0s autopkgtest [22:19:57]: starting date and time: 2024-11-15 22:19:57+0000 0s autopkgtest [22:19:57]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [22:19:57]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ibd_k9gj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-pybedtools --apt-upgrade mirtop --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-pybedtools/0.10.0-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-20.secgroup --name adt-plucky-amd64-mirtop-20241115-221957-juju-7f2275-prod-proposed-migration-environment-15-59115e38-3907-45c3-ade5-f9b9868cbba7 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 61s autopkgtest [22:20:58]: testbed dpkg architecture: amd64 61s autopkgtest [22:20:58]: testbed apt version: 2.9.8 61s autopkgtest [22:20:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 62s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 62s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [93.0 kB] 62s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1029 kB] 62s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 62s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB] 62s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [111 kB] 62s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 62s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [297 kB] 62s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [811 kB] 62s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 62s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 62s Fetched 2655 kB in 1s (3086 kB/s) 63s Reading package lists... 65s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 66s The following NEW packages will be installed: 66s libassuan9 66s The following packages will be upgraded: 66s libgpgme11t64 libseccomp2 python3-cffi-backend 66s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 66s Need to get 348 kB of archives. 66s After this operation, 361 kB of additional disk space will be used. 66s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu5 [53.3 kB] 69s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build1 [96.7 kB] 69s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 69s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.1-2 [42.9 kB] 69s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.0-2ubuntu1 [155 kB] 69s Fetched 348 kB in 0s (723 kB/s) 69s (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 ... 75576 files and directories currently installed.) 69s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu5_amd64.deb ... 69s Unpacking libseccomp2:amd64 (2.5.5-1ubuntu5) over (2.5.5-1ubuntu4) ... 69s Setting up libseccomp2:amd64 (2.5.5-1ubuntu5) ... 69s (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 ... 75576 files and directories currently installed.) 69s Preparing to unpack .../python3-cffi-backend_1.17.1-2build1_amd64.deb ... 69s Unpacking python3-cffi-backend:amd64 (1.17.1-2build1) over (1.17.1-2) ... 69s Selecting previously unselected package libassuan9:amd64. 69s Preparing to unpack .../libassuan9_3.0.1-2_amd64.deb ... 69s Unpacking libassuan9:amd64 (3.0.1-2) ... 69s Preparing to unpack .../libgpgme11t64_1.24.0-2ubuntu1_amd64.deb ... 69s Unpacking libgpgme11t64:amd64 (1.24.0-2ubuntu1) over (1.23.2-5ubuntu4) ... 69s Setting up libassuan9:amd64 (3.0.1-2) ... 69s Setting up libgpgme11t64:amd64 (1.24.0-2ubuntu1) ... 69s Setting up python3-cffi-backend:amd64 (1.17.1-2build1) ... 69s Processing triggers for libc-bin (2.40-1ubuntu3) ... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 69s Reading package lists... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s Calculating upgrade... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [22:21:11]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 74s autopkgtest [22:21:11]: @@@@@@@@@@@@@@@@@@@@ apt-source mirtop 76s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (dsc) [2340 B] 76s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (tar) [718 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (diff) [10.4 kB] 76s gpgv: Signature made Sat Oct 12 13:35:08 2024 UTC 76s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 76s gpgv: issuer "tchet@debian.org" 76s gpgv: Can't check signature: No public key 76s dpkg-source: warning: cannot verify inline signature for ./mirtop_0.4.28-1.dsc: no acceptable signature found 77s autopkgtest [22:21:14]: testing package mirtop version 0.4.28-1 77s autopkgtest [22:21:14]: build not needed 78s autopkgtest [22:21:15]: 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 113s The following additional packages will be installed: 113s bedtools fontconfig-config fonts-dejavu-core fonts-dejavu-mono 113s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 113s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 113s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 113s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 113s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mirtop 113s python3-all python3-biopython python3-cairo python3-dateutil 113s python3-freetype python3-iniconfig python3-mirtop python3-numpy 113s python3-packaging python3-pandas python3-pandas-lib python3-pil 113s python3-pluggy python3-pybedtools python3-pysam python3-pytest 113s python3-reportlab python3-rlpycairo python3-six python3-tz samtools 113s seqan-apps sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils 113s xml-core 113s Suggested packages: 113s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 113s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 113s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 113s python3-rdflib python3-psycopg2 python3-scipy raxml t-coffee wise gcc 113s gfortran