0s autopkgtest [15:47:10]: starting date and time: 2024-07-12 15:47:10+0000 0s autopkgtest [15:47:10]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [15:47:10]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hqd75avi/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:glibc --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- lxd -r lxd-armhf-10.145.243.242 lxd-armhf-10.145.243.242:autopkgtest/ubuntu/oracular/armhf 98s autopkgtest [15:48:48]: testbed dpkg architecture: armhf 102s autopkgtest [15:48:52]: testbed apt version: 2.9.6 102s autopkgtest [15:48:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 198s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 202s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [343 kB] 203s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 203s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [46.6 kB] 203s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 203s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [58.3 kB] 203s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf c-n-f Metadata [1444 B] 203s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf Packages [1368 B] 203s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf c-n-f Metadata [120 B] 203s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [303 kB] 203s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf c-n-f Metadata [6176 B] 203s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1448 B] 203s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf c-n-f Metadata [120 B] 215s Fetched 899 kB in 17s (53.3 kB/s) 215s Reading package lists... 280s tee: /proc/self/fd/2: Permission denied 341s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 341s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 341s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 341s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 344s Reading package lists... 344s Reading package lists... 345s Building dependency tree... 345s Reading state information... 345s Calculating upgrade... 346s The following packages will be upgraded: 346s inetutils-telnet libc-bin libc6 libssl3t64 locales openssh-client 346s openssh-server openssh-sftp-server openssl telnet 346s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 346s Need to get 11.9 MB of archives. 346s After this operation, 285 kB of additional disk space will be used. 346s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc6 armhf 2.39-3.1ubuntu3 [2825 kB] 346s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc-bin armhf 2.39-3.1ubuntu3 [527 kB] 346s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libssl3t64 armhf 3.2.2-1ubuntu1 [1729 kB] 346s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu17 [35.6 kB] 346s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-server armhf 1:9.6p1-3ubuntu17 [502 kB] 346s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-client armhf 1:9.6p1-3ubuntu17 [888 kB] 346s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf locales all 2.39-3.1ubuntu3 [4220 kB] 347s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf openssl armhf 3.2.2-1ubuntu1 [1095 kB] 347s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf inetutils-telnet armhf 2:2.5-5ubuntu1 [94.4 kB] 347s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf telnet all 0.17+2.5-5ubuntu1 [3688 B] 348s Preconfiguring packages ... 348s Fetched 11.9 MB in 1s (11.2 MB/s) 349s (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 ... 58437 files and directories currently installed.) 349s Preparing to unpack .../libc6_2.39-3.1ubuntu3_armhf.deb ... 349s Unpacking libc6:armhf (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 350s Setting up libc6:armhf (2.39-3.1ubuntu3) ... 350s Error: Could not restart systemd, systemd binary not working 350s (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 ... 58437 files and directories currently installed.) 350s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_armhf.deb ... 350s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 350s Setting up libc-bin (2.39-3.1ubuntu3) ... 351s (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 ... 58437 files and directories currently installed.) 351s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_armhf.deb ... 351s Unpacking libssl3t64:armhf (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 351s Setting up libssl3t64:armhf (3.2.2-1ubuntu1) ... 351s (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 ... 58437 files and directories currently installed.) 351s Preparing to unpack .../0-openssh-sftp-server_1%3a9.6p1-3ubuntu17_armhf.deb ... 351s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 352s Preparing to unpack .../1-openssh-server_1%3a9.6p1-3ubuntu17_armhf.deb ... 352s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 353s Preparing to unpack .../2-openssh-client_1%3a9.6p1-3ubuntu17_armhf.deb ... 353s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 353s Preparing to unpack .../3-locales_2.39-3.1ubuntu3_all.deb ... 353s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 355s Preparing to unpack .../4-openssl_3.2.2-1ubuntu1_armhf.deb ... 355s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 356s Preparing to unpack .../5-inetutils-telnet_2%3a2.5-5ubuntu1_armhf.deb ... 356s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ... 357s Preparing to unpack .../6-telnet_0.17+2.5-5ubuntu1_all.deb ... 357s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ... 358s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 358s Setting up inetutils-telnet (2:2.5-5ubuntu1) ... 358s Setting up locales (2.39-3.1ubuntu3) ... 374s Generating locales (this might take a while)... 