4s autopkgtest [15:33:24]: starting date and time: 2024-08-07 15:33:24+0000 4s autopkgtest [15:33:24]: git checkout: fd3bed09 nova: allow more retries for quota issues 4s autopkgtest [15:33:24]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.38_1gtt6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy,src:sphinx --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11build1 sphinx/7.4.7-2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-91.secgroup --name adt-oracular-amd64-cyvcf2-20240807-153312-juju-7f2275-prod-proposed-migration-environment-3-cbaf4d47-ce78-4cf6-960f-16287a188764 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 150s autopkgtest [15:35:50]: testbed dpkg architecture: amd64 158s autopkgtest [15:35:58]: testbed apt version: 2.9.7 158s autopkgtest [15:35:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 167s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 167s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [8756 B] 167s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [624 kB] 167s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [10.1 kB] 167s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [80.8 kB] 167s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [122 kB] 167s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [159 kB] 167s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [3920 B] 167s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [13.3 kB] 167s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [51.5 kB] 167s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 167s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [738 kB] 167s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [356 kB] 167s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [22.5 kB] 167s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [4040 B] 167s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [12.0 kB] 167s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [552 B] 168s Fetched 2333 kB in 0s (5816 kB/s) 168s Reading package lists... 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 173s Calculating upgrade... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 198s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 198s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 198s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 200s Reading package lists... 200s Reading package lists... 200s Building dependency tree... 200s Reading state information... 200s Calculating upgrade... 200s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 201s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 227s autopkgtest [15:37:07]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 227s autopkgtest [15:37:07]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 244s Get:1 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.1-2 (dsc) [2337 B] 244s Get:2 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.1-2 (tar) [420 kB] 244s Get:3 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.1-2 (diff) [6764 B] 244s gpgv: Signature made Wed Jul 31 09:42:06 2024 UTC 244s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 244s gpgv: Can't check signature: No public key 244s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.1-2.dsc: no acceptable signature found 244s autopkgtest [15:37:24]: testing package cyvcf2 version 0.31.1-2 261s autopkgtest [15:37:41]: build not needed 309s autopkgtest [15:38:29]: test run-unit-test: preparing testbed 324s Reading package lists... 325s Building dependency tree... 325s Reading state information... 325s Starting pkgProblemResolver with broken count: 0 325s Starting 2 pkgProblemResolver with broken count: 0 325s Done 325s The following additional packages will be installed: 325s libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 python3-all 325s python3-click python3-colorama python3-coloredlogs python3-cyvcf2 325s python3-humanfriendly python3-iniconfig python3-numpy python3-packaging 325s python3-pluggy python3-pytest 325s Suggested packages: 325s gcc gfortran python-numpy-doc python3-dev 325s The following NEW packages will be installed: 325s autopkgtest-satdep libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 325s python3-all python3-click python3-colorama python3-coloredlogs 325s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 325s python3-packaging python3-pluggy python3-pytest 325s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 325s Need to get 10.3 MB/10.3 MB of archives. 325s After this operation, 45.0 MB of additional disk space will be used. 325s Get:1 /tmp/autopkgtest.fXYvVA/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [724 B] 325s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 325s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.2.0-1ubuntu1 [910 kB] 325s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 325s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 325s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 325s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-all amd64 3.12.4-1 [882 B] 325s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 325s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-click all 8.1.7-2 [79.5 kB] 325s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-humanfriendly all 10.0-5 [70.5 kB] 325s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 325s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 326s Get:13 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cyvcf2 amd64 0.31.1-2 [925 kB] 326s Get:14 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 326s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.1-1 [41.4 kB] 326s Get:16 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 326s Get:17 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pytest all 7.4.4-1 [305 kB] 326s Fetched 10.3 MB in 0s (46.0 MB/s) 326s Selecting previously unselected package libblas3:amd64. 326s (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 ... 74252 files and directories currently installed.) 326s Preparing to unpack .../00-libblas3_3.12.0-3build1_amd64.deb ... 326s Unpacking libblas3:amd64 (3.12.0-3build1) ... 326s Selecting previously unselected package libgfortran5:amd64. 326s Preparing to unpack .../01-libgfortran5_14.2.0-1ubuntu1_amd64.deb ... 326s Unpacking libgfortran5:amd64 (14.2.0-1ubuntu1) ... 326s Selecting previously unselected package libhtscodecs2:amd64. 326s Preparing to unpack .../02-libhtscodecs2_1.6.0-1build1_amd64.deb ... 