0s autopkgtest [15:26:58]: starting date and time: 2024-11-02 15:26:58+0000 0s autopkgtest [15:26:58]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [15:26:58]: host juju-7f2275-prod-proposed-migration-environment-14; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.haqzts6j/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib --apt-upgrade python-pyfaidx --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.20+ds-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-14@bos03-s390x-27.secgroup --name adt-plucky-s390x-python-pyfaidx-20241102-152658-juju-7f2275-prod-proposed-migration-environment-14-8a5310b5-44fb-409a-b96b-fdd0de513288 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-14 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 97s autopkgtest [15:28:35]: testbed dpkg architecture: s390x 97s autopkgtest [15:28:35]: testbed apt version: 2.9.8 97s autopkgtest [15:28:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 98s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 98s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2555 kB] 99s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 99s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [40.4 kB] 99s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [172 kB] 99s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [212 kB] 99s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [1819 kB] 99s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [33.3 kB] 99s Fetched 4913 kB in 1s (4558 kB/s) 99s Reading package lists... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Calculating upgrade... 101s The following packages will be upgraded: 101s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 101s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 101s libblockdev3 libevdev2 libftdi1-2 libinih1 libpipeline1 nano 101s python3-lazr.uri 102s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 611 kB of archives. 102s After this operation, 52.2 kB of additional disk space will be used. 102s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libevdev2 s390x 1.13.3+dfsg-1 [35.9 kB] 102s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpipeline1 s390x 1.5.8-1 [32.5 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x nano s390x 8.2-1 [298 kB] 102s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-utils3 s390x 3.2.0-2 [19.3 kB] 102s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-crypto3 s390x 3.2.0-2 [23.7 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-fs3 s390x 3.2.0-2 [36.1 kB] 102s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-loop3 s390x 3.2.0-2 [7092 B] 102s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-mdraid3 s390x 3.2.0-2 [12.8 kB] 102s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-nvme3 s390x 3.2.0-2 [18.1 kB] 102s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-part3 s390x 3.2.0-2 [15.3 kB] 102s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-swap3 s390x 3.2.0-2 [7704 B] 102s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev3 s390x 3.2.0-2 [53.8 kB] 102s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libftdi1-2 s390x 1.5-7 [29.2 kB] 102s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libinih1 s390x 58-1ubuntu1 [7602 B] 102s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x python3-lazr.uri all 1.0.6-4 [13.6 kB] 102s Fetched 611 kB in 1s (1156 kB/s) 102s (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 ... 55483 files and directories currently installed.) 102s Preparing to unpack .../00-libevdev2_1.13.3+dfsg-1_s390x.deb ... 102s Unpacking libevdev2:s390x (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 102s Preparing to unpack .../01-libpipeline1_1.5.8-1_s390x.deb ... 102s Unpacking libpipeline1:s390x (1.5.8-1) over (1.5.7-2) ... 102s Preparing to unpack .../02-nano_8.2-1_s390x.deb ... 102s Unpacking nano (8.2-1) over (8.1-1) ... 102s Preparing to unpack .../03-libblockdev-utils3_3.2.0-2_s390x.deb ... 102s Unpacking libblockdev-utils3:s390x (3.2.0-2) over (3.1.1-2) ... 102s Preparing to unpack .../04-libblockdev-crypto3_3.2.0-2_s390x.deb ... 102s Unpacking libblockdev-crypto3:s390x (3.2.0-2) over (3.1.1-2) ... 102s Preparing to unpack .../05-libblockdev-fs3_3.2.0-2_s390x.deb ... 102s Unpacking libblockdev-fs3:s390x (3.2.0-2) over (3.1.1-2) ... 102s Preparing to unpack .../06-libblockdev-loop3_3.2.0-2_s390x.deb ... 102s Unpacking libblockdev-loop3:s390x (3.2.0-2) over (3.1.1-2) ... 102s Preparing to unpack .../07-libblockdev-mdraid3_3.2.0-2_s390x.deb ... 102s Unpacking libblockdev-mdraid3:s390x (3.2.0-2) over (3.1.1-2) ... 102s Preparing to unpack .../08-libblockdev-nvme3_3.2.0-2_s390x.deb ... 102s Unpacking libblockdev-nvme3:s390x (3.2.0-2) over (3.1.1-2) ... 102s Preparing to unpack .../09-libblockdev-part3_3.2.0-2_s390x.deb ... 102s Unpacking libblockdev-part3:s390x (3.2.0-2) over (3.1.1-2) ... 102s Preparing to unpack .../10-libblockdev-swap3_3.2.0-2_s390x.deb ... 102s Unpacking libblockdev-swap3:s390x (3.2.0-2) over (3.1.1-2) ... 102s Preparing to unpack .../11-libblockdev3_3.2.0-2_s390x.deb ... 102s Unpacking libblockdev3:s390x (3.2.0-2) over (3.1.1-2) ... 102s Preparing to unpack .../12-libftdi1-2_1.5-7_s390x.deb ... 102s Unpacking libftdi1-2:s390x (1.5-7) over (1.5-6build5) ... 102s Preparing to unpack .../13-libinih1_58-1ubuntu1_s390x.deb ... 102s Unpacking libinih1:s390x (58-1ubuntu1) over (55-1ubuntu2) ... 102s Preparing to unpack .../14-python3-lazr.uri_1.0.6-4_all.deb ... 103s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 103s Setting up libpipeline1:s390x (1.5.8-1) ... 103s Setting up libinih1:s390x (58-1ubuntu1) ... 103s Setting up python3-lazr.uri (1.0.6-4) ... 103s Setting up libftdi1-2:s390x (1.5-7) ... 103s Setting up libblockdev-utils3:s390x (3.2.0-2) ... 103s Setting up libblockdev-nvme3:s390x (3.2.0-2) ... 103s Setting up nano (8.2-1) ... 103s Setting up libblockdev-fs3:s390x (3.2.0-2) ... 103s Setting up libevdev2:s390x (1.13.3+dfsg-1) ... 103s Setting up libblockdev-mdraid3:s390x (3.2.0-2) ... 103s Setting up libblockdev-crypto3:s390x (3.2.0-2) ... 