384s en_US.UTF-8... done 384s Generation complete. 385s Setting up openssl (3.2.2-1ubuntu1) ... 385s Installing new version of config file /etc/ssl/openssl.cnf ... 385s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 385s Setting up telnet (0.17+2.5-5ubuntu1) ... 385s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 385s Installing new version of config file /etc/pam.d/sshd ... 402s Processing triggers for ufw (0.36.2-6) ... 403s Processing triggers for systemd (256-1ubuntu1) ... 416s Processing triggers for man-db (2.12.1-2) ... 420s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 423s Reading package lists... 424s Building dependency tree... 424s Reading state information... 426s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 429s autopkgtest [15:54:19]: rebooting testbed after setup commands that affected boot 525s autopkgtest [15:55:55]: testbed running kernel: Linux 6.5.0-41-generic #41~22.04.2-Ubuntu SMP PREEMPT_DYNAMIC Mon Jun 3 16:28:24 UTC 2 554s autopkgtest [15:56:24]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 578s Get:1 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (dsc) [2486 B] 578s Get:2 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (tar) [420 kB] 578s Get:3 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (diff) [6696 B] 581s gpgv: Signature made Sat Jun 1 08:34:30 2024 UTC 581s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 581s gpgv: issuer "emollier@debian.org" 581s gpgv: Can't check signature: No public key 582s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.0-1.dsc: no acceptable signature found 599s autopkgtest [15:57:09]: testing package cyvcf2 version 0.31.0-1 603s autopkgtest [15:57:13]: build not needed 606s autopkgtest [15:57:16]: test run-unit-test: preparing testbed 617s Reading package lists... 617s Building dependency tree... 617s Reading state information... 617s Starting pkgProblemResolver with broken count: 0 617s Starting 2 pkgProblemResolver with broken count: 0 617s Done 618s The following additional packages will be installed: 618s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 618s python3-all python3-click python3-colorama python3-coloredlogs 618s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 618s python3-packaging python3-pluggy python3-pytest 618s Suggested packages: 618s gcc gfortran python-numpy-doc python3-dev 618s The following NEW packages will be installed: 618s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 618s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 618s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-iniconfig 618s python3-numpy python3-packaging python3-pluggy python3-pytest 618s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 618s Need to get 7977 kB/7978 kB of archives. 618s After this operation, 30.0 MB of additional disk space will be used. 618s Get:1 /tmp/autopkgtest.YJxzsf/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [720 B] 618s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 619s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate0 armhf 1.20-1 [38.3 kB] 619s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-1ubuntu1 [311 kB] 619s Get:5 http://ftpmaster.internal/ubuntu oracular/universe armhf libhtscodecs2 armhf 1.6.0-1build1 [65.8 kB] 619s Get:6 http://ftpmaster.internal/ubuntu oracular/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 619s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 619s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf python3-all armhf 3.12.3-0ubuntu1 [886 B] 619s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 619s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf python3-click all 8.1.7-1 [79.1 kB] 619s Get:11 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-humanfriendly all 10.0-5 [70.5 kB] 619s Get:12 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-coloredlogs all 15.0.1-1 [38.2 kB] 619s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf python3-numpy armhf 1:1.26.4+ds-10 [3541 kB] 619s Get:14 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cyvcf2 armhf 0.31.0-1 [827 kB] 619s Get:15 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 619s Get:16 http://ftpmaster.internal/ubuntu oracular/main armhf python3-packaging all 24.1-1 [41.4 kB] 619s Get:17 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 619s Get:18 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pytest all 7.4.4-1 [305 kB] 620s Fetched 7977 kB in 1s (7077 kB/s) 620s Selecting previously unselected package libblas3:armhf. 620s (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 ... 58436 files and directories currently installed.) 620s Preparing to unpack .../00-libblas3_3.12.0-3build1_armhf.deb ... 620s Unpacking libblas3:armhf (3.12.0-3build1) ... 620s Selecting previously unselected package libdeflate0:armhf. 621s Preparing to unpack .../01-libdeflate0_1.20-1_armhf.deb ... 621s Unpacking libdeflate0:armhf (1.20-1) ... 621s Selecting previously unselected package libgfortran5:armhf. 621s Preparing to unpack .../02-libgfortran5_14.1.0-1ubuntu1_armhf.deb ... 621s Unpacking libgfortran5:armhf (14.1.0-1ubuntu1) ... 621s Selecting previously unselected package libhtscodecs2:armhf. 621s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_armhf.deb ... 621s Unpacking libhtscodecs2:armhf (1.6.0-1build1) ... 621s Selecting previously unselected package libhts3t64:armhf. 621s Preparing to unpack .../04-libhts3t64_1.20+ds-1_armhf.deb ... 621s Unpacking libhts3t64:armhf (1.20+ds-1) ... 622s Selecting previously unselected package liblapack3:armhf. 622s Preparing to unpack .../05-liblapack3_3.12.0-3build1_armhf.deb ... 622s Unpacking liblapack3:armhf (3.12.0-3build1) ... 