0s autopkgtest [20:41:23]: starting date and time: 2024-11-23 20:41:23+0000 0s autopkgtest [20:41:23]: git checkout: 6408f825 Correct logic in old-systemd fallback code 0s autopkgtest [20:41:23]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.89vgrpzv/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:python3-defaults --apt-upgrade pyfastx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 -- lxd -r lxd-armhf-10.145.243.142 lxd-armhf-10.145.243.142:autopkgtest/ubuntu/plucky/armhf 53s autopkgtest [20:42:16]: testbed dpkg architecture: armhf 55s autopkgtest [20:42:18]: testbed apt version: 2.9.8 55s autopkgtest [20:42:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 64s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9704 B] 64s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [925 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [53.2 kB] 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.6 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [61.7 kB] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [756 B] 64s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [721 kB] 64s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [5924 B] 64s Fetched 1865 kB in 1s (1940 kB/s) 65s Reading package lists... 84s tee: /proc/self/fd/2: Permission denied 106s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 106s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 106s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 106s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 107s Reading package lists... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s Calculating upgrade... 108s The following packages will be upgraded: 108s bash debconf debconf-i18n dracut-install libpython3-stdlib pinentry-curses 108s python3 python3-blinker python3-debconf python3-minimal vim-common vim-tiny 108s xxd 108s 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 2311 kB of archives. 108s After this operation, 4096 B of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf bash armhf 5.2.32-1ubuntu2 [673 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 109s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 109s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 109s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf debconf-i18n all 1.5.87ubuntu1 [204 kB] 109s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-debconf all 1.5.87ubuntu1 [4156 B] 109s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf debconf all 1.5.87ubuntu1 [124 kB] 109s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0861-1ubuntu1 [694 kB] 109s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0861-1ubuntu1 [395 kB] 109s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0861-1ubuntu1 [67.0 kB] 109s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf dracut-install armhf 105-2ubuntu2 [37.5 kB] 109s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-0ubuntu2 [40.0 kB] 109s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf python3-blinker all 1.9.0-1 [10.7 kB] 109s Preconfiguring packages ... 109s Fetched 2311 kB in 1s (3459 kB/s) 109s (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 ... 59616 files and directories currently installed.) 109s Preparing to unpack .../bash_5.2.32-1ubuntu2_armhf.deb ... 109s Unpacking bash (5.2.32-1ubuntu2) over (5.2.32-1ubuntu1) ... 110s Setting up bash (5.2.32-1ubuntu2) ... 110s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 110s (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 ... 59616 files and directories currently installed.) 110s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 110s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Setting up python3-minimal (3.12.7-1) ... 110s (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 ... 59616 files and directories currently installed.) 110s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 110s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 110s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Preparing to unpack .../debconf-i18n_1.5.87ubuntu1_all.deb ... 110s Unpacking debconf-i18n (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 110s Preparing to unpack .../python3-debconf_1.5.87ubuntu1_all.deb ... 110s Unpacking python3-debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 110s Preparing to unpack .../debconf_1.5.87ubuntu1_all.deb ... 110s Unpacking debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 110s Setting up debconf (1.5.87ubuntu1) ... 111s (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 ... 