103s Setting up libblockdev-swap3:s390x (3.2.0-2) ... 103s Setting up libblockdev-loop3:s390x (3.2.0-2) ... 103s Setting up libblockdev3:s390x (3.2.0-2) ... 103s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 103s Setting up libblockdev-part3:s390x (3.2.0-2) ... 103s Processing triggers for libc-bin (2.40-1ubuntu3) ... 103s Processing triggers for man-db (2.12.1-3) ... 103s Processing triggers for install-info (7.1.1-1) ... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 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 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s autopkgtest [15:28:46]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 108s autopkgtest [15:28:46]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pyfaidx 110s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pyfaidx 0.8.1.2-1 (dsc) [2578 B] 110s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pyfaidx 0.8.1.2-1 (tar) [96.5 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pyfaidx 0.8.1.2-1 (diff) [7004 B] 110s gpgv: Signature made Sun Aug 11 17:37:37 2024 UTC 110s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 110s gpgv: issuer "emollier@debian.org" 110s gpgv: Can't check signature: No public key 110s dpkg-source: warning: cannot verify inline signature for ./python-pyfaidx_0.8.1.2-1.dsc: no acceptable signature found 110s autopkgtest [15:28:48]: testing package python-pyfaidx version 0.8.1.2-1 110s autopkgtest [15:28:48]: build not needed 111s autopkgtest [15:28:49]: test run-unit-test: preparing testbed 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Starting pkgProblemResolver with broken count: 0 112s Starting 2 pkgProblemResolver with broken count: 0 112s Done 112s The following additional packages will be installed: 112s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 112s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 112s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhtscodecs2 112s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 112s libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 112s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 112s python-pyfaidx-examples python3-all python3-biopython python3-cairo 112s python3-freetype python3-importlib-metadata python3-iniconfig python3-numpy 112s python3-packaging python3-pil python3-pluggy python3-pyfaidx python3-pytest 112s python3-reportlab python3-rlpycairo sgml-base tabix w3c-sgml-lib x11-common 112s xfonts-encodings xfonts-utils xml-core 112s Suggested packages: 112s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 112s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 112s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 112s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 112s gcc gfortran python-numpy-doc python3-dev python-pil-doc pdf-viewer 112s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 112s sgml-base-doc debhelper 112s Recommended packages: 112s python-biopython-doc ncbi-blast+ python3-olefile fonts-dejavu-extra 112s The following NEW packages will be installed: 112s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 112s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 112s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 112s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 112s liblcms2-2 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 112s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 112s python-pyfaidx-examples python3-all python3-biopython python3-cairo 112s python3-freetype python3-importlib-metadata python3-iniconfig python3-numpy 112s python3-packaging python3-pil python3-pluggy python3-pyfaidx python3-pytest 112s python3-reportlab python3-rlpycairo sgml-base tabix w3c-sgml-lib x11-common 112s xfonts-encodings xfonts-utils xml-core 112s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 29.1 MB/29.1 MB of archives. 112s After this operation, 89.6 MB of additional disk space will be used. 112s Get:1 /tmp/autopkgtest.v2Uuxc/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [756 B] 112s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x sgml-base all 1.31 [11.4 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 113s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 113s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 113s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 113s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 113s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 113s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 113s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB] 113s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 113s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB] 113s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.42.2-1build1 [206 kB] 113s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 113s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 113s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 113s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 113s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.21-1 [46.1 kB] 113s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-7ubuntu1 [587 kB] 113s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 14.2.0-7ubuntu1 [151 kB] 113s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 113s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 9.0.0-1 [533 kB] 113s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x libhtscodecs2 s390x 1.6.0-1build1 [87.0 kB] 113s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 113s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu2 [150 kB] 113s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 113s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 113s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.14-2build1 [172 kB] 113s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.1-1build1 [16.2 kB] 113s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.4.0-0.1 [16.2 kB] 113s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 113s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.4.0-0.1 [204 kB] 