0s autopkgtest [13:45:12]: starting date and time: 2024-11-04 13:45:12+0000 0s autopkgtest [13:45:12]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [13:45:12]: host juju-7f2275-prod-proposed-migration-environment-14; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ofgm23zv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.20+ds-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-14@lcy02-18.secgroup --name adt-plucky-amd64-cyvcf2-20241104-124021-juju-7f2275-prod-proposed-migration-environment-14-68e1661f-3e05-4379-9d2b-fc3dce715ac8 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-14 --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/ 240s autopkgtest [13:49:12]: testbed dpkg architecture: amd64 240s autopkgtest [13:49:12]: testbed apt version: 2.9.8 240s autopkgtest [13:49:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 241s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 241s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 241s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 241s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 241s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 241s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB] 241s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB] 241s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 241s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB] 241s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB] 241s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB] 241s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB] 241s Fetched 5618 kB in 1s (9857 kB/s) 241s Reading package lists... 243s Reading package lists... 243s Building dependency tree... 243s Reading state information... 244s Calculating upgrade... 244s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 244s Reading package lists... 244s Building dependency tree... 244s Reading state information... 245s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 245s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 245s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 245s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 245s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 246s Reading package lists... 246s Reading package lists... 246s Building dependency tree... 246s Reading state information... 247s Calculating upgrade... 247s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 247s Reading package lists... 247s Building dependency tree... 247s Reading state information... 247s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 248s autopkgtest [13:49:20]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 248s autopkgtest [13:49:20]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 249s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (dsc) [2337 B] 249s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (tar) [420 kB] 249s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (diff) [6764 B] 249s gpgv: Signature made Wed Jul 31 09:42:06 2024 UTC 249s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 249s gpgv: Can't check signature: No public key 249s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.1-2.dsc: no acceptable signature found 249s autopkgtest [13:49:21]: testing package cyvcf2 version 0.31.1-2 249s autopkgtest [13:49:21]: build not needed 249s autopkgtest [13:49:21]: test run-unit-test: preparing testbed 250s Reading package lists... 250s Building dependency tree... 250s Reading state information... 251s Starting pkgProblemResolver with broken count: 0 251s Starting 2 pkgProblemResolver with broken count: 0 251s Done 251s The following additional packages will be installed: 251s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 251s python3-all python3-click python3-colorama python3-coloredlogs 251s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 251s python3-packaging python3-pluggy python3-pytest 251s Suggested packages: 251s gcc gfortran python-numpy-doc python3-dev 251s The following NEW packages will be installed: 251s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 251s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 251s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-iniconfig 251s python3-numpy python3-packaging python3-pluggy python3-pytest 251s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 251s Need to get 10.4 MB/10.4 MB of archives. 251s After this operation, 45.5 MB of additional disk space will be used. 251s Get:1 /tmp/autopkgtest.zvcr7A/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [724 B] 251s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 251s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 251s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-7ubuntu1 [909 kB] 251s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 251s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 251s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 251s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 251s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 251s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB] 251s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-humanfriendly all 10.0-6 [70.8 kB] 251s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 251s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 251s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cyvcf2 amd64 0.31.1-2 [925 kB] 251s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 251s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 251s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 251s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.2-1 [251 kB] 252s Fetched 10.4 MB in 0s (41.6 MB/s) 252s Selecting previously unselected package libblas3:amd64. 252s (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 ... 75323 files and directories currently installed.) 252s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 252s Unpacking libblas3:amd64 (3.12.0-3build2) ... 252s Selecting previously unselected package libdeflate0:amd64. 252s Preparing to unpack .../01-libdeflate0_1.21-1_amd64.deb ... 252s Unpacking libdeflate0:amd64 (1.21-1) ... 252s Selecting previously unselected package libgfortran5:amd64. 252s Preparing to unpack .../02-libgfortran5_14.2.0-7ubuntu1_amd64.deb ... 252s Unpacking libgfortran5:amd64 (14.2.0-7ubuntu1) ... 252s Selecting previously unselected package libhtscodecs2:amd64. 