622s Selecting previously unselected package python3-all. 622s Preparing to unpack .../06-python3-all_3.12.3-0ubuntu1_armhf.deb ... 622s Unpacking python3-all (3.12.3-0ubuntu1) ... 623s Selecting previously unselected package python3-colorama. 623s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 623s Unpacking python3-colorama (0.4.6-4) ... 623s Selecting previously unselected package python3-click. 623s Preparing to unpack .../08-python3-click_8.1.7-1_all.deb ... 623s Unpacking python3-click (8.1.7-1) ... 624s Selecting previously unselected package python3-humanfriendly. 624s Preparing to unpack .../09-python3-humanfriendly_10.0-5_all.deb ... 624s Unpacking python3-humanfriendly (10.0-5) ... 624s Selecting previously unselected package python3-coloredlogs. 625s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 625s Unpacking python3-coloredlogs (15.0.1-1) ... 625s Selecting previously unselected package python3-numpy. 626s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-10_armhf.deb ... 626s Unpacking python3-numpy (1:1.26.4+ds-10) ... 626s Selecting previously unselected package python3-cyvcf2. 627s Preparing to unpack .../12-python3-cyvcf2_0.31.0-1_armhf.deb ... 627s Unpacking python3-cyvcf2 (0.31.0-1) ... 627s Selecting previously unselected package python3-iniconfig. 627s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 627s Unpacking python3-iniconfig (1.1.1-2) ... 627s Selecting previously unselected package python3-packaging. 628s Preparing to unpack .../14-python3-packaging_24.1-1_all.deb ... 628s Unpacking python3-packaging (24.1-1) ... 628s Selecting previously unselected package python3-pluggy. 628s Preparing to unpack .../15-python3-pluggy_1.5.0-1_all.deb ... 628s Unpacking python3-pluggy (1.5.0-1) ... 628s Selecting previously unselected package python3-pytest. 628s Preparing to unpack .../16-python3-pytest_7.4.4-1_all.deb ... 628s Unpacking python3-pytest (7.4.4-1) ... 629s Selecting previously unselected package autopkgtest-satdep. 629s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 629s Unpacking autopkgtest-satdep (0) ... 629s Setting up libhtscodecs2:armhf (1.6.0-1build1) ... 629s Setting up python3-iniconfig (1.1.1-2) ... 629s Setting up python3-colorama (0.4.6-4) ... 629s Setting up libdeflate0:armhf (1.20-1) ... 629s Setting up python3-all (3.12.3-0ubuntu1) ... 629s Setting up python3-click (8.1.7-1) ... 629s Setting up libblas3:armhf (3.12.0-3build1) ... 629s 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 629s Setting up python3-packaging (24.1-1) ... 629s Setting up python3-humanfriendly (10.0-5) ... 630s Setting up libgfortran5:armhf (14.1.0-1ubuntu1) ... 630s Setting up python3-pluggy (1.5.0-1) ... 630s Setting up libhts3t64:armhf (1.20+ds-1) ... 630s Setting up python3-coloredlogs (15.0.1-1) ... 630s Setting up liblapack3:armhf (3.12.0-3build1) ... 630s 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 630s Setting up python3-pytest (7.4.4-1) ... 630s Setting up python3-numpy (1:1.26.4+ds-10) ... 632s Setting up python3-cyvcf2 (0.31.0-1) ... 633s Setting up autopkgtest-satdep (0) ... 633s Processing triggers for man-db (2.12.1-2) ... 633s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 648s (Reading database ... 59703 files and directories currently installed.) 648s Removing autopkgtest-satdep (0) ... 658s autopkgtest [15:58:08]: test run-unit-test: [----------------------- 670s Testing with python3.12 in /tmp/autopkgtest.YJxzsf/autopkgtest_tmp: 670s ============================= test session starts ============================== 670s platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.5.0 -- /usr/bin/python3.12 670s cachedir: .pytest_cache 670s rootdir: /tmp/autopkgtest.YJxzsf/autopkgtest_tmp 673s collecting ... collected 112 items 673s 673s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 673s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 673s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 673s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 673s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 673s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 674s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 674s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 674s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 674s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 674s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 674s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 674s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 674s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 674s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 674s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 674s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 674s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 674s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 674s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 674s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 674s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 674s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 674s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 674s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 674s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 674s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 674s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 674s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 674s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 674s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 674s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 674s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 