0s autopkgtest [17:55:41]: starting date and time: 2025-01-03 17:55:41+0000 0s autopkgtest [17:55:41]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:55:41]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.131cgf1u/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 autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-6.secgroup --name adt-plucky-s390x-python-gffutils-20250103-175541-juju-7f2275-prod-proposed-migration-environment-20-9627e475-3952-4bec-9cec-66720f119831 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 103s autopkgtest [17:57:24]: testbed dpkg architecture: s390x 103s autopkgtest [17:57:24]: testbed apt version: 2.9.18 103s autopkgtest [17:57:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s autopkgtest [17:57:24]: testbed release detected to be: None 104s autopkgtest [17:57:25]: updating testbed package index (apt update) 104s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 104s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 104s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 104s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [73.5 kB] 105s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [780 kB] 105s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [82.8 kB] 105s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x Packages [756 B] 105s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [684 kB] 105s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [4080 B] 105s Fetched 1721 kB in 1s (1957 kB/s) 105s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 106s The following packages will be upgraded: 106s binutils binutils-common binutils-s390x-linux-gnu libbinutils libctf-nobfd0 106s libctf0 libsframe1 106s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 3250 kB of archives. 106s After this operation, 0 B of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libctf0 s390x 2.43.50.20241230-1ubuntu1 [101 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libctf-nobfd0 s390x 2.43.50.20241230-1ubuntu1 [101 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x binutils-s390x-linux-gnu s390x 2.43.50.20241230-1ubuntu1 [2328 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libbinutils s390x 2.43.50.20241230-1ubuntu1 [481 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x binutils s390x 2.43.50.20241230-1ubuntu1 [3068 B] 107s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x binutils-common s390x 2.43.50.20241230-1ubuntu1 [222 kB] 107s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libsframe1 s390x 2.43.50.20241230-1ubuntu1 [13.9 kB] 107s Fetched 3250 kB in 1s (4828 kB/s) 107s (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 ... 55616 files and directories currently installed.) 107s Preparing to unpack .../0-libctf0_2.43.50.20241230-1ubuntu1_s390x.deb ... 107s Unpacking libctf0:s390x (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 107s Preparing to unpack .../1-libctf-nobfd0_2.43.50.20241230-1ubuntu1_s390x.deb ... 107s Unpacking libctf-nobfd0:s390x (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 107s Preparing to unpack .../2-binutils-s390x-linux-gnu_2.43.50.20241230-1ubuntu1_s390x.deb ... 107s Unpacking binutils-s390x-linux-gnu (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 107s Preparing to unpack .../3-libbinutils_2.43.50.20241230-1ubuntu1_s390x.deb ... 107s Unpacking libbinutils:s390x (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 107s Preparing to unpack .../4-binutils_2.43.50.20241230-1ubuntu1_s390x.deb ... 107s Unpacking binutils (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 107s Preparing to unpack .../5-binutils-common_2.43.50.20241230-1ubuntu1_s390x.deb ... 107s Unpacking binutils-common:s390x (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 107s Preparing to unpack .../6-libsframe1_2.43.50.20241230-1ubuntu1_s390x.deb ... 107s Unpacking libsframe1:s390x (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 107s Setting up binutils-common:s390x (2.43.50.20241230-1ubuntu1) ... 107s Setting up libctf-nobfd0:s390x (2.43.50.20241230-1ubuntu1) ... 107s Setting up libsframe1:s390x (2.43.50.20241230-1ubuntu1) ... 107s Setting up libbinutils:s390x (2.43.50.20241230-1ubuntu1) ... 107s Setting up libctf0:s390x (2.43.50.20241230-1ubuntu1) ... 107s Setting up binutils-s390x-linux-gnu (2.43.50.20241230-1ubuntu1) ... 107s Setting up binutils (2.43.50.20241230-1ubuntu1) ... 107s Processing triggers for libc-bin (2.40-4ubuntu1) ... 107s Processing triggers for man-db (2.13.0-1) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 108s autopkgtest [17:57:29]: upgrading testbed (apt dist-upgrade and autopurge) 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 109s Starting 2 pkgProblemResolver with broken count: 0 109s Done 109s Entering ResolveByKeep 109s 109s The following packages were automatically installed and are no longer required: 109s python3.12 python3.12-minimal 109s Use 'sudo apt autoremove' to remove them. 109s The following NEW packages will be installed: 109s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 109s The following packages will be upgraded: 109s libpython3-stdlib python3 python3-minimal 109s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 6108 kB of archives. 