113s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 113s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.4.0-0.1 [12.2 kB] 113s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.4.0-0.1 [25.3 kB] 113s Get:37 http://ftpmaster.internal/ubuntu plucky/universe s390x python-pyfaidx-examples all 0.8.1.2-1 [38.0 kB] 114s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.12.6-0ubuntu1 [890 B] 114s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 114s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.0-2ubuntu1 [208 kB] 114s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 10.4.0-1ubuntu1 [492 kB] 114s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x python3-cairo s390x 1.26.1-2 [119 kB] 114s Get:43 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-freetype all 2.4.0-2 [81.3 kB] 114s Get:44 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 114s Get:45 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-reportlab all 4.2.2-1 [1130 kB] 114s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x xml-core all 0.19 [20.3 kB] 114s Get:47 http://ftpmaster.internal/ubuntu plucky/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 114s Get:48 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython s390x 1.83+dfsg1-3 [1680 kB] 114s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x python3-importlib-metadata all 8.2.0-2 [20.3 kB] 114s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 114s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.1-1 [41.4 kB] 114s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] 114s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfaidx all 0.8.1.2-1 [29.6 kB] 114s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest all 8.3.2-1 [251 kB] 114s Get:55 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x tabix s390x 1.20+ds-2 [544 kB] 114s Fetched 29.1 MB in 2s (16.9 MB/s) 114s Selecting previously unselected package sgml-base. 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 ... 55483 files and directories currently installed.) 114s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 114s Unpacking sgml-base (1.31) ... 114s Selecting previously unselected package fonts-dejavu-mono. 114s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 114s Unpacking fonts-dejavu-mono (2.37-8) ... 114s Selecting previously unselected package fonts-dejavu-core. 114s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 114s Unpacking fonts-dejavu-core (2.37-8) ... 114s Selecting previously unselected package libfontenc1:s390x. 114s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 114s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 114s Selecting previously unselected package libfreetype6:s390x. 114s Preparing to unpack .../04-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 114s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 114s Selecting previously unselected package x11-common. 114s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 114s Unpacking x11-common (1:7.7+23ubuntu3) ... 114s Selecting previously unselected package xfonts-encodings. 114s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 114s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 114s Selecting previously unselected package xfonts-utils. 114s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_s390x.deb ... 114s Unpacking xfonts-utils (1:7.7+7) ... 114s Selecting previously unselected package fonts-urw-base35. 114s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 114s Unpacking fonts-urw-base35 (20200910-8) ... 114s Selecting previously unselected package fontconfig-config. 114s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_s390x.deb ... 115s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 115s Selecting previously unselected package libblas3:s390x. 115s Preparing to unpack .../10-libblas3_3.12.0-3build2_s390x.deb ... 115s Unpacking libblas3:s390x (3.12.0-3build2) ... 115s Selecting previously unselected package libfontconfig1:s390x. 115s Preparing to unpack .../11-libfontconfig1_2.15.0-1.1ubuntu2_s390x.deb ... 115s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 115s Selecting previously unselected package libpixman-1-0:s390x. 115s Preparing to unpack .../12-libpixman-1-0_0.42.2-1build1_s390x.deb ... 115s Unpacking libpixman-1-0:s390x (0.42.2-1build1) ... 115s Selecting previously unselected package libxcb-render0:s390x. 115s Preparing to unpack .../13-libxcb-render0_1.17.0-2_s390x.deb ... 115s Unpacking libxcb-render0:s390x (1.17.0-2) ... 115s Selecting previously unselected package libxcb-shm0:s390x. 115s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_s390x.deb ... 115s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 115s Selecting previously unselected package libxrender1:s390x. 115s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 115s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 115s Selecting previously unselected package libcairo2:s390x. 115s Preparing to unpack .../16-libcairo2_1.18.2-2_s390x.deb ... 115s Unpacking libcairo2:s390x (1.18.2-2) ... 115s Selecting previously unselected package libdeflate0:s390x. 115s Preparing to unpack .../17-libdeflate0_1.21-1_s390x.deb ... 115s Unpacking libdeflate0:s390x (1.21-1) ... 115s Selecting previously unselected package libgfortran5:s390x. 115s Preparing to unpack .../18-libgfortran5_14.2.0-7ubuntu1_s390x.deb ... 115s Unpacking libgfortran5:s390x (14.2.0-7ubuntu1) ... 115s Selecting previously unselected package libgomp1:s390x. 115s Preparing to unpack .../19-libgomp1_14.2.0-7ubuntu1_s390x.deb ... 115s Unpacking libgomp1:s390x (14.2.0-7ubuntu1) ... 115s Selecting previously unselected package libgraphite2-3:s390x. 115s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 115s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 115s Selecting previously unselected package libharfbuzz0b:s390x. 115s Preparing to unpack .../21-libharfbuzz0b_9.0.0-1_s390x.deb ... 115s Unpacking libharfbuzz0b:s390x (9.0.0-1) ... 115s Selecting previously unselected package libhtscodecs2:s390x. 115s Preparing to unpack .../22-libhtscodecs2_1.6.0-1build1_s390x.deb ... 