326s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 326s Selecting previously unselected package libhts3t64:amd64. 326s Preparing to unpack .../03-libhts3t64_1.20+ds-1_amd64.deb ... 326s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 326s Selecting previously unselected package liblapack3:amd64. 326s Preparing to unpack .../04-liblapack3_3.12.0-3build1_amd64.deb ... 326s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 326s Selecting previously unselected package python3-all. 326s Preparing to unpack .../05-python3-all_3.12.4-1_amd64.deb ... 326s Unpacking python3-all (3.12.4-1) ... 326s Selecting previously unselected package python3-colorama. 326s Preparing to unpack .../06-python3-colorama_0.4.6-4_all.deb ... 326s Unpacking python3-colorama (0.4.6-4) ... 326s Selecting previously unselected package python3-click. 326s Preparing to unpack .../07-python3-click_8.1.7-2_all.deb ... 326s Unpacking python3-click (8.1.7-2) ... 326s Selecting previously unselected package python3-humanfriendly. 326s Preparing to unpack .../08-python3-humanfriendly_10.0-5_all.deb ... 326s Unpacking python3-humanfriendly (10.0-5) ... 326s Selecting previously unselected package python3-coloredlogs. 326s Preparing to unpack .../09-python3-coloredlogs_15.0.1-1_all.deb ... 326s Unpacking python3-coloredlogs (15.0.1-1) ... 326s Selecting previously unselected package python3-numpy. 326s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 326s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 327s Selecting previously unselected package python3-cyvcf2. 327s Preparing to unpack .../11-python3-cyvcf2_0.31.1-2_amd64.deb ... 327s Unpacking python3-cyvcf2 (0.31.1-2) ... 327s Selecting previously unselected package python3-iniconfig. 327s Preparing to unpack .../12-python3-iniconfig_1.1.1-2_all.deb ... 327s Unpacking python3-iniconfig (1.1.1-2) ... 327s Selecting previously unselected package python3-packaging. 327s Preparing to unpack .../13-python3-packaging_24.1-1_all.deb ... 327s Unpacking python3-packaging (24.1-1) ... 327s Selecting previously unselected package python3-pluggy. 327s Preparing to unpack .../14-python3-pluggy_1.5.0-1_all.deb ... 327s Unpacking python3-pluggy (1.5.0-1) ... 327s Selecting previously unselected package python3-pytest. 327s Preparing to unpack .../15-python3-pytest_7.4.4-1_all.deb ... 327s Unpacking python3-pytest (7.4.4-1) ... 327s Selecting previously unselected package autopkgtest-satdep. 327s Preparing to unpack .../16-1-autopkgtest-satdep.deb ... 327s Unpacking autopkgtest-satdep (0) ... 327s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 327s Setting up python3-iniconfig (1.1.1-2) ... 327s Setting up python3-colorama (0.4.6-4) ... 327s Setting up python3-all (3.12.4-1) ... 327s Setting up python3-click (8.1.7-2) ... 327s Setting up libblas3:amd64 (3.12.0-3build1) ... 327s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 327s Setting up python3-packaging (24.1-1) ... 327s Setting up python3-humanfriendly (10.0-5) ... 328s Setting up libgfortran5:amd64 (14.2.0-1ubuntu1) ... 328s Setting up python3-pluggy (1.5.0-1) ... 328s Setting up libhts3t64:amd64 (1.20+ds-1) ... 328s Setting up python3-coloredlogs (15.0.1-1) ... 328s Setting up liblapack3:amd64 (3.12.0-3build1) ... 328s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 328s Setting up python3-pytest (7.4.4-1) ... 328s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 330s Setting up python3-cyvcf2 (0.31.1-2) ... 330s Setting up autopkgtest-satdep (0) ... 330s Processing triggers for man-db (2.12.1-2) ... 331s Processing triggers for libc-bin (2.39-0ubuntu9) ... 345s (Reading database ... 75514 files and directories currently installed.) 345s Removing autopkgtest-satdep (0) ... 348s autopkgtest [15:39:08]: test run-unit-test: [----------------------- 348s Testing with python3.12 in /tmp/autopkgtest.fXYvVA/autopkgtest_tmp: 349s ============================= test session starts ============================== 349s platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.5.0 -- /usr/bin/python3.12 349s cachedir: .pytest_cache 349s rootdir: /tmp/autopkgtest.fXYvVA/autopkgtest_tmp 349s collecting ... collected 112 items 349s 349s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 349s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 349s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 349s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 349s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 349s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 349s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 349s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 349s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 349s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 349s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 349s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 349s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 349s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 349s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 349s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 349s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 349s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 349s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 349s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 349s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 349s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 349s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 349s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 349s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 349s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 349s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 349s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 349s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 349s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 349s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 349s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 349s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 349s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 349s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 349s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 349s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 349s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 350s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 