python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 113s python-pil-doc python-pybedtools-doc pdf-viewer python3-egenix-mxtexttools 113s python-reportlab-doc rl-accel rl-renderpm cwltool cwltool | cwl-runner 113s sgml-base-doc debhelper 113s Recommended packages: 113s python-biopython-doc ncbi-blast+ python3-scipy python3-matplotlib 113s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 113s python3-html5lib python3-lxml python3-tables python3-numba python3-olefile 113s fonts-dejavu-extra 113s The following NEW packages will be installed: 113s autopkgtest-satdep bedtools fontconfig-config fonts-dejavu-core 113s fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 libdeflate0 113s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 113s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 113s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 113s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 113s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mirtop python3-all 113s python3-biopython python3-cairo python3-dateutil python3-freetype 113s python3-iniconfig python3-mirtop python3-numpy python3-packaging 113s python3-pandas python3-pandas-lib python3-pil python3-pluggy 113s python3-pybedtools python3-pysam python3-pytest python3-reportlab 113s python3-rlpycairo python3-six python3-tz samtools seqan-apps sgml-base 113s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 113s 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. 113s Need to get 67.3 MB/67.3 MB of archives. 113s After this operation, 262 MB of additional disk space will be used. 113s Get:1 /tmp/autopkgtest.wOu7bp/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [744 B] 113s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 113s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 bedtools amd64 2.31.1+dfsg-2 [674 kB] 113s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 114s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 114s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 114s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 114s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 114s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 114s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 114s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 114s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 114s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 114s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 114s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 114s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 114s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 114s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 114s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 114s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 114s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 114s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 114s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 114s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 114s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 114s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 114s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 114s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 114s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 114s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 114s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 114s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 114s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 114s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 114s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 114s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 114s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 114s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 114s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 114s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 114s Get:42 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-pybedtools amd64 0.10.0-2 [12.4 MB] 115s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 115s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 115s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 115s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 115s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 115s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 115s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 115s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 115s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 115s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 115s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 115s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 115s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 115s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mirtop all 0.4.28-1 [61.9 kB] 115s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 mirtop all 0.4.28-1 [13.5 kB] 115s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 115s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 115s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 115s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 115s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 115s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 115s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 seqan-apps amd64 2.4.0+dfsg-16 [12.3 MB] 116s Fetched 67.3 MB in 2s (27.4 MB/s) 116s Selecting previously unselected package sgml-base. 116s (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 ... 75582 files and directories currently installed.) 