115s Unpacking libhtscodecs2:s390x (1.6.0-1build1) ... 115s Selecting previously unselected package libimagequant0:s390x. 115s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_s390x.deb ... 115s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 115s Selecting previously unselected package libjpeg-turbo8:s390x. 115s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu2_s390x.deb ... 115s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 115s Selecting previously unselected package libjpeg8:s390x. 115s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_s390x.deb ... 115s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 115s Selecting previously unselected package liblapack3:s390x. 115s Preparing to unpack .../26-liblapack3_3.12.0-3build2_s390x.deb ... 115s Unpacking liblapack3:s390x (3.12.0-3build2) ... 115s Selecting previously unselected package liblcms2-2:s390x. 115s Preparing to unpack .../27-liblcms2-2_2.14-2build1_s390x.deb ... 115s Unpacking liblcms2-2:s390x (2.14-2build1) ... 115s Selecting previously unselected package libraqm0:s390x. 115s Preparing to unpack .../28-libraqm0_0.10.1-1build1_s390x.deb ... 115s Unpacking libraqm0:s390x (0.10.1-1build1) ... 115s Selecting previously unselected package libsharpyuv0:s390x. 115s Preparing to unpack .../29-libsharpyuv0_1.4.0-0.1_s390x.deb ... 115s Unpacking libsharpyuv0:s390x (1.4.0-0.1) ... 115s Selecting previously unselected package libjbig0:s390x. 115s Preparing to unpack .../30-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 115s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 115s Selecting previously unselected package libwebp7:s390x. 115s Preparing to unpack .../31-libwebp7_1.4.0-0.1_s390x.deb ... 115s Unpacking libwebp7:s390x (1.4.0-0.1) ... 115s Selecting previously unselected package libtiff6:s390x. 115s Preparing to unpack .../32-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 115s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 115s Selecting previously unselected package libwebpdemux2:s390x. 115s Preparing to unpack .../33-libwebpdemux2_1.4.0-0.1_s390x.deb ... 115s Unpacking libwebpdemux2:s390x (1.4.0-0.1) ... 115s Selecting previously unselected package libwebpmux3:s390x. 115s Preparing to unpack .../34-libwebpmux3_1.4.0-0.1_s390x.deb ... 115s Unpacking libwebpmux3:s390x (1.4.0-0.1) ... 115s Selecting previously unselected package python-pyfaidx-examples. 115s Preparing to unpack .../35-python-pyfaidx-examples_0.8.1.2-1_all.deb ... 115s Unpacking python-pyfaidx-examples (0.8.1.2-1) ... 115s Selecting previously unselected package python3-all. 115s Preparing to unpack .../36-python3-all_3.12.6-0ubuntu1_s390x.deb ... 115s Unpacking python3-all (3.12.6-0ubuntu1) ... 115s Selecting previously unselected package python3-numpy. 115s Preparing to unpack .../37-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ... 115s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 115s Selecting previously unselected package libopenjp2-7:s390x. 115s Preparing to unpack .../38-libopenjp2-7_2.5.0-2ubuntu1_s390x.deb ... 115s Unpacking libopenjp2-7:s390x (2.5.0-2ubuntu1) ... 115s Selecting previously unselected package python3-pil:s390x. 115s Preparing to unpack .../39-python3-pil_10.4.0-1ubuntu1_s390x.deb ... 115s Unpacking python3-pil:s390x (10.4.0-1ubuntu1) ... 115s Selecting previously unselected package python3-cairo. 115s Preparing to unpack .../40-python3-cairo_1.26.1-2_s390x.deb ... 115s Unpacking python3-cairo (1.26.1-2) ... 115s Selecting previously unselected package python3-freetype. 115s Preparing to unpack .../41-python3-freetype_2.4.0-2_all.deb ... 115s Unpacking python3-freetype (2.4.0-2) ... 115s Selecting previously unselected package python3-rlpycairo. 115s Preparing to unpack .../42-python3-rlpycairo_0.3.0-3_all.deb ... 115s Unpacking python3-rlpycairo (0.3.0-3) ... 115s Selecting previously unselected package python3-reportlab. 115s Preparing to unpack .../43-python3-reportlab_4.2.2-1_all.deb ... 115s Unpacking python3-reportlab (4.2.2-1) ... 115s Selecting previously unselected package xml-core. 115s Preparing to unpack .../44-xml-core_0.19_all.deb ... 115s Unpacking xml-core (0.19) ... 115s Selecting previously unselected package w3c-sgml-lib. 115s Preparing to unpack .../45-w3c-sgml-lib_1.3-3_all.deb ... 115s Unpacking w3c-sgml-lib (1.3-3) ... 115s Selecting previously unselected package python3-biopython. 115s Preparing to unpack .../46-python3-biopython_1.83+dfsg1-3_s390x.deb ... 115s Unpacking python3-biopython (1.83+dfsg1-3) ... 115s Selecting previously unselected package python3-importlib-metadata. 115s Preparing to unpack .../47-python3-importlib-metadata_8.2.0-2_all.deb ... 115s Unpacking python3-importlib-metadata (8.2.0-2) ... 115s Selecting previously unselected package python3-iniconfig. 115s Preparing to unpack .../48-python3-iniconfig_1.1.1-2_all.deb ... 115s Unpacking python3-iniconfig (1.1.1-2) ... 115s Selecting previously unselected package python3-packaging. 115s Preparing to unpack .../49-python3-packaging_24.1-1_all.deb ... 115s Unpacking python3-packaging (24.1-1) ... 115s Selecting previously unselected package python3-pluggy. 115s Preparing to unpack .../50-python3-pluggy_1.5.0-1_all.deb ... 115s Unpacking python3-pluggy (1.5.0-1) ... 115s Selecting previously unselected package python3-pyfaidx. 115s Preparing to unpack .../51-python3-pyfaidx_0.8.1.2-1_all.deb ... 115s Unpacking python3-pyfaidx (0.8.1.2-1) ... 115s Selecting previously unselected package python3-pytest. 115s Preparing to unpack .../52-python3-pytest_8.3.2-1_all.deb ... 115s Unpacking python3-pytest (8.3.2-1) ... 115s Selecting previously unselected package tabix. 115s Preparing to unpack .../53-tabix_1.20+ds-2_s390x.deb ... 115s Unpacking tabix (1.20+ds-2) ... 115s Selecting previously unselected package autopkgtest-satdep. 115s Preparing to unpack .../54-1-autopkgtest-satdep.deb ... 115s Unpacking autopkgtest-satdep (0) ... 115s Setting up libhtscodecs2:s390x (1.6.0-1build1) ... 115s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 115s Setting up liblcms2-2:s390x (2.14-2build1) ... 