0s autopkgtest [09:16:29]: starting date and time: 2025-01-17 09:16:29+0000 0s autopkgtest [09:16:29]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [09:16:29]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lfb5k6ah/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade python-gffutils --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.13.1-1~exp2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-27.secgroup --name adt-plucky-amd64-python-gffutils-20250117-091629-juju-7f2275-prod-proposed-migration-environment-15-b0b16473-5137-4200-9d96-e5b3498ac23c --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 52s autopkgtest [09:17:21]: testbed dpkg architecture: amd64 52s autopkgtest [09:17:21]: testbed apt version: 2.9.18 52s autopkgtest [09:17:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 52s autopkgtest [09:17:21]: testbed release detected to be: None 53s autopkgtest [09:17:22]: updating testbed package index (apt update) 54s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 54s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 54s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 54s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.0 kB] 54s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [886 kB] 54s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [171 kB] 54s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [327 kB] 54s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [223 kB] 54s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 54s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 54s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [461 kB] 54s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1080 kB] 54s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [27.1 kB] 54s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [7684 B] 54s Fetched 3326 kB in 1s (3295 kB/s) 55s Reading package lists... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s The following packages will be upgraded: 56s libgudev-1.0-0 usb.ids 56s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Need to get 239 kB of archives. 56s After this operation, 0 B of additional disk space will be used. 56s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 usb.ids all 2025.01.14-1 [223 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgudev-1.0-0 amd64 1:238-6 [15.8 kB] 57s Fetched 239 kB in 0s (505 kB/s) 57s (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 ... 75824 files and directories currently installed.) 57s Preparing to unpack .../usb.ids_2025.01.14-1_all.deb ... 57s Unpacking usb.ids (2025.01.14-1) over (2024.12.04-1) ... 57s Preparing to unpack .../libgudev-1.0-0_1%3a238-6_amd64.deb ... 57s Unpacking libgudev-1.0-0:amd64 (1:238-6) over (1:238-5ubuntu1) ... 57s Setting up usb.ids (2025.01.14-1) ... 57s Setting up libgudev-1.0-0:amd64 (1:238-6) ... 57s Processing triggers for libc-bin (2.40-4ubuntu1) ... 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 58s autopkgtest [09:17:27]: upgrading testbed (apt dist-upgrade and autopurge) 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 59s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 59s Starting 2 pkgProblemResolver with broken count: 0 59s Done 59s Entering ResolveByKeep 59s 59s The following packages were automatically installed and are no longer required: 59s python3.12 python3.12-minimal 59s Use 'sudo apt autoremove' to remove them. 59s The following NEW packages will be installed: 59s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 59s The following packages will be upgraded: 59s libpython3-stdlib python3 python3-minimal 59s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 59s Need to get 6118 kB of archives. 59s After this operation, 22.7 MB of additional disk space will be used. 59s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.1-2 [881 kB] 60s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.1-2 [2358 kB] 60s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.13.1-1~exp2 [27.6 kB] 60s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.13.1-1~exp2 [23.9 kB] 60s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.1-2 [2088 kB] 60s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.1-2 [729 kB] 60s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.13.1-1~exp2 [10.2 kB] 60s Fetched 6118 kB in 1s (7327 kB/s) 60s Selecting previously unselected package libpython3.13-minimal:amd64. 60s (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 ... 75824 files and directories currently installed.) 60s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_amd64.deb ... 60s Unpacking libpython3.13-minimal:amd64 (3.13.1-2) ... 60s Selecting previously unselected package python3.13-minimal. 60s Preparing to unpack .../python3.13-minimal_3.13.1-2_amd64.deb ... 60s Unpacking python3.13-minimal (3.13.1-2) ... 60s Setting up libpython3.13-minimal:amd64 (3.13.1-2) ... 60s Setting up python3.13-minimal (3.13.1-2) ... 61s (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 ... 76144 files and directories currently installed.) 61s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_amd64.deb ... 61s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 61s Setting up python3-minimal (3.13.1-1~exp2) ... 61s (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 ... 76144 files and directories currently installed.) 61s Preparing to unpack .../python3_3.13.1-1~exp2_amd64.deb ... 61s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 61s Selecting previously unselected package libpython3.13-stdlib:amd64. 61s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_amd64.deb ... 61s Unpacking libpython3.13-stdlib:amd64 (3.13.1-2) ... 61s Selecting previously unselected package python3.13. 61s Preparing to unpack .../python3.13_3.13.1-2_amd64.deb ... 