109s After this operation, 22.7 MB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.1-2 [880 kB] 110s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.1-2 [2364 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.13.1-1~exp2 [27.6 kB] 110s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.13.1-1~exp2 [23.9 kB] 110s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.1-2 [2074 kB] 110s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.1-2 [729 kB] 110s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.13.1-1~exp2 [10.2 kB] 110s Fetched 6108 kB in 1s (7595 kB/s) 110s Selecting previously unselected package libpython3.13-minimal:s390x. 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 ... 55616 files and directories currently installed.) 110s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_s390x.deb ... 110s Unpacking libpython3.13-minimal:s390x (3.13.1-2) ... 110s Selecting previously unselected package python3.13-minimal. 110s Preparing to unpack .../python3.13-minimal_3.13.1-2_s390x.deb ... 110s Unpacking python3.13-minimal (3.13.1-2) ... 110s Setting up libpython3.13-minimal:s390x (3.13.1-2) ... 110s Setting up python3.13-minimal (3.13.1-2) ... 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 ... 55936 files and directories currently installed.) 111s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_s390x.deb ... 111s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 111s Setting up python3-minimal (3.13.1-1~exp2) ... 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 ... 55936 files and directories currently installed.) 111s Preparing to unpack .../python3_3.13.1-1~exp2_s390x.deb ... 111s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 111s Selecting previously unselected package libpython3.13-stdlib:s390x. 111s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_s390x.deb ... 111s Unpacking libpython3.13-stdlib:s390x (3.13.1-2) ... 111s Selecting previously unselected package python3.13. 111s Preparing to unpack .../python3.13_3.13.1-2_s390x.deb ... 111s Unpacking python3.13 (3.13.1-2) ... 111s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_s390x.deb ... 111s Unpacking libpython3-stdlib:s390x (3.13.1-1~exp2) over (3.12.8-1) ... 111s Setting up libpython3.13-stdlib:s390x (3.13.1-2) ... 111s Setting up libpython3-stdlib:s390x (3.13.1-1~exp2) ... 111s Setting up python3.13 (3.13.1-2) ... 112s Setting up python3 (3.13.1-1~exp2) ... 112s /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. 112s for fn in glob1(directory, "%s.*" % fname): 112s Processing triggers for man-db (2.13.0-1) ... 112s Processing triggers for systemd (257-2ubuntu1) ... 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 113s The following packages will be REMOVED: 113s python3.12* python3.12-minimal* 113s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 113s After this operation, 9190 kB disk space will be freed. 113s (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 ... 56353 files and directories currently installed.) 113s Removing python3.12 (3.12.8-3) ... 113s Removing python3.12-minimal (3.12.8-3) ... 113s /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. 113s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 114s Processing triggers for man-db (2.13.0-1) ... 114s Processing triggers for systemd (257-2ubuntu1) ... 114s (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 ... 56325 files and directories currently installed.) 114s Purging configuration files for python3.12-minimal (3.12.8-3) ... 116s autopkgtest [17:57:37]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 116s autopkgtest [17:57:37]: @@@@@@@@@@@@@@@@@@@@ apt-source python-gffutils 118s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-gffutils 0.13-1 (dsc) [2351 B] 118s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-gffutils 0.13-1 (tar) [1560 kB] 118s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-gffutils 0.13-1 (diff) [5024 B] 118s gpgv: Signature made Sat Apr 13 20:25:45 2024 UTC 118s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 118s gpgv: issuer "tchet@debian.org" 118s gpgv: Can't check signature: No public key 118s dpkg-source: warning: cannot verify inline signature for ./python-gffutils_0.13-1.dsc: no acceptable signature found 118s autopkgtest [17:57:39]: testing package python-gffutils version 0.13-1 119s autopkgtest [17:57:40]: build not needed 119s autopkgtest [17:57:40]: test run-unit-test: preparing testbed 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s Starting pkgProblemResolver with broken count: 0 120s Starting 2 pkgProblemResolver with broken count: 0 120s Done 120s The following NEW packages will be installed: 