115s Setting up python3-iniconfig (1.1.1-2) ... 115s Setting up libpixman-1-0:s390x (0.42.2-1build1) ... 115s Setting up libsharpyuv0:s390x (1.4.0-0.1) ... 115s Setting up python3-importlib-metadata (8.2.0-2) ... 115s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 115s Setting up python-pyfaidx-examples (0.8.1.2-1) ... 115s Setting up libxcb-render0:s390x (1.17.0-2) ... 115s Setting up x11-common (1:7.7+23ubuntu3) ... 116s Setting up libdeflate0:s390x (1.21-1) ... 116s Setting up python3-all (3.12.6-0ubuntu1) ... 116s Setting up libxcb-shm0:s390x (1.17.0-2) ... 116s Setting up libgomp1:s390x (14.2.0-7ubuntu1) ... 116s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 116s Setting up libfontenc1:s390x (1:1.1.8-1build1) ... 116s Setting up libblas3:s390x (3.12.0-3build2) ... 116s 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 116s Setting up python3-packaging (24.1-1) ... 116s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 116s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 116s Setting up libimagequant0:s390x (2.18.0-1build1) ... 116s Setting up fonts-dejavu-mono (2.37-8) ... 116s Setting up fonts-dejavu-core (2.37-8) ... 116s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 116s Setting up libgfortran5:s390x (14.2.0-7ubuntu1) ... 116s Setting up python3-pluggy (1.5.0-1) ... 116s Setting up libwebp7:s390x (1.4.0-0.1) ... 116s Setting up libopenjp2-7:s390x (2.5.0-2ubuntu1) ... 116s Setting up libharfbuzz0b:s390x (9.0.0-1) ... 116s Setting up sgml-base (1.31) ... 116s Setting up libwebpmux3:s390x (1.4.0-0.1) ... 116s Setting up tabix (1.20+ds-2) ... 116s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 116s Setting up python3-pyfaidx (0.8.1.2-1) ... 116s Setting up liblapack3:s390x (3.12.0-3build2) ... 116s 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 116s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 116s Setting up python3-pytest (8.3.2-1) ... 116s Setting up libwebpdemux2:s390x (1.4.0-0.1) ... 116s Setting up python3-freetype (2.4.0-2) ... 117s Setting up xfonts-utils (1:7.7+7) ... 117s Setting up libraqm0:s390x (0.10.1-1build1) ... 117s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 118s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 118s Setting up xml-core (0.19) ... 119s Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 119s Setting up fonts-urw-base35 (20200910-8) ... 119s Setting up libcairo2:s390x (1.18.2-2) ... 119s Setting up python3-pil:s390x (10.4.0-1ubuntu1) ... 119s Setting up python3-cairo (1.26.1-2) ... 119s Setting up python3-rlpycairo (0.3.0-3) ... 119s Setting up python3-reportlab (4.2.2-1) ... 120s Processing triggers for libc-bin (2.40-1ubuntu3) ... 120s Processing triggers for man-db (2.12.1-3) ... 120s Processing triggers for sgml-base (1.31) ... 120s Setting up w3c-sgml-lib (1.3-3) ... 140s Setting up python3-biopython (1.83+dfsg1-3) ... 141s Setting up autopkgtest-satdep (0) ... 144s (Reading database ... 58927 files and directories currently installed.) 144s Removing autopkgtest-satdep (0) ... 144s autopkgtest [15:29:22]: test run-unit-test: [----------------------- 144s Testing with python3.12 in /tmp/autopkgtest.v2Uuxc/build.9WZ/src: 145s ============================= test session starts ============================== 145s platform linux -- Python 3.12.7, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3.12 145s cachedir: .pytest_cache 145s rootdir: /tmp/autopkgtest.v2Uuxc/build.9WZ/src 145s configfile: pyproject.toml 145s plugins: typeguard-4.3.0 145s collecting ... collected 136 items 145s 145s tests/test_FastaRecord.py::test_sequence_uppercase PASSED [ 0%] 145s tests/test_FastaRecord.py::test_long_names PASSED [ 1%] 145s tests/test_FastaRecord.py::test_issue_62 PASSED [ 2%] 145s tests/test_FastaRecord.py::test_unpadded_length PASSED [ 2%] 145s tests/test_FastaRecord.py::test_numpy_array PASSED [ 3%] 145s tests/test_FastaRecord_iter.py::test_fetch_whole_fasta PASSED [ 4%] 145s tests/test_FastaRecord_iter.py::test_line_len PASSED [ 5%] 145s tests/test_FastaRecord_iter.py::test_reverse_iter PASSED [ 5%] 145s tests/test_FastaVariant.py::test_fetch_variant SKIPPED (pysam not in...) [ 6%] 145s tests/test_FastaVariant.py::test_fetch_hom_variant SKIPPED (pysam no...) [ 7%] 145s tests/test_FastaVariant.py::test_fetch_het_variant SKIPPED (pysam no...) [ 8%] 145s tests/test_FastaVariant.py::test_fetch_chr_not_in_vcf SKIPPED (pysam...) [ 8%] 145s tests/test_FastaVariant.py::test_all_pos SKIPPED (pysam not installed.) [ 9%] 145s tests/test_FastaVariant.py::test_all_diff SKIPPED (pysam not installed.) [ 10%] 145s tests/test_Fasta_bgzip.py::test_build_issue_126 XFAIL [ 11%] 145s tests/test_Fasta_bgzip.py::test_integer_slice PASSED [ 11%] 145s tests/test_Fasta_bgzip.py::test_integer_index PASSED [ 12%] 145s tests/test_Fasta_bgzip.py::test_fetch_whole_fasta PASSED [ 13%] 145s tests/test_Fasta_bgzip.py::test_line_len PASSED [ 13%] 145s tests/test_Fasta_bgzip.py::test_mutable_bgzf PASSED [ 14%] 145s tests/test_Fasta_bgzip.py::test_long_names XFAIL [ 15%] 145s tests/test_Fasta_bgzip.py::test_fetch_whole_entry PASSED [ 16%] 145s tests/test_Fasta_bgzip.py::test_fetch_middle PASSED [ 16%] 145s tests/test_Fasta_bgzip.py::test_fetch_end PASSED [ 17%] 145s tests/test_Fasta_bgzip.py::test_fetch_border PASSED [ 18%] 145s tests/test_Fasta_bgzip.py::test_rev PASSED [ 19%] 145s tests/test_Fasta_bgzip.py::test_fetch_past_bounds PASSED [ 19%] 145s tests/test_Fasta_bgzip.py::test_fetch_negative PASSED [ 20%] 145s tests/test_Fasta_bgzip.py::test_fetch_reversed_coordinates PASSED [ 21%] 145s tests/test_Fasta_bgzip.py::test_fetch_keyerror PASSED [ 22%] 145s tests/test_Fasta_bgzip.py::test_blank_string PASSED [ 22%] 145s tests/test_Fasta_bgzip.py::test_slice_from_beginning PASSED [ 23%] 145s tests/test_Fasta_bgzip.py::test_slice_from_end PASSED [ 24%] 145s tests/test_Fasta_bgzip.py::test_issue_74_start PASSED [ 25%] 145s tests/test_Fasta_bgzip.py::test_issue_74_consistency PASSED [ 25%] 145s tests/test_Fasta_bgzip.py::test_issue_74_end_faidx PASSED [ 26%] 145s