Diff of the two buildlogs: -- --- b1/build.log 2025-01-25 15:41:51.754804812 +0000 +++ b2/build.log 2025-01-25 16:03:51.855456814 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 27 09:56:31 -12 2026 -I: pbuilder-time-stamp: 1772229391 +I: Current time: Sun Jan 26 05:41:56 +14 2025 +I: pbuilder-time-stamp: 1737819716 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying reproducible_build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/981311/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2796068/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 Jan 25 15:42 /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/2796068/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2796068/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='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='f2ba4c367d83461791d39164ab92d348' - 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='981311' - PS1='# ' - PS2='> ' + INVOCATION_ID=c35bb91e3fcf4857803e38dd2107e820 + 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=2796068 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.JdCvRfPM/pbuilderrc_Lad8 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JdCvRfPM/b1 --logfile b1/build.log infernal_1.1.5-3.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.JdCvRfPM/pbuilderrc_x9kP --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JdCvRfPM/b2 --logfile b2/build.log infernal_1.1.5-3.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 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/981311/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2796068/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -164,7 +196,7 @@ Get: 52 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libperl4-corelibs-perl all 0.005-1 [39.0 kB] -Fetched 26.7 MB in 0s (193 MB/s) +Fetched 26.7 MB in 0s (87.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.12-minimal: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 ... 19970 files and directories currently installed.) @@ -361,8 +393,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Feb 27 21:56:48 UTC 2026. -Universal Time is now: Fri Feb 27 21:56:48 UTC 2026. +Local time is now: Sat Jan 25 15:42:38 UTC 2025. +Universal Time is now: Sat Jan 25 15:42:38 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -409,7 +441,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/infernal-1.1.5/ && 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 > ../infernal_1.1.5-3_source.changes +I: user script /srv/workspace/pbuilder/2796068/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2796068/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/infernal-1.1.5/ && 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 > ../infernal_1.1.5-3_source.changes dpkg-buildpackage: info: source package infernal dpkg-buildpackage: info: source version 1.1.5-3 dpkg-buildpackage: info: source distribution unstable @@ -701,8 +737,6 @@ gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_sqio_ascii.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_sqio_ncbi.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_ssi.c -gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_stack.c -gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_stats.c In file included from esl_scorematrix.c:22: esl_scorematrix.c: In function 'esl_scorematrix_Create': easel.h:179:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] @@ -715,6 +749,8 @@ /usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ +gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_stack.c +gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_stats.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_stopwatch.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_stretchexp.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/infernal-1.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pthread -c esl_subcmd.c @@ -998,17 +1034,17 @@ make[1]: Entering directory '/build/reproducible-path/infernal-1.1.5' SUBDIR easel make[2]: Entering directory '/build/reproducible-path/infernal-1.1.5/easel' + GEN easel_utest GEN esl_alloc_utest + GEN esl_alphabet_utest GEN esl_bitfield_utest - GEN easel_utest GEN esl_buffer_utest - GEN esl_cpu_utest - GEN esl_alphabet_utest GEN esl_cluster_utest + GEN esl_cpu_utest + GEN esl_dirichlet_utest GEN esl_distance_utest GEN esl_dmatrix_utest GEN esl_dsqdata_utest - GEN esl_dirichlet_utest GEN esl_exponential_utest GEN esl_fileparser_utest GEN esl_gamma_utest @@ -1017,8 +1053,8 @@ GEN