116s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 116s Unpacking sgml-base (1.31) ... 116s Selecting previously unselected package bedtools. 116s Preparing to unpack .../01-bedtools_2.31.1+dfsg-2_amd64.deb ... 116s Unpacking bedtools (2.31.1+dfsg-2) ... 116s Selecting previously unselected package fonts-dejavu-mono. 116s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 116s Unpacking fonts-dejavu-mono (2.37-8) ... 116s Selecting previously unselected package fonts-dejavu-core. 116s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 116s Unpacking fonts-dejavu-core (2.37-8) ... 116s Selecting previously unselected package libfontenc1:amd64. 116s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 116s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 116s Selecting previously unselected package x11-common. 116s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 116s Unpacking x11-common (1:7.7+23ubuntu3) ... 116s Selecting previously unselected package xfonts-encodings. 116s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 116s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 116s Selecting previously unselected package xfonts-utils. 116s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_amd64.deb ... 116s Unpacking xfonts-utils (1:7.7+7) ... 116s Selecting previously unselected package fonts-urw-base35. 116s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 116s Unpacking fonts-urw-base35 (20200910-8) ... 116s Selecting previously unselected package fontconfig-config. 116s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 116s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 116s Selecting previously unselected package libblas3:amd64. 116s Preparing to unpack .../10-libblas3_3.12.0-3build2_amd64.deb ... 116s Unpacking libblas3:amd64 (3.12.0-3build2) ... 116s Selecting previously unselected package libfontconfig1:amd64. 117s Preparing to unpack .../11-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 117s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 117s Selecting previously unselected package libpixman-1-0:amd64. 117s Preparing to unpack .../12-libpixman-1-0_0.44.0-3_amd64.deb ... 117s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 117s Selecting previously unselected package libxcb-render0:amd64. 117s Preparing to unpack .../13-libxcb-render0_1.17.0-2_amd64.deb ... 117s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 117s Selecting previously unselected package libxcb-shm0:amd64. 117s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_amd64.deb ... 117s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 117s Selecting previously unselected package libxrender1:amd64. 117s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 117s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 117s Selecting previously unselected package libcairo2:amd64. 117s Preparing to unpack .../16-libcairo2_1.18.2-2_amd64.deb ... 117s Unpacking libcairo2:amd64 (1.18.2-2) ... 117s Selecting previously unselected package libdeflate0:amd64. 117s Preparing to unpack .../17-libdeflate0_1.22-1_amd64.deb ... 117s Unpacking libdeflate0:amd64 (1.22-1) ... 117s Selecting previously unselected package libgfortran5:amd64. 117s Preparing to unpack .../18-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package libgomp1:amd64. 117s Preparing to unpack .../19-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 117s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package libgraphite2-3:amd64. 117s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 117s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 117s Selecting previously unselected package libharfbuzz0b:amd64. 117s Preparing to unpack .../21-libharfbuzz0b_10.0.1-1_amd64.deb ... 117s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 117s Selecting previously unselected package libhtscodecs2:amd64. 117s Preparing to unpack .../22-libhtscodecs2_1.6.1-1_amd64.deb ... 117s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 117s Selecting previously unselected package libhts3t64:amd64. 117s Preparing to unpack .../23-libhts3t64_1.20+ds-1_amd64.deb ... 117s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 117s Selecting previously unselected package libimagequant0:amd64. 117s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_amd64.deb ... 117s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 117s Selecting previously unselected package libjpeg-turbo8:amd64. 117s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 117s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 117s Selecting previously unselected package libjpeg8:amd64. 117s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_amd64.deb ... 117s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 117s Selecting previously unselected package liblapack3:amd64. 117s Preparing to unpack .../27-liblapack3_3.12.0-3build2_amd64.deb ... 117s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 117s Selecting previously unselected package liblcms2-2:amd64. 117s Preparing to unpack .../28-liblcms2-2_2.16-2_amd64.deb ... 117s Unpacking liblcms2-2:amd64 (2.16-2) ... 117s Selecting previously unselected package liblerc4:amd64. 117s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 117s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 117s Selecting previously unselected package libraqm0:amd64. 117s Preparing to unpack .../30-libraqm0_0.10.1-1build1_amd64.deb ... 117s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 117s Selecting previously unselected package libsharpyuv0:amd64. 117s Preparing to unpack .../31-libsharpyuv0_1.4.0-0.1_amd64.deb ... 