120s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 120s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 120s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 120s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 libopenjp2-7 libpixman-1-0 120s libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 120s libxcb-render0 libxcb-shm0 libxrender1 python3-argcomplete python3-argh 120s python3-biopython python3-cairo python3-freetype python3-gffutils 120s python3-importlib-metadata python3-iniconfig python3-numpy python3-packaging 120s python3-pil python3-pluggy python3-pyfaidx python3-pytest python3-reportlab 120s python3-rlpycairo python3-simplejson sgml-base w3c-sgml-lib x11-common 120s xfonts-encodings xfonts-utils xml-core 120s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 120s Need to get 30.2 MB of archives. 120s After this operation, 109 MB of additional disk space will be used. 120s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x sgml-base all 1.31 [11.4 kB] 120s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 120s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 121s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 121s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 121s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 121s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 121s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 121s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 122s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB] 122s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-4 [238 kB] 122s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB] 122s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 122s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 122s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 122s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 122s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 122s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.22-1 [46.1 kB] 122s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-12ubuntu1 [587 kB] 122s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 14.2.0-12ubuntu1 [151 kB] 122s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 122s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.1.0-1 [537 kB] 122s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 122s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 122s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 122s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-4 [2964 kB] 122s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 122s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 122s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.4.0-0.1 [16.2 kB] 122s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 122s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.4.0-0.1 [204 kB] 122s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 122s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.4.0-0.1 [12.2 kB] 122s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.4.0-0.1 [25.3 kB] 122s Get:35 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-argcomplete all 3.5.1-1ubuntu1 [35.6 kB] 122s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-12 [4601 kB] 122s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.0-2ubuntu2 [208 kB] 122s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 10.4.0-1ubuntu2 [515 kB] 123s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x python3-cairo s390x 1.26.1-2build1 [138 kB] 123s Get:40 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 123s Get:41 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 123s Get:42 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-reportlab all 4.2.5-1 [1107 kB] 123s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x xml-core all 0.19 [20.3 kB] 123s Get:44 http://ftpmaster.internal/ubuntu plucky/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 123s Get:45 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython s390x 1.84+dfsg-4build1 [1728 kB] 123s Get:46 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-argh all 0.31.3-1 [27.0 kB] 123s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x python3-importlib-metadata all 8.5.0-1 [20.7 kB] 123s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.2-1 [51.5 kB] 123s Get:49 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 123s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x python3-simplejson s390x 3.19.3-1build1 [55.6 kB] 123s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-gffutils all 0.13-1 [1081 kB] 123s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 123s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] 123s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest all 8.3.3-1 [251 kB] 123s Fetched 30.2 MB in 3s (10.9 MB/s) 123s Selecting previously unselected package sgml-base. 123s (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 ... 