61s Unpacking python3.13 (3.13.1-2) ... 61s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_amd64.deb ... 61s Unpacking libpython3-stdlib:amd64 (3.13.1-1~exp2) over (3.12.8-1) ... 61s Setting up libpython3.13-stdlib:amd64 (3.13.1-2) ... 61s Setting up libpython3-stdlib:amd64 (3.13.1-1~exp2) ... 61s Setting up python3.13 (3.13.1-2) ... 62s Setting up python3 (3.13.1-1~exp2) ... 62s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 62s for fn in glob1(directory, "%s.*" % fname): 62s Processing triggers for man-db (2.13.0-1) ... 63s Processing triggers for systemd (257-2ubuntu1) ... 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 64s Starting pkgProblemResolver with broken count: 0 64s Starting 2 pkgProblemResolver with broken count: 0 64s Done 64s The following packages will be REMOVED: 64s python3.12* python3.12-minimal* 64s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 64s After this operation, 8926 kB disk space will be freed. 64s (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 ... 76561 files and directories currently installed.) 64s Removing python3.12 (3.12.8-3) ... 64s Removing python3.12-minimal (3.12.8-3) ... 64s /usr/bin/py3clean:125: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 64s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 65s Processing triggers for man-db (2.13.0-1) ... 65s Processing triggers for systemd (257-2ubuntu1) ... 65s (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 ... 76533 files and directories currently installed.) 65s Purging configuration files for python3.12-minimal (3.12.8-3) ... 68s autopkgtest [09:17:37]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 68s autopkgtest [09:17:37]: @@@@@@@@@@@@@@@@@@@@ apt-source python-gffutils 70s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-gffutils 0.13-1 (dsc) [2351 B] 70s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-gffutils 0.13-1 (tar) [1560 kB] 70s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-gffutils 0.13-1 (diff) [5024 B] 70s gpgv: Signature made Sat Apr 13 20:25:45 2024 UTC 70s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 70s gpgv: issuer "tchet@debian.org" 70s gpgv: Can't check signature: No public key 70s dpkg-source: warning: cannot verify inline signature for ./python-gffutils_0.13-1.dsc: no acceptable signature found 70s autopkgtest [09:17:39]: testing package python-gffutils version 0.13-1 70s autopkgtest [09:17:39]: build not needed 71s autopkgtest [09:17:40]: test run-unit-test: preparing testbed 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 72s Starting pkgProblemResolver with broken count: 0 72s Starting 2 pkgProblemResolver with broken count: 0 72s Done 72s The following NEW packages will be installed: 72s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 72s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 72s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 72s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 72s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 72s libxcb-shm0 libxrender1 python3-argcomplete python3-argh python3-biopython 72s python3-cairo python3-freetype python3-gffutils python3-importlib-metadata 72s python3-iniconfig python3-numpy python3-packaging python3-pil python3-pluggy 72s python3-pyfaidx python3-pytest python3-reportlab python3-rlpycairo 72s python3-simplejson sgml-base w3c-sgml-lib x11-common xfonts-encodings 72s xfonts-utils xml-core 72s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 31.8 MB of archives. 72s After this operation, 120 MB of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 72s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 73s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 73s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 73s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 73s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 73s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 74s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 74s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 74s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 74s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 74s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 74s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 74s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 74s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 74s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 74s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-12ubuntu1 [909 kB] 74s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-12ubuntu1 [148 kB] 74s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 74s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.1.0-1 [541 kB] 74s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 74s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 74s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 74s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 75s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 75s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 75s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 75s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 75s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 75s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 75s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 75s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 75s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 75s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-argcomplete all 3.5.3-1 [35.6 kB] 75s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [5319 kB] 75s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu2 [217 kB] 75s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu2 [580 kB] 75s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build1 [143 kB] 75s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 75s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 75s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 75s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 75s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 75s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB] 76s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-argh all 0.31.3-1 [27.0 kB] 76s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 76s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 76s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 76s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-simplejson amd64 3.19.3-1build1 [59.3 kB] 76s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-gffutils all 0.13-1 [1081 kB] 76s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 76s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 76s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 76s Fetched 31.8 MB in 4s (8619 kB/s) 76s Selecting previously unselected package sgml-base. 76s (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 ... 76533 files and directories currently installed.) 76s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 76s Unpacking sgml-base (1.31) ... 76s Selecting previously unselected package fonts-dejavu-mono. 76s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 76s Unpacking fonts-dejavu-mono (2.37-8) ... 76s Selecting previously unselected package fonts-dejavu-core. 76s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 76s Unpacking fonts-dejavu-core (2.37-8) ... 76s Selecting previously unselected package libfontenc1:amd64. 76s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 76s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 76s Selecting previously unselected package x11-common. 76s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 76s Unpacking x11-common (1:7.7+23ubuntu3) ... 76s Selecting previously unselected package xfonts-encodings. 76s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 76s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 76s Selecting previously unselected package xfonts-utils. 76s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_amd64.deb ... 76s Unpacking xfonts-utils (1:7.7+7) ... 76s Selecting previously unselected package fonts-urw-base35. 76s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 76s Unpacking fonts-urw-base35 (20200910-8) ... 77s Selecting previously unselected package fontconfig-config. 77s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 77s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 77s Selecting previously unselected package libblas3:amd64. 77s Preparing to unpack .../09-libblas3_3.12.0-4_amd64.deb ... 77s Unpacking libblas3:amd64 (3.12.0-4) ... 77s Selecting previously unselected package libfontconfig1:amd64. 77s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 77s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 77s Selecting previously unselected package libpixman-1-0:amd64. 77s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_amd64.deb ... 77s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 77s Selecting previously unselected package libxcb-render0:amd64. 77s Preparing to unpack .../12-libxcb-render0_1.17.0-2_amd64.deb ... 77s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 77s Selecting previously unselected package libxcb-shm0:amd64. 77s Preparing to unpack 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unselected package liblapack3:amd64. 77s Preparing to unpack .../24-liblapack3_3.12.0-4_amd64.deb ... 77s Unpacking liblapack3:amd64 (3.12.0-4) ... 77s Selecting previously unselected package liblcms2-2:amd64. 77s Preparing to unpack .../25-liblcms2-2_2.16-2_amd64.deb ... 77s Unpacking liblcms2-2:amd64 (2.16-2) ... 77s Selecting previously unselected package liblerc4:amd64. 77s Preparing to unpack .../26-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 77s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 77s Selecting previously unselected package libraqm0:amd64. 77s Preparing to unpack .../27-libraqm0_0.10.2-1_amd64.deb ... 77s Unpacking libraqm0:amd64 (0.10.2-1) ... 77s Selecting previously unselected package libsharpyuv0:amd64. 77s Preparing to unpack .../28-libsharpyuv0_1.4.0-0.1_amd64.deb ... 77s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 77s Selecting previously unselected package libjbig0:amd64. 77s Preparing to unpack .../29-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 77s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 77s Selecting previously unselected package libwebp7:amd64. 77s Preparing to unpack .../30-libwebp7_1.4.0-0.1_amd64.deb ... 77s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 77s Selecting previously unselected package libtiff6:amd64. 77s Preparing to unpack .../31-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 77s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 77s Selecting previously unselected package libwebpdemux2:amd64. 77s Preparing to unpack .../32-libwebpdemux2_1.4.0-0.1_amd64.deb ... 77s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 77s Selecting previously unselected package libwebpmux3:amd64. 77s Preparing to unpack .../33-libwebpmux3_1.4.0-0.1_amd64.deb ... 77s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 77s Selecting previously unselected package python3-argcomplete. 77s Preparing to unpack .../34-python3-argcomplete_3.5.3-1_all.deb ... 77s Unpacking python3-argcomplete (3.5.3-1) ... 77s Selecting previously unselected package 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up libdeflate0:amd64 (1.22-1) ... 79s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 79s Setting up libgomp1:amd64 (14.2.0-12ubuntu1) ... 79s Setting up python3-freetype (2.5.1-1) ... 