59616 files and directories currently installed.) 111s Preparing to unpack .../0-vim-tiny_2%3a9.1.0861-1ubuntu1_armhf.deb ... 111s Unpacking vim-tiny (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 111s Preparing to unpack .../1-vim-common_2%3a9.1.0861-1ubuntu1_all.deb ... 111s Unpacking vim-common (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 111s Preparing to unpack .../2-xxd_2%3a9.1.0861-1ubuntu1_armhf.deb ... 111s Unpacking xxd (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 111s Preparing to unpack .../3-dracut-install_105-2ubuntu2_armhf.deb ... 111s Unpacking dracut-install (105-2ubuntu2) over (105-1ubuntu1) ... 111s Preparing to unpack .../4-pinentry-curses_1.3.1-0ubuntu2_armhf.deb ... 111s Unpacking pinentry-curses (1.3.1-0ubuntu2) over (1.2.1-3ubuntu5) ... 111s Preparing to unpack .../5-python3-blinker_1.9.0-1_all.deb ... 111s Unpacking python3-blinker (1.9.0-1) over (1.8.2-1) ... 111s Setting up pinentry-curses (1.3.1-0ubuntu2) ... 111s Setting up debconf-i18n (1.5.87ubuntu1) ... 111s Setting up xxd (2:9.1.0861-1ubuntu1) ... 111s Setting up vim-common (2:9.1.0861-1ubuntu1) ... 111s Setting up dracut-install (105-2ubuntu2) ... 111s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 111s Setting up python3 (3.12.7-1) ... 111s Setting up vim-tiny (2:9.1.0861-1ubuntu1) ... 111s Setting up python3-blinker (1.9.0-1) ... 111s Setting up python3-debconf (1.5.87ubuntu1) ... 111s Processing triggers for debianutils (5.21) ... 112s Processing triggers for install-info (7.1.1-1) ... 112s Processing triggers for man-db (2.13.0-1) ... 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s autopkgtest [20:43:19]: rebooting testbed after setup commands that affected boot 185s autopkgtest [20:44:28]: testbed running kernel: Linux 6.8.0-49-generic #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 6 18:12:14 UTC 2 212s autopkgtest [20:44:55]: @@@@@@@@@@@@@@@@@@@@ apt-source pyfastx 226s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (dsc) [2289 B] 226s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (tar) [230 kB] 226s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyfastx 2.1.0-2 (diff) [7412 B] 226s gpgv: Signature made Fri Aug 30 18:49:12 2024 UTC 226s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 226s gpgv: issuer "emollier@debian.org" 226s gpgv: Can't check signature: No public key 226s dpkg-source: warning: cannot verify inline signature for ./pyfastx_2.1.0-2.dsc: no acceptable signature found 226s autopkgtest [20:45:09]: testing package pyfastx version 2.1.0-2 228s autopkgtest [20:45:11]: build not needed 230s autopkgtest [20:45:13]: test run-unit-test: preparing testbed 241s Reading package lists... 241s Building dependency tree... 241s Reading state information... 242s Starting pkgProblemResolver with broken count: 0 242s Starting 2 pkgProblemResolver with broken count: 0 242s Done 242s The following additional packages will be installed: 242s libpython3.13-minimal libpython3.13-stdlib pyfastx python3-all 242s python3-importlib-metadata python3-packaging python3-pyfaidx python3-pyfastx 242s python3.13 python3.13-minimal 242s Suggested packages: 242s python3.13-venv python3.13-doc binfmt-support 242s Recommended packages: 242s python3-biopython 242s The following NEW packages will be installed: 242s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib pyfastx 242s python3-all python3-importlib-metadata python3-packaging python3-pyfaidx 242s python3-pyfastx python3.13 python3.13-minimal 243s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 243s Need to get 5688 kB/5689 kB of archives. 243s After this operation, 19.8 MB of additional disk space will be used. 243s Get:1 /tmp/autopkgtest.z6pyp3/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [712 B] 243s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 243s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 243s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 243s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-importlib-metadata all 8.5.0-1 [20.7 kB] 243s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.2-1 [51.5 kB] 243s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 243s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyfastx armhf 2.1.0-2 [52.7 kB] 243s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf pyfastx armhf 2.1.0-2 [122 kB] 243s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 243s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 244s Fetched 5688 kB in 1s (7078 kB/s) 244s Selecting previously unselected package libpython3.13-minimal:armhf. 