56325 files and directories currently installed.) 123s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 123s Unpacking sgml-base (1.31) ... 123s Selecting previously unselected package fonts-dejavu-mono. 123s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 123s Unpacking fonts-dejavu-mono (2.37-8) ... 123s Selecting previously unselected package fonts-dejavu-core. 123s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 123s Unpacking fonts-dejavu-core (2.37-8) ... 123s Selecting previously unselected package libfontenc1:s390x. 123s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 123s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 123s Selecting previously unselected package libfreetype6:s390x. 123s Preparing to unpack .../04-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 123s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 123s Selecting previously unselected package x11-common. 123s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 123s Unpacking x11-common (1:7.7+23ubuntu3) ... 123s Selecting previously unselected package xfonts-encodings. 123s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 123s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 123s Selecting previously unselected package xfonts-utils. 123s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_s390x.deb ... 123s Unpacking xfonts-utils (1:7.7+7) ... 123s Selecting previously unselected package fonts-urw-base35. 123s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 123s Unpacking fonts-urw-base35 (20200910-8) ... 123s Selecting previously unselected package fontconfig-config. 123s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_s390x.deb ... 123s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 123s Selecting previously unselected package libblas3:s390x. 123s Preparing to unpack .../10-libblas3_3.12.0-4_s390x.deb ... 123s Unpacking libblas3:s390x (3.12.0-4) ... 123s Selecting previously unselected package libfontconfig1:s390x. 123s Preparing to unpack .../11-libfontconfig1_2.15.0-1.1ubuntu2_s390x.deb ... 123s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 123s Selecting previously unselected package libpixman-1-0:s390x. 123s Preparing to unpack .../12-libpixman-1-0_0.44.0-3_s390x.deb ... 123s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 123s Selecting previously unselected package libxcb-render0:s390x. 123s Preparing to unpack .../13-libxcb-render0_1.17.0-2_s390x.deb ... 123s Unpacking libxcb-render0:s390x (1.17.0-2) ... 123s Selecting previously unselected package libxcb-shm0:s390x. 123s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_s390x.deb ... 123s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 123s Selecting previously unselected package libxrender1:s390x. 123s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 123s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 123s Selecting previously unselected package libcairo2:s390x. 123s Preparing to unpack .../16-libcairo2_1.18.2-2_s390x.deb ... 123s Unpacking libcairo2:s390x (1.18.2-2) ... 123s Selecting previously unselected package libdeflate0:s390x. 123s Preparing to unpack .../17-libdeflate0_1.22-1_s390x.deb ... 123s Unpacking libdeflate0:s390x (1.22-1) ... 123s Selecting previously unselected package libgfortran5:s390x. 123s Preparing to unpack .../18-libgfortran5_14.2.0-12ubuntu1_s390x.deb ... 123s Unpacking libgfortran5:s390x (14.2.0-12ubuntu1) ... 123s Selecting previously unselected package libgomp1:s390x. 123s Preparing to unpack .../19-libgomp1_14.2.0-12ubuntu1_s390x.deb ... 123s Unpacking libgomp1:s390x (14.2.0-12ubuntu1) ... 123s Selecting previously unselected package libgraphite2-3:s390x. 123s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 123s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 123s Selecting previously unselected package libharfbuzz0b:s390x. 123s Preparing to unpack .../21-libharfbuzz0b_10.1.0-1_s390x.deb ... 123s Unpacking libharfbuzz0b:s390x (10.1.0-1) ... 123s Selecting previously unselected package libimagequant0:s390x. 123s Preparing to unpack .../22-libimagequant0_2.18.0-1build1_s390x.deb ... 123s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 123s Selecting previously unselected package libjpeg-turbo8:s390x. 123s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 123s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 124s Selecting previously unselected package libjpeg8:s390x. 124s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_s390x.deb ... 124s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 124s Selecting previously unselected package liblapack3:s390x. 124s Preparing to unpack .../25-liblapack3_3.12.0-4_s390x.deb ... 124s Unpacking liblapack3:s390x (3.12.0-4) ... 124s Selecting previously unselected package liblcms2-2:s390x. 124s Preparing to unpack .../26-liblcms2-2_2.16-2_s390x.deb ... 124s Unpacking liblcms2-2:s390x (2.16-2) ... 