0s autopkgtest [17:53:28]: starting date and time: 2024-11-01 17:53:28+0000 0s autopkgtest [17:53:28]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [17:53:28]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vab6dsi5/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-2@bos03-arm64-22.secgroup --name adt-plucky-arm64-cyvcf2-20241101-175328-juju-7f2275-prod-proposed-migration-environment-2-94a9d5dd-efc1-4c92-af5e-afd5d8441ef1 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 68s autopkgtest [17:54:36]: testbed dpkg architecture: arm64 68s autopkgtest [17:54:36]: testbed apt version: 2.9.8 68s autopkgtest [17:54:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 69s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 69s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [183 kB] 70s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 70s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [44.0 kB] 70s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2775 kB] 70s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [241 kB] 70s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 70s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [2023 kB] 70s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [36.5 kB] 70s Fetched 5433 kB in 1s (4433 kB/s) 70s Reading package lists... 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 74s Calculating upgrade... 74s The following packages will be upgraded: 74s libevdev2 libftdi1-2 libinih1 nano python3-lazr.uri 74s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Need to get 374 kB of archives. 74s After this operation, 17.4 kB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libevdev2 arm64 1.13.3+dfsg-1 [36.0 kB] 75s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 nano arm64 8.2-1 [289 kB] 75s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libftdi1-2 arm64 1.5-7 [28.4 kB] 75s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libinih1 arm64 58-1ubuntu1 [7412 B] 75s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lazr.uri all 1.0.6-4 [13.6 kB] 75s Fetched 374 kB in 1s (748 kB/s) 75s (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 ... 79705 files and directories currently installed.) 75s Preparing to unpack .../libevdev2_1.13.3+dfsg-1_arm64.deb ... 75s Unpacking libevdev2:arm64 (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 76s Preparing to unpack .../archives/nano_8.2-1_arm64.deb ... 76s Unpacking nano (8.2-1) over (8.1-1) ... 76s Preparing to unpack .../libftdi1-2_1.5-7_arm64.deb ... 76s Unpacking libftdi1-2:arm64 (1.5-7) over (1.5-6build5) ... 76s Preparing to unpack .../libinih1_58-1ubuntu1_arm64.deb ... 76s Unpacking libinih1:arm64 (58-1ubuntu1) over (55-1ubuntu2) ... 76s Preparing to unpack .../python3-lazr.uri_1.0.6-4_all.deb ... 76s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 76s Setting up libinih1:arm64 (58-1ubuntu1) ... 76s Setting up python3-lazr.uri (1.0.6-4) ... 76s Setting up libftdi1-2:arm64 (1.5-7) ... 76s Setting up nano (8.2-1) ... 76s Setting up libevdev2:arm64 (1.13.3+dfsg-1) ... 76s Processing triggers for man-db (2.12.1-3) ... 77s Processing triggers for install-info (7.1.1-1) ... 77s Processing triggers for libc-bin (2.40-1ubuntu3) ... 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 78s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 79s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 80s Reading package lists... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s autopkgtest [17:54:53]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 85s autopkgtest [17:54:53]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 87s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (dsc) [2337 B] 87s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (tar) [420 kB] 87s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (diff) [6764 B] 87s gpgv: Signature made Wed Jul 31 09:42:06 2024 UTC 87s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 87s gpgv: Can't check signature: No public key 87s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.1-2.dsc: no acceptable signature found 88s autopkgtest [17:54:56]: testing package cyvcf2 version 0.31.1-2 89s autopkgtest [17:54:57]: build not needed 91s autopkgtest [17:54:59]: test run-unit-test: preparing testbed 92s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Starting pkgProblemResolver with broken count: 0 93s Starting 2 pkgProblemResolver with broken count: 0 93s Done 94s The following additional packages will be installed: 94s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 94s python3-all python3-click python3-colorama python3-coloredlogs 94s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 94s python3-packaging python3-pluggy python3-pytest 94s Suggested packages: 94s gcc gfortran python-numpy-doc python3-dev 94s The following NEW packages will be installed: 94s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 94s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 94s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-iniconfig 94s python3-numpy python3-packaging python3-pluggy python3-pytest 94s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 8547 kB/8547 kB of archives. 