117s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 117s Selecting previously unselected package libjbig0:amd64. 117s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 117s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 117s Selecting previously unselected package libwebp7:amd64. 117s Preparing to unpack .../33-libwebp7_1.4.0-0.1_amd64.deb ... 117s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 117s Selecting previously unselected package libtiff6:amd64. 117s Preparing to unpack .../34-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 117s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 117s Selecting previously unselected package libwebpdemux2:amd64. 117s Preparing to unpack .../35-libwebpdemux2_1.4.0-0.1_amd64.deb ... 117s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 117s Selecting previously unselected package libwebpmux3:amd64. 117s Preparing to unpack .../36-libwebpmux3_1.4.0-0.1_amd64.deb ... 117s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 117s Selecting previously unselected package python3-six. 117s Preparing to unpack .../37-python3-six_1.16.0-7_all.deb ... 117s Unpacking python3-six (1.16.0-7) ... 117s Selecting previously unselected package python3-pysam. 117s Preparing to unpack .../38-python3-pysam_0.22.1+ds-2_amd64.deb ... 117s Unpacking python3-pysam (0.22.1+ds-2) ... 118s Selecting previously unselected package python3-numpy. 118s Preparing to unpack .../39-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 118s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 118s Selecting previously unselected package python3-pybedtools. 118s Preparing to unpack .../40-python3-pybedtools_0.10.0-2_amd64.deb ... 118s Unpacking python3-pybedtools (0.10.0-2) ... 118s Selecting previously unselected package python3-dateutil. 118s Preparing to unpack .../41-python3-dateutil_2.9.0-2_all.deb ... 118s Unpacking python3-dateutil (2.9.0-2) ... 118s Selecting previously unselected package python3-tz. 118s Preparing to unpack .../42-python3-tz_2024.1-2_all.deb ... 118s Unpacking python3-tz (2024.1-2) ... 118s Selecting previously unselected package python3-pandas-lib:amd64. 118s Preparing to unpack .../43-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ... 118s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 118s Selecting previously unselected package python3-pandas. 118s Preparing to unpack .../44-python3-pandas_2.2.3+dfsg-5_all.deb ... 118s Unpacking python3-pandas (2.2.3+dfsg-5) ... 118s Selecting previously unselected package libopenjp2-7:amd64. 118s Preparing to unpack .../45-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 118s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 118s Selecting previously unselected package python3-pil:amd64. 118s Preparing to unpack .../46-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 118s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 118s Selecting previously unselected package python3-cairo. 118s Preparing to unpack .../47-python3-cairo_1.26.1-2_amd64.deb ... 118s Unpacking python3-cairo (1.26.1-2) ... 118s Selecting previously unselected package python3-freetype. 118s Preparing to unpack .../48-python3-freetype_2.5.1-1_all.deb ... 118s Unpacking python3-freetype (2.5.1-1) ... 118s Selecting previously unselected package python3-rlpycairo. 119s Preparing to unpack .../49-python3-rlpycairo_0.3.0-3_all.deb ... 119s Unpacking python3-rlpycairo (0.3.0-3) ... 119s Selecting previously unselected package python3-reportlab. 119s Preparing to unpack .../50-python3-reportlab_4.2.5-1_all.deb ... 119s Unpacking python3-reportlab (4.2.5-1) ... 119s Selecting previously unselected package xml-core. 119s Preparing to unpack .../51-xml-core_0.19_all.deb ... 119s Unpacking xml-core (0.19) ... 119s Selecting previously unselected package w3c-sgml-lib. 119s Preparing to unpack .../52-w3c-sgml-lib_1.3-3_all.deb ... 119s Unpacking w3c-sgml-lib (1.3-3) ... 119s Selecting previously unselected package python3-biopython. 119s Preparing to unpack .../53-python3-biopython_1.84+dfsg-4_amd64.deb ... 119s Unpacking python3-biopython (1.84+dfsg-4) ... 119s Selecting previously unselected package python3-mirtop. 119s Preparing to unpack .../54-python3-mirtop_0.4.28-1_all.deb ... 119s Unpacking python3-mirtop (0.4.28-1) ... 119s Selecting previously unselected package mirtop. 119s Preparing to unpack .../55-mirtop_0.4.28-1_all.deb ... 119s Unpacking mirtop (0.4.28-1) ... 119s Selecting previously unselected package python3-all. 119s Preparing to unpack .../56-python3-all_3.12.6-0ubuntu1_amd64.deb ... 119s Unpacking python3-all (3.12.6-0ubuntu1) ... 119s Selecting previously unselected package python3-iniconfig. 119s Preparing to unpack .../57-python3-iniconfig_1.1.1-2_all.deb ... 119s Unpacking python3-iniconfig (1.1.1-2) ... 119s Selecting previously unselected package python3-packaging. 119s Preparing to unpack .../58-python3-packaging_24.1-1_all.deb ... 119s Unpacking python3-packaging (24.1-1) ... 119s Selecting previously unselected package python3-pluggy. 119s Preparing to unpack .../59-python3-pluggy_1.5.0-1_all.deb ... 119s Unpacking python3-pluggy (1.5.0-1) ... 119s Selecting previously unselected package python3-pytest. 119s Preparing to unpack .../60-python3-pytest_8.3.3-1_all.deb ... 119s Unpacking python3-pytest (8.3.3-1) ... 119s Selecting previously unselected package samtools. 119s Preparing to unpack .../61-samtools_1.20-3_amd64.deb ... 119s Unpacking samtools (1.20-3) ... 119s Selecting previously unselected package seqan-apps. 119s Preparing to unpack .../62-seqan-apps_2.4.0+dfsg-16_amd64.deb ... 119s Unpacking seqan-apps (2.4.0+dfsg-16) ... 119s Selecting previously unselected package autopkgtest-satdep. 