tests/test_Fasta_bgzip.py::test_issue_74_end_fasta PASSED [ 27%] 145s tests/test_Fasta_bgzip.py::test_issue_79_fix PASSED [ 27%] 145s tests/test_Fasta_bgzip.py::test_issue_79_fix_negate PASSED [ 28%] 145s tests/test_Fasta_bgzip.py::test_issue_79_fix_one_based_false PASSED [ 29%] 145s tests/test_Fasta_bgzip.py::test_issue_79_fix_one_based_false_negate PASSED [ 30%] 145s tests/test_Fasta_bgzip.py::test_fetch_border_padded PASSED [ 30%] 145s tests/test_Fasta_integer_index.py::test_integer_slice PASSED [ 31%] 145s tests/test_Fasta_integer_index.py::test_integer_index PASSED [ 32%] 145s tests/test_Fasta_synchronization.py::TestFastaIntIndex::test_simultaneous_reads PASSED [ 33%] 145s tests/test_Fasta_synchronization.py::TestFastaIntIndex::test_simultaneous_reads_and_writes PASSED [ 33%] 145s tests/test_Fasta_synchronization.py::TestFastaIntIndex::test_simultaneous_writes PASSED [ 34%] 145s tests/test_Path.py::test_Faidx PASSED [ 35%] 145s tests/test_Path.py::test_Fasta PASSED [ 36%] 145s tests/test_bio_seqio.py::test_fetch_whole_entry PASSED [ 36%] 145s tests/test_bio_seqio.py::test_slice_whole_entry PASSED [ 37%] 145s tests/test_bio_seqio.py::test_revcomp_whole_entry PASSED [ 38%] 145s tests/test_faidx.py::test_short_line_lengths PASSED [ 38%] 145s tests/test_faidx.py::test_fetch_whole_file PASSED [ 39%] 145s tests/test_faidx.py::test_split_entry PASSED [ 40%] 145s tests/test_faidx.py::test_fetch_error PASSED [ 41%] 145s tests/test_faidx.py::test_key_warning PASSED [ 41%] 145s tests/test_faidx.py::test_auto_strand PASSED [ 42%] 145s tests/test_faidx.py::test_regexp PASSED [ 43%] 145s tests/test_faidx.py::test_not_regexp PASSED [ 44%] 145s tests/test_faidx.py::test_not_regexp_multi PASSED [ 44%] 145s tests/test_feature_bounds_check.py::test_index_zero_length PASSED [ 45%] 145s tests/test_feature_bounds_check.py::test_fetch_zero_length PASSED [ 46%] 145s tests/test_feature_bounds_check.py::test_as_raw_zero_length_subsequence PASSED [ 47%] 145s tests/test_feature_bounds_check.py::test_zero_length_subsequence PASSED [ 47%] 145s tests/test_feature_bounds_check.py::test_fetch_whole_entry PASSED [ 48%] 145s tests/test_feature_bounds_check.py::test_fetch_middle PASSED [ 49%] 145s tests/test_feature_bounds_check.py::test_fetch_end PASSED [ 50%] 145s tests/test_feature_bounds_check.py::test_fetch_border PASSED [ 50%] 145s tests/test_feature_bounds_check.py::test_rev PASSED [ 51%] 145s tests/test_feature_bounds_check.py::test_fetch_past_bounds PASSED [ 52%] 145s tests/test_feature_bounds_check.py::test_fetch_negative PASSED [ 52%] 145s tests/test_feature_bounds_check.py::test_fetch_reversed_coordinates PASSED [ 53%] 145s tests/test_feature_bounds_check.py::test_fetch_keyerror PASSED [ 54%] 145s tests/test_feature_bounds_check.py::test_blank_string PASSED [ 55%] 145s tests/test_feature_bounds_check.py::test_slice_from_beginning PASSED [ 55%] 145s tests/test_feature_bounds_check.py::test_slice_from_end PASSED [ 56%] 145s tests/test_feature_bounds_check.py::test_issue_74_start PASSED [ 57%] 145s tests/test_feature_bounds_check.py::test_issue_74_consistency PASSED [ 58%] 145s tests/test_feature_bounds_check.py::test_issue_74_end_faidx PASSED [ 58%] 145s tests/test_feature_bounds_check.py::test_issue_74_end_fasta PASSED [ 59%] 145s tests/test_feature_bounds_check.py::test_issue_79_fix PASSED [ 60%] 145s tests/test_feature_bounds_check.py::test_issue_79_fix_negate PASSED [ 61%] 145s tests/test_feature_bounds_check.py::test_issue_79_fix_one_based_false PASSED [ 61%] 145s tests/test_feature_bounds_check.py::test_issue_79_fix_one_based_false_negate PASSED [ 62%] 145s tests/test_feature_default_seq.py::test_fetch_border_padded PASSED [ 63%] 145s tests/test_feature_indexing.py::test_version_issue_206 PASSED [ 63%] 145s tests/test_feature_indexing.py::test_build PASSED [ 64%] 145s tests/test_feature_indexing.py::test_build_issue_141 PASSED [ 65%] 145s tests/test_feature_indexing.py::test_build_issue_111 PASSED [ 66%] 145s tests/test_feature_indexing.py::test_order PASSED [ 66%] 147s tests/test_feature_indexing.py::test_valgrind_short_lines PASSED [ 67%] 148s tests/test_feature_indexing.py::test_valgrind_long_lines PASSED [ 68%] 149s tests/test_feature_indexing.py::test_valgrind_blank_lines PASSED [ 69%] 151s tests/test_feature_indexing.py::test_reindex_on_modification PASSED [ 69%] 151s tests/test_feature_indexing.py::test_build_issue_83 PASSED [ 70%] 151s tests/test_feature_indexing.py::test_build_issue_96_fail_build_faidx PASSED [ 71%] 151s tests/test_feature_indexing.py::test_build_issue_96_fail_read_malformed_index_duplicate_key PASSED [ 72%] 151s tests/test_feature_indexing.py::test_read_back_index PASSED [ 72%] 152s tests/test_feature_indexing.py::test_issue_134_no_build_index PASSED [ 73%] 152s tests/test_feature_indexing.py::test_issue_144_no_defline PASSED [ 74%] 152s tests/test_feature_key_function.py::test_keys PASSED [ 75%] 152s tests/test_feature_key_function.py::test_key_function_by_dictionary_get_key PASSED [ 75%] 152s tests/test_feature_key_function.py::test_key_function_by_fetch PASSED [ 76%] 152s tests/test_feature_key_function.py::test_duplicated_keys PASSED [ 77%] 152s tests/test_feature_key_function.py::test_duplicated_keys_shortest PASSED [ 77%] 152s tests/test_feature_key_function.py::test_duplicated_keys_longest PASSED [ 78%] 152s tests/test_feature_read_ahead_buffer.py::test_buffer_false PASSED [ 79%] 152s tests/test_feature_read_ahead_buffer.py::test_buffer_true PASSED [ 80%] 152s tests/test_feature_read_ahead_buffer.py::test_buffer_exceed PASSED [ 80%] 152s tests/test_feature_read_ahead_buffer.py::test_bounds_error PASSED [ 81%] 152s tests/test_feature_read_ahead_buffer.py::test_buffer_value PASSED [ 82%] 152s tests/test_feature_sequence_as_raw.py::test_as_raw_false PASSED [ 83%] 152s tests/test_feature_sequence_as_raw.py::test_as_raw_true PASSED [ 83%] 152s tests/test_feature_sequence_as_raw.py::test_as_raw_false_error PASSED [ 84%] 152s tests/test_feature_sequence_as_raw.py::test_as_raw_true_error PASSED [ 85%] 152s tests/test_feature_sequence_as_raw.py::test_as_raw_type_when_blen_lt_0 