0s autopkgtest [21:27:14]: starting date and time: 2025-10-21 21:27:14+0000 0s autopkgtest [21:27:14]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [21:27:14]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3kwk57uz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-4.secgroup --name adt-resolute-ppc64el-cyvcf2-20251021-212714-juju-7f2275-prod-proposed-migration-environment-15-c7992d54-1004-43c0-8cf1-a2e06ace144f --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-cyvcf2-20251021-212714-juju-7f2275-prod-proposed-migration-environment-15-c7992d54-1004-43c0-8cf1-a2e06ace144f from image adt/ubuntu-resolute-ppc64el-server-20251021.img (UUID c177abc7-cbc1-4b1f-967f-196ea722a402)... 53s autopkgtest [21:28:07]: testbed dpkg architecture: ppc64el 54s autopkgtest [21:28:08]: testbed apt version: 3.1.8ubuntu1 54s autopkgtest [21:28:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 54s autopkgtest [21:28:08]: testbed release detected to be: None 55s autopkgtest [21:28:09]: updating testbed package index (apt update) 55s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 56s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 56s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [627 kB] 56s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [62.2 kB] 56s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [119 kB] 56s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 56s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [427 kB] 56s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [4596 B] 56s Fetched 1344 kB in 1s (1175 kB/s) 57s Reading package lists... 58s Failed to check for VM: Permission denied 58s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 58s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 58s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 58s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 59s Reading package lists... 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s autopkgtest [21:28:13]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Solving dependencies... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s autopkgtest [21:28:17]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 63s autopkgtest [21:28:17]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 65s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build3 (dsc) [2361 B] 65s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build3 (tar) [420 kB] 65s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build3 (diff) [6888 B] 65s gpgv: Signature made Tue Mar 4 17:10:01 2025 UTC 65s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 65s gpgv: Can't check signature: No public key 65s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.1-2build3.dsc: no acceptable signature found 65s autopkgtest [21:28:19]: testing package cyvcf2 version 0.31.1-2build3 66s autopkgtest [21:28:20]: build not needed 66s autopkgtest [21:28:20]: test run-unit-test: preparing testbed 66s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Solving dependencies... 67s The following NEW packages will be installed: 67s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 67s python3-all python3-click python3-coloredlogs python3-cyvcf2 67s python3-humanfriendly python3-iniconfig python3-numpy python3-numpy-dev 67s python3-packaging python3-pluggy python3-pytest 67s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 11.2 MB of archives. 67s After this operation, 48.8 MB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.2.4+ds-1ubuntu1 [153 kB] 67s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-6build1 [291 kB] 67s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-5ubuntu1 [620 kB] 68s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-6build1 [2960 kB] 68s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.2.4+ds-1ubuntu1 [4887 kB] 69s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 69s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2 [113 kB] 69s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.21+ds-1 [585 kB] 69s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-all ppc64el 3.13.7-1 [884 B] 69s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 69s Get:11 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-humanfriendly all 10.0-6 [70.8 kB] 69s Get:12 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-coloredlogs all 15.0.1-1 [38.2 kB] 69s Get:13 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-cyvcf2 ppc64el 0.31.1-2build3 [972 kB] 69s Get:14 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 69s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-packaging all 25.0-1 [52.8 kB] 69s Get:16 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pluggy all 1.6.0-1 [21.0 kB] 69s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el python3-pytest all 8.4.2-1 [268 kB] 69s Fetched 11.2 MB in 2s (5482 kB/s) 69s Selecting previously unselected package python3-numpy-dev:ppc64el. 69s (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 ... 76480 files and directories currently installed.) 69s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 69s Unpacking python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 69s Selecting previously unselected package libblas3:ppc64el. 69s Preparing to unpack .../01-libblas3_3.12.1-6build1_ppc64el.deb ... 69s Unpacking libblas3:ppc64el (3.12.1-6build1) ... 69s Selecting previously unselected package libgfortran5:ppc64el. 69s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_ppc64el.deb ... 69s Unpacking libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 69s Selecting previously unselected package liblapack3:ppc64el. 69s Preparing to unpack .../03-liblapack3_3.12.1-6build1_ppc64el.deb ... 69s Unpacking liblapack3:ppc64el (3.12.1-6build1) ... 69s Selecting previously unselected package python3-numpy. 