Diff of the two buildlogs: -- --- b1/build.log 2025-07-11 07:31:38.931800575 +0000 +++ b2/build.log 2025-07-11 07:34:30.416940324 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 10 19:27:21 -12 2025 -I: pbuilder-time-stamp: 1752218841 +I: Current time: Fri Aug 14 03:54:40 +14 2026 +I: pbuilder-time-stamp: 1786629280 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying numpy2.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3084800/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/89175/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 Aug 13 13:54 /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/89175/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/89175/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='863570e8a0f34225b99d76a2494c2495' - 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='3084800' - PS1='# ' - PS2='> ' + INVOCATION_ID=e5520bbc272c419781998e8e73878090 + 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=89175 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.DmScg5Va/pbuilderrc_Mx7F --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.DmScg5Va/b1 --logfile b1/build.log python-pbcore_2.1.2+dfsg-11.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.DmScg5Va/pbuilderrc_FBLa --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.DmScg5Va/b2 --logfile b2/build.log python-pbcore_2.1.2+dfsg-11.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 6.1.0-37-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 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3084800/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/89175/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -342,7 +374,7 @@ Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 8.1.3-5 [468 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-uritools all 4.0.3-1 [28.6 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-xmlschema all 3.4.5-1 [239 kB] -Fetched 73.1 MB in 0s (186 MB/s) +Fetched 73.1 MB in 0s (211 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 ... 19964 files and directories currently installed.) @@ -976,8 +1008,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jul 11 07:28:20 UTC 2025. -Universal Time is now: Fri Jul 11 07:28:20 UTC 2025. +Local time is now: Thu Aug 13 13:55:11 UTC 2026. +Universal Time is now: Thu Aug 13 13:55:11 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:arm64 (1:1.1.8-1+b2) ... @@ -1160,7 +1192,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/python-pbcore-2.1.2+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 > ../python-pbcore_2.1.2+dfsg-11_source.changes +I: user script /srv/workspace/pbuilder/89175/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/89175/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-pbcore-2.1.2+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 > ../python-pbcore_2.1.2+dfsg-11_source.changes dpkg-buildpackage: info: source package python-pbcore dpkg-buildpackage: info: source version 2.1.2+dfsg-11 dpkg-buildpackage: info: source distribution unstable @@ -1178,8 +1214,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - By 2026-Mar-03, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1196,8 +1232,8 @@ versions. Please use the underscore name 'description_file' instead. (Affected: pbcore). - By 2026-Mar-03, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1236,8 +1272,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - By 2026-Mar-03, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1254,8 +1290,8 @@ versions. Please use the underscore name 'description_file' instead. (Affected: pbcore). - By 2026-Mar-03, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1274,8 +1310,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - By 2026-Mar-03, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1292,8 +1328,8 @@ versions. Please use the underscore name 'description_file' instead. (Affected: pbcore). - By 2026-Mar-03, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1572,248 +1608,248 @@ scheduling tests via LoadScopeScheduling -tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse -[gw8] [ 0%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement -[gw8] [ 1%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement -[gw8] [ 2%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations +tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str -[gw5] [ 2%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str +[gw7] [ 0%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str +tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification -[gw5] [ 3%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification +[gw7] [ 1%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString -tests/test_pbdataset_split.py::TestDataSetSplit::test_split -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ -[gw3] [ 4%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ -tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency +tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse +[gw6] [ 2%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement +[gw6] [ 2%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement +[gw6] [ 3%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement +[gw11] [ 4%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 +tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 +[gw11] [ 5%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 +tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs +[gw7] [ 5%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations +tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency +tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid +[gw9] [ 6%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid +[gw0] [ 7%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation +[gw0] [ 7%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName +[gw0] [ 8%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead +[gw0] [ 9%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration -[gw6] [ 5%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration -tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName -[gw6] [ 5%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName -tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById -[gw5] [ 6%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString -[gw9] [ 7%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid +[gw0] [ 10%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference +[gw4] [ 10%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype -tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs -[gw10] [ 7%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs -tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted -[gw10] [ 8%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted -tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ +[gw5] [ 11%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ +tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName +[gw4] [ 12%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName +[gw2] [ 12%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation +[gw2] [ 13%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac -[gw8] [ 9%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac +[gw6] [ 14%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error +[gw6] [ 15%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error +tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById +[gw4] [ 15%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById +tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition +[gw4] [ 16%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition +[gw5] [ 17%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString +[gw5] [ 17%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 +[gw5] [ 18%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 +[gw9] [ 19%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype +tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix +[gw9] [ 20%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix +[gw0] [ 20%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference +[gw0] [ 21%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV +[gw0] [ 22%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript +[gw0] [ 22%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments +[gw0] [ 23%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName +[gw2] [ 24%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead +[gw10] [ 25%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency +tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming +tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice +[gw4] [ 25%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice +tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get -[gw5] [ 10%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get +[gw7] [ 26%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get tests/test_pbcore_io_FofnIO.py::test_simple -[gw3] [ 10%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString -[gw3] [ 11%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString -[gw8] [ 12%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error -tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 -[gw11] [ 12%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 -tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 -[gw11] [ 13%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 -tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ -[gw4] [ 14%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ +[gw7] [ 27%] PASSED tests/test_pbcore_io_FofnIO.py::test_simple +tests/test_pbcore_io_FofnIO.py::test_empty_lines +[gw7] [ 27%] PASSED tests/test_pbcore_io_FofnIO.py::test_empty_lines +[gw5] [ 28%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len +[gw5] [ 29%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq +[gw5] [ 30%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq +[gw8] [ 30%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs +tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted +[gw8] [ 31%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted +tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff +[gw8] [ 32%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff +[gw10] [ 32%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming +tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire +[gw2] [ 33%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead +[gw2] [ 34%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead +tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 +[gw11] [ 35%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 +tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations +[gw11] [ 35%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations +[gw10] [ 36%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire +[gw3] [ 37%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ -[gw4] [ 15%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ +[gw3] [ 37%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString -[gw4] [ 15%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString +[gw3] [ 38%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 -[gw6] [ 16%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById -tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition -[gw6] [ 17%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition -tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice -[gw5] [ 17%] PASSED tests/test_pbcore_io_FofnIO.py::test_simple -tests/test_pbcore_io_FofnIO.py::test_empty_lines -[gw5] [ 18%] PASSED tests/test_pbcore_io_FofnIO.py::test_empty_lines -[gw9] [ 19%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype -tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error -[gw8] [ 20%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error -tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties -tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 -[gw11] [ 20%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 -tests/test_pbcore_io_BlasrIO.py::test_m4 -[gw4] [ 21%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 +[gw3] [ 39%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 -[gw4] [ 22%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 +[gw3] [ 40%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len -[gw10] [ 22%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff -tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file -[gw4] [ 23%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len +[gw3] [ 40%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq -[gw4] [ 24%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 -[gw3] [ 25%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 -[gw10] [ 25%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file -tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations -[gw9] [ 26%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix +[gw3] [ 41%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq +[gw4] [ 42%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference +[gw2] [ 42%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference +[gw2] [ 43%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error +[gw6] [ 44%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error +[gw2] [ 45%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV +tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript +[gw2] [ 45%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments +[gw2] [ 46%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges -[gw9] [ 27%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges -tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 -tests/test_pbcore_io_FofnIO.py::test_absolutifying -[gw5] [ 27%] PASSED tests/test_pbcore_io_FofnIO.py::test_absolutifying +[gw9] [ 47%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges +tests/test_pbcore_io_BlasrIO.py::test_m4 +[gw6] [ 47%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange +[gw9] [ 48%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m4 +tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex +[gw4] [ 49%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta -[gw11] [ 28%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m4 -tests/test_pbcore_io_BlasrIO.py::test_m5 -[gw11] [ 29%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m5 +tests/test_pbcore_io_FofnIO.py::test_absolutifying +[gw7] [ 50%] PASSED tests/test_pbcore_io_FofnIO.py::test_absolutifying +tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 +[gw7] [ 50%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 +[gw4] [ 51%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal +[gw5] [ 52%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal +tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs +[gw5] [ 52%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs +tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file +tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index +[gw10] [ 53%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index +tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers +[gw10] [ 54%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers +[gw8] [ 55%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 -[gw0] [ 30%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 -[gw3] [ 30%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len -[gw6] [ 31%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice -tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta -[gw5] [ 32%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta -[gw9] [ 32%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 -[gw2] [ 33%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation -[gw10] [ 34%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations +[gw8] [ 55%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable -tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 -[gw9] [ 35%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 -tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations -[gw3] [ 35%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq -[gw3] [ 36%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal -[gw4] [ 37%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal -tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers -tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta -[gw8] [ 37%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties +[gw11] [ 56%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable +tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader +[gw11] [ 57%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader +[gw1] [ 57%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split +[gw3] [ 58%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal +tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations +[gw3] [ 59%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations +tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names -[gw8] [ 38%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names -tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs -[gw8] [ 39%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation -[gw0] [ 40%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName -[gw11] [ 40%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 -tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 -[gw11] [ 41%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 -[gw9] [ 42%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations -tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd -[gw9] [ 42%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd -[gw0] [ 43%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead -[gw0] [ 44%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal -[gw2] [ 45%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName -[gw2] [ 45%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName -[gw5] [ 46%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta -[gw4] [ 47%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers -tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support +[gw6] [ 60%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names +tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv +[gw6] [ 60%] PASSED tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv +tests/test_pbcore_io_BlasrIO.py::test_m5 +[gw9] [ 61%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m5 +tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii -[gw10] [ 47%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable -[gw6] [ 48%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta -[gw9] [ 49%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support -[gw3] [ 50%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead -[gw8] [ 50%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii +[gw5] [ 62%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii +[gw4] [ 62%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta +tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support tests/test_dataset_run_split.py::test -[gw7] [ 51%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency -tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv +[gw9] [ 63%] SKIPPED tests/test_dataset_run_split.py::test +[gw4] [ 64%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ -[gw11] [ 52%] SKIPPED tests/test_dataset_run_split.py::test -[gw2] [ 52%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead -tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader -tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex -[gw5] [ 53%] PASSED tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv +tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 +[gw7] [ 65%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range -[gw4] [ 54%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead +[gw7] [ 65%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range +tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam +[gw5] [ 66%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam +[gw10] [ 67%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 -tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping -[gw10] [ 55%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader -[gw6] [ 55%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex -[gw3] [ 56%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range -[gw9] [ 57%] SKIPPED tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 -[gw0] [ 57%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead -tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming -[gw8] [ 58%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping -[gw7] [ 59%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead -[gw2] [ 60%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference -[gw2] [ 60%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference -[gw2] [ 61%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV -tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire -[gw7] [ 62%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference -[gw0] [ 62%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference -[gw0] [ 63%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV -[gw0] [ 64%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript -[gw0] [ 65%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments -[gw0] [ 65%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange -[gw2] [ 66%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV +[gw10] [ 67%] SKIPPED tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 +tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 +[gw8] [ 68%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord -[gw10] [ 67%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord -tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam -[gw8] [ 67%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam -tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index -tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted -[gw11] [ 68%] PASSED tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted -tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement -tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties -[gw4] [ 69%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties -[gw7] [ 70%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript -[gw2] [ 70%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments -[gw2] [ 71%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments +[gw11] [ 69%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy -[gw5] [ 72%] PASSED tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy -[gw6] [ 72%] PASSED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange -[gw1] [ 73%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split -tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws -[gw0] [ 74%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange +[gw6] [ 70%] PASSED tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy +tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties +[gw7] [ 70%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties +tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd +[gw3] [ 71%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd +tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement +[gw9] [ 72%] PASSED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement +tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping +[gw4] [ 72%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping +[gw0] [ 73%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable -[gw0] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable +[gw0] [ 74%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry [gw0] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV -[gw0] [ 76%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV +[gw0] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers -[gw0] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts -[gw0] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName -[gw0] [ 78%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam -[gw0] [ 79%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity -[gw0] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed -[gw2] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange +tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted +[gw5] [ 76%] PASSED tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted +[gw2] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable -[gw2] [ 81%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable +[gw2] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry -[gw2] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry +[gw2] [ 78%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion -[gw2] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion +[gw2] [ 79%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore -[gw2] [ 83%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore +[gw2] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default -[gw2] [ 84%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default +[gw2] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default -[gw1] [ 85%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws -[gw2] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default +[gw2] [ 81%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default +[gw0] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts +[gw0] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName +[gw1] [ 83%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize +[gw0] [ 84%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam +[gw0] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity +[gw0] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw0] [ 86%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw1] [ 87%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws @@ -1854,15 +1890,15 @@ [gw1] [100%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups =============================== warnings summary =============================== +tests/test_pbcore_io_FastqIO.py: 11 warnings + /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/FastqIO.py:239: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. + return (np.clip(a, 0, 93).astype(np.uint8) + 33).tostring().decode("ascii") + tests/test_pbdataset_utils.py: 10 warnings tests/test_pbdataset_split.py: 249 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset/utils.py:24: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). time = datetime.datetime.utcnow().strftime("%y%m%d_%H%M%S%f")[:-3] -tests/test_pbcore_io_FastqIO.py: 11 warnings - /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/FastqIO.py:239: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. - return (np.clip(a, 0, 93).astype(np.uint8) + 33).tostring().decode("ascii") - tests/test_pbcore_io_AlnFileReaders.py: 3 warnings tests/test_pbdataset_split.py: 16 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align/PacBioBamIndex.py:159: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) @@ -1899,27 +1935,27 @@ Coverage XML written to file coverage.xml ============================= slowest 20 durations ============================= -0.52s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split_and_maxChunks -0.43s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split -0.39s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange -0.36s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split -0.34s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize -0.32s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws -0.29s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange -0.20s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split -0.14s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency -0.10s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed -0.09s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations -0.08s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations -0.06s call tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows -0.06s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta -0.05s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity -0.04s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name -0.04s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice +0.25s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split_and_maxChunks +0.20s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split +0.16s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize +0.16s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange +0.14s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split +0.13s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split +0.12s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange +0.10s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws +0.06s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency +0.06s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations +0.05s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed 0.03s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid -0.03s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers -0.02s call tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable -================ 122 passed, 18 skipped, 461 warnings in 8.20s ================= +0.03s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations +0.03s call tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows +0.02s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity +0.02s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration +0.02s call tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs +0.02s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name +0.02s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers +0.02s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta +================ 122 passed, 18 skipped, 461 warnings in 4.02s ================= I: pybuild pybuild:334: rm -rfv /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/coverage.xml /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/nosetests.xml removed '/build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/coverage.xml' removed '/build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/nosetests.xml' @@ -1943,8 +1979,8 @@ Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. - By 2026-Mar-03, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -1961,8 +1997,8 @@ versions. Please use the underscore name 'description_file' instead. (Affected: pbcore). - By 2026-Mar-03, you need to update your project and remove deprecated calls - or your builds will no longer be supported. + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** @@ -2304,12 +2340,14 @@ 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/89175/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/89175/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/3084800 and its subdirectories -I: Current time: Thu Jul 10 19:31:37 -12 2025 -I: pbuilder-time-stamp: 1752219097 +I: removing directory /srv/workspace/pbuilder/89175 and its subdirectories +I: Current time: Fri Aug 14 03:57:28 +14 2026 +I: pbuilder-time-stamp: 1786629448