PASSED [ 86%] 152s tests/test_feature_spliced_seq.py::test_split_seq PASSED [ 86%] 152s tests/test_feature_spliced_seq.py::test_get_seq_rc PASSED [ 87%] 152s tests/test_feature_split_char.py::test_keys PASSED [ 88%] 152s tests/test_feature_split_char.py::test_key_function_by_dictionary_get_key PASSED [ 88%] 152s tests/test_feature_split_char.py::test_key_function_by_fetch PASSED [ 89%] 152s tests/test_feature_split_char.py::test_stop PASSED [ 90%] 152s tests/test_fsspec.py::test_fsspec_fetch_whole_file SKIPPED (uncondit...) [ 91%] 152s tests/test_fsspec.py::test_fsspec_default_index SKIPPED (uncondition...) [ 91%] 152s tests/test_fsspec.py::test_fsspec_local_index SKIPPED (unconditional...) [ 92%] 152s tests/test_fsspec.py::test_fsspec_remote_index SKIPPED (unconditiona...) [ 93%] 152s tests/test_sequence_class.py::test_negate PASSED [ 94%] 152s tests/test_sequence_class.py::test_negate_metadata PASSED [ 94%] 152s tests/test_sequence_class.py::test_seq_invalid PASSED [ 95%] 152s tests/test_sequence_class.py::test_integer_index PASSED [ 96%] 152s tests/test_sequence_class.py::test_slice_index PASSED [ 97%] 152s tests/test_sequence_class.py::test_comp_invalid PASSED [ 97%] 152s tests/test_sequence_class.py::test_check_coordinates PASSED [ 98%] 152s tests/test_sequence_class.py::test_comp_valid PASSED [ 99%] 152s tests/test_sequence_class.py::test_comp_empty PASSED [100%] 152s 152s ================== 124 passed, 10 skipped, 2 xfailed in 6.99s ================== 152s autopkgtest [15:29:30]: test run-unit-test: -----------------------] 152s autopkgtest [15:29:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 152s run-unit-test PASS 153s autopkgtest [15:29:31]: test autodep8-python3: preparing testbed 228s autopkgtest [15:30:46]: testbed dpkg architecture: s390x 229s autopkgtest [15:30:47]: testbed apt version: 2.9.8 229s autopkgtest [15:30:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 229s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 230s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 230s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [172 kB] 230s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2555 kB] 230s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [40.4 kB] 230s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [212 kB] 230s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [1819 kB] 230s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [33.3 kB] 231s Fetched 4913 kB in 1s (3695 kB/s) 231s Reading package lists... 233s Reading package lists... 233s Building dependency tree... 233s Reading state information... 234s Calculating upgrade... 234s The following packages will be upgraded: 234s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 234s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 234s libblockdev3 libevdev2 libftdi1-2 libinih1 libpipeline1 nano 234s python3-lazr.uri 234s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 234s Need to get 611 kB of archives. 234s After this operation, 52.2 kB of additional disk space will be used. 234s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libevdev2 s390x 1.13.3+dfsg-1 [35.9 kB] 234s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpipeline1 s390x 1.5.8-1 [32.5 kB] 234s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x nano s390x 8.2-1 [298 kB] 234s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-utils3 s390x 3.2.0-2 [19.3 kB] 234s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-crypto3 s390x 3.2.0-2 [23.7 kB] 234s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-fs3 s390x 3.2.0-2 [36.1 kB] 234s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-loop3 s390x 3.2.0-2 [7092 B] 234s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-mdraid3 s390x 3.2.0-2 [12.8 kB] 234s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-nvme3 s390x 3.2.0-2 [18.1 kB] 234s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-part3 s390x 3.2.0-2 [15.3 kB] 234s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev-swap3 s390x 3.2.0-2 [7704 B] 234s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libblockdev3 s390x 3.2.0-2 [53.8 kB] 234s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libftdi1-2 s390x 1.5-7 [29.2 kB] 234s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libinih1 s390x 58-1ubuntu1 [7602 B] 234s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x python3-lazr.uri all 1.0.6-4 [13.6 kB] 235s Fetched 611 kB in 1s (1016 kB/s) 235s (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 ... 55483 files and directories currently installed.) 235s Preparing to unpack .../00-libevdev2_1.13.3+dfsg-1_s390x.deb ... 235s Unpacking libevdev2:s390x (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 235s Preparing to unpack .../01-libpipeline1_1.5.8-1_s390x.deb ... 235s Unpacking libpipeline1:s390x (1.5.8-1) over (1.5.7-2) ... 235s Preparing to unpack .../02-nano_8.2-1_s390x.deb ... 235s Unpacking nano (8.2-1) over (8.1-1) ... 235s Preparing to unpack .../03-libblockdev-utils3_3.2.0-2_s390x.deb ... 235s Unpacking libblockdev-utils3:s390x (3.2.0-2) over (3.1.1-2) ... 235s Preparing to unpack .../04-libblockdev-crypto3_3.2.0-2_s390x.deb ... 235s Unpacking libblockdev-crypto3:s390x (3.2.0-2) over (3.1.1-2) ... 235s Preparing to unpack .../05-libblockdev-fs3_3.2.0-2_s390x.deb ... 235s Unpacking libblockdev-fs3:s390x (3.2.0-2) over (3.1.1-2) ... 235s Preparing to unpack .../06-libblockdev-loop3_3.2.0-2_s390x.deb ... 235s Unpacking libblockdev-loop3:s390x (3.2.0-2) over (3.1.1-2) ... 235s Preparing to unpack .../07-libblockdev-mdraid3_3.2.0-2_s390x.deb ... 235s Unpacking libblockdev-mdraid3:s390x (3.2.0-2) over (3.1.1-2) ... 235s Preparing to unpack .../08-libblockdev-nvme3_3.2.0-2_s390x.deb ... 235s Unpacking libblockdev-nvme3:s390x (3.2.0-2) over (3.1.1-2) ... 235s Preparing to unpack .../09-libblockdev-part3_3.2.0-2_s390x.deb ... 235s Unpacking libblockdev-part3:s390x (3.2.0-2) over (3.1.1-2) ... 235s Preparing to unpack .../10-libblockdev-swap3_3.2.0-2_s390x.deb ... 235s Unpacking libblockdev-swap3:s390x (3.2.0-2) over (3.1.1-2) ... 