350s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 350s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 350s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 350s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 350s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 350s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 350s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 350s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 350s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 350s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 350s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 350s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 350s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 350s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 350s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 350s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 350s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 350s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 350s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 350s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 350s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 350s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 350s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 350s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 350s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 350s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 350s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 350s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 350s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 350s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 350s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 350s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 350s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 350s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 350s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 350s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 350s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 350s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 350s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 350s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 350s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 350s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 350s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 350s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 350s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 350s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 350s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 350s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 350s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 350s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 350s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 350s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 350s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 350s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 350s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 350s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 350s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 350s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 350s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 350s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 350s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 350s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 350s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 350s 350s ============================= 112 passed in 1.04s ============================== 350s autopkgtest [15:39:10]: test run-unit-test: -----------------------] 373s run-unit-test PASS 373s autopkgtest [15:39:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 385s autopkgtest [15:39:45]: test autodep8-python3: preparing testbed 629s autopkgtest [15:43:49]: testbed dpkg architecture: amd64 629s autopkgtest [15:43:49]: testbed apt version: 2.9.7 629s autopkgtest [15:43:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 629s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 629s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [8756 B] 629s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [624 kB] 629s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [80.8 kB] 629s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [10.1 kB] 629s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [122 kB] 629s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [159 kB] 629s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [3920 B] 629s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [51.5 kB] 629s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [13.3 kB] 629s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 629s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [738 kB] 629s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [356 kB] 629s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [22.5 kB] 629s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [4040 B] 629s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [12.0 kB] 629s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [552 B] 631s Fetched 2333 kB in 0s (5338 kB/s) 631s Reading package lists... 635s Reading package lists... 636s Building dependency tree... 636s Reading state information... 636s Calculating upgrade... 636s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 636s Reading package lists... 637s Building dependency tree... 637s Reading state information... 637s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 637s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 637s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 637s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 637s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 639s Reading package lists... 639s Reading package lists... 639s Building dependency tree... 639s Reading state information... 639s Calculating upgrade... 640s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 640s Reading package lists... 640s Building dependency tree... 640s Reading state information... 641s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 669s Reading package lists... 670s Building dependency tree... 670s Reading state information... 