674s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 674s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 674s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 674s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 674s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 675s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 675s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 675s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 675s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 675s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 675s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 675s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 675s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 675s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 675s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 675s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 675s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 675s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 675s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 675s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 675s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 675s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 675s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 675s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 675s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 675s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 675s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 675s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 675s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 675s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 676s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 676s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 676s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 676s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 676s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 676s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 676s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 676s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 676s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 676s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 676s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 676s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 676s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 676s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 676s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 676s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 676s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 676s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 676s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 676s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 676s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 676s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 676s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 676s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 676s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 676s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 676s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 676s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 676s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 676s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 676s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 676s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 676s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 676s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 676s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 676s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 676s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 676s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 676s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 676s 676s ============================= 112 passed in 6.11s ============================== 679s autopkgtest [15:58:29]: test run-unit-test: -----------------------] 685s run-unit-test PASS 685s autopkgtest [15:58:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 689s autopkgtest [15:58:39]: test autodep8-python3: preparing testbed 781s autopkgtest [16:00:11]: testbed dpkg architecture: armhf 784s autopkgtest [16:00:14]: testbed apt version: 2.9.6 784s autopkgtest [16:00:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 795s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 797s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 797s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [343 kB] 797s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [46.6 kB] 797s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 797s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [58.3 kB] 798s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf c-n-f Metadata [1444 B] 798s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf Packages [1368 B] 798s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf c-n-f Metadata [120 B] 798s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [303 kB] 798s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf c-n-f Metadata [6176 B] 798s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1448 B] 798s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf c-n-f Metadata [120 B] 801s Fetched 899 kB in 3s (303 kB/s) 801s Reading package lists... 