235s Preparing to unpack .../11-libblockdev3_3.2.0-2_s390x.deb ... 235s Unpacking libblockdev3:s390x (3.2.0-2) over (3.1.1-2) ... 235s Preparing to unpack .../12-libftdi1-2_1.5-7_s390x.deb ... 235s Unpacking libftdi1-2:s390x (1.5-7) over (1.5-6build5) ... 235s Preparing to unpack .../13-libinih1_58-1ubuntu1_s390x.deb ... 235s Unpacking libinih1:s390x (58-1ubuntu1) over (55-1ubuntu2) ... 235s Preparing to unpack .../14-python3-lazr.uri_1.0.6-4_all.deb ... 235s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 235s Setting up libpipeline1:s390x (1.5.8-1) ... 235s Setting up libinih1:s390x (58-1ubuntu1) ... 235s Setting up python3-lazr.uri (1.0.6-4) ... 235s Setting up libftdi1-2:s390x (1.5-7) ... 235s Setting up libblockdev-utils3:s390x (3.2.0-2) ... 235s Setting up libblockdev-nvme3:s390x (3.2.0-2) ... 235s Setting up nano (8.2-1) ... 235s Setting up libblockdev-fs3:s390x (3.2.0-2) ... 235s Setting up libevdev2:s390x (1.13.3+dfsg-1) ... 235s Setting up libblockdev-mdraid3:s390x (3.2.0-2) ... 235s Setting up libblockdev-crypto3:s390x (3.2.0-2) ... 235s Setting up libblockdev-swap3:s390x (3.2.0-2) ... 235s Setting up libblockdev-loop3:s390x (3.2.0-2) ... 235s Setting up libblockdev3:s390x (3.2.0-2) ... 235s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 235s Setting up libblockdev-part3:s390x (3.2.0-2) ... 235s Processing triggers for libc-bin (2.40-1ubuntu3) ... 235s Processing triggers for man-db (2.12.1-3) ... 236s Processing triggers for install-info (7.1.1-1) ... 236s Reading package lists... 236s Building dependency tree... 236s Reading state information... 236s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 237s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 237s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 237s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 237s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 238s Reading package lists... 238s Reading package lists... 238s Building dependency tree... 238s Reading state information... 238s Calculating upgrade... 238s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 238s Reading package lists... 238s Building dependency tree... 238s Reading state information... 239s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 242s Reading package lists... 243s Building dependency tree... 243s Reading state information... 243s Starting pkgProblemResolver with broken count: 0 243s Starting 2 pkgProblemResolver with broken count: 0 243s Done 243s The following additional packages will be installed: 243s python3-all python3-importlib-metadata python3-packaging python3-pyfaidx 243s Recommended packages: 243s python3-biopython 243s The following NEW packages will be installed: 243s autopkgtest-satdep python3-all python3-importlib-metadata python3-packaging 243s python3-pyfaidx 243s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 243s Need to get 92.1 kB/92.8 kB of archives. 243s After this operation, 410 kB of additional disk space will be used. 243s Get:1 /tmp/autopkgtest.v2Uuxc/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 243s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.12.6-0ubuntu1 [890 B] 243s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-importlib-metadata all 8.2.0-2 [20.3 kB] 243s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.1-1 [41.4 kB] 243s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyfaidx all 0.8.1.2-1 [29.6 kB] 244s Fetched 92.1 kB in 0s (275 kB/s) 244s Selecting previously unselected package python3-all. 244s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 55483 files and directories currently installed.) 244s Preparing to unpack .../python3-all_3.12.6-0ubuntu1_s390x.deb ... 244s Unpacking python3-all (3.12.6-0ubuntu1) ... 244s Selecting previously unselected package python3-importlib-metadata. 244s Preparing to unpack .../python3-importlib-metadata_8.2.0-2_all.deb ... 244s Unpacking python3-importlib-metadata (8.2.0-2) ... 244s Selecting previously unselected package python3-packaging. 244s Preparing to unpack .../python3-packaging_24.1-1_all.deb ... 244s Unpacking python3-packaging (24.1-1) ... 244s Selecting previously unselected package python3-pyfaidx. 244s Preparing to unpack .../python3-pyfaidx_0.8.1.2-1_all.deb ... 244s Unpacking python3-pyfaidx (0.8.1.2-1) ... 244s Selecting previously unselected package autopkgtest-satdep. 244s Preparing to unpack .../2-autopkgtest-satdep.deb ... 244s Unpacking autopkgtest-satdep (0) ... 244s Setting up python3-importlib-metadata (8.2.0-2) ... 244s Setting up python3-all (3.12.6-0ubuntu1) ... 244s Setting up python3-packaging (24.1-1) ... 244s Setting up python3-pyfaidx (0.8.1.2-1) ... 244s Setting up autopkgtest-satdep (0) ... 244s Processing triggers for man-db (2.12.1-3) ... 246s (Reading database ... 55544 files and directories currently installed.) 246s Removing autopkgtest-satdep (0) ... 248s autopkgtest [15:31:06]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pyfaidx; print(pyfaidx)" ; done 248s autopkgtest [15:31:06]: test autodep8-python3: [----------------------- 248s Testing with python3.12: 248s 249s autopkgtest [15:31:07]: test autodep8-python3: -----------------------] 249s autopkgtest [15:31:07]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 249s autodep8-python3 PASS (superficial) 250s autopkgtest [15:31:08]: @@@@@@@@@@@@@@@@@@@@ summary 250s run-unit-test PASS 250s autodep8-python3 PASS (superficial) 261s nova [W] Using flock in prodstack6-s390x 261s flock: timeout while waiting to get lock 261s Creating nova instance adt-plucky-s390x-python-pyfaidx-20241102-152658-juju-7f2275-prod-proposed-migration-environment-14-8a5310b5-44fb-409a-b96b-fdd0de513288 from image adt/ubuntu-plucky-s390x-server-20241101.img (UUID efc880a6-ff20-4207-a161-b1113fd9bea7)... 261s nova [W] Using flock in prodstack6-s390x 261s Creating nova instance adt-plucky-s390x-python-pyfaidx-20241102-152658-juju-7f2275-prod-proposed-migration-environment-14-8a5310b5-44fb-409a-b96b-fdd0de513288 from image adt/ubuntu-plucky-s390x-server-20241101.img (UUID efc880a6-ff20-4207-a161-b1113fd9bea7)...