252s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_amd64.deb ... 252s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 252s Selecting previously unselected package libhts3t64:amd64. 252s Preparing to unpack .../04-libhts3t64_1.20+ds-2_amd64.deb ... 252s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 252s Selecting previously unselected package liblapack3:amd64. 252s Preparing to unpack .../05-liblapack3_3.12.0-3build2_amd64.deb ... 252s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 252s Selecting previously unselected package python3-all. 252s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_amd64.deb ... 252s Unpacking python3-all (3.12.6-0ubuntu1) ... 252s Selecting previously unselected package python3-colorama. 252s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 252s Unpacking python3-colorama (0.4.6-4) ... 252s Selecting previously unselected package python3-click. 252s Preparing to unpack .../08-python3-click_8.1.7-2_all.deb ... 252s Unpacking python3-click (8.1.7-2) ... 252s Selecting previously unselected package python3-humanfriendly. 252s Preparing to unpack .../09-python3-humanfriendly_10.0-6_all.deb ... 252s Unpacking python3-humanfriendly (10.0-6) ... 252s Selecting previously unselected package python3-coloredlogs. 252s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 252s Unpacking python3-coloredlogs (15.0.1-1) ... 252s Selecting previously unselected package python3-numpy. 252s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 252s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 252s Selecting previously unselected package python3-cyvcf2. 252s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2_amd64.deb ... 252s Unpacking python3-cyvcf2 (0.31.1-2) ... 252s Selecting previously unselected package python3-iniconfig. 253s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 253s Unpacking python3-iniconfig (1.1.1-2) ... 253s Selecting previously unselected package python3-packaging. 253s Preparing to unpack .../14-python3-packaging_24.1-1_all.deb ... 253s Unpacking python3-packaging (24.1-1) ... 253s Selecting previously unselected package python3-pluggy. 253s Preparing to unpack .../15-python3-pluggy_1.5.0-1_all.deb ... 253s Unpacking python3-pluggy (1.5.0-1) ... 253s Selecting previously unselected package python3-pytest. 253s Preparing to unpack .../16-python3-pytest_8.3.2-1_all.deb ... 253s Unpacking python3-pytest (8.3.2-1) ... 253s Selecting previously unselected package autopkgtest-satdep. 253s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 253s Unpacking autopkgtest-satdep (0) ... 253s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 253s Setting up python3-iniconfig (1.1.1-2) ... 253s Setting up python3-colorama (0.4.6-4) ... 253s Setting up libdeflate0:amd64 (1.21-1) ... 253s Setting up python3-all (3.12.6-0ubuntu1) ... 253s Setting up python3-click (8.1.7-2) ... 253s Setting up libblas3:amd64 (3.12.0-3build2) ... 253s 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 253s Setting up python3-packaging (24.1-1) ... 253s Setting up python3-humanfriendly (10.0-6) ... 253s Setting up libgfortran5:amd64 (14.2.0-7ubuntu1) ... 253s Setting up python3-pluggy (1.5.0-1) ... 253s Setting up libhts3t64:amd64 (1.20+ds-2) ... 253s Setting up python3-coloredlogs (15.0.1-1) ... 254s Setting up liblapack3:amd64 (3.12.0-3build2) ... 254s 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 254s Setting up python3-pytest (8.3.2-1) ... 254s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 256s Setting up python3-cyvcf2 (0.31.1-2) ... 256s Setting up autopkgtest-satdep (0) ... 256s Processing triggers for man-db (2.12.1-3) ... 257s Processing triggers for libc-bin (2.40-1ubuntu3) ... 258s (Reading database ... 76589 files and directories currently installed.) 258s Removing autopkgtest-satdep (0) ... 258s autopkgtest [13:49:30]: test run-unit-test: [----------------------- 259s Testing with python3.12 in /tmp/autopkgtest.zvcr7A/autopkgtest_tmp: 259s ============================= test session starts ============================== 259s platform linux -- Python 3.12.7, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3.12 259s cachedir: .pytest_cache 259s rootdir: /tmp/autopkgtest.zvcr7A/autopkgtest_tmp 259s plugins: typeguard-4.3.0 259s collecting ... collected 112 items 259s 259s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 259s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 259s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 259s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 259s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 259s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 259s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 259s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 259s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 259s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 259s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 259s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 259s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 259s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 259s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 259s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 259s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 259s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 259s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 259s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 259s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 259s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 259s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 259s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 259s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 259s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 259s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 259s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 259s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 259s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 259s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 259s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 259s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 259s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 259s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 259s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 