94s After this operation, 37.3 MB of additional disk space will be used. 94s Get:1 /tmp/autopkgtest.JL5rqN/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 94s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 94s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.21-1 [46.2 kB] 94s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-7ubuntu1 [438 kB] 94s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.0-1build1 [78.0 kB] 94s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libhts3t64 arm64 1.20+ds-2 [437 kB] 94s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 95s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 95s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 95s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 95s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-humanfriendly all 10.0-5 [70.5 kB] 95s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 95s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 95s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cyvcf2 arm64 0.31.1-2 [908 kB] 95s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 95s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 95s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 95s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.2-1 [251 kB] 95s Fetched 8547 kB in 1s (9174 kB/s) 95s Selecting previously unselected package libblas3:arm64. 95s (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 ... 79705 files and directories currently installed.) 95s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 95s Unpacking libblas3:arm64 (3.12.0-3build2) ... 95s Selecting previously unselected package libdeflate0:arm64. 95s Preparing to unpack .../01-libdeflate0_1.21-1_arm64.deb ... 95s Unpacking libdeflate0:arm64 (1.21-1) ... 95s Selecting previously unselected package libgfortran5:arm64. 95s Preparing to unpack .../02-libgfortran5_14.2.0-7ubuntu1_arm64.deb ... 95s Unpacking libgfortran5:arm64 (14.2.0-7ubuntu1) ... 95s Selecting previously unselected package libhtscodecs2:arm64. 95s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_arm64.deb ... 95s Unpacking libhtscodecs2:arm64 (1.6.0-1build1) ... 95s Selecting previously unselected package libhts3t64:arm64. 95s Preparing to unpack .../04-libhts3t64_1.20+ds-2_arm64.deb ... 95s Unpacking libhts3t64:arm64 (1.20+ds-2) ... 95s Selecting previously unselected package liblapack3:arm64. 95s Preparing to unpack .../05-liblapack3_3.12.0-3build2_arm64.deb ... 95s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 95s Selecting previously unselected package python3-all. 95s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_arm64.deb ... 95s Unpacking python3-all (3.12.6-0ubuntu1) ... 95s Selecting previously unselected package python3-colorama. 95s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 95s Unpacking python3-colorama (0.4.6-4) ... 95s Selecting previously unselected package python3-click. 95s Preparing to unpack .../08-python3-click_8.1.7-2_all.deb ... 95s Unpacking python3-click (8.1.7-2) ... 95s Selecting previously unselected package python3-humanfriendly. 96s Preparing to unpack .../09-python3-humanfriendly_10.0-5_all.deb ... 96s Unpacking python3-humanfriendly (10.0-5) ... 96s Selecting previously unselected package python3-coloredlogs. 96s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 96s Unpacking python3-coloredlogs (15.0.1-1) ... 96s Selecting previously unselected package python3-numpy. 96s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 96s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 96s Selecting previously unselected package python3-cyvcf2. 96s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2_arm64.deb ... 96s Unpacking python3-cyvcf2 (0.31.1-2) ... 96s Selecting previously unselected package python3-iniconfig. 96s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 96s Unpacking python3-iniconfig (1.1.1-2) ... 96s Selecting previously unselected package python3-packaging. 96s Preparing to unpack .../14-python3-packaging_24.1-1_all.deb ... 96s Unpacking python3-packaging (24.1-1) ... 96s Selecting previously unselected package python3-pluggy. 96s Preparing to unpack .../15-python3-pluggy_1.5.0-1_all.deb ... 96s Unpacking python3-pluggy (1.5.0-1) ... 96s Selecting previously unselected package python3-pytest. 96s Preparing to unpack .../16-python3-pytest_8.3.2-1_all.deb ... 96s Unpacking python3-pytest (8.3.2-1) ... 96s Selecting previously unselected package autopkgtest-satdep. 96s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 96s Unpacking autopkgtest-satdep (0) ... 96s Setting up libhtscodecs2:arm64 (1.6.0-1build1) ... 96s Setting up python3-iniconfig (1.1.1-2) ... 96s Setting up python3-colorama (0.4.6-4) ... 96s Setting up libdeflate0:arm64 (1.21-1) ... 96s Setting up python3-all (3.12.6-0ubuntu1) ... 96s Setting up python3-click (8.1.7-2) ... 96s Setting up libblas3:arm64 (3.12.0-3build2) ... 96s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 96s Setting up python3-packaging (24.1-1) ... 97s Setting up python3-humanfriendly (10.0-5) ... 97s Setting up libgfortran5:arm64 (14.2.0-7ubuntu1) ... 97s Setting up python3-pluggy (1.5.0-1) ... 97s Setting up libhts3t64:arm64 (1.20+ds-2) ... 97s Setting up python3-coloredlogs (15.0.1-1) ... 97s Setting up liblapack3:arm64 (3.12.0-3build2) ... 97s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 97s Setting up python3-pytest (8.3.2-1) ... 97s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 99s Setting up python3-cyvcf2 (0.31.1-2) ... 99s Setting up autopkgtest-satdep (0) ... 99s Processing triggers for man-db (2.12.1-3) ... 100s Processing triggers for libc-bin (2.40-1ubuntu3) ... 103s (Reading database ... 80971 files and directories currently installed.) 103s Removing autopkgtest-satdep (0) ... 