244s (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 ... 59616 files and directories currently installed.) 244s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_armhf.deb ... 244s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 244s Selecting previously unselected package python3.13-minimal. 244s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_armhf.deb ... 244s Unpacking python3.13-minimal (3.13.0-2) ... 244s Selecting previously unselected package libpython3.13-stdlib:armhf. 244s Preparing to unpack .../02-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 244s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 244s Selecting previously unselected package python3-importlib-metadata. 244s Preparing to unpack .../03-python3-importlib-metadata_8.5.0-1_all.deb ... 244s Unpacking python3-importlib-metadata (8.5.0-1) ... 244s Selecting previously unselected package python3-packaging. 244s Preparing to unpack .../04-python3-packaging_24.2-1_all.deb ... 244s Unpacking python3-packaging (24.2-1) ... 244s Selecting previously unselected package python3-pyfaidx. 244s Preparing to unpack .../05-python3-pyfaidx_0.8.1.3-1_all.deb ... 244s Unpacking python3-pyfaidx (0.8.1.3-1) ... 244s Selecting previously unselected package python3-pyfastx. 244s Preparing to unpack .../06-python3-pyfastx_2.1.0-2_armhf.deb ... 244s Unpacking python3-pyfastx (2.1.0-2) ... 244s Selecting previously unselected package pyfastx. 244s Preparing to unpack .../07-pyfastx_2.1.0-2_armhf.deb ... 244s Unpacking pyfastx (2.1.0-2) ... 244s Selecting previously unselected package python3.13. 244s Preparing to unpack .../08-python3.13_3.13.0-2_armhf.deb ... 244s Unpacking python3.13 (3.13.0-2) ... 244s Selecting previously unselected package python3-all. 244s Preparing to unpack .../09-python3-all_3.12.7-1_armhf.deb ... 244s Unpacking python3-all (3.12.7-1) ... 244s Selecting previously unselected package autopkgtest-satdep. 244s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 244s Unpacking autopkgtest-satdep (0) ... 244s Setting up python3-importlib-metadata (8.5.0-1) ... 245s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 245s Setting up python3-packaging (24.2-1) ... 245s Setting up python3.13-minimal (3.13.0-2) ... 246s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 246s Setting up python3-pyfaidx (0.8.1.3-1) ... 246s Setting up python3.13 (3.13.0-2) ... 247s Setting up python3-pyfastx (2.1.0-2) ... 247s Setting up python3-all (3.12.7-1) ... 247s Setting up pyfastx (2.1.0-2) ... 247s Setting up autopkgtest-satdep (0) ... 247s Processing triggers for man-db (2.13.0-1) ... 247s Processing triggers for systemd (256.5-2ubuntu4) ... 261s (Reading database ... 60451 files and directories currently installed.) 261s Removing autopkgtest-satdep (0) ... 267s autopkgtest [20:45:50]: test run-unit-test: [----------------------- 269s tests.test_fakeys (unittest.loader._FailedTest.tests.test_fakeys) ... ERROR 269s tests.test_fasta (unittest.loader._FailedTest.tests.test_fasta) ... ERROR 269s tests.test_fastq (unittest.loader._FailedTest.tests.test_fastq) ... ERROR 269s tests.test_fastx (unittest.loader._FailedTest.tests.test_fastx) ... ERROR 269s tests.test_fqkeys (unittest.loader._FailedTest.tests.test_fqkeys) ... ERROR 269s tests.test_read (unittest.loader._FailedTest.tests.test_read) ... ERROR 269s tests.test_sequence (unittest.loader._FailedTest.tests.test_sequence) ... ERROR 270s autopkgtest [20:45:53]: test run-unit-test: -----------------------] 274s run-unit-test FAIL non-zero exit status 1 274s autopkgtest [20:45:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 277s autopkgtest [20:46:00]: test test-cli: preparing testbed 331s autopkgtest [20:46:54]: testbed dpkg architecture: armhf 333s autopkgtest [20:46:56]: testbed apt version: 2.9.8 333s autopkgtest [20:46:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 341s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 341s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9704 B] 341s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [53.2 kB] 341s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [925 kB] 342s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.6 kB] 342s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [61.7 kB] 342s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [756 B] 342s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [721 kB] 342s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [5924 B] 342s Fetched 1865 kB in 2s (1183 kB/s) 342s Reading package lists... 