Diff of the two buildlogs: -- --- b1/build.log 2023-05-08 10:18:27.288640491 +0000 +++ b2/build.log 2023-05-08 10:35:01.149118316 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 7 22:01:18 -12 2023 -I: pbuilder-time-stamp: 1683540078 +I: Current time: Mon Jun 10 06:41:32 +14 2024 +I: pbuilder-time-stamp: 1717951292 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./python-pysam_0.20.0+ds.orig.tar.xz] I: copying [./python-pysam_0.20.0+ds-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Dec 31 05:45:09 2022 -12 +gpgv: Signature made Sun Jan 1 07:45:09 2023 +14 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.20.0+ds-3.dsc: no acceptable signature found @@ -31,52 +31,84 @@ dpkg-source: info: applying python3.11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/15183/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/19221/tmp/hooks/D01_modify_environment starting +debug: Running on codethink15-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 Jun 10 06:41 /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/19221/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/19221/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + 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='15183' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=19221 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.mYze8wk1/pbuilderrc_sd07 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mYze8wk1/b1 --logfile b1/build.log python-pysam_0.20.0+ds-3.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.mYze8wk1/pbuilderrc_3SlN --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mYze8wk1/b2 --logfile b2/build.log --extrapackages usrmerge python-pysam_0.20.0+ds-3.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink12-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 5 22:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/15183/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 9 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/19221/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -222,7 +254,7 @@ Get: 86 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 samtools arm64 1.16.1-1 [580 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 tabix arm64 1.16+ds-3 [427 kB] -Fetched 40.9 MB in 2s (24.5 MB/s) +Fetched 40.9 MB in 1s (39.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-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 ... 19616 files and directories currently installed.) @@ -590,8 +622,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/python-pysam-0.20.0+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_0.20.0+ds-3_source.changes +I: user script /srv/workspace/pbuilder/19221/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/19221/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/python-pysam-0.20.0+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_0.20.0+ds-3_source.changes dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.20.0+ds-3 dpkg-buildpackage: info: source distribution unstable @@ -600,17 +641,17 @@ dpkg-buildpackage: info: host architecture arm64 debian/rules clean cd tests/pysam_data && /usr/bin/make clean -make[1]: Entering directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[1]: Map '/build/python-pysam-0.20.0+ds/tests/pysam_data' wordt binnengegaan rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[1]: Map '/build/python-pysam-0.20.0+ds/tests/pysam_data' wordt verlaten cd tests/cbcf_data && /usr/bin/make clean -make[1]: Entering directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[1]: Map '/build/python-pysam-0.20.0+ds/tests/cbcf_data' wordt binnengegaan rm -f all.stamp *.gz *.tbi *.csi *.bcf -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[1]: Map '/build/python-pysam-0.20.0+ds/tests/cbcf_data' wordt verlaten find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete @@ -633,7 +674,7 @@ rm -rf .pytest_cache/ dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/python-pysam-0.20.0+ds' +make[1]: Map '/build/python-pysam-0.20.0+ds' wordt binnengegaan dh_auto_clean I: pybuild base:240: python3.11 setup.py clean # pysam: cython is available - using cythonize if necessary @@ -650,7 +691,7 @@ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds' +make[1]: Map '/build/python-pysam-0.20.0+ds' wordt verlaten dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary @@ -1007,9 +1048,9 @@ | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pysam-0.20.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-cpython-311/pysam/libcvcf.o -L/build/python-pysam-0.20.0+ds/pysam -L/usr/lib/aarch64-linux-gnu -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/aarch64-linux-gnu -lz -lhts -lchtslib.cpython-311-aarch64-linux-gnu -lcutils.cpython-311-aarch64-linux-gnu -o /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test -make[1]: Entering directory '/build/python-pysam-0.20.0+ds' +make[1]: Map '/build/python-pysam-0.20.0+ds' wordt binnengegaan cd tests/pysam_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: Map '/build/python-pysam-0.20.0+ds/tests/pysam_data' wordt binnengegaan samtools faidx ex1.fa samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz @@ -1161,9 +1202,9 @@ samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 -1+0 records in -1+0 records out -122292 bytes (122 kB, 119 KiB) copied, 0.000340224 s, 359 MB/s +1+0 records gelezen +1+0 records geschreven +122292 bytes (122 kB, 119 KiB) gekopieerd, 0.000397 s, 308 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 @@ -1176,9 +1217,9 @@ samtools index -c ex1_csi.bam touch all.stamp rm with_md.sam -make[2]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: Map '/build/python-pysam-0.20.0+ds/tests/pysam_data' wordt verlaten cd tests/cbcf_data && /usr/bin/make all -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: Map '/build/python-pysam-0.20.0+ds/tests/cbcf_data' wordt binnengegaan bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index @@ -1227,7 +1268,7 @@ bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf touch all.stamp -make[2]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: Map '/build/python-pysam-0.20.0+ds/tests/cbcf_data' wordt verlaten dh_auto_test I: pybuild base:240: cd /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build; python3.11 -m pytest tests ============================= test