104s autopkgtest [17:55:12]: test run-unit-test: [----------------------- 104s Testing with python3.12 in /tmp/autopkgtest.JL5rqN/autopkgtest_tmp: 105s ============================= test session starts ============================== 105s platform linux -- Python 3.12.7, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3.12 105s cachedir: .pytest_cache 105s rootdir: /tmp/autopkgtest.JL5rqN/autopkgtest_tmp 105s plugins: typeguard-4.3.0 105s collecting ... collected 112 items 105s 105s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 105s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 105s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 105s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 105s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 105s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 105s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 105s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 105s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 105s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 105s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 105s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 105s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 105s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 105s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 105s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 105s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 105s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 105s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 105s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 105s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 105s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 105s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 105s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 105s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 105s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 105s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 105s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 105s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 105s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 105s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 105s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 105s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 105s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 105s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 105s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 105s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 105s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 106s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 106s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 106s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 106s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 106s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 106s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 106s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 106s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 106s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 106s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 106s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 106s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 106s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 106s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 106s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 106s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 106s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 106s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 106s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 106s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 106s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 106s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 106s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 106s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 106s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 106s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 106s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 106s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 106s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 106s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 106s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 106s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 106s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 106s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 106s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 106s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 106s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 106s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 106s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 106s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 106s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 106s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 106s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 106s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 106s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 106s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 106s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 106s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 