0s autopkgtest [22:23:22]: starting date and time: 2024-03-20 22:23:22+0000 0s autopkgtest [22:23:22]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [22:23:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.oo8wi49z/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:pytest --apt-upgrade python-gffutils --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=pytest/8.0.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-8.secgroup --name adt-noble-s390x-python-gffutils-20240320-222322-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 99s autopkgtest [22:25:01]: testbed dpkg architecture: s390x 99s autopkgtest [22:25:01]: testbed apt version: 2.7.12 99s autopkgtest [22:25:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 100s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 101s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3819 kB] 101s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB] 101s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [500 kB] 101s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 101s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [679 kB] 101s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 101s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 101s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 101s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4073 kB] 101s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 101s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [45.3 kB] 101s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 104s Fetched 9307 kB in 3s (3066 kB/s) 104s Reading package lists... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s Calculating upgrade... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Unknown architecture, assuming PC-style ttyS0 109s sh: Attempting to set up Debian/Ubuntu apt sources automatically 109s sh: Distribution appears to be Ubuntu 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s eatmydata is already the newest version (131-1). 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s dbus is already the newest version (1.14.10-4ubuntu1). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s rng-tools-debian is already the newest version (2.4). 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s The following packages will be REMOVED: 112s cloud-init* python3-configobj* python3-debconf* 112s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 112s After this operation, 3252 kB disk space will be freed. 112s (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 ... 52171 files and directories currently installed.) 112s Removing cloud-init (24.1.1-0ubuntu1) ... 112s Removing python3-configobj (5.0.8-3) ... 112s Removing python3-debconf (1.5.86) ... 113s Processing triggers for man-db (2.12.0-3) ... 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 ... 51782 files and directories currently installed.) 113s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 113s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 114s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 114s invoke-rc.d: policy-rc.d denied execution of try-restart. 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s linux-generic is already the newest version (6.8.0-11.11+1). 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 115s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 115s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 117s Reading package lists... 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s autopkgtest [22:25:21]: rebooting testbed after setup commands that affected boot 133s autopkgtest [22:25:35]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 135s autopkgtest [22:25:37]: @@@@@@@@@@@@@@@@@@@@ apt-source python-gffutils 138s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-gffutils 0.12-2 (dsc) [1748 B] 138s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-gffutils 0.12-2 (tar) [1556 kB] 138s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-gffutils 0.12-2 (diff) [5360 B] 138s gpgv: Signature made Sun Nov 5 01:04:40 2023 UTC 138s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 138s gpgv: issuer "nilesh@debian.org" 138s gpgv: Can't check signature: No public key 138s dpkg-source: warning: cannot verify inline signature for ./python-gffutils_0.12-2.dsc: no acceptable signature found 138s autopkgtest [22:25:40]: testing package python-gffutils version 0.12-2 138s autopkgtest [22:25:40]: build not needed 140s autopkgtest [22:25:42]: test run-unit-test: preparing testbed 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Starting pkgProblemResolver with broken count: 0 153s Starting 2 pkgProblemResolver with broken count: 0 153s Done 154s The following additional packages will be installed: 154s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 154s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 154s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 154s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 154s libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 154s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 154s python3-argcomplete python3-argh python3-biopython python3-cairo 154s python3-freetype python3-gffutils python3-importlib-metadata 154s