session starts ============================== @@ -1310,7 +1351,7 @@ tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED -tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp___enter___92gj1odinegative_integers.bam' +tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp___enter____yz7tgcknegative_integers.bam' PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED @@ -1389,22 +1430,22 @@ tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED 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 [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_mjtl842c' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_mjtl842c +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_97i_t1n5' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_97i_t1n5 PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_7ykpez9u' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_7ykpez9u +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_e6xiiynm' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_e6xiiynm PASSED -tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_e26kym73 +tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_77c6o68g PASSED -tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ygk98ojj' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ygk98ojj +tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_hen109qn' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_hen109qn 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/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_adzzdsvp' -/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_adzzdsvp +[E::cram_index_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ylqtno5l' +/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_ylqtno5l PASSED -tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write__o48mpz3 +tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_dpsv91my PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED @@ -1766,7 +1807,7 @@ tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED -tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_vdef3m4rtmp_ex2.bam' +tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_ko3e9f3wtmp_ex2.bam' PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused @@ -1880,8 +1921,8 @@ tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED -tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_qntbfyk_tmp_single.bam' -[E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_1qtsuo2otmp_multi.bam' +tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_4xjmvwjitmp_single.bam' +[E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_ol54puvbtmp_multi.bam' PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED @@ -1998,7 +2039,7 @@ tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED -tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_yfwq54lttmp_largecigar.bam' +tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_fcniv80btmp_largecigar.bam' PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED @@ -2071,7 +2112,7 @@ 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/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_1ugzmo2y.bcf' +tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/build/python-pysam-0.20.0+ds/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_ouhmtz9c.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.) @@ -2589,8 +2630,8 @@ return self.run(*args, **kwds) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -=========== 938 passed, 11 skipped, 4 warnings in 111.68s (0:01:51) ============ -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds' +=========== 938 passed, 11 skipped, 4 warnings in 112.32s (0:01:52) ============ +make[1]: Map '/build/python-pysam-0.20.0+ds' wordt verlaten create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -2782,19 +2823,19 @@ Skipping SOURCES.txt running install_scripts debian/rules override_dh_install -make[1]: Entering directory '/build/python-pysam-0.20.0+ds' +make[1]: Map '/build/python-pysam-0.20.0+ds' wordt binnengegaan cd tests/pysam_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: Map '/build/python-pysam-0.20.0+ds/tests/pysam_data' wordt binnengegaan rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz -make[2]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/pysam_data' +make[2]: Map '/build/python-pysam-0.20.0+ds/tests/pysam_data' wordt verlaten cd tests/cbcf_data && /usr/bin/make clean -make[2]: Entering directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: Map '/build/python-pysam-0.20.0+ds/tests/cbcf_data' wordt binnengegaan rm -f all.stamp *.gz *.tbi *.csi *.bcf -make[2]: Leaving directory '/build/python-pysam-0.20.0+ds/tests/cbcf_data' +make[2]: Map '/build/python-pysam-0.20.0+ds/tests/cbcf_data' wordt verlaten find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete @@ -2817,7 +2858,7 @@ rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz find debian -name log.txt -delete -make[1]: Leaving directory '/build/python-pysam-0.20.0+ds' +make[1]: Map '/build/python-pysam-0.20.0+ds' wordt verlaten dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild @@ -2838,9 +2879,9 @@ dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.20.0+ds-3_arm64.deb'. -dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.20.0+ds-3_arm64.deb'. -dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.20.0+ds-3_all.deb'. +dpkg-deb: pakket 'python-pysam-tests' wordt gebouwd in '../python-pysam-tests_0.20.0+ds-3_all.deb'. +dpkg-deb: pakket 'python3-pysam-dbgsym' wordt gebouwd in '../python3-pysam-dbgsym_0.20.0+ds-3_arm64.deb'. +dpkg-deb: pakket 'python3-pysam' wordt gebouwd in '../python3-pysam_0.20.0+ds-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../python-pysam_0.20.0+ds-3_arm64.buildinfo dpkg-genchanges --build=binary -O../python-pysam_0.20.0+ds-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2848,12 +2889,14 @@ 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/19221/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/19221/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/15183 and its subdirectories -I: Current time: Sun May 7 22:18:25 -12 2023 -I: pbuilder-time-stamp: 1683541105 +I: removing directory /srv/workspace/pbuilder/19221 and its subdirectories +I: Current time: Mon Jun 10 06:57:59 +14 2024 +I: pbuilder-time-stamp: 1717952279