106s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 106s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 106s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 106s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 106s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 106s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 106s 106s ============================= 112 passed in 1.21s ============================== 106s autopkgtest [17:55:14]: test run-unit-test: -----------------------] 107s run-unit-test PASS 107s autopkgtest [17:55:15]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 107s autopkgtest [17:55:15]: test autodep8-python3: preparing testbed 198s autopkgtest [17:56:46]: testbed dpkg architecture: arm64 198s autopkgtest [17:56:46]: testbed apt version: 2.9.8 198s autopkgtest [17:56:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 199s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 200s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 200s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2775 kB] 200s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [44.0 kB] 200s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [183 kB] 200s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [241 kB] 200s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 200s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [2023 kB] 200s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [36.5 kB] 201s Fetched 5433 kB in 1s (3719 kB/s) 201s Reading package lists... 204s Reading package lists... 205s Building dependency tree... 205s Reading state information... 206s Calculating upgrade... 207s The following packages will be upgraded: 207s libevdev2 libftdi1-2 libinih1 nano python3-lazr.uri 207s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 207s Need to get 374 kB of archives. 207s After this operation, 17.4 kB of additional disk space will be used. 207s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libevdev2 arm64 1.13.3+dfsg-1 [36.0 kB] 207s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 nano arm64 8.2-1 [289 kB] 207s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libftdi1-2 arm64 1.5-7 [28.4 kB] 207s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libinih1 arm64 58-1ubuntu1 [7412 B] 207s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lazr.uri all 1.0.6-4 [13.6 kB] 208s Fetched 374 kB in 0s (848 kB/s) 208s (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 ... 79705 files and directories currently installed.) 208s Preparing to unpack .../libevdev2_1.13.3+dfsg-1_arm64.deb ... 208s Unpacking libevdev2:arm64 (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 208s Preparing to unpack .../archives/nano_8.2-1_arm64.deb ... 208s Unpacking nano (8.2-1) over (8.1-1) ... 208s Preparing to unpack .../libftdi1-2_1.5-7_arm64.deb ... 208s Unpacking libftdi1-2:arm64 (1.5-7) over (1.5-6build5) ... 208s Preparing to unpack .../libinih1_58-1ubuntu1_arm64.deb ... 208s Unpacking libinih1:arm64 (58-1ubuntu1) over (55-1ubuntu2) ... 208s Preparing to unpack .../python3-lazr.uri_1.0.6-4_all.deb ... 209s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 209s Setting up libinih1:arm64 (58-1ubuntu1) ... 209s Setting up python3-lazr.uri (1.0.6-4) ... 209s Setting up libftdi1-2:arm64 (1.5-7) ... 209s Setting up nano (8.2-1) ... 209s Setting up libevdev2:arm64 (1.13.3+dfsg-1) ... 209s Processing triggers for man-db (2.12.1-3) ... 210s Processing triggers for install-info (7.1.1-1) ... 210s Processing triggers for libc-bin (2.40-1ubuntu3) ... 210s Reading package lists... 211s Building dependency tree... 211s Reading state information... 213s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 213s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 213s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 213s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 213s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 215s Reading package lists... 215s Reading package lists... 215s Building dependency tree... 215s Reading state information... 217s Calculating upgrade... 218s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 218s Reading package lists... 218s Building dependency tree... 218s Reading state information... 220s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 226s Starting pkgProblemResolver with broken count: 0 226s Starting 2 pkgProblemResolver with broken count: 0 226s Done 227s The following additional packages will be installed: 227s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 227s python3-all python3-click python3-colorama python3-coloredlogs 227s python3-cyvcf2 python3-humanfriendly python3-numpy 227s Suggested packages: 227s gcc gfortran python-numpy-doc python3-dev python3-pytest 227s The following NEW packages will be installed: 227s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 227s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 227s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-numpy 228s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 228s Need to get 8227 kB/8228 kB of archives. 