esl_graph_utest GEN esl_gumbel_utest GEN esl_heap_utest - GEN esl_hmm_utest GEN esl_histogram_utest + GEN esl_hmm_utest GEN esl_huffman_utest GEN esl_hyperexp_utest GEN esl_iset_utest @@ -1030,8 +1066,8 @@ GEN esl_minimizer_utest GEN esl_mixdchlet_utest GEN esl_msa_utest - GEN esl_msafile_utest GEN esl_msacluster_utest + GEN esl_msafile_utest GEN esl_msafile2_utest GEN esl_msafile_a2m_utest GEN esl_msafile_afa_utest @@ -1040,24 +1076,23 @@ GEN esl_msafile_psiblast_utest GEN esl_msafile_selex_utest GEN esl_msafile_stockholm_utest - GEN esl_normal_utest GEN esl_msaweight_utest + GEN esl_normal_utest GEN esl_quicksort_utest GEN esl_random_utest GEN esl_rand64_utest GEN esl_randomseq_utest - GEN esl_red_black_utest GEN esl_ratematrix_utest + GEN esl_red_black_utest GEN esl_recorder_utest GEN esl_regexp_utest GEN esl_rootfinder_utest GEN esl_scorematrix_utest GEN esl_sq_utest GEN esl_sqio_utest - GEN esl_stack_utest GEN esl_ssi_utest + GEN esl_stack_utest GEN esl_stats_utest - GEN esl_stretchexp_utest In file included from ./esl_scorematrix.c:22: ./esl_scorematrix.c: In function 'esl_scorematrix_Create': ./easel.h:179:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] @@ -1070,14 +1105,15 @@ /usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ + GEN esl_stretchexp_utest GEN esl_tree_utest GEN esl_varint_utest GEN esl_vectorops_utest - GEN esl_wuss_utest GEN esl_weibull_utest + GEN esl_wuss_utest GEN esl_sse_utest - GEN esl_avx512_utest GEN esl_avx_utest + GEN esl_avx512_utest GEN esl_neon_utest GEN esl_vmx_utest SUBDIR miniapps @@ -1093,17 +1129,17 @@ SUBDIR src SUBDIR impl_neon CC itest_brute.o + GEN build_utest + GEN generic_msv_utest + GEN generic_fwdback_chk_utest + GEN generic_fwdback_utest + GEN generic_stotrace_utest GEN generic_viterbi_utest + GEN hmmer_utest GEN logsum_utest - GEN generic_fwdback_utest - GEN generic_fwdback_chk_utest - GEN generic_msv_utest - GEN build_utest GEN modelconfig_utest - GEN p7_alidisplay_utest - GEN hmmer_utest GEN seqmodel_utest - GEN generic_stotrace_utest + GEN p7_alidisplay_utest GEN p7_bg_utest GEN p7_domain_utest GEN p7_gmx_utest @@ -1111,23 +1147,23 @@ GEN p7_hit_utest GEN p7_hmmd_search_stats_utest GEN p7_hmm_utest - GEN p7_profile_utest GEN p7_hmmfile_utest GEN p7_tophits_utest + GEN p7_profile_utest GEN p7_trace_utest GEN p7_scoredata_utest GEN hmmpgmd2msa_utest - GEN hmmd_search_status_utest GEN itest_brute + GEN hmmd_search_status_utest SUBDIR impl_neon - GEN null2_utest - GEN fwdback_utest - GEN io_utest GEN decoding_utest - GEN optacc_utest + GEN fwdback_utest GEN msvfilter_utest + GEN io_utest + GEN null2_utest GEN stotrace_utest GEN vitfilter_utest + GEN optacc_utest make[2]: Leaving directory '/build/reproducible-path/infernal-1.1.5/hmmer' SUBDIR src make[2]: Entering directory '/build/reproducible-path/infernal-1.1.5/src' @@ -1234,8 +1270,8 @@ System information: -Fri Feb 27 09:58:33 -12 2026 -Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux +Sun Jan 26 05:47:24 +14 2025 +Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux make[2]: Leaving directory '/build/reproducible-path/infernal-1.1.5/easel' SUBDIR hmmer/testsuite make[2]: Entering directory '/build/reproducible-path/infernal-1.1.5/hmmer/testsuite' @@ -1554,8 +1590,8 @@ System information: -Fri Feb 27 09:58:52 -12 2026 -Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux +Sun Jan 26 05:48:17 +14 2025 +Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux make[2]: Leaving directory '/build/reproducible-path/infernal-1.1.5/hmmer/testsuite' SUBDIR testsuite make[2]: Entering directory '/build/reproducible-path/infernal-1.1.5/testsuite' @@ -1737,8 +1773,8 @@ System information: -Fri Feb 27 10:03:49 -12 2026 -Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux +Sun Jan 26 06:01:51 +14 2025 +Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux make[2]: Leaving directory '/build/reproducible-path/infernal-1.1.5/testsuite' make[1]: Leaving directory '/build/reproducible-path/infernal-1.1.5' create-stamp debian/debhelper-build-stamp @@ -1833,12 +1869,14 @@ 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/2796068/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2796068/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/981311 and its subdirectories -I: Current time: Fri Feb 27 10:04:50 -12 2026 -I: pbuilder-time-stamp: 1772229890 +I: removing directory /srv/workspace/pbuilder/2796068 and its subdirectories +I: Current time: Sun Jan 26 06:03:50 +14 2025 +I: pbuilder-time-stamp: 1737821030