259s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 259s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 260s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 260s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 260s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 260s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 260s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 260s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 260s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 260s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 260s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 260s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 260s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 260s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 260s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 260s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 260s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 260s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 260s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 260s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 260s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 260s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 260s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 260s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 260s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 260s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 260s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 260s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 260s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 260s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 260s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 260s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 260s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 260s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 260s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 260s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 260s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 260s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 260s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 260s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 260s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 260s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 260s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 260s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 260s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 260s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 260s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 260s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 260s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 260s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 260s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 260s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 260s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 260s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 260s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 260s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 260s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 260s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 260s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 260s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 260s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 260s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 260s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 260s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 260s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 260s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 260s 260s ============================= 112 passed in 1.01s ============================== 260s autopkgtest [13:49:32]: test run-unit-test: -----------------------] 260s autopkgtest [13:49:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 260s run-unit-test PASS 261s autopkgtest [13:49:33]: test autodep8-python3: preparing testbed 479s autopkgtest [13:53:11]: testbed dpkg architecture: amd64 479s autopkgtest [13:53:11]: testbed apt version: 2.9.8 479s autopkgtest [13:53:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 479s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 479s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 479s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 479s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 479s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 479s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB] 479s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB] 479s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 479s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB] 479s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB] 479s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB] 479s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB] 480s Fetched 5618 kB in 1s (9584 kB/s) 480s Reading package lists... 481s Reading package lists... 482s Building dependency tree... 482s Reading state information... 482s Calculating upgrade... 482s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 482s Reading package lists... 483s Building dependency tree... 483s Reading state information... 483s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 483s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 483s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 483s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 483s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 484s Reading package lists... 484s Reading package lists... 485s Building dependency tree... 485s Reading state information... 485s Calculating upgrade... 485s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 485s Reading package lists... 486s Building dependency tree... 486s Reading state information... 486s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 487s Reading package lists... 487s Building dependency tree... 487s Reading state information... 