0s autopkgtest [10:58:58]: starting date and time: 2024-05-29 10:58:58+0000 0s autopkgtest [10:58:58]: git checkout: d60bd36 autopkgtest-build-lxd: Add missing remote prefix in get_boot_id(). 0s autopkgtest [10:58:58]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5_8zs6rt/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:pytest,src:astropy,src:sunpy --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.1-2 astropy/6.0.1-4 sunpy/5.1.3-1' -- lxd -r lxd-armhf-10.145.243.183 lxd-armhf-10.145.243.183:autopkgtest/ubuntu/oracular/armhf 30s autopkgtest [10:59:28]: testbed dpkg architecture: armhf 32s autopkgtest [10:59:30]: testbed apt version: 2.9.3 32s autopkgtest [10:59:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 40s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB] 40s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [1964 B] 40s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [60.8 kB] 40s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2568 B] 40s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [498 kB] 40s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [107 kB] 40s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [486 kB] 40s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1392 B] 40s Fetched 1232 kB in 1s (1180 kB/s) 40s Reading package lists... 57s tee: /proc/self/fd/2: Permission denied 80s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 80s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 80s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 81s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 82s Reading package lists... 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 84s Calculating upgrade... 84s The following packages will be upgraded: 84s python3-typing-extensions 85s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 65.4 kB of archives. 85s After this operation, 26.6 kB of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu oracular/main armhf python3-typing-extensions all 4.12.0-1 [65.4 kB] 85s Fetched 65.4 kB in 0s (235 kB/s) 86s (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 ... 58333 files and directories currently installed.) 86s Preparing to unpack .../python3-typing-extensions_4.12.0-1_all.deb ... 86s Unpacking python3-typing-extensions (4.12.0-1) over (4.11.0-1) ... 86s Setting up python3-typing-extensions (4.12.0-1) ... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s autopkgtest [11:00:27]: rebooting testbed after setup commands that affected boot 130s autopkgtest [11:01:08]: testbed running kernel: Linux 6.5.0-35-generic #35~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue May 7 11:19:33 UTC 2 162s autopkgtest [11:01:40]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 175s Get:1 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.30.28-1build2 (dsc) [2415 B] 175s Get:2 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.30.28-1build2 (tar) [420 kB] 175s Get:3 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.30.28-1build2 (diff) [6784 B] 175s gpgv: Signature made Mon Apr 1 05:42:45 2024 UTC 175s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 175s gpgv: Can't check signature: No public key 175s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.30.28-1build2.dsc: no acceptable signature found 175s autopkgtest [11:01:53]: testing package cyvcf2 version 0.30.28-1build2 177s autopkgtest [11:01:55]: build not needed 180s autopkgtest [11:01:58]: test run-unit-test: preparing testbed 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 191s The following additional packages will be installed: 191s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 191s python3-all python3-click python3-colorama python3-coloredlogs 191s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 191s python3-packaging python3-pluggy python3-pytest 191s Suggested packages: 191s gcc gfortran python-numpy-doc python3-dev 191s The following NEW packages will be installed: 191s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 191s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 191s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-iniconfig 191s python3-numpy python3-packaging python3-pluggy python3-pytest 191s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 7918 kB/7919 kB of archives. 191s After this operation, 30.0 MB of additional disk space will be used. 191s Get:1 /tmp/autopkgtest.qxXmCw/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [724 B] 192s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 192s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate0 armhf 1.20-1 [38.3 kB] 192s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-1ubuntu1 [311 kB] 192s Get:5 http://ftpmaster.internal/ubuntu oracular/universe armhf libhtscodecs2 armhf 1.6.0-1build1 [65.8 kB] 192s Get:6 http://ftpmaster.internal/ubuntu oracular/universe armhf libhts3t64 armhf 1.19+ds-1.1build3 [389 kB] 192s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 193s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf python3-all armhf 3.12.3-0ubuntu1 [886 B] 193s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 193s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf python3-click