124s Selecting previously unselected package libraqm0:s390x. 124s Preparing to unpack .../27-libraqm0_0.10.2-1_s390x.deb ... 124s Unpacking libraqm0:s390x (0.10.2-1) ... 124s Selecting previously unselected package libsharpyuv0:s390x. 124s Preparing to unpack .../28-libsharpyuv0_1.4.0-0.1_s390x.deb ... 124s Unpacking libsharpyuv0:s390x (1.4.0-0.1) ... 124s Selecting previously unselected package libjbig0:s390x. 124s Preparing to unpack .../29-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 124s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 124s Selecting previously unselected package libwebp7:s390x. 124s Preparing to unpack .../30-libwebp7_1.4.0-0.1_s390x.deb ... 124s Unpacking libwebp7:s390x (1.4.0-0.1) ... 124s Selecting previously unselected package libtiff6:s390x. 124s Preparing to unpack .../31-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 124s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 124s Selecting previously unselected package libwebpdemux2:s390x. 124s Preparing to unpack .../32-libwebpdemux2_1.4.0-0.1_s390x.deb ... 124s Unpacking libwebpdemux2:s390x (1.4.0-0.1) ... 124s Selecting previously unselected package libwebpmux3:s390x. 124s Preparing to unpack .../33-libwebpmux3_1.4.0-0.1_s390x.deb ... 124s Unpacking libwebpmux3:s390x (1.4.0-0.1) ... 124s Selecting previously unselected package python3-argcomplete. 124s Preparing to unpack .../34-python3-argcomplete_3.5.1-1ubuntu1_all.deb ... 124s Unpacking python3-argcomplete (3.5.1-1ubuntu1) ... 124s Selecting previously unselected package python3-numpy. 124s Preparing to unpack .../35-python3-numpy_1%3a1.26.4+ds-12_s390x.deb ... 124s Unpacking python3-numpy (1:1.26.4+ds-12) ... 124s Selecting previously unselected package libopenjp2-7:s390x. 124s Preparing to unpack .../36-libopenjp2-7_2.5.0-2ubuntu2_s390x.deb ... 124s Unpacking libopenjp2-7:s390x (2.5.0-2ubuntu2) ... 124s Selecting previously unselected package python3-pil:s390x. 124s Preparing to unpack .../37-python3-pil_10.4.0-1ubuntu2_s390x.deb ... 124s Unpacking python3-pil:s390x (10.4.0-1ubuntu2) ... 124s Selecting previously unselected package python3-cairo. 124s Preparing to unpack .../38-python3-cairo_1.26.1-2build1_s390x.deb ... 124s Unpacking python3-cairo (1.26.1-2build1) ... 124s Selecting previously unselected package python3-freetype. 124s Preparing to unpack .../39-python3-freetype_2.5.1-1_all.deb ... 124s Unpacking python3-freetype (2.5.1-1) ... 124s 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Unpacking python3-argh (0.31.3-1) ... 124s Selecting previously unselected package python3-importlib-metadata. 124s Preparing to unpack .../46-python3-importlib-metadata_8.5.0-1_all.deb ... 124s Unpacking python3-importlib-metadata (8.5.0-1) ... 124s Selecting previously unselected package python3-packaging. 124s Preparing to unpack .../47-python3-packaging_24.2-1_all.deb ... 124s Unpacking python3-packaging (24.2-1) ... 124s Selecting previously unselected package python3-pyfaidx. 124s Preparing to unpack .../48-python3-pyfaidx_0.8.1.3-1_all.deb ... 124s Unpacking python3-pyfaidx (0.8.1.3-1) ... 124s Selecting previously unselected package python3-simplejson. 124s Preparing to unpack .../49-python3-simplejson_3.19.3-1build1_s390x.deb ... 124s Unpacking python3-simplejson (3.19.3-1build1) ... 124s Selecting previously unselected package python3-gffutils. 124s Preparing to unpack .../50-python3-gffutils_0.13-1_all.deb ... 124s Unpacking python3-gffutils (0.13-1) ... 124s Selecting previously unselected package python3-iniconfig. 124s Preparing to unpack .../51-python3-iniconfig_1.1.1-2_all.deb ... 124s Unpacking python3-iniconfig (1.1.1-2) ... 124s Selecting previously unselected package python3-pluggy. 124s Preparing to unpack .../52-python3-pluggy_1.5.0-1_all.deb ... 124s Unpacking python3-pluggy (1.5.0-1) ... 124s Selecting previously unselected package python3-pytest. 124s Preparing to unpack .../53-python3-pytest_8.3.3-1_all.deb ... 124s Unpacking python3-pytest (8.3.3-1) ... 124s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 124s Setting up liblcms2-2:s390x (2.16-2) ... 124s Setting up python3-iniconfig (1.1.1-2) ... 124s Setting up libpixman-1-0:s390x (0.44.0-3) ... 124s Setting up python3-argh (0.31.3-1) ... 124s Setting up libsharpyuv0:s390x (1.4.0-0.1) ... 124s Setting up python3-importlib-metadata (8.5.0-1) ... 124s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 124s Setting up libxcb-render0:s390x (1.17.0-2) ... 124s Setting up x11-common (1:7.7+23ubuntu3) ... 125s Setting up libdeflate0:s390x (1.22-1) ... 125s Setting up libxcb-shm0:s390x (1.17.0-2) ... 125s Setting up libgomp1:s390x (14.2.0-12ubuntu1) ... 125s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 125s Setting up python3-simplejson (3.19.3-1build1) ... 125s Setting up libfontenc1:s390x (1:1.1.8-1build1) ... 125s Setting up libblas3:s390x (3.12.0-4) ... 125s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 125s Setting up python3-packaging (24.2-1) ... 