358s tee: /proc/self/fd/2: Permission denied 382s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 382s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 382s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 382s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 383s Reading package lists... 383s Reading package lists... 384s Building dependency tree... 384s Reading state information... 384s Calculating upgrade... 385s The following packages will be upgraded: 385s bash debconf debconf-i18n dracut-install libpython3-stdlib pinentry-curses 385s python3 python3-blinker python3-debconf python3-minimal vim-common vim-tiny 385s xxd 385s 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 385s Need to get 2311 kB of archives. 385s After this operation, 4096 B of additional disk space will be used. 385s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf bash armhf 5.2.32-1ubuntu2 [673 kB] 385s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 385s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 385s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 385s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf debconf-i18n all 1.5.87ubuntu1 [204 kB] 385s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-debconf all 1.5.87ubuntu1 [4156 B] 385s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf debconf all 1.5.87ubuntu1 [124 kB] 385s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0861-1ubuntu1 [694 kB] 385s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0861-1ubuntu1 [395 kB] 385s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0861-1ubuntu1 [67.0 kB] 385s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf dracut-install armhf 105-2ubuntu2 [37.5 kB] 385s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-0ubuntu2 [40.0 kB] 385s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf python3-blinker all 1.9.0-1 [10.7 kB] 386s Preconfiguring packages ... 386s Fetched 2311 kB in 1s (3485 kB/s) 386s (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 ... 59616 files and directories currently installed.) 386s Preparing to unpack .../bash_5.2.32-1ubuntu2_armhf.deb ... 386s Unpacking bash (5.2.32-1ubuntu2) over (5.2.32-1ubuntu1) ... 386s Setting up bash (5.2.32-1ubuntu2) ... 386s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 386s (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 ... 59616 files and directories currently installed.) 386s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 386s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 386s Setting up python3-minimal (3.12.7-1) ... 386s (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 ... 59616 files and directories currently installed.) 386s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 386s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 386s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 386s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 386s Preparing to unpack .../debconf-i18n_1.5.87ubuntu1_all.deb ... 386s Unpacking debconf-i18n (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 386s Preparing to unpack .../python3-debconf_1.5.87ubuntu1_all.deb ... 386s Unpacking python3-debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 386s Preparing to unpack .../debconf_1.5.87ubuntu1_all.deb ... 386s Unpacking debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 386s Setting up debconf (1.5.87ubuntu1) ... 387s (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 ... 59616 files and directories currently installed.) 387s Preparing to unpack .../0-vim-tiny_2%3a9.1.0861-1ubuntu1_armhf.deb ... 387s Unpacking vim-tiny (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 387s Preparing to unpack .../1-vim-common_2%3a9.1.0861-1ubuntu1_all.deb ... 387s Unpacking vim-common (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 387s Preparing to unpack .../2-xxd_2%3a9.1.0861-1ubuntu1_armhf.deb ... 387s Unpacking xxd (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 387s Preparing to unpack .../3-dracut-install_105-2ubuntu2_armhf.deb ... 387s Unpacking dracut-install (105-2ubuntu2) over (105-1ubuntu1) ... 387s Preparing to unpack .../4-pinentry-curses_1.3.1-0ubuntu2_armhf.deb ... 387s Unpacking pinentry-curses (1.3.1-0ubuntu2) over (1.2.1-3ubuntu5) ... 387s Preparing to unpack .../5-python3-blinker_1.9.0-1_all.deb ... 387s Unpacking python3-blinker (1.9.0-1) over (1.8.2-1) ... 387s Setting up pinentry-curses (1.3.1-0ubuntu2) ... 