all 8.1.7-1 [79.1 kB] 193s Get:11 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-humanfriendly all 10.0-5 [70.5 kB] 193s Get:12 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-coloredlogs all 15.0.1-1 [38.2 kB] 193s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf python3-numpy armhf 1:1.26.4+ds-10 [3541 kB] 193s Get:14 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cyvcf2 armhf 0.30.28-1build2 [827 kB] 193s Get:15 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 193s Get:16 http://ftpmaster.internal/ubuntu oracular/main armhf python3-packaging all 24.0-1 [41.1 kB] 193s Get:17 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 193s Get:18 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf python3-pytest all 8.2.1-2 [249 kB] 195s Fetched 7918 kB in 2s (3293 kB/s) 195s Selecting previously unselected package libblas3:armhf. 195s (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 ... 58333 files and directories currently installed.) 195s Preparing to unpack .../00-libblas3_3.12.0-3build1_armhf.deb ... 195s Unpacking libblas3:armhf (3.12.0-3build1) ... 195s Selecting previously unselected package libdeflate0:armhf. 195s Preparing to unpack .../01-libdeflate0_1.20-1_armhf.deb ... 195s Unpacking libdeflate0:armhf (1.20-1) ... 195s Selecting previously unselected package libgfortran5:armhf. 195s Preparing to unpack .../02-libgfortran5_14.1.0-1ubuntu1_armhf.deb ... 195s Unpacking libgfortran5:armhf (14.1.0-1ubuntu1) ... 195s Selecting previously unselected package libhtscodecs2:armhf. 196s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_armhf.deb ... 196s Unpacking libhtscodecs2:armhf (1.6.0-1build1) ... 196s Selecting previously unselected package libhts3t64:armhf. 196s Preparing to unpack .../04-libhts3t64_1.19+ds-1.1build3_armhf.deb ... 196s Unpacking libhts3t64:armhf (1.19+ds-1.1build3) ... 196s Selecting previously unselected package liblapack3:armhf. 196s Preparing to unpack .../05-liblapack3_3.12.0-3build1_armhf.deb ... 196s Unpacking liblapack3:armhf (3.12.0-3build1) ... 196s Selecting previously unselected package python3-all. 196s Preparing to unpack .../06-python3-all_3.12.3-0ubuntu1_armhf.deb ... 196s Unpacking python3-all (3.12.3-0ubuntu1) ... 196s Selecting previously unselected package python3-colorama. 196s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 196s Unpacking python3-colorama (0.4.6-4) ... 196s Selecting previously unselected package python3-click. 196s Preparing to unpack .../08-python3-click_8.1.7-1_all.deb ... 196s Unpacking python3-click (8.1.7-1) ... 196s Selecting previously unselected package python3-humanfriendly. 196s Preparing to unpack .../09-python3-humanfriendly_10.0-5_all.deb ... 196s Unpacking python3-humanfriendly (10.0-5) ... 196s Selecting previously unselected package python3-coloredlogs. 196s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 196s Unpacking python3-coloredlogs (15.0.1-1) ... 196s Selecting previously unselected package python3-numpy. 196s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-10_armhf.deb ... 196s Unpacking python3-numpy (1:1.26.4+ds-10) ... 197s Selecting previously unselected package python3-cyvcf2. 197s Preparing to unpack .../12-python3-cyvcf2_0.30.28-1build2_armhf.deb ... 197s Unpacking python3-cyvcf2 (0.30.28-1build2) ... 197s Selecting previously unselected package python3-iniconfig. 197s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 197s Unpacking python3-iniconfig (1.1.1-2) ... 197s Selecting previously unselected package python3-packaging. 197s Preparing to unpack .../14-python3-packaging_24.0-1_all.deb ... 197s Unpacking python3-packaging (24.0-1) ... 197s Selecting previously unselected package python3-pluggy. 197s Preparing to unpack .../15-python3-pluggy_1.5.0-1_all.deb ... 197s Unpacking python3-pluggy (1.5.0-1) ... 197s Selecting previously unselected package python3-pytest. 197s Preparing to unpack .../16-python3-pytest_8.2.1-2_all.deb ... 197s Unpacking python3-pytest (8.2.1-2) ... 198s Selecting previously unselected package autopkgtest-satdep. 199s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 199s Unpacking autopkgtest-satdep (0) ... 200s Setting up libhtscodecs2:armhf (1.6.0-1build1) ... 200s Setting up python3-iniconfig (1.1.1-2) ... 200s Setting up python3-colorama (0.4.6-4) ... 201s Setting up libdeflate0:armhf (1.20-1) ... 201s Setting up python3-all (3.12.3-0ubuntu1) ... 201s Setting up python3-click (8.1.7-1) ... 202s Setting up libblas3:armhf (3.12.0-3build1) ... 202s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 202s Setting up python3-packaging (24.0-1) ... 202s Setting up python3-humanfriendly (10.0-5) ... 203s Setting up libgfortran5:armhf (14.1.0-1ubuntu1) ... 203s Setting up python3-pluggy (1.5.0-1) ... 203s Setting up libhts3t64:armhf (1.19+ds-1.1build3) ... 203s Setting up python3-coloredlogs (15.0.1-1) ... 203s Setting up liblapack3:armhf (3.12.0-3build1) ... 203s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 203s Setting up python3-pytest (8.2.1-2) ... 203s Setting up python3-numpy (1:1.26.4+ds-10) ... 205s Setting up python3-cyvcf2 (0.30.28-1build2) ... 206s Setting up autopkgtest-satdep (0) ... 