python3-iniconfig python3-more-itertools python3-numpy python3-packaging 154s python3-pil python3-pluggy python3-pyfaidx python3-pytest python3-reportlab 154s python3-rlpycairo python3-simplejson python3-zipp sgml-base w3c-sgml-lib 154s x11-common xfonts-encodings xfonts-utils xml-core 154s Suggested packages: 154s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 154s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 154s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 154s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 154s gcc gfortran python3-dev python-pil-doc pdf-viewer 154s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 154s sgml-base-doc debhelper 154s Recommended packages: 154s python-biopython-doc ncbi-blast+ python3-pybedtools python3-olefile 154s The following NEW packages will be installed: 154s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-extra 154s fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 libdeflate0 154s libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 154s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 154s liblcms2-2 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 154s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 154s python3-argcomplete python3-argh python3-biopython python3-cairo 154s python3-freetype python3-gffutils python3-importlib-metadata 154s python3-iniconfig python3-more-itertools python3-numpy python3-packaging 154s python3-pil python3-pluggy python3-pyfaidx python3-pytest python3-reportlab 154s python3-rlpycairo python3-simplejson python3-zipp sgml-base w3c-sgml-lib 154s x11-common xfonts-encodings xfonts-utils xml-core 154s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 154s Need to get 32.9 MB/32.9 MB of archives. 154s After this operation, 114 MB of additional disk space will be used. 154s Get:1 /tmp/autopkgtest.hDMdZo/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 154s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x sgml-base all 1.31 [11.4 kB] 154s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 155s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 155s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libfontenc1 s390x 1:1.1.8-1 [14.8 kB] 155s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB] 155s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB] 155s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 155s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-utils s390x 1:7.7+6build2 [94.8 kB] 155s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 157s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB] 157s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-extra all 2.37-8 [1947 kB] 157s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 157s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB] 157s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB] 157s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB] 157s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B] 157s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB] 157s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB] 157s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 157s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 157s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 157s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB] 157s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB] 157s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libimagequant0 s390x 2.18.0-1 [42.9 kB] 157s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB] 157s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 157s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 157s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB] 157s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libraqm0 s390x 0.10.1-1 [14.4 kB] 157s Get:31 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB] 157s Get:32 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB] 157s Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB] 157s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB] 157s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libwebpdemux2 s390x 1.3.2-0.4 [12.4 kB] 157s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libwebpmux3 s390x 1.3.2-0.4 [25.4 kB] 157s Get:37 http://ftpmaster.internal/ubuntu noble/universe s390x python3-argcomplete all 3.1.4-1 [33.5 kB] 157s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB] 157s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libopenjp2-7 s390x 2.5.0-2 [169 kB] 157s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x python3-pil s390x 10.2.0-1 [519 kB] 157s Get:41 http://ftpmaster.internal/ubuntu noble/main s390x python3-cairo s390x 1.25.1-2 [150 kB] 157s Get:42 http://ftpmaster.internal/ubuntu noble/universe s390x python3-freetype all 2.4.0-1 [83.1 kB] 157s Get:43 http://ftpmaster.internal/ubuntu noble/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 157s Get:44 http://ftpmaster.internal/ubuntu noble/universe s390x python3-reportlab all 4.1.0-1 [683 kB] 157s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x xml-core all 0.19 [20.3 kB] 157s Get:46 http://ftpmaster.internal/ubuntu noble/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 157s Get:47 