69s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 69s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 70s Selecting previously unselected package libdeflate0:ppc64el. 70s Preparing to unpack .../05-libdeflate0_1.23-2_ppc64el.deb ... 70s Unpacking libdeflate0:ppc64el (1.23-2) ... 70s Selecting previously unselected package libhtscodecs2:ppc64el. 70s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_ppc64el.deb ... 70s Unpacking libhtscodecs2:ppc64el (1.6.1-2) ... 70s Selecting previously unselected package libhts3t64:ppc64el. 70s Preparing to unpack .../07-libhts3t64_1.21+ds-1_ppc64el.deb ... 70s Unpacking libhts3t64:ppc64el (1.21+ds-1) ... 70s Selecting previously unselected package python3-all. 70s Preparing to unpack .../08-python3-all_3.13.7-1_ppc64el.deb ... 70s Unpacking python3-all (3.13.7-1) ... 70s Selecting previously unselected package python3-click. 70s Preparing to unpack .../09-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 70s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 70s Selecting previously unselected package python3-humanfriendly. 70s Preparing to unpack .../10-python3-humanfriendly_10.0-6_all.deb ... 70s Unpacking python3-humanfriendly (10.0-6) ... 70s Selecting previously unselected package python3-coloredlogs. 70s Preparing to unpack .../11-python3-coloredlogs_15.0.1-1_all.deb ... 70s Unpacking python3-coloredlogs (15.0.1-1) ... 70s Selecting previously unselected package python3-cyvcf2. 70s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2build3_ppc64el.deb ... 70s Unpacking python3-cyvcf2 (0.31.1-2build3) ... 70s Selecting previously unselected package python3-iniconfig. 70s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 70s Unpacking python3-iniconfig (1.1.1-2) ... 70s Selecting previously unselected package python3-packaging. 70s Preparing to unpack .../14-python3-packaging_25.0-1_all.deb ... 70s Unpacking python3-packaging (25.0-1) ... 70s Selecting previously unselected package python3-pluggy. 70s Preparing to unpack .../15-python3-pluggy_1.6.0-1_all.deb ... 70s Unpacking python3-pluggy (1.6.0-1) ... 70s Selecting previously unselected package python3-pytest. 70s Preparing to unpack .../16-python3-pytest_8.4.2-1_all.deb ... 70s Unpacking python3-pytest (8.4.2-1) ... 70s Setting up libhtscodecs2:ppc64el (1.6.1-2) ... 70s Setting up python3-iniconfig (1.1.1-2) ... 70s Setting up libdeflate0:ppc64el (1.23-2) ... 70s Setting up python3-all (3.13.7-1) ... 70s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 70s Setting up libblas3:ppc64el (3.12.1-6build1) ... 70s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 70s Setting up python3-packaging (25.0-1) ... 70s Setting up python3-humanfriendly (10.0-6) ... 70s Setting up python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 70s Setting up libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 70s Setting up python3-pluggy (1.6.0-1) ... 71s Setting up libhts3t64:ppc64el (1.21+ds-1) ... 71s Setting up python3-coloredlogs (15.0.1-1) ... 71s Setting up liblapack3:ppc64el (3.12.1-6build1) ... 71s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 71s Setting up python3-pytest (8.4.2-1) ... 71s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 73s Setting up python3-cyvcf2 (0.31.1-2build3) ... 73s Processing triggers for man-db (2.13.1-1) ... 74s Processing triggers for libc-bin (2.42-0ubuntu3) ... 75s autopkgtest [21:28:29]: test run-unit-test: [----------------------- 75s Testing with python3.13 in /tmp/autopkgtest.9jrutI/autopkgtest_tmp: 75s ============================= test session starts ============================== 75s platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13 75s cachedir: .pytest_cache 75s rootdir: /tmp/autopkgtest.9jrutI/autopkgtest_tmp 75s plugins: typeguard-4.4.2 76s collecting ... collected 112 items 76s 76s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 76s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 76s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 76s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 76s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 76s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 76s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 76s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 76s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 76s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 76s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 76s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 76s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 76s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 76s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 76s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 76s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 76s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 76s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 76s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 76s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 76s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 76s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 76s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 76s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 76s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 76s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 76s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 76s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 76s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 76s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 76s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 76s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 76s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 76s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 76s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 76s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 