206s Processing triggers for man-db (2.12.1-1) ... 207s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 236s (Reading database ... 59600 files and directories currently installed.) 236s Removing autopkgtest-satdep (0) ... 245s autopkgtest [11:03:03]: test run-unit-test: [----------------------- 248s Testing with python3.12 in /tmp/autopkgtest.qxXmCw/autopkgtest_tmp: 249s ============================= test session starts ============================== 249s platform linux -- Python 3.12.3, pytest-8.2.1, pluggy-1.5.0 -- /usr/bin/python3.12 249s cachedir: .pytest_cache 249s rootdir: /tmp/autopkgtest.qxXmCw/autopkgtest_tmp 249s collecting ... collected 112 items 249s 249s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 249s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 249s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 249s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 249s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 249s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 249s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 249s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 249s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 249s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 249s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 249s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 249s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 249s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 249s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 249s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 249s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 249s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 249s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 249s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 249s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 249s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 249s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 249s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 249s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 249s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 249s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 249s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 249s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 249s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 249s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 249s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 249s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 249s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 249s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 249s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 249s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 249s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 250s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 250s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 250s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 250s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 250s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 250s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 250s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 250s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 250s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 250s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 250s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 250s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 250s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 250s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 250s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 250s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 250s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 250s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 250s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 250s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 250s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 250s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 250s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 250s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 250s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 250s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 250s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 250s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 250s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 250s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 250s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 250s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 250s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 250s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 250s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 250s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 250s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 250s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 250s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 250s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 