http://ftpmaster.internal/ubuntu noble/universe s390x python3-biopython s390x 1.81+dfsg-3 [2234 kB] 158s Get:48 http://ftpmaster.internal/ubuntu noble/universe s390x python3-argh all 0.31.2-1 [26.9 kB] 158s Get:49 http://ftpmaster.internal/ubuntu noble/main s390x python3-more-itertools all 10.2.0-1 [52.9 kB] 158s Get:50 http://ftpmaster.internal/ubuntu noble/main s390x python3-zipp all 1.0.0-6 [6090 B] 158s Get:51 http://ftpmaster.internal/ubuntu noble/main s390x python3-importlib-metadata all 4.12.0-1 [17.8 kB] 158s Get:52 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pyfaidx all 0.8.1.1-1 [29.6 kB] 158s Get:53 http://ftpmaster.internal/ubuntu noble/main s390x python3-simplejson s390x 3.19.2-1build1 [63.6 kB] 158s Get:54 http://ftpmaster.internal/ubuntu noble/universe s390x python3-gffutils all 0.12-2 [1078 kB] 158s Get:55 http://ftpmaster.internal/ubuntu noble/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 158s Get:56 http://ftpmaster.internal/ubuntu noble/main s390x python3-packaging all 23.2-1 [40.6 kB] 158s Get:57 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pluggy all 1.4.0-1 [20.4 kB] 158s Get:58 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pytest all 7.4.4-1 [305 kB] 158s Fetched 32.9 MB in 4s (8837 kB/s) 158s Selecting previously unselected package sgml-base. 158s (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 ... 51727 files and directories currently installed.) 158s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 158s Unpacking sgml-base (1.31) ... 158s Selecting previously unselected package fonts-dejavu-mono. 158s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-mono (2.37-8) ... 158s Selecting previously unselected package fonts-dejavu-core. 158s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-core (2.37-8) ... 158s Selecting previously unselected package libfontenc1:s390x. 158s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1_s390x.deb ... 158s Unpacking libfontenc1:s390x (1:1.1.8-1) ... 158s Selecting previously unselected package libfreetype6:s390x. 158s Preparing to unpack .../04-libfreetype6_2.13.2+dfsg-1_s390x.deb ... 158s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ... 158s Selecting previously unselected package x11-common. 158s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu2_all.deb ... 158s Unpacking x11-common (1:7.7+23ubuntu2) ... 158s Selecting previously unselected package xfonts-encodings. 158s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 158s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 158s Selecting previously unselected package xfonts-utils. 158s Preparing to unpack .../07-xfonts-utils_1%3a7.7+6build2_s390x.deb ... 158s Unpacking xfonts-utils (1:7.7+6build2) ... 158s Selecting previously unselected package fonts-urw-base35. 158s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 158s Unpacking fonts-urw-base35 (20200910-8) ... 159s Selecting previously unselected package fontconfig-config. 159s Preparing to unpack .../09-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ... 159s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 159s Selecting previously unselected package fonts-dejavu-extra. 159s Preparing to unpack .../10-fonts-dejavu-extra_2.37-8_all.deb ... 159s Unpacking fonts-dejavu-extra (2.37-8) ... 159s Selecting previously unselected package libblas3:s390x. 159s Preparing to unpack .../11-libblas3_3.12.0-3_s390x.deb ... 159s Unpacking libblas3:s390x (3.12.0-3) ... 159s Selecting previously unselected package libfontconfig1:s390x. 159s Preparing to unpack .../12-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ... 159s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ... 159s Selecting previously unselected package libpixman-1-0:s390x. 159s Preparing to unpack .../13-libpixman-1-0_0.42.2-1_s390x.deb ... 159s Unpacking libpixman-1-0:s390x (0.42.2-1) ... 159s Selecting previously unselected package libxcb-render0:s390x. 159s Preparing to unpack .../14-libxcb-render0_1.15-1_s390x.deb ... 159s Unpacking libxcb-render0:s390x (1.15-1) ... 159s Selecting previously unselected package libxcb-shm0:s390x. 159s Preparing to unpack .../15-libxcb-shm0_1.15-1_s390x.deb ... 159s Unpacking libxcb-shm0:s390x (1.15-1) ... 159s Selecting previously unselected package libxrender1:s390x. 159s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1_s390x.deb ... 159s Unpacking libxrender1:s390x (1:0.9.10-1.1) ... 159s Selecting previously unselected package libcairo2:s390x. 159s Preparing to unpack .../17-libcairo2_1.18.0-1_s390x.deb ... 159s Unpacking libcairo2:s390x (1.18.0-1) ... 159s Selecting previously unselected package libdeflate0:s390x. 159s Preparing to unpack .../18-libdeflate0_1.19-1_s390x.deb ... 159s Unpacking libdeflate0:s390x (1.19-1) ... 159s Selecting previously unselected package libgfortran5:s390x. 159s Preparing to unpack .../19-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 159s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 159s Selecting previously unselected package libgomp1:s390x. 159s Preparing to unpack .../20-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 159s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 159s Selecting previously unselected package libgraphite2-3:s390x. 159s Preparing to unpack .../21-libgraphite2-3_1.3.14-2_s390x.deb ... 