76s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 76s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 76s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 76s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 76s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 76s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 76s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 76s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 76s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 76s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 76s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 76s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 76s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 76s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 76s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 76s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 76s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 76s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 76s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 76s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 76s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 76s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 76s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 76s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 76s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 76s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 76s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 76s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 76s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 76s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 76s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 76s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 76s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 76s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 76s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 76s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 76s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 76s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 76s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 76s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 76s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 76s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 76s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 76s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 76s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 76s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 76s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 76s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 76s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 76s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 76s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 76s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 76s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 76s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 76s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 76s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 76s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 76s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 76s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 76s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 76s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 76s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 76s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 76s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 76s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 76s 76s ============================= 112 passed in 1.10s ============================== 77s autopkgtest [21:28:31]: test run-unit-test: -----------------------] 77s run-unit-test PASS 77s autopkgtest [21:28:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 78s autopkgtest [21:28:32]: test autodep8-python3: preparing testbed 98s Creating nova instance adt-resolute-ppc64el-cyvcf2-20251021-212714-juju-7f2275-prod-proposed-migration-environment-15-c7992d54-1004-43c0-8cf1-a2e06ace144f from image adt/ubuntu-resolute-ppc64el-server-20251021.img (UUID c177abc7-cbc1-4b1f-967f-196ea722a402)... 156s autopkgtest [21:29:50]: testbed dpkg architecture: ppc64el 156s autopkgtest [21:29:50]: testbed apt version: 3.1.8ubuntu1 156s autopkgtest [21:29:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 156s autopkgtest [21:29:50]: testbed release detected to be: resolute 157s autopkgtest [21:29:51]: updating testbed package index (apt update) 158s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 158s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 158s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 158s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 158s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 158s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [62.2 kB] 158s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 158s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [627 kB] 158s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [119 kB] 158s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 158s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [427 kB] 159s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [4596 B] 159s Fetched 1344 kB in 1s (1011 kB/s) 160s Reading package lists... 160s Failed to check for VM: Permission denied 160s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 161s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 161s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 161s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 162s Reading package lists... 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s Calculating upgrade... 