488s Starting pkgProblemResolver with broken count: 0 488s Starting 2 pkgProblemResolver with broken count: 0 488s Done 488s The following additional packages will be installed: 488s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 488s python3-all python3-click python3-colorama python3-coloredlogs 488s python3-cyvcf2 python3-humanfriendly python3-numpy 488s Suggested packages: 488s gcc gfortran python-numpy-doc python3-dev python3-pytest 488s The following NEW packages will be installed: 488s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 488s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 488s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-numpy 488s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 488s Need to get 10.1 MB/10.1 MB of archives. 488s After this operation, 43.9 MB of additional disk space will be used. 488s Get:1 /tmp/autopkgtest.zvcr7A/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 488s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 488s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 488s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-7ubuntu1 [909 kB] 488s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 488s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 488s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 488s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 488s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 488s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB] 488s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-humanfriendly all 10.0-6 [70.8 kB] 488s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 488s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 488s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cyvcf2 amd64 0.31.1-2 [925 kB] 489s Fetched 10.1 MB in 0s (63.6 MB/s) 489s Selecting previously unselected package libblas3:amd64. 489s (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 ... 75323 files and directories currently installed.) 489s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 489s Unpacking libblas3:amd64 (3.12.0-3build2) ... 489s Selecting previously unselected package libdeflate0:amd64. 489s Preparing to unpack .../01-libdeflate0_1.21-1_amd64.deb ... 489s Unpacking libdeflate0:amd64 (1.21-1) ... 489s Selecting previously unselected package libgfortran5:amd64. 489s Preparing to unpack .../02-libgfortran5_14.2.0-7ubuntu1_amd64.deb ... 489s Unpacking libgfortran5:amd64 (14.2.0-7ubuntu1) ... 489s Selecting previously unselected package libhtscodecs2:amd64. 489s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_amd64.deb ... 489s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 489s Selecting previously unselected package libhts3t64:amd64. 489s Preparing to unpack .../04-libhts3t64_1.20+ds-2_amd64.deb ... 489s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 489s Selecting previously unselected package liblapack3:amd64. 489s Preparing to unpack .../05-liblapack3_3.12.0-3build2_amd64.deb ... 489s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 489s Selecting previously unselected package python3-all. 489s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_amd64.deb ... 489s Unpacking python3-all (3.12.6-0ubuntu1) ... 489s Selecting previously unselected package python3-colorama. 489s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 489s Unpacking python3-colorama (0.4.6-4) ... 489s Selecting previously unselected package python3-click. 489s Preparing to unpack .../08-python3-click_8.1.7-2_all.deb ... 489s Unpacking python3-click (8.1.7-2) ... 489s Selecting previously unselected package python3-humanfriendly. 489s Preparing to unpack .../09-python3-humanfriendly_10.0-6_all.deb ... 489s Unpacking python3-humanfriendly (10.0-6) ... 489s Selecting previously unselected package python3-coloredlogs. 489s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 489s Unpacking python3-coloredlogs (15.0.1-1) ... 489s Selecting previously unselected package python3-numpy. 489s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 489s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 490s Selecting previously unselected package python3-cyvcf2. 490s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2_amd64.deb ... 490s Unpacking python3-cyvcf2 (0.31.1-2) ... 490s Selecting previously unselected package autopkgtest-satdep. 490s Preparing to unpack .../13-2-autopkgtest-satdep.deb ... 490s Unpacking autopkgtest-satdep (0) ... 490s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 490s Setting up python3-colorama (0.4.6-4) ... 490s Setting up libdeflate0:amd64 (1.21-1) ... 490s Setting up python3-all (3.12.6-0ubuntu1) ... 490s Setting up python3-click (8.1.7-2) ... 490s Setting up libblas3:amd64 (3.12.0-3build2) ... 490s 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 490s Setting up python3-humanfriendly (10.0-6) ... 490s Setting up libgfortran5:amd64 (14.2.0-7ubuntu1) ... 490s Setting up libhts3t64:amd64 (1.20+ds-2) ... 490s Setting up python3-coloredlogs (15.0.1-1) ... 490s Setting up liblapack3:amd64 (3.12.0-3build2) ... 490s 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 490s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 492s Setting up python3-cyvcf2 (0.31.1-2) ... 492s Setting up autopkgtest-satdep (0) ... 492s Processing triggers for man-db (2.12.1-3) ... 493s Processing triggers for libc-bin (2.40-1ubuntu3) ... 495s (Reading database ... 76425 files and directories currently installed.) 495s Removing autopkgtest-satdep (0) ... 495s autopkgtest [13:53:27]: 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 495s autopkgtest [13:53:27]: test autodep8-python3: [----------------------- 495s Testing with python3.12: 496s 496s autopkgtest [13:53:28]: test autodep8-python3: -----------------------] 496s autopkgtest [13:53:28]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 496s autodep8-python3 PASS (superficial) 496s autopkgtest [13:53:28]: @@@@@@@@@@@@@@@@@@@@ summary 496s run-unit-test PASS 496s autodep8-python3 PASS (superficial) 507s nova [W] Skipping flock for amd64 507s Creating nova instance adt-plucky-amd64-cyvcf2-20241104-124021-juju-7f2275-prod-proposed-migration-environment-14-68e1661f-3e05-4379-9d2b-fc3dce715ac8 from image adt/ubuntu-plucky-amd64-server-20241104.img (UUID 0ab90577-a6b7-4a72-9ab8-957838d495c0)... 507s nova [W] Skipping flock for amd64 507s Creating nova instance adt-plucky-amd64-cyvcf2-20241104-124021-juju-7f2275-prod-proposed-migration-environment-14-68e1661f-3e05-4379-9d2b-fc3dce715ac8 from image adt/ubuntu-plucky-amd64-server-20241104.img (UUID 0ab90577-a6b7-4a72-9ab8-957838d495c0)...