79s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 79s Setting up python3-simplejson (3.19.3-1build1) ... 79s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 79s Setting up libblas3:amd64 (3.12.0-4) ... 79s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 79s Setting up python3-packaging (24.2-1) ... 79s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 79s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 79s Setting up fonts-dejavu-mono (2.37-8) ... 79s Setting up fonts-dejavu-core (2.37-8) ... 79s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 79s Setting up libgfortran5:amd64 (14.2.0-12ubuntu1) ... 79s Setting up python3-pluggy (1.5.0-1) ... 79s Setting up libwebp7:amd64 (1.4.0-0.1) ... 79s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu2) ... 79s Setting up libharfbuzz0b:amd64 (10.1.0-1) ... 79s Setting up sgml-base (1.31) ... 79s Setting up python3-argcomplete (3.5.3-1) ... 80s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 80s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 80s Setting up python3-pyfaidx (0.8.1.3-1) ... 80s Setting up liblapack3:amd64 (3.12.0-4) ... 80s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 80s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 80s Setting up python3-pytest (8.3.4-1) ... 80s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 80s Setting up xfonts-utils (1:7.7+7) ... 80s Setting up libraqm0:amd64 (0.10.2-1) ... 80s Setting up python3-numpy (1:1.26.4+ds-12) ... 81s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 81s Setting up xml-core (0.19) ... 82s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 82s Setting up fonts-urw-base35 (20200910-8) ... 82s Setting up libcairo2:amd64 (1.18.2-2) ... 82s Setting up python3-pil:amd64 (10.4.0-1ubuntu2) ... 82s Setting up python3-cairo (1.26.1-2build1) ... 82s Setting up python3-rlpycairo (0.3.0-3) ... 82s Setting up python3-reportlab (4.2.5-1) ... 83s Processing triggers for libc-bin (2.40-4ubuntu1) ... 83s Processing triggers for man-db (2.13.0-1) ... 84s Processing triggers for sgml-base (1.31) ... 84s Setting up w3c-sgml-lib (1.3-3) ... 106s Setting up python3-biopython (1.84+dfsg-4build1) ... 107s Setting up python3-gffutils (0.13-1) ... 108s autopkgtest [09:18:17]: test run-unit-test: [----------------------- 108s + pkg=python-gffutils 108s + [ /tmp/autopkgtest.bLmfHN/autopkgtest_tmp = ] 108s + cd /tmp/autopkgtest.bLmfHN/autopkgtest_tmp 108s + export HOME=/tmp/autopkgtest.bLmfHN/autopkgtest_tmp 108s + cp -r /usr/lib/python3/dist-packages/gffutils/test ./ 108s + pytest --doctest-modules -m not slow test 109s ============================= test session starts ============================== 109s platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 109s rootdir: /tmp/autopkgtest.bLmfHN/autopkgtest_tmp 109s plugins: typeguard-4.4.1 109s collected 110 items 109s 109s test/feature_test.py ........... [ 10%] 109s test/helpers_test.py .. [ 11%] 109s test/parser_test.py .................. [ 28%] 110s test/test_1.py ...........x..........s........... [ 59%] 110s test/test_biopython_integration.py . [ 60%] 111s test/test_cli.py . [ 60%] 111s test/test_issues.py ........................ [ 82%] 111s test/test_iterators.py .... [ 86%] 111s test/test_merge.py ......... [ 94%] 111s test/test_merge_all.py ...... [100%] 111s 111s =============================== warnings summary =============================== 111s test/performance_evaluation.py:190 111s /tmp/autopkgtest.bLmfHN/autopkgtest_tmp/test/performance_evaluation.py:190: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 111s @pytest.mark.slow 111s 111s test/performance_evaluation.py:208 111s /tmp/autopkgtest.bLmfHN/autopkgtest_tmp/test/performance_evaluation.py:208: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 111s @pytest.mark.slow 111s 111s test/test_1.py:485 111s test/test_1.py:485: PytestCollectionWarning: yield tests were removed in pytest 4.0 - test_region will be ignored 111s def test_region(): 111s 111s test/parser_test.py::test_parser_from_string 111s /usr/lib/python3/dist-packages/_pytest/python.py:163: PytestReturnNotNoneWarning: Expected None, but test/parser_test.py::test_parser_from_string returned True, which will be an error in a future version of pytest. Did you mean to use `assert` instead of `return`? 111s warnings.warn( 111s 111s test/parser_test.py::test_inconsistent_dialect 111s test/test_1.py::test_disable_infer 111s test/test_issues.py::test_pr_172 111s /usr/lib/python3/dist-packages/gffutils/create.py:770: UserWarning: It appears you have a gene feature in your GTF file. You may want to use the `disable_infer_genes=True` option to speed up database creation 111s warnings.warn( 111s 111s test/test_1.py::test_disable_infer 111s /usr/lib/python3/dist-packages/gffutils/create.py:763: UserWarning: It appears you have a transcript feature in your GTF file. You may want to use the `disable_infer_transcripts=True` option to speed up database creation 111s warnings.warn( 111s 111s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 111s ============ 108 passed, 1 skipped, 1 xfailed, 8 warnings in 2.94s ============= 112s autopkgtest [09:18:21]: test run-unit-test: -----------------------] 112s autopkgtest [09:18:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 112s run-unit-test PASS 113s autopkgtest [09:18:22]: @@@@@@@@@@@@@@@@@@@@ summary 113s run-unit-test PASS 118s nova [W] Skipping flock for amd64 118s Creating nova instance adt-plucky-amd64-python-gffutils-20250117-091629-juju-7f2275-prod-proposed-migration-environment-15-b0b16473-5137-4200-9d96-e5b3498ac23c from image adt/ubuntu-plucky-amd64-server-20250117.img (UUID 8f35863a-398a-4b7d-9594-544c7b7656c3)... 118s nova [W] Timed out waiting for ae45273b-90e5-411a-9c59-e0777872601c to get deleted.