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s autopkgtest [21:29:56]: upgrading testbed (apt dist-upgrade and autopurge) 162s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Calculating upgrade... 163s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Solving dependencies... 163s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s Solving dependencies... 167s The following NEW packages will be installed: 167s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 167s python3-all python3-click python3-coloredlogs python3-cyvcf2 167s python3-humanfriendly python3-numpy python3-numpy-dev 167s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 167s Need to get 10.8 MB of archives. 167s After this operation, 47.1 MB of additional disk space will be used. 167s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.2.4+ds-1ubuntu1 [153 kB] 167s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-6build1 [291 kB] 167s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-5ubuntu1 [620 kB] 168s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-6build1 [2960 kB] 169s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.2.4+ds-1ubuntu1 [4887 kB] 171s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2 [63.3 kB] 171s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2 [113 kB] 171s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libhts3t64 ppc64el 1.21+ds-1 [585 kB] 171s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-all ppc64el 3.13.7-1 [884 B] 171s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 171s Get:11 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-humanfriendly all 10.0-6 [70.8 kB] 171s Get:12 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-coloredlogs all 15.0.1-1 [38.2 kB] 171s Get:13 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-cyvcf2 ppc64el 0.31.1-2build3 [972 kB] 172s Fetched 10.8 MB in 5s (2383 kB/s) 172s Selecting previously unselected package python3-numpy-dev:ppc64el. 172s (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 ... 76480 files and directories currently installed.) 172s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 172s Unpacking python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 172s Selecting previously unselected package libblas3:ppc64el. 172s Preparing to unpack .../01-libblas3_3.12.1-6build1_ppc64el.deb ... 172s Unpacking libblas3:ppc64el (3.12.1-6build1) ... 172s Selecting previously unselected package libgfortran5:ppc64el. 172s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_ppc64el.deb ... 172s Unpacking libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 172s Selecting previously unselected package liblapack3:ppc64el. 172s Preparing to unpack .../03-liblapack3_3.12.1-6build1_ppc64el.deb ... 172s Unpacking liblapack3:ppc64el (3.12.1-6build1) ... 172s Selecting previously unselected package python3-numpy. 172s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 172s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 172s Selecting previously unselected package libdeflate0:ppc64el. 172s Preparing to unpack .../05-libdeflate0_1.23-2_ppc64el.deb ... 172s Unpacking libdeflate0:ppc64el (1.23-2) ... 172s Selecting previously unselected package libhtscodecs2:ppc64el. 172s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_ppc64el.deb ... 172s Unpacking libhtscodecs2:ppc64el (1.6.1-2) ... 172s Selecting previously unselected package libhts3t64:ppc64el. 172s Preparing to unpack .../07-libhts3t64_1.21+ds-1_ppc64el.deb ... 172s Unpacking libhts3t64:ppc64el (1.21+ds-1) ... 172s Selecting previously unselected package python3-all. 172s Preparing to unpack .../08-python3-all_3.13.7-1_ppc64el.deb ... 172s Unpacking python3-all (3.13.7-1) ... 172s Selecting previously unselected package python3-click. 172s Preparing to unpack .../09-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 172s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 172s Selecting previously unselected package python3-humanfriendly. 172s Preparing to unpack .../10-python3-humanfriendly_10.0-6_all.deb ... 172s Unpacking python3-humanfriendly (10.0-6) ... 172s Selecting previously unselected package python3-coloredlogs. 172s Preparing to unpack .../11-python3-coloredlogs_15.0.1-1_all.deb ... 172s Unpacking python3-coloredlogs (15.0.1-1) ... 172s Selecting previously unselected package python3-cyvcf2. 172s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2build3_ppc64el.deb ... 172s Unpacking python3-cyvcf2 (0.31.1-2build3) ... 172s Setting up libhtscodecs2:ppc64el (1.6.1-2) ... 172s Setting up libdeflate0:ppc64el (1.23-2) ... 172s Setting up python3-all (3.13.7-1) ... 172s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 173s Setting up libblas3:ppc64el (3.12.1-6build1) ... 173s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 173s Setting up python3-humanfriendly (10.0-6) ... 173s Setting up python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 173s Setting up libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 173s Setting up libhts3t64:ppc64el (1.21+ds-1) ... 173s Setting up python3-coloredlogs (15.0.1-1) ... 173s Setting up liblapack3:ppc64el (3.12.1-6build1) ... 173s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 173s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 175s Setting up python3-cyvcf2 (0.31.1-2build3) ... 175s Processing triggers for man-db (2.13.1-1) ... 176s Processing triggers for libc-bin (2.42-0ubuntu3) ... 178s autopkgtest [21:30:12]: 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 178s autopkgtest [21:30:12]: test autodep8-python3: [----------------------- 179s Testing with python3.13: 179s 179s autopkgtest [21:30:13]: test autodep8-python3: -----------------------] 179s autodep8-python3 PASS (superficial) 179s autopkgtest [21:30:13]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 180s autopkgtest [21:30:14]: @@@@@@@@@@@@@@@@@@@@ summary 180s run-unit-test PASS 180s autodep8-python3 PASS (superficial)