387s Setting up debconf-i18n (1.5.87ubuntu1) ... 387s Setting up xxd (2:9.1.0861-1ubuntu1) ... 387s Setting up vim-common (2:9.1.0861-1ubuntu1) ... 387s Setting up dracut-install (105-2ubuntu2) ... 387s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 387s Setting up python3 (3.12.7-1) ... 387s Setting up vim-tiny (2:9.1.0861-1ubuntu1) ... 387s Setting up python3-blinker (1.9.0-1) ... 387s Setting up python3-debconf (1.5.87ubuntu1) ... 388s Processing triggers for debianutils (5.21) ... 388s Processing triggers for install-info (7.1.1-1) ... 388s Processing triggers for man-db (2.13.0-1) ... 389s Reading package lists... 389s Building dependency tree... 389s Reading state information... 390s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 392s autopkgtest [20:47:55]: rebooting testbed after setup commands that affected boot 499s Reading package lists... 500s Building dependency tree... 500s Reading state information... 500s Starting pkgProblemResolver with broken count: 0 500s Starting 2 pkgProblemResolver with broken count: 0 500s Done 501s The following additional packages will be installed: 501s pyfastx python3-importlib-metadata python3-packaging python3-pyfaidx 501s python3-pyfastx 501s Recommended packages: 501s python3-biopython 501s The following NEW packages will be installed: 501s autopkgtest-satdep pyfastx python3-importlib-metadata python3-packaging 501s python3-pyfaidx python3-pyfastx 501s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 501s Need to get 276 kB/277 kB of archives. 501s After this operation, 766 kB of additional disk space will be used. 501s Get:1 /tmp/autopkgtest.z6pyp3/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [716 B] 501s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf python3-importlib-metadata all 8.5.0-1 [20.7 kB] 502s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.2-1 [51.5 kB] 502s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 502s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyfastx armhf 2.1.0-2 [52.7 kB] 502s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf pyfastx armhf 2.1.0-2 [122 kB] 502s Fetched 276 kB in 0s (573 kB/s) 502s Selecting previously unselected package python3-importlib-metadata. 502s (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 ... 59616 files and directories currently installed.) 502s Preparing to unpack .../0-python3-importlib-metadata_8.5.0-1_all.deb ... 502s Unpacking python3-importlib-metadata (8.5.0-1) ... 502s Selecting previously unselected package python3-packaging. 502s Preparing to unpack .../1-python3-packaging_24.2-1_all.deb ... 502s Unpacking python3-packaging (24.2-1) ... 502s Selecting previously unselected package python3-pyfaidx. 502s Preparing to unpack .../2-python3-pyfaidx_0.8.1.3-1_all.deb ... 502s Unpacking python3-pyfaidx (0.8.1.3-1) ... 502s Selecting previously unselected package python3-pyfastx. 502s Preparing to unpack .../3-python3-pyfastx_2.1.0-2_armhf.deb ... 502s Unpacking python3-pyfastx (2.1.0-2) ... 502s Selecting previously unselected package pyfastx. 502s Preparing to unpack .../4-pyfastx_2.1.0-2_armhf.deb ... 502s Unpacking pyfastx (2.1.0-2) ... 502s Selecting previously unselected package autopkgtest-satdep. 502s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 502s Unpacking autopkgtest-satdep (0) ... 502s Setting up python3-importlib-metadata (8.5.0-1) ... 502s Setting up python3-packaging (24.2-1) ... 503s Setting up python3-pyfaidx (0.8.1.3-1) ... 503s Setting up python3-pyfastx (2.1.0-2) ... 503s Setting up pyfastx (2.1.0-2) ... 503s Setting up autopkgtest-satdep (0) ... 503s Processing triggers for man-db (2.13.0-1) ... 520s (Reading database ... 59716 files and directories currently installed.) 520s Removing autopkgtest-satdep (0) ... 532s autopkgtest [20:50:15]: test test-cli: [----------------------- 534s $ pyfastx --help 534s usage: pyfastx COMMAND [OPTIONS] 534s 534s A command line tool for FASTA/Q file manipulation 534s 534s options: 534s -h, --help show this help message and exit 534s -v, --version show program's version number and exit 534s 534s Commands: 534s 534s index build index for fasta/q file 534s stat show detailed statistics information of fasta/q file 534s split split fasta/q file into multiple files 534s fq2fa convert fastq file to fasta file 534s subseq get subsequences from fasta file by region 534s sample randomly sample sequences from fasta or fastq file 534s extract extract full sequences or reads from fasta/q file 534s $ # Found pyfastx commands: 'index stat split fq2fa subseq sample extract' 534s $ pyfastx index --help 534s usage: pyfastx index [-h] [-f] fastx [fastx ...] 