Diff of the two buildlogs: -- --- b1/build.log 2025-02-07 12:26:32.959131675 +0000 +++ b2/build.log 2025-02-07 12:40:17.897770980 +0000 @@ -1,7 +1,6 @@ -W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 7 00:13:43 -12 2025 -I: pbuilder-time-stamp: 1738930423 +I: Current time: Fri Mar 13 08:49:36 +14 2026 +I: pbuilder-time-stamp: 1773341376 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,51 +26,84 @@ dpkg-source: info: applying skip-test-on-32-bit.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3937062/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1555161/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 Mar 12 18:49 /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/1555161/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1555161/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='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=' ' - 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='3937062' - PS1='# ' - PS2='> ' + INVOCATION_ID=b6baca75d930441aa72b7806c4ad8fad + 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=1555161 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.PiJ9EIeA/pbuilderrc_RffW --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.PiJ9EIeA/b1 --logfile b1/build.log python-pysam_0.23.0+ds-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - 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.PiJ9EIeA/pbuilderrc_Raku --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.PiJ9EIeA/b2 --logfile b2/build.log python-pysam_0.23.0+ds-1.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 codethink04-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 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3937062/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1555161/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -277,7 +309,7 @@ Get: 148 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.4-1 [250 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.21-1 [637 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 tabix arm64 1.21+ds-1 [461 kB] -Fetched 72.4 MB in 1s (126 MB/s) +Fetched 72.4 MB in 0s (199 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-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 ... 19920 files and directories currently installed.) @@ -769,8 +801,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Feb 7 12:14:15 UTC 2025. -Universal Time is now: Fri Feb 7 12:14:15 UTC 2025. +Local time is now: Thu Mar 12 18:50:02 UTC 2026. +Universal Time is now: Thu Mar 12 18:50:02 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -906,7 +938,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/python-pysam-0.23.0+ds/ && 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 > ../python-pysam_0.23.0+ds-1_source.changes +I: user script /srv/workspace/pbuilder/1555161/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1555161/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-pysam-0.23.0+ds/ && 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 > ../python-pysam_0.23.0+ds-1_source.changes dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.23.0+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -2474,7 +2510,7 @@ dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 1+0 records in 1+0 records out -122288 bytes (122 kB, 119 KiB) copied, 0.000150201 s, 814 MB/s +122288 bytes (122 kB, 119 KiB) copied, 0.00031908 s, 383 MB/s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - samtools index empty.bam @@ -2712,12 +2748,12 @@ tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_t7uue8w8' +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_1i794zpv' PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 -[E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_72yieaff' +[E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_72q90xew' PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED @@ -3299,8 +3335,7 @@ tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED -tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.12_pysam/build/tests/pysam_data/ex1.bam.bai -PASSED +tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED @@ -3377,7 +3412,7 @@ tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED -tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult__x_9en0r.bcf' +tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.12_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_b8sqzail.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) @@ -3878,7 +3913,7 @@ tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED -======================= 947 passed, 14 skipped in 20.71s ======================= +======================= 947 passed, 14 skipped in 21.86s ======================= I: pybuild base:311: cd /build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.13_pysam/build; python3.13 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.13 @@ -4051,12 +4086,12 @@ tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.13_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_h4ihtjy6' +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.13_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_slw0f4e8' PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 -[E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.13_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_02trpdb4' +[E::cram_index_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.13_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_6dd7jbc0' PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED @@ -4638,8 +4673,7 @@ tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED -tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load3] The index file is older than the data file: /build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.13_pysam/build/tests/pysam_data/ex1.bam.bai -PASSED +tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED @@ -4716,7 +4750,7 @@ tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED -tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.13_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_h04f_wvv.bcf' +tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/reproducible-path/python-pysam-0.23.0+ds/.pybuild/cpython3_3.13_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_ts_4ujqd.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) @@ -5217,7 +5251,7 @@ tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED -======================= 947 passed, 14 skipped in 19.39s ======================= +======================= 947 passed, 14 skipped in 19.35s ======================= make[1]: Leaving directory '/build/reproducible-path/python-pysam-0.23.0+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -6275,12 +6309,14 @@ 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/1555161/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1555161/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/3937062 and its subdirectories -I: Current time: Fri Feb 7 00:26:31 -12 2025 -I: pbuilder-time-stamp: 1738931191 +I: removing directory /srv/workspace/pbuilder/1555161 and its subdirectories +I: Current time: Fri Mar 13 09:03:16 +14 2026 +I: pbuilder-time-stamp: 1773342196