228s After this operation, 35.7 MB of additional disk space will be used. 228s Get:1 /tmp/autopkgtest.JL5rqN/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 228s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 228s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.21-1 [46.2 kB] 228s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-7ubuntu1 [438 kB] 228s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.0-1build1 [78.0 kB] 228s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libhts3t64 arm64 1.20+ds-2 [437 kB] 228s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 228s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 228s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 228s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 228s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-humanfriendly all 10.0-5 [70.5 kB] 228s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 228s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 228s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cyvcf2 arm64 0.31.1-2 [908 kB] 229s Fetched 8227 kB in 1s (8842 kB/s) 229s Selecting previously unselected package libblas3:arm64. 229s (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 ... 79705 files and directories currently installed.) 229s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 229s Unpacking libblas3:arm64 (3.12.0-3build2) ... 229s Selecting previously unselected package libdeflate0:arm64. 229s Preparing to unpack .../01-libdeflate0_1.21-1_arm64.deb ... 229s Unpacking libdeflate0:arm64 (1.21-1) ... 229s Selecting previously unselected package libgfortran5:arm64. 229s Preparing to unpack .../02-libgfortran5_14.2.0-7ubuntu1_arm64.deb ... 229s Unpacking libgfortran5:arm64 (14.2.0-7ubuntu1) ... 229s Selecting previously unselected package libhtscodecs2:arm64. 229s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_arm64.deb ... 229s Unpacking libhtscodecs2:arm64 (1.6.0-1build1) ... 229s Selecting previously unselected package libhts3t64:arm64. 229s Preparing to unpack .../04-libhts3t64_1.20+ds-2_arm64.deb ... 229s Unpacking libhts3t64:arm64 (1.20+ds-2) ... 229s Selecting previously unselected package liblapack3:arm64. 229s Preparing to unpack .../05-liblapack3_3.12.0-3build2_arm64.deb ... 229s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 230s Selecting previously unselected package python3-all. 230s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_arm64.deb ... 230s Unpacking python3-all (3.12.6-0ubuntu1) ... 230s Selecting previously unselected package python3-colorama. 230s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 230s Unpacking python3-colorama (0.4.6-4) ... 230s Selecting previously unselected package python3-click. 230s Preparing to unpack .../08-python3-click_8.1.7-2_all.deb ... 230s Unpacking python3-click (8.1.7-2) ... 230s Selecting previously unselected package python3-humanfriendly. 230s Preparing to unpack .../09-python3-humanfriendly_10.0-5_all.deb ... 230s Unpacking python3-humanfriendly (10.0-5) ... 230s Selecting previously unselected package python3-coloredlogs. 230s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 230s Unpacking python3-coloredlogs (15.0.1-1) ... 230s Selecting previously unselected package python3-numpy. 230s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 230s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 230s Selecting previously unselected package python3-cyvcf2. 230s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2_arm64.deb ... 230s Unpacking python3-cyvcf2 (0.31.1-2) ... 230s Selecting previously unselected package autopkgtest-satdep. 230s Preparing to unpack .../13-2-autopkgtest-satdep.deb ... 230s Unpacking autopkgtest-satdep (0) ... 230s Setting up libhtscodecs2:arm64 (1.6.0-1build1) ... 230s Setting up python3-colorama (0.4.6-4) ... 231s Setting up libdeflate0:arm64 (1.21-1) ... 231s Setting up python3-all (3.12.6-0ubuntu1) ... 231s Setting up python3-click (8.1.7-2) ... 231s Setting up libblas3:arm64 (3.12.0-3build2) ... 231s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 231s Setting up python3-humanfriendly (10.0-5) ... 231s Setting up libgfortran5:arm64 (14.2.0-7ubuntu1) ... 231s Setting up libhts3t64:arm64 (1.20+ds-2) ... 231s Setting up python3-coloredlogs (15.0.1-1) ... 231s Setting up liblapack3:arm64 (3.12.0-3build2) ... 231s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 231s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 234s Setting up python3-cyvcf2 (0.31.1-2) ... 234s Setting up autopkgtest-satdep (0) ... 234s Processing triggers for man-db (2.12.1-3) ... 235s Processing triggers for libc-bin (2.40-1ubuntu3) ... 240s (Reading database ... 80807 files and directories currently installed.) 240s Removing autopkgtest-satdep (0) ... 242s autopkgtest [17:57:30]: 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 242s autopkgtest [17:57:30]: test autodep8-python3: [----------------------- 243s Testing with python3.12: 243s 243s autopkgtest [17:57:31]: test autodep8-python3: -----------------------] 244s autopkgtest [17:57:32]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 244s autodep8-python3 PASS (superficial) 245s autopkgtest [17:57:33]: @@@@@@@@@@@@@@@@@@@@ summary 245s run-unit-test PASS 245s autodep8-python3 PASS (superficial) 254s nova [W] Skipping flock in bos03-arm64 254s Creating nova instance adt-plucky-arm64-cyvcf2-20241101-175328-juju-7f2275-prod-proposed-migration-environment-2-94a9d5dd-efc1-4c92-af5e-afd5d8441ef1 from image adt/ubuntu-plucky-arm64-server-20241101.img (UUID 520a937f-514a-4e80-b76b-163a8c247e3e)... 254s nova [W] Skipping flock in bos03-arm64 254s Creating nova instance adt-plucky-arm64-cyvcf2-20241101-175328-juju-7f2275-prod-proposed-migration-environment-2-94a9d5dd-efc1-4c92-af5e-afd5d8441ef1 from image adt/ubuntu-plucky-arm64-server-20241101.img (UUID 520a937f-514a-4e80-b76b-163a8c247e3e)...