250s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 250s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 250s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 250s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 250s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 250s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 250s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 250s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 250s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 250s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 250s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 250s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 250s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 250s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 250s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 250s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 250s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 250s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 250s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 250s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 250s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 250s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 250s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 250s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 250s 250s ============================= 112 passed in 1.70s ============================== 251s autopkgtest [11:03:09]: test run-unit-test: -----------------------] 255s autopkgtest [11:03:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 255s run-unit-test PASS 258s autopkgtest [11:03:16]: test autodep8-python3: preparing testbed 295s autopkgtest [11:03:53]: testbed dpkg architecture: armhf 297s autopkgtest [11:03:55]: testbed apt version: 2.9.3 297s autopkgtest [11:03:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 304s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB] 305s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [1964 B] 305s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [498 kB] 305s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2568 B] 305s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [60.8 kB] 305s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [107 kB] 305s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [486 kB] 305s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1392 B] 305s Fetched 1232 kB in 1s (1477 kB/s) 305s Reading package lists... 320s tee: /proc/self/fd/2: Permission denied 342s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 342s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 342s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 342s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 344s Reading package lists... 344s Reading package lists... 344s Building dependency tree... 344s Reading state information... 345s Calculating upgrade... 345s The following packages will be upgraded: 345s python3-typing-extensions 346s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 346s Need to get 65.4 kB of archives. 346s After this operation, 26.6 kB of additional disk space will be used. 346s Get:1 http://ftpmaster.internal/ubuntu oracular/main armhf python3-typing-extensions all 4.12.0-1 [65.4 kB] 346s Fetched 65.4 kB in 0s (232 kB/s) 347s (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 ... 58333 files and directories currently installed.) 347s Preparing to unpack .../python3-typing-extensions_4.12.0-1_all.deb ... 347s Unpacking python3-typing-extensions (4.12.0-1) over (4.11.0-1) ... 347s Setting up python3-typing-extensions (4.12.0-1) ... 347s Reading package lists... 347s Building dependency tree... 347s Reading state information... 349s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 351s autopkgtest [11:04:49]: rebooting testbed after setup commands that affected boot 443s Reading package lists... 444s Building dependency tree... 444s Reading state information... 444s Starting pkgProblemResolver with broken count: 0 445s Starting 2 pkgProblemResolver with broken count: 0 445s Done 445s The following additional packages will be installed: 445s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 445s python3-all python3-click python3-colorama python3-coloredlogs 445s python3-cyvcf2 python3-humanfriendly python3-numpy 445s Suggested packages: 445s gcc gfortran python-numpy-doc python3-dev python3-pytest 446s The following NEW packages will be installed: 446s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 446s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 446s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-numpy 447s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 447s Need to get 7600 kB/7601 kB of archives. 