159s Unpacking libgraphite2-3:s390x (1.3.14-2) ... 159s Selecting previously unselected package libharfbuzz0b:s390x. 159s Preparing to unpack .../22-libharfbuzz0b_8.3.0-2_s390x.deb ... 159s Unpacking libharfbuzz0b:s390x (8.3.0-2) ... 159s Selecting previously unselected package libimagequant0:s390x. 159s Preparing to unpack .../23-libimagequant0_2.18.0-1_s390x.deb ... 159s Unpacking libimagequant0:s390x (2.18.0-1) ... 159s Selecting previously unselected package libjpeg-turbo8:s390x. 159s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ... 159s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 159s Selecting previously unselected package libjpeg8:s390x. 159s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_s390x.deb ... 159s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 159s Selecting previously unselected package liblapack3:s390x. 159s Preparing to unpack .../26-liblapack3_3.12.0-3_s390x.deb ... 159s Unpacking liblapack3:s390x (3.12.0-3) ... 159s Selecting previously unselected package liblcms2-2:s390x. 159s Preparing to unpack .../27-liblcms2-2_2.14-2_s390x.deb ... 159s Unpacking liblcms2-2:s390x (2.14-2) ... 159s Selecting previously unselected package libraqm0:s390x. 159s Preparing to unpack .../28-libraqm0_0.10.1-1_s390x.deb ... 159s Unpacking libraqm0:s390x (0.10.1-1) ... 159s Selecting previously unselected package libsharpyuv0:s390x. 159s Preparing to unpack .../29-libsharpyuv0_1.3.2-0.4_s390x.deb 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previously unselected package python3-argcomplete. 159s Preparing to unpack .../35-python3-argcomplete_3.1.4-1_all.deb ... 159s Unpacking python3-argcomplete (3.1.4-1) ... 159s Selecting previously unselected package python3-numpy. 159s Preparing to unpack .../36-python3-numpy_1%3a1.24.2-2_s390x.deb ... 159s Unpacking python3-numpy (1:1.24.2-2) ... 160s Selecting previously unselected package libopenjp2-7:s390x. 160s Preparing to unpack .../37-libopenjp2-7_2.5.0-2_s390x.deb ... 160s Unpacking libopenjp2-7:s390x (2.5.0-2) ... 160s Selecting previously unselected package python3-pil:s390x. 160s Preparing to unpack .../38-python3-pil_10.2.0-1_s390x.deb ... 160s Unpacking python3-pil:s390x (10.2.0-1) ... 160s Selecting previously unselected package python3-cairo. 160s Preparing to unpack .../39-python3-cairo_1.25.1-2_s390x.deb ... 160s Unpacking python3-cairo (1.25.1-2) ... 160s Selecting previously unselected package python3-freetype. 160s Preparing to unpack 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(1:1.1.8-1) ... 162s Setting up libblas3:s390x (3.12.0-3) ... 162s 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 162s Setting up python3-packaging (23.2-1) ... 162s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ... 162s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 162s Setting up libimagequant0:s390x (2.18.0-1) ... 162s Setting up fonts-dejavu-mono (2.37-8) ... 162s Setting up fonts-dejavu-core (2.37-8) ... 162s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ... 162s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 162s Setting up python3-pluggy (1.4.0-1) ... 162s Setting up libwebp7:s390x (1.3.2-0.4) ... 162s Setting up fonts-dejavu-extra (2.37-8) ... 162s Setting up libopenjp2-7:s390x (2.5.0-2) ... 162s Setting up libharfbuzz0b:s390x (8.3.0-2) ... 162s Setting up sgml-base (1.31) ... 162s Setting up python3-argcomplete (3.1.4-1) ... 162s Setting up 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(1.18.0-1) ... 165s Setting up python3-pil:s390x (10.2.0-1) ... 166s Setting up python3-cairo (1.25.1-2) ... 166s Setting up python3-rlpycairo (0.3.0-3) ... 166s Setting up python3-reportlab (4.1.0-1) ... 167s Processing triggers for libc-bin (2.39-0ubuntu2) ... 167s Processing triggers for man-db (2.12.0-3) ... 168s Processing triggers for sgml-base (1.31) ... 168s Setting up w3c-sgml-lib (1.3-3) ... 201s Setting up python3-biopython (1.81+dfsg-3) ... 202s Setting up python3-gffutils (0.12-2) ... 202s Setting up autopkgtest-satdep (0) ... 205s (Reading database ... 55400 files and directories currently installed.) 205s Removing autopkgtest-satdep (0) ... 206s autopkgtest [22:26:48]: test run-unit-test: [----------------------- 206s + pkg=python-gffutils 206s + [ /tmp/autopkgtest.hDMdZo/autopkgtest_tmp = ] 206s + cd /tmp/autopkgtest.hDMdZo/autopkgtest_tmp 206s + export HOME=/tmp/autopkgtest.hDMdZo/autopkgtest_tmp 206s + cp -r /usr/lib/python3/dist-packages/gffutils/test ./ 206s + pytest --doctest-modules -m not slow test 207s ============================= test session starts ============================== 207s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 207s rootdir: /tmp/autopkgtest.hDMdZo/autopkgtest_tmp 207s collected 110 items 207s 207s test/feature_test.py ........... [ 10%] 207s test/helpers_test.py .. [ 11%] 207s test/parser_test.py .................. [ 28%] 208s test/test_1.py ...........x..........s............ [ 60%] 208s test/test_biopython_integration.py . [ 60%] 208s test/test_issues.py ........................ [ 82%] 208s test/test_iterators.py .... [ 86%] 208s test/test_merge.py ......... [ 94%] 208s test/test_merge_all.py ...... [100%] 208s 208s =============================== warnings summary =============================== 208s test/performance_evaluation.py:190 208s /tmp/autopkgtest.hDMdZo/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 208s @pytest.mark.slow 208s 208s test/performance_evaluation.py:208 208s /tmp/autopkgtest.hDMdZo/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 208s @pytest.mark.slow 208s 208s test/test_1.py:486 208s test/test_1.py:486: PytestCollectionWarning: yield tests were removed in pytest 4.0 - test_region will be ignored 208s def test_region(): 208s 208s test/parser_test.py::test_parser_from_string 208s /usr/lib/python3/dist-packages/_pytest/python.py:198: 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`? 208s warnings.warn( 208s 208s test/parser_test.py::test_inconsistent_dialect 208s test/test_1.py::test_disable_infer 208s test/test_issues.py::test_pr_172 208s /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 208s warnings.warn( 208s 208s test/test_1.py::TestGFFClass::test_parents_level_1 208s /usr/lib/python3/dist-packages/_pytest/fixtures.py:895: PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release. 208s test/test_1.py::TestGFFClass::test_parents_level_1 is using nose-specific method: `setup(self)` 208s To remove this warning, rename it to `setup_method(self)` 208s See docs: https://docs.pytest.org/en/stable/deprecations.html#support-for-tests-written-for-nose 208s fixture_result = next(generator) 208s 208s test/test_1.py::TestGFFClass::test_parents_level_2 208s /usr/lib/python3/dist-packages/_pytest/fixtures.py:895: PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release. 208s test/test_1.py::TestGFFClass::test_parents_level_2 is using nose-specific method: `setup(self)` 208s To remove this warning, rename it to `setup_method(self)` 208s See docs: https://docs.pytest.org/en/stable/deprecations.html#support-for-tests-written-for-nose 208s fixture_result = next(generator) 208s 208s test/test_1.py::TestGFFClass::test_bed12 208s /usr/lib/python3/dist-packages/_pytest/fixtures.py:895: PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release. 208s test/test_1.py::TestGFFClass::test_bed12 is using nose-specific method: `setup(self)` 208s To remove this warning, rename it to `setup_method(self)` 208s See docs: https://docs.pytest.org/en/stable/deprecations.html#support-for-tests-written-for-nose 208s fixture_result = next(generator) 208s 208s test/test_1.py::TestGTFClass::test_parents_level_1 208s /usr/lib/python3/dist-packages/_pytest/fixtures.py:895: PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release. 208s test/test_1.py::TestGTFClass::test_parents_level_1 is using nose-specific method: `setup(self)` 208s To remove this warning, rename it to `setup_method(self)` 208s See docs: https://docs.pytest.org/en/stable/deprecations.html#support-for-tests-written-for-nose 208s fixture_result = next(generator) 208s 208s test/test_1.py::TestGTFClass::test_parents_level_2 208s /usr/lib/python3/dist-packages/_pytest/fixtures.py:895: PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release. 208s test/test_1.py::TestGTFClass::test_parents_level_2 is using nose-specific method: `setup(self)` 208s To remove this warning, rename it to `setup_method(self)` 208s See docs: https://docs.pytest.org/en/stable/deprecations.html#support-for-tests-written-for-nose 208s fixture_result = next(generator) 208s 208s test/test_1.py::TestGTFClass::test_bed12 208s /usr/lib/python3/dist-packages/_pytest/fixtures.py:895: PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release. 208s test/test_1.py::TestGTFClass::test_bed12 is using nose-specific method: `setup(self)` 208s To remove this warning, rename it to `setup_method(self)` 208s See docs: https://docs.pytest.org/en/stable/deprecations.html#support-for-tests-written-for-nose 208s fixture_result = next(generator) 208s 208s test/test_1.py::test_disable_infer 208s /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 208s warnings.warn( 208s 208s test/test_biopython_integration.py::test_roundtrip 208s /usr/lib/python3/dist-packages/Bio/SeqFeature.py:257: BiopythonDeprecationWarning: Using the strand argument is deprecated, and will be removed in a future release. Please set it via the location object instead. 208s warnings.warn( 208s 208s test/test_biopython_integration.py::test_roundtrip 208s /usr/lib/python3/dist-packages/Bio/SeqFeature.py:1940: BiopythonDeprecationWarning: Alias location.position is deprecated and will be removed in a future release. Use location directly, or int(location). However, that will fail for UnknownPosition, and for OneOfPosition and WithinPosition will give the default rather than left-most value. 208s warnings.warn( 208s 208s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 208s ============ 108 passed, 1 skipped, 1 xfailed, 16 warnings in 1.41s ============ 208s autopkgtest [22:26:50]: test run-unit-test: -----------------------] 209s autopkgtest [22:26:51]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 209s run-unit-test PASS 209s autopkgtest [22:26:51]: @@@@@@@@@@@@@@@@@@@@ summary 209s run-unit-test PASS 222s Creating nova instance adt-noble-s390x-python-gffutils-20240320-222322-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240320.img (UUID 6569a0ff-4984-4a4c-a4d0-b93f21cb5de9)...