125s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 125s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 125s Setting up libimagequant0:s390x (2.18.0-1build1) ... 125s Setting up fonts-dejavu-mono (2.37-8) ... 125s Setting up fonts-dejavu-core (2.37-8) ... 125s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 125s Setting up libgfortran5:s390x (14.2.0-12ubuntu1) ... 125s Setting up python3-pluggy (1.5.0-1) ... 125s Setting up libwebp7:s390x (1.4.0-0.1) ... 125s Setting up libopenjp2-7:s390x (2.5.0-2ubuntu2) ... 125s Setting up libharfbuzz0b:s390x (10.1.0-1) ... 125s Setting up sgml-base (1.31) ... 125s Setting up python3-argcomplete (3.5.1-1ubuntu1) ... 125s Setting up libwebpmux3:s390x (1.4.0-0.1) ... 125s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 125s Setting up python3-pyfaidx (0.8.1.3-1) ... 125s Setting up liblapack3:s390x (3.12.0-4) ... 125s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 125s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 125s Setting up python3-pytest (8.3.3-1) ... 125s Setting up libwebpdemux2:s390x (1.4.0-0.1) ... 125s Setting up python3-freetype (2.5.1-1) ... 125s Setting up xfonts-utils (1:7.7+7) ... 125s Setting up libraqm0:s390x (0.10.2-1) ... 125s Setting up python3-numpy (1:1.26.4+ds-12) ... 127s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 127s Setting up xml-core (0.19) ... 127s Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 127s Setting up fonts-urw-base35 (20200910-8) ... 127s Setting up libcairo2:s390x (1.18.2-2) ... 127s Setting up python3-pil:s390x (10.4.0-1ubuntu2) ... 127s Setting up python3-cairo (1.26.1-2build1) ... 127s Setting up python3-rlpycairo (0.3.0-3) ... 127s Setting up python3-reportlab (4.2.5-1) ... 128s Processing triggers for libc-bin (2.40-4ubuntu1) ... 128s Processing triggers for man-db (2.13.0-1) ... 128s Processing triggers for sgml-base (1.31) ... 128s Setting up w3c-sgml-lib (1.3-3) ... 148s Setting up python3-biopython (1.84+dfsg-4build1) ... 148s Setting up python3-gffutils (0.13-1) ... 149s autopkgtest [17:58:10]: test run-unit-test: [----------------------- 149s + pkg=python-gffutils 149s + [ /tmp/autopkgtest.kD03Nj/autopkgtest_tmp = ] 149s + cd /tmp/autopkgtest.kD03Nj/autopkgtest_tmp 149s + export HOME=/tmp/autopkgtest.kD03Nj/autopkgtest_tmp 149s + cp -r /usr/lib/python3/dist-packages/gffutils/test ./ 149s + pytest --doctest-modules -m not slow test 150s ============================= test session starts ============================== 150s platform linux -- Python 3.13.1, pytest-8.3.3, pluggy-1.5.0 150s rootdir: /tmp/autopkgtest.kD03Nj/autopkgtest_tmp 150s plugins: typeguard-4.4.1 150s collected 110 items 150s 150s test/feature_test.py ........... [ 10%] 150s test/helpers_test.py .. [ 11%] 150s test/parser_test.py .................. [ 28%] 151s test/test_1.py ...........x..........s........... [ 59%] 151s test/test_biopython_integration.py . [ 60%] 152s test/test_cli.py . [ 60%] 152s test/test_issues.py ........................ [ 82%] 152s test/test_iterators.py .... [ 86%] 152s test/test_merge.py ......... [ 94%] 152s test/test_merge_all.py ...... [100%] 152s 152s =============================== warnings summary =============================== 152s test/performance_evaluation.py:190 152s /tmp/autopkgtest.kD03Nj/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 152s @pytest.mark.slow 152s 152s test/performance_evaluation.py:208 152s /tmp/autopkgtest.kD03Nj/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 152s @pytest.mark.slow 152s 152s test/test_1.py:485 152s test/test_1.py:485: PytestCollectionWarning: yield tests were removed in pytest 4.0 - test_region will be ignored 152s def test_region(): 152s 152s test/parser_test.py::test_parser_from_string 152s /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`? 152s warnings.warn( 152s 152s test/parser_test.py::test_inconsistent_dialect 152s test/test_1.py::test_disable_infer 152s test/test_issues.py::test_pr_172 152s /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 152s warnings.warn( 152s 152s test/test_1.py::test_disable_infer 152s /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 152s warnings.warn( 152s 152s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 152s ============ 108 passed, 1 skipped, 1 xfailed, 8 warnings in 2.05s ============= 152s autopkgtest [17:58:13]: test run-unit-test: -----------------------] 152s run-unit-test PASS 152s autopkgtest [17:58:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 153s autopkgtest [17:58:14]: @@@@@@@@@@@@@@@@@@@@ summary 153s run-unit-test PASS 169s nova [W] Using flock in prodstack6-s390x 169s Creating nova instance adt-plucky-s390x-python-gffutils-20250103-175541-juju-7f2275-prod-proposed-migration-environment-20-9627e475-3952-4bec-9cec-66720f119831 from image adt/ubuntu-plucky-s390x-server-20250103.img (UUID 9816a864-89cd-473a-b7ab-55eae81bf00a)... 169s nova [W] Timed out waiting for c701bca4-8581-439b-a52c-05b25ad09f08 to get deleted.