447s After this operation, 28.4 MB of additional disk space will be used. 447s Get:1 /tmp/autopkgtest.qxXmCw/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [720 B] 447s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 447s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate0 armhf 1.20-1 [38.3 kB] 447s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-1ubuntu1 [311 kB] 447s Get:5 http://ftpmaster.internal/ubuntu oracular/universe armhf libhtscodecs2 armhf 1.6.0-1build1 [65.8 kB] 447s Get:6 http://ftpmaster.internal/ubuntu oracular/universe armhf libhts3t64 armhf 1.19+ds-1.1build3 [389 kB] 447s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 447s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf python3-all armhf 3.12.3-0ubuntu1 [886 B] 447s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 447s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf python3-click all 8.1.7-1 [79.1 kB] 447s Get:11 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-humanfriendly all 10.0-5 [70.5 kB] 447s Get:12 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-coloredlogs all 15.0.1-1 [38.2 kB] 447s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf python3-numpy armhf 1:1.26.4+ds-10 [3541 kB] 447s Get:14 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cyvcf2 armhf 0.30.28-1build2 [827 kB] 456s Fetched 7600 kB in 1s (5932 kB/s) 457s Selecting previously unselected package libblas3:armhf. 457s (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 ... 58333 files and directories currently installed.) 457s Preparing to unpack .../00-libblas3_3.12.0-3build1_armhf.deb ... 457s Unpacking libblas3:armhf (3.12.0-3build1) ... 457s Selecting previously unselected package libdeflate0:armhf. 460s Preparing to unpack .../01-libdeflate0_1.20-1_armhf.deb ... 460s Unpacking libdeflate0:armhf (1.20-1) ... 460s Selecting previously unselected package libgfortran5:armhf. 461s Preparing to unpack .../02-libgfortran5_14.1.0-1ubuntu1_armhf.deb ... 461s Unpacking libgfortran5:armhf (14.1.0-1ubuntu1) ... 461s Selecting previously unselected package libhtscodecs2:armhf. 463s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_armhf.deb ... 463s Unpacking libhtscodecs2:armhf (1.6.0-1build1) ... 464s Selecting previously unselected package libhts3t64:armhf. 468s Preparing to unpack .../04-libhts3t64_1.19+ds-1.1build3_armhf.deb ... 468s Unpacking libhts3t64:armhf (1.19+ds-1.1build3) ... 468s Selecting previously unselected package liblapack3:armhf. 472s Preparing to unpack .../05-liblapack3_3.12.0-3build1_armhf.deb ... 472s Unpacking liblapack3:armhf (3.12.0-3build1) ... 473s Selecting previously unselected package python3-all. 477s Preparing to unpack .../06-python3-all_3.12.3-0ubuntu1_armhf.deb ... 477s Unpacking python3-all (3.12.3-0ubuntu1) ... 478s Selecting previously unselected package python3-colorama. 480s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 480s Unpacking python3-colorama (0.4.6-4) ... 481s Selecting previously unselected package python3-click. 483s Preparing to unpack .../08-python3-click_8.1.7-1_all.deb ... 483s Unpacking python3-click (8.1.7-1) ... 484s Selecting previously unselected package python3-humanfriendly. 487s Preparing to unpack .../09-python3-humanfriendly_10.0-5_all.deb ... 487s Unpacking python3-humanfriendly (10.0-5) ... 488s Selecting previously unselected package python3-coloredlogs. 492s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 492s Unpacking python3-coloredlogs (15.0.1-1) ... 492s Selecting previously unselected package python3-numpy. 494s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-10_armhf.deb ... 494s Unpacking python3-numpy (1:1.26.4+ds-10) ... 495s Selecting previously unselected package python3-cyvcf2. 499s Preparing to unpack .../12-python3-cyvcf2_0.30.28-1build2_armhf.deb ... 499s Unpacking python3-cyvcf2 (0.30.28-1build2) ... 500s Selecting previously unselected package autopkgtest-satdep. 502s Preparing to unpack .../13-2-autopkgtest-satdep.deb ... 502s Unpacking autopkgtest-satdep (0) ... 505s Setting up libhtscodecs2:armhf (1.6.0-1build1) ... 505s Setting up python3-colorama (0.4.6-4) ... 506s Setting up libdeflate0:armhf (1.20-1) ... 506s Setting up python3-all (3.12.3-0ubuntu1) ... 506s Setting up python3-click (8.1.7-1) ... 507s Setting up libblas3:armhf (3.12.0-3build1) ... 507s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 507s Setting up python3-humanfriendly (10.0-5) ... 508s Setting up libgfortran5:armhf (14.1.0-1ubuntu1) ... 508s Setting up libhts3t64:armhf (1.19+ds-1.1build3) ... 508s Setting up python3-coloredlogs (15.0.1-1) ... 509s Setting up liblapack3:armhf (3.12.0-3build1) ... 511s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 511s Setting up python3-numpy (1:1.26.4+ds-10) ... 513s Setting up python3-cyvcf2 (0.30.28-1build2) ... 513s Setting up autopkgtest-satdep (0) ... 513s Processing triggers for man-db (2.12.1-1) ... 515s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 536s (Reading database ... 59436 files and directories currently installed.) 536s Removing autopkgtest-satdep (0) ... 555s autopkgtest [11:08:13]: 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 555s autopkgtest [11:08:13]: test autodep8-python3: [----------------------- 562s Testing with python3.12: 564s 565s autopkgtest [11:08:23]: test autodep8-python3: -----------------------] 569s autopkgtest [11:08:27]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 569s autodep8-python3 PASS (superficial) 575s autopkgtest [11:08:33]: @@@@@@@@@@@@@@@@@@@@ summary 575s run-unit-test PASS 575s autodep8-python3 PASS (superficial)