818s tee: /proc/self/fd/2: Permission denied 847s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 847s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 847s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 847s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 850s Reading package lists... 850s Reading package lists... 850s Building dependency tree... 850s Reading state information... 851s Calculating upgrade... 851s The following packages will be upgraded: 851s inetutils-telnet libc-bin libc6 libssl3t64 locales openssh-client 851s openssh-server openssh-sftp-server openssl telnet 851s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 851s Need to get 11.9 MB of archives. 851s After this operation, 285 kB of additional disk space will be used. 851s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc6 armhf 2.39-3.1ubuntu3 [2825 kB] 852s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libc-bin armhf 2.39-3.1ubuntu3 [527 kB] 852s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libssl3t64 armhf 3.2.2-1ubuntu1 [1729 kB] 852s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-sftp-server armhf 1:9.6p1-3ubuntu17 [35.6 kB] 852s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-server armhf 1:9.6p1-3ubuntu17 [502 kB] 852s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf openssh-client armhf 1:9.6p1-3ubuntu17 [888 kB] 852s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf locales all 2.39-3.1ubuntu3 [4220 kB] 852s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf openssl armhf 3.2.2-1ubuntu1 [1095 kB] 852s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf inetutils-telnet armhf 2:2.5-5ubuntu1 [94.4 kB] 852s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf telnet all 0.17+2.5-5ubuntu1 [3688 B] 854s Preconfiguring packages ... 855s Fetched 11.9 MB in 1s (10.6 MB/s) 855s (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 ... 58437 files and directories currently installed.) 855s Preparing to unpack .../libc6_2.39-3.1ubuntu3_armhf.deb ... 856s Unpacking libc6:armhf (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 856s Setting up libc6:armhf (2.39-3.1ubuntu3) ... 856s Error: Could not restart systemd, systemd binary not working 856s (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 ... 58437 files and directories currently installed.) 856s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_armhf.deb ... 856s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 856s Setting up libc-bin (2.39-3.1ubuntu3) ... 857s (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 ... 58437 files and directories currently installed.) 857s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_armhf.deb ... 857s Unpacking libssl3t64:armhf (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 857s Setting up libssl3t64:armhf (3.2.2-1ubuntu1) ... 857s (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 ... 58437 files and directories currently installed.) 857s Preparing to unpack .../0-openssh-sftp-server_1%3a9.6p1-3ubuntu17_armhf.deb ... 857s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 858s Preparing to unpack .../1-openssh-server_1%3a9.6p1-3ubuntu17_armhf.deb ... 858s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 859s Preparing to unpack .../2-openssh-client_1%3a9.6p1-3ubuntu17_armhf.deb ... 859s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 860s Preparing to unpack .../3-locales_2.39-3.1ubuntu3_all.deb ... 860s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 861s Preparing to unpack .../4-openssl_3.2.2-1ubuntu1_armhf.deb ... 861s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 862s Preparing to unpack .../5-inetutils-telnet_2%3a2.5-5ubuntu1_armhf.deb ... 862s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ... 863s Preparing to unpack .../6-telnet_0.17+2.5-5ubuntu1_all.deb ... 863s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ... 863s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 863s Setting up inetutils-telnet (2:2.5-5ubuntu1) ... 863s Setting up locales (2.39-3.1ubuntu3) ... 867s Generating locales (this might take a while)... 874s en_US.UTF-8... done 874s Generation complete. 875s Setting up openssl (3.2.2-1ubuntu1) ... 875s Installing new version of config file /etc/ssl/openssl.cnf ... 875s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 875s Setting up telnet (0.17+2.5-5ubuntu1) ... 875s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 875s Installing new version of config file /etc/pam.d/sshd ... 878s Processing triggers for ufw (0.36.2-6) ... 879s Processing triggers for systemd (256-1ubuntu1) ... 881s Processing triggers for man-db (2.12.1-2) ... 882s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 883s Reading package lists... 883s Building dependency tree... 883s Reading state information... 884s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 886s autopkgtest [16:01:56]: rebooting testbed after setup commands that affected boot 1233s Reading package lists... 1234s Building dependency tree... 1234s Reading state information... 1234s Starting pkgProblemResolver with broken count: 0 1234s Starting 2 pkgProblemResolver with broken count: 0 1234s Done 1235s The following additional packages will be installed: 1235s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 1235s python3-all python3-click python3-colorama python3-coloredlogs 1235s python3-cyvcf2 python3-humanfriendly python3-numpy 1235s Suggested packages: 1235s gcc gfortran python-numpy-doc python3-dev python3-pytest 1236s The following NEW packages will be installed: 1236s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 1236s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 1236s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-numpy 1238s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 1238s Need to get 7603 kB/7604 kB of archives. 