926 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -32,53 +32,85 @@ 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/2564246/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2684756/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 4 19:35 /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/2684756/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2684756/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=40 ' - 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=42 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='6440a444cb4e44b39952d62e35c9b42d' - 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='2564246' - PS1='# ' - PS2='> ' + INVOCATION_ID=cc371eae86614f6e94b15f34904c33eb + 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=2684756 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.D0SB7cjV/pbuilderrc_lC5e --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.D0SB7cjV/b1 --logfile b1/build.log aegean_0.16.0+dfsg-5.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.D0SB7cjV/pbuilderrc_UgTh --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.D0SB7cjV/b2 --logfile b2/build.log aegean_0.16.0+dfsg-5.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.48+deb13-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/2564246/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2684756/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -250,7 +282,7 @@ Get: 128 http://deb.debian.org/debian forky/main amd64 lua-md5 amd64 1.3-2 [15.1 kB] Get: 129 http://deb.debian.org/debian forky/main amd64 libgenometools0t64 amd64 1.6.6+ds-1 [1421 kB] Get: 130 http://deb.debian.org/debian forky/main amd64 libgenometools0-dev amd64 1.6.6+ds-1 [95.3 kB] -Fetched 40.6 MB in 17s (2430 kB/s) +Fetched 40.6 MB in 1s (46.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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.) @@ -685,8 +717,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Nov 1 13:11:43 UTC 2025. -Universal Time is now: Sat Nov 1 13:11:43 UTC 2025. +Local time is now: Fri Dec 4 19:37:46 UTC 2026. +Universal Time is now: Fri Dec 4 19:37:46 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libsysprof-capture-4-dev:amd64 (49.0-1) ... @@ -801,7 +833,11 @@ 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_source.changes +I: user script /srv/workspace/pbuilder/2684756/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2684756/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_source.changes dpkg-buildpackage: info: source package aegean dpkg-buildpackage: info: source version 0.16.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -813,7 +849,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_auto_clean - make -j40 clean + make -j42 clean make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' rm -rf bin/parseval bin/canon-gff3 bin/locuspocus bin/gaeval bin/xtractore bin/pmrna bin/tidygff3 bin/unittests libaegean.a obj/AgnAttributeFilterStream.o obj/AgnCliquePair.o obj/AgnCompareReportHTML.o obj/AgnCompareReportText.o obj/AgnComparison.o obj/AgnFilterStream.o obj/AgnGaevalVisitor.o obj/AgnGeneStream.o obj/AgnInferCDSVisitor.o obj/AgnInferExonsVisitor.o obj/AgnInferParentStream.o obj/AgnLocus.o obj/AgnLocusFilterStream.o obj/AgnLocusMapVisitor.o obj/AgnLocusRefineStream.o obj/AgnLocusStream.o obj/AgnMrnaRepVisitor.o obj/AgnPseudogeneFixVisitor.o obj/AgnRemoveChildrenVisitor.o obj/AgnTranscriptClique.o obj/AgnTypecheck.o obj/AgnUnitTest.o obj/AgnUtils.o inc/core/AgnVersion.h bin/*.dSYM make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' @@ -828,7 +864,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_auto_build -- prefix=/build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp 64bit=yes errorcheck=no - make -j40 INSTALL="install --strip-program=true" prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp 64bit=yes errorcheck=no + make -j42 INSTALL="install --strip-program=true" prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp 64bit=yes errorcheck=no make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' [print inc/core/AgnVersion.h] /build/reproducible-path/aegean-0.16.0+dfsg/data/scripts/version.py:31: SyntaxWarning: invalid escape sequence '\S' @@ -854,6 +890,10 @@ [compile AgnMrnaRepVisitor] [compile AgnPseudogeneFixVisitor] [compile AgnRemoveChildrenVisitor] +[compile AgnTranscriptClique] +[compile AgnTypecheck] +[compile AgnUnitTest] +[compile AgnUtils] 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)); @@ -861,10 +901,6 @@ src/core/AgnCompareReportText.c:287:30: note: length computed here 287 | strncpy(header + 4, label, strlen(label)); | ^~~~~~~~~~~~~ -[compile AgnTranscriptClique] -[compile AgnTypecheck] -[compile AgnUnitTest] -[compile AgnUtils] 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)); @@ -891,142 +927,12 @@ ar: creating libaegean.a make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' -dh_auto_test -- useshared=yes 64bit=yes testthreads=5 - make -j40 test useshared=yes 64bit=yes testthreads=5 -make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' -AEGeAn Unit Tests - AEGeAn::AgnAttributeFilterStream | SUCCESS - | Pogonomyrmex barbatus (partial) | PASS - AEGeAn::AgnPseudogeneFixVisitor | SUCCESS - | Gene, no pseudo attribute | PASS - | Gene, bogus pseudo attribute | PASS - | Corrected pseudogene | PASS - | Uncorrected pseudogene | PASS - | iLocus with gene & pseudogene | PASS - AEGeAn::AgnInferParentStream | SUCCESS - | Test 1: basic | PASS - | Test 2: 2 top-level | PASS - | Test 3: 2 top-level, inferred parent | PASS - | Test 4: multichild | PASS - | Test 5: multichild, inferred parent | PASS - AEGeAn::AgnMrnaRepVisitor | SUCCESS - | TAIR10: test 1 | PASS - AEGeAn::AgnRemoveChildrenVisitor | SUCCESS - | Test 1: grape (Gaze) | PASS - AEGeAn::AgnTranscriptClique | SUCCESS - | simple check | PASS - | two mRNAs | PASS - | copy check | PASS - AEGeAn::AgnCliquePair | SUCCESS - | perfect match vs. self | PASS - | CDS match | PASS - | non-match | PASS - AEGeAn::AgnLocus | SUCCESS - | grape test 1 | PASS - | grape test 2 | PASS - | filter by CDS length | PASS - | filter by exon number | PASS - AEGeAn::AgnFilterStream | SUCCESS - | mRNA | PASS - | exon | PASS - | CDS | PASS - | intron | PASS - | exon+intron | PASS - | CDS+intron | PASS - AEGeAn::AgnInferCDSVisitor | SUCCESS - | grape test sans UTRs | PASS - | grape test with UTRs, strand check | PASS - | grape test 3 | PASS - | grape test 4 | PASS - AEGeAn::AgnInferExonsVisitor | SUCCESS - | grape test sans UTRs | PASS - | grape test with UTRs, strand check | PASS - | grape test 3 | PASS - | grape test 4 | PASS - AEGeAn::AgnGeneStream | SUCCESS - | 1 gene, 2 mRNAs | PASS - | 1 gene, 2 mRNAs (one sans CDS) | PASS - | mRNA only | PASS - | mRNA boundaries | PASS - AEGeAn::AgnLocusStream | SUCCESS - | grape test (pairwise) | PASS - | Pdom test (pairwise) | PASS - | Amel test (Augustus) | PASS - | Delta=200 | PASS - AEGeAn::AgnLocusRefineStream | SUCCESS - | Atta cephalotes (syndrome): coords | PASS - | Atta cephalotes (syndrome): elen | PASS - | Megachile rotundata CST: coords | PASS - | Megachile rotundata CST: elen | PASS - AEGeAn::AgnGaevalVisitor | SUCCESS - | range intersect (1) | PASS - | range intersect (2) | PASS - | range intersect (3) | PASS - | union (1) | PASS - | union (2) | PASS - | union (3) | PASS - | intersect (1) | PASS - | intersect (2) | PASS - | intersect (3) | PASS - | intersect (4) | PASS - | intersect (5) | PASS - | calculate coverage | PASS - | introns confirmed (no gaps) | PASS - | introns confirmed (gaps) | PASS - | calculate integrity | PASS - -===== Unit tests passed for all 15 classes! ===== - -AEGeAn Functional Tests - GFF3 I/O: 'AT1G05320' - | codons | PASS - | sansexons | PASS - | sansutrs | PASS - | withprot | PASS - GFF3 I/O: 'FBgn0035002' - | codons | PASS - | sansexons | PASS - | sansutrs | PASS - AEGeAn::LocusPocus - | default | PASS - | end skip | PASS - | Apis mellifera plap | PASS - | Apis mellifera plap (CDS) | PASS - | Apis mellifera LSM | PASS - | Megachile rotundata CST (intron) | PASS - | iiLocus lengths (Amel OGS Group7.16) | PASS - | Nasonia vitripennis (intron gene) | PASS - | A. echinatior (intron gene + ncRNA) | PASS - AEGeAn::Xtractore - | major royal jelly | PASS - AEGeAn::CanonGFF3 - | A. mellifera gene multitrans | PASS - AEGeAn::GAEVAL - | sans CDS | PASS - | Pdom | PASS - AEGeAn::ParsEval - | Amel Group7.16 (text) | PASS - | Amel Group7.16 (delta=500) | PASS - | Amel Group7.16 (HTML) | PASS - AEGeAn::align-convert.py - | GAEVAL example1 | PASS - | GAEVAL example5 | PASS - AEGeAn::pmrna - | A. mellifera Shal | PASS - | A. mellifera dock | PASS - | A. mellifera pseudo | PASS - AEGeAn::tidygff3 - | A. dorsata exception | PASS -make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' -make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_auto_install -- 64bit=yes prefix=/build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp - make -j40 install DESTDIR=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/aegean AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" 64bit=yes prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp + make -j42 install DESTDIR=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/aegean AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" 64bit=yes prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' cp bin/parseval bin/canon-gff3 bin/locuspocus bin/gaeval bin/xtractore bin/pmrna bin/tidygff3 /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/bin/. cp libaegean.a /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/lib/. @@ -1110,8 +1016,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'aegean' in '../aegean_0.16.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'aegean-dbgsym' in '../aegean-dbgsym_0.16.0+dfsg-5_amd64.deb'. +dpkg-deb: building package 'aegean' in '../aegean_0.16.0+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../aegean_0.16.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../aegean_0.16.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1119,12 +1025,14 @@ 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/2684756/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2684756/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/2564246 and its subdirectories -I: Current time: Sat Nov 1 01:12:24 -12 2025 -I: pbuilder-time-stamp: 1762002744 +I: removing directory /srv/workspace/pbuilder/2684756 and its subdirectories +I: Current time: Sat Dec 5 09:38:22 +14 2026 +I: pbuilder-time-stamp: 1796413102