670s Starting pkgProblemResolver with broken count: 0 670s Starting 2 pkgProblemResolver with broken count: 0 670s Done 671s The following additional packages will be installed: 671s libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 python3-all 671s python3-click python3-colorama python3-coloredlogs python3-cyvcf2 671s python3-humanfriendly python3-numpy 671s Suggested packages: 671s gcc gfortran python-numpy-doc python3-dev python3-pytest 671s The following NEW packages will be installed: 671s autopkgtest-satdep libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 671s python3-all python3-click python3-colorama python3-coloredlogs 671s python3-cyvcf2 python3-humanfriendly python3-numpy 671s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 671s Need to get 9961 kB/9962 kB of archives. 671s After this operation, 43.5 MB of additional disk space will be used. 671s Get:1 /tmp/autopkgtest.fXYvVA/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 671s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 671s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.2.0-1ubuntu1 [910 kB] 671s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 671s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 671s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 671s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-all amd64 3.12.4-1 [882 B] 671s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 671s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-click all 8.1.7-2 [79.5 kB] 671s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-humanfriendly all 10.0-5 [70.5 kB] 671s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 671s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 671s Get:13 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cyvcf2 amd64 0.31.1-2 [925 kB] 672s Fetched 9961 kB in 1s (18.6 MB/s) 672s Selecting previously unselected package libblas3:amd64. 672s (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 ... 74252 files and directories currently installed.) 672s Preparing to unpack .../00-libblas3_3.12.0-3build1_amd64.deb ... 672s Unpacking libblas3:amd64 (3.12.0-3build1) ... 672s Selecting previously unselected package libgfortran5:amd64. 672s Preparing to unpack .../01-libgfortran5_14.2.0-1ubuntu1_amd64.deb ... 672s Unpacking libgfortran5:amd64 (14.2.0-1ubuntu1) ... 672s Selecting previously unselected package libhtscodecs2:amd64. 672s Preparing to unpack .../02-libhtscodecs2_1.6.0-1build1_amd64.deb ... 672s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 672s Selecting previously unselected package libhts3t64:amd64. 672s Preparing to unpack .../03-libhts3t64_1.20+ds-1_amd64.deb ... 672s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 672s Selecting previously unselected package liblapack3:amd64. 672s Preparing to unpack .../04-liblapack3_3.12.0-3build1_amd64.deb ... 672s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 672s Selecting previously unselected package python3-all. 672s Preparing to unpack .../05-python3-all_3.12.4-1_amd64.deb ... 672s Unpacking python3-all (3.12.4-1) ... 672s Selecting previously unselected package python3-colorama. 672s Preparing to unpack .../06-python3-colorama_0.4.6-4_all.deb ... 672s Unpacking python3-colorama (0.4.6-4) ... 672s Selecting previously unselected package python3-click. 672s Preparing to unpack .../07-python3-click_8.1.7-2_all.deb ... 672s Unpacking python3-click (8.1.7-2) ... 672s Selecting previously unselected package python3-humanfriendly. 672s Preparing to unpack .../08-python3-humanfriendly_10.0-5_all.deb ... 672s Unpacking python3-humanfriendly (10.0-5) ... 672s Selecting previously unselected package python3-coloredlogs. 672s Preparing to unpack .../09-python3-coloredlogs_15.0.1-1_all.deb ... 672s Unpacking python3-coloredlogs (15.0.1-1) ... 672s Selecting previously unselected package python3-numpy. 672s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 672s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 672s Selecting previously unselected package python3-cyvcf2. 672s Preparing to unpack .../11-python3-cyvcf2_0.31.1-2_amd64.deb ... 672s Unpacking python3-cyvcf2 (0.31.1-2) ... 672s Selecting previously unselected package autopkgtest-satdep. 672s Preparing to unpack .../12-2-autopkgtest-satdep.deb ... 672s Unpacking autopkgtest-satdep (0) ... 672s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 672s Setting up python3-colorama (0.4.6-4) ... 673s Setting up python3-all (3.12.4-1) ... 673s Setting up python3-click (8.1.7-2) ... 673s Setting up libblas3:amd64 (3.12.0-3build1) ... 673s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 673s Setting up python3-humanfriendly (10.0-5) ... 673s Setting up libgfortran5:amd64 (14.2.0-1ubuntu1) ... 673s Setting up libhts3t64:amd64 (1.20+ds-1) ... 673s Setting up python3-coloredlogs (15.0.1-1) ... 673s Setting up liblapack3:amd64 (3.12.0-3build1) ... 673s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 673s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 675s Setting up python3-cyvcf2 (0.31.1-2) ... 675s Setting up autopkgtest-satdep (0) ... 675s Processing triggers for man-db (2.12.1-2) ... 676s Processing triggers for libc-bin (2.39-0ubuntu9) ... 709s (Reading database ... 75350 files and directories currently installed.) 709s Removing autopkgtest-satdep (0) ... 757s autopkgtest [15:45:57]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import cyvcf2; print(cyvcf2)" ; done 757s autopkgtest [15:45:57]: test autodep8-python3: [----------------------- 758s Testing with python3.12: 758s 758s autopkgtest [15:45:58]: test autodep8-python3: -----------------------] 762s autodep8-python3 PASS (superficial) 762s autopkgtest [15:46:02]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 766s autopkgtest [15:46:06]: @@@@@@@@@@@@@@@@@@@@ summary 766s run-unit-test PASS 766s autodep8-python3 PASS (superficial) 789s nova [W] Skipping flock for amd64 789s Creating nova instance adt-oracular-amd64-cyvcf2-20240807-153312-juju-7f2275-prod-proposed-migration-environment-3-cbaf4d47-ce78-4cf6-960f-16287a188764 from image adt/ubuntu-oracular-amd64-server-20240807.img (UUID 9ba463ea-7914-46a4-a1eb-b149e31532e6)... 789s nova [W] Skipping flock for amd64 789s Creating nova instance adt-oracular-amd64-cyvcf2-20240807-153312-juju-7f2275-prod-proposed-migration-environment-3-cbaf4d47-ce78-4cf6-960f-16287a188764 from image adt/ubuntu-oracular-amd64-server-20240807.img (UUID 9ba463ea-7914-46a4-a1eb-b149e31532e6)...