534s 534s positional arguments: 534s fastx fasta or fastq file, gzip support 534s 534s options: 534s -h, --help show this help message and exit 534s -f, --full build full index, base composition will be calculated 534s $ pyfastx stat --help 535s usage: pyfastx stat [-h] fastx [fastx ...] 535s 535s positional arguments: 535s fastx fasta or fastq file, gzip support 535s 535s options: 535s -h, --help show this help message and exit 535s $ pyfastx split --help 535s usage: pyfastx split [-h] (-n int | -c int) [-o str] fastx 535s 535s positional arguments: 535s fastx fasta or fastq file, gzip support 535s 535s options: 535s -h, --help show this help message and exit 535s -n int split a fasta/q file into N new files with even size 535s -c int split a fasta/q file into multiple files containing 535s the same sequence counts 535s -o str, --out-dir str 535s output directory, default is current folder 535s $ pyfastx fq2fa --help 535s usage: pyfastx fq2fa [-h] [-o str] fastx 535s 535s positional arguments: 535s fastx fastq file, gzip support 535s 535s options: 535s -h, --help show this help message and exit 535s -o str, --out-file str 535s output file, default: output to stdout 535s $ pyfastx subseq --help 535s usage: pyfastx subseq [-h] [-r str | -b str] [-o str] fastx [region ...] 535s 535s positional arguments: 535s fastx input fasta file, gzip support 535s region format is chr:start-end, start and end position is 535s 1-based, multiple regions were separated by space 535s 535s options: 535s -h, --help show this help message and exit 535s -r str, --region-file str 535s tab-delimited file, one region per line, both start 535s and end position are 1-based 535s -b str, --bed-file str 535s tab-delimited BED file, 0-based start position and 535s 1-based end position 535s -o str, --out-file str 535s output file, default: output to stdout 535s $ pyfastx sample --help 535s usage: pyfastx sample [-h] (-n int | -p float) [-s int] [--sequential-read] 535s [-o str] 535s fastx 535s 535s positional arguments: 535s fastx fasta or fastq file, gzip support 535s 535s options: 535s -h, --help show this help message and exit 535s -n int number of sequences to be sampled 535s -p float proportion of sequences to be sampled, 0~1 535s -s int, --seed int random seed, default is the current system time 535s --sequential-read start sequential reading, particularly suitable for 535s sampling large numbers of sequences 535s -o str, --out-file str 535s output file, default: output to stdout 535s $ pyfastx extract --help 535s usage: pyfastx extract [-h] [-l str] [--reverse-complement] [--out-fasta] 535s [-o str] [--sequential-read] 535s fastx [name ...] 535s 535s positional arguments: 535s fastx fasta or fastq file, gzip support 535s name sequence name or read name, multiple names were 535s separated by space 535s 535s options: 535s -h, --help show this help message and exit 535s -l str, --list-file str 535s a file containing sequence or read names, one name per 535s line 535s --reverse-complement output reverse complement sequence 535s --out-fasta output fasta format when extract reads from fastq, 535s default output fastq format 535s -o str, --out-file str 535s output file, default: output to stdout 535s --sequential-read start sequential reading, particularly suitable for 535s extracting large numbers of sequences 535s $ pyfastx --version 535s pyfastx version 2.1.0 535s $ pyfastx index protein.fa 535s $ pyfastx index rna.fa 535s $ pyfastx index test.fa 536s $ pyfastx index test.fq 536s $ pyfastx index test.fa.gz 536s $ pyfastx index test.fq.gz 536s $ pyfastx stat protein.fa 536s fileName seqType seqCounts totalBases GC% avgLen medianLen maxLen minLen N50 L50 536s protein.fa protein 17 2265 - 133.235 80.0 419 23 263 4 536s $ pyfastx split -n 2 protein.fa 536s $ pyfastx fq2fa test.fq -o test.fa 536s $ pyfastx subseq protein.fa UPI0000000011:1-4 537s >UPI0000000011:1-4 537s MVDA 537s $ pyfastx sample -n 1 test.fq.gz -o sample.fq 537s $ pyfastx extract protein.fa UPI0000000011 537s >UPI0000000011 status=active 537s MVDAITVLTAIGITVLMLLMVISGAAMIVKELNPNDIFTMQSLKFNRAVTIFKYIGLFIY 537s IPGTIILYATYVKSLLMKS 537s autopkgtest [20:50:20]: test test-cli: -----------------------] 541s autopkgtest [20:50:24]: test test-cli: - - - - - - - - - - results - - - - - - - - - - 541s test-cli PASS 545s autopkgtest [20:50:28]: @@@@@@@@@@@@@@@@@@@@ summary 545s run-unit-test FAIL non-zero exit status 1 545s test-cli PASS