1238s After this operation, 28.4 MB of additional disk space will be used. 1238s Get:1 /tmp/autopkgtest.YJxzsf/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [712 B] 1238s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 1238s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate0 armhf 1.20-1 [38.3 kB] 1238s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-1ubuntu1 [311 kB] 1238s Get:5 http://ftpmaster.internal/ubuntu oracular/universe armhf libhtscodecs2 armhf 1.6.0-1build1 [65.8 kB] 1238s Get:6 http://ftpmaster.internal/ubuntu oracular/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 1238s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 1239s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf python3-all armhf 3.12.3-0ubuntu1 [886 B] 1239s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 1239s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf python3-click all 8.1.7-1 [79.1 kB] 1239s Get:11 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-humanfriendly all 10.0-5 [70.5 kB] 1239s Get:12 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-coloredlogs all 15.0.1-1 [38.2 kB] 1239s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf python3-numpy armhf 1:1.26.4+ds-10 [3541 kB] 1239s Get:14 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cyvcf2 armhf 0.31.0-1 [827 kB] 1266s Fetched 7603 kB in 3s (2658 kB/s) 1271s Selecting previously unselected package libblas3:armhf. 1271s (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 ... 58436 files and directories currently installed.) 1271s Preparing to unpack .../00-libblas3_3.12.0-3build1_armhf.deb ... 1271s Unpacking libblas3:armhf (3.12.0-3build1) ... 1273s Selecting previously unselected package libdeflate0:armhf. 1279s Preparing to unpack .../01-libdeflate0_1.20-1_armhf.deb ... 1279s Unpacking libdeflate0:armhf (1.20-1) ... 1281s Selecting previously unselected package libgfortran5:armhf. 1286s Preparing to unpack .../02-libgfortran5_14.1.0-1ubuntu1_armhf.deb ... 1286s Unpacking libgfortran5:armhf (14.1.0-1ubuntu1) ... 1293s Selecting previously unselected package libhtscodecs2:armhf. 1297s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_armhf.deb ... 1297s Unpacking libhtscodecs2:armhf (1.6.0-1build1) ... 1298s Selecting previously unselected package libhts3t64:armhf. 1301s Preparing to unpack .../04-libhts3t64_1.20+ds-1_armhf.deb ... 1301s Unpacking libhts3t64:armhf (1.20+ds-1) ... 1303s Selecting previously unselected package liblapack3:armhf. 1308s Preparing to unpack .../05-liblapack3_3.12.0-3build1_armhf.deb ... 1308s Unpacking liblapack3:armhf (3.12.0-3build1) ... 1309s Selecting previously unselected package python3-all. 1316s Preparing to unpack .../06-python3-all_3.12.3-0ubuntu1_armhf.deb ... 1316s Unpacking python3-all (3.12.3-0ubuntu1) ... 1316s Selecting previously unselected package python3-colorama. 1321s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 1321s Unpacking python3-colorama (0.4.6-4) ... 1323s Selecting previously unselected package python3-click. 1328s Preparing to unpack .../08-python3-click_8.1.7-1_all.deb ... 1328s Unpacking python3-click (8.1.7-1) ... 1330s Selecting previously unselected package python3-humanfriendly. 1333s Preparing to unpack .../09-python3-humanfriendly_10.0-5_all.deb ... 1333s Unpacking python3-humanfriendly (10.0-5) ... 1334s Selecting previously unselected package python3-coloredlogs. 1336s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 1336s Unpacking python3-coloredlogs (15.0.1-1) ... 1338s Selecting previously unselected package python3-numpy. 1340s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-10_armhf.deb ... 1340s Unpacking python3-numpy (1:1.26.4+ds-10) ... 1351s Selecting previously unselected package python3-cyvcf2. 1353s Preparing to unpack .../12-python3-cyvcf2_0.31.0-1_armhf.deb ... 1353s Unpacking python3-cyvcf2 (0.31.0-1) ... 1354s Selecting previously unselected package autopkgtest-satdep. 1356s Preparing to unpack .../13-2-autopkgtest-satdep.deb ... 1356s Unpacking autopkgtest-satdep (0) ... 1357s Setting up libhtscodecs2:armhf (1.6.0-1build1) ... 1357s Setting up python3-colorama (0.4.6-4) ... 1366s Setting up libdeflate0:armhf (1.20-1) ... 1366s Setting up python3-all (3.12.3-0ubuntu1) ... 1366s Setting up python3-click (8.1.7-1) ... 1369s Setting up libblas3:armhf (3.12.0-3build1) ... 1369s 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 1369s Setting up python3-humanfriendly (10.0-5) ... 1371s Setting up libgfortran5:armhf (14.1.0-1ubuntu1) ... 1371s Setting up libhts3t64:armhf (1.20+ds-1) ... 1371s Setting up python3-coloredlogs (15.0.1-1) ... 1372s Setting up liblapack3:armhf (3.12.0-3build1) ... 1372s 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 1372s Setting up python3-numpy (1:1.26.4+ds-10) ... 1377s Setting up python3-cyvcf2 (0.31.0-1) ... 1383s Setting up autopkgtest-satdep (0) ... 1383s Processing triggers for man-db (2.12.1-2) ... 1385s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 1425s (Reading database ... 59539 files and directories currently installed.) 1425s Removing autopkgtest-satdep (0) ... 1455s autopkgtest [16:11:25]: 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 1455s autopkgtest [16:11:25]: test autodep8-python3: [----------------------- 1463s Testing with python3.12: 1465s 1466s autopkgtest [16:11:36]: test autodep8-python3: -----------------------] 1473s autopkgtest [16:11:43]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 1473s autodep8-python3 PASS (superficial) 1478s autopkgtest [16:11:48]: @@@@@@@@@@@@@@@@@@@@ summary 1478s run-unit-test PASS 1478s autodep8-python3 PASS (superficial)