119s Preparing to unpack .../63-1-autopkgtest-satdep.deb ... 119s Unpacking autopkgtest-satdep (0) ... 119s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 119s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 119s Setting up liblcms2-2:amd64 (2.16-2) ... 119s Setting up python3-iniconfig (1.1.1-2) ... 120s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 120s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 120s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 120s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 120s Setting up libxcb-render0:amd64 (1.17.0-2) ... 120s Setting up x11-common (1:7.7+23ubuntu3) ... 120s Setting up libdeflate0:amd64 (1.22-1) ... 120s Setting up python3-all (3.12.6-0ubuntu1) ... 120s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 120s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 120s Setting up python3-freetype (2.5.1-1) ... 120s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 120s Setting up python3-tz (2024.1-2) ... 120s Setting up python3-six (1.16.0-7) ... 120s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 120s Setting up libblas3:amd64 (3.12.0-3build2) ... 120s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 120s Setting up python3-packaging (24.1-1) ... 120s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 120s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 120s Setting up seqan-apps (2.4.0+dfsg-16) ... 120s Setting up fonts-dejavu-mono (2.37-8) ... 120s Setting up fonts-dejavu-core (2.37-8) ... 120s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 120s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 120s Setting up python3-pluggy (1.5.0-1) ... 120s Setting up libwebp7:amd64 (1.4.0-0.1) ... 120s Setting up libhts3t64:amd64 (1.20+ds-1) ... 120s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 120s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 120s Setting up python3-dateutil (2.9.0-2) ... 121s Setting up sgml-base (1.31) ... 121s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 121s Setting up bedtools (2.31.1+dfsg-2) ... 121s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 121s Setting up liblapack3:amd64 (3.12.0-3build2) ... 121s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 121s Setting up python3-pysam (0.22.1+ds-2) ... 121s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 121s Setting up python3-pytest (8.3.3-1) ... 121s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 121s Setting up xfonts-utils (1:7.7+7) ... 121s Setting up samtools (1.20-3) ... 121s Setting up libraqm0:amd64 (0.10.1-1build1) ... 121s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 123s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 123s Setting up xml-core (0.19) ... 123s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 123s Setting up python3-pybedtools (0.10.0-2) ... 123s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 123s Setting up fonts-urw-base35 (20200910-8) ... 123s Setting up libcairo2:amd64 (1.18.2-2) ... 123s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 124s Setting up python3-pandas (2.2.3+dfsg-5) ... 127s Setting up python3-cairo (1.26.1-2) ... 128s Setting up python3-rlpycairo (0.3.0-3) ... 128s Setting up python3-reportlab (4.2.5-1) ... 128s Processing triggers for libc-bin (2.40-1ubuntu3) ... 128s Processing triggers for man-db (2.13.0-1) ... 129s Processing triggers for sgml-base (1.31) ... 129s Setting up w3c-sgml-lib (1.3-3) ... 153s Setting up python3-biopython (1.84+dfsg-4) ... 154s Setting up python3-mirtop (0.4.28-1) ... 154s /usr/lib/python3/dist-packages/mirtop/sql/sql.py:478: SyntaxWarning: invalid escape sequence '\(' 154s print("Usage: mirtop sql --create --gff --db \(Default: mirtop.db\)") 154s Setting up mirtop (0.4.28-1) ... 154s Setting up autopkgtest-satdep (0) ... 158s (Reading database ... 81759 files and directories currently installed.) 158s Removing autopkgtest-satdep (0) ... 160s autopkgtest [22:22:37]: test run-unit-test: [----------------------- 160s Testing with python3.12 in /tmp/autopkgtest.wOu7bp/autopkgtest_tmp: 160s ============================= test session starts ============================== 160s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 160s cachedir: .pytest_cache 160s rootdir: /tmp/autopkgtest.wOu7bp/autopkgtest_tmp 160s plugins: typeguard-4.4.1 160s collecting ... collected 62 items 160s 161s test/test_automated_analysis.py::AutomatedAnalysisTest::test_count PASSED [ 1%] 162s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_fasta PASSED [ 3%] 162s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_seqbuster PASSED [ 4%] 163s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_vcf PASSED [ 6%] 164s test/test_automated_analysis.py::AutomatedAnalysisTest::test_merge_bam PASSED [ 8%] 164s test/test_automated_analysis.py::AutomatedAnalysisTest::test_simulate PASSED [ 9%] 165s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_create_1_cmd PASSED [ 11%] 165s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_create_2_cmd PASSED [ 12%] 166s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectColumns_cmd PASSED [ 14%] 167s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectCount_cmd PASSED [ 16%] 167s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectFilter_cmd PASSED [ 17%] 168s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectLimit_cmd PASSED [ 19%] 168s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectMirna_cmd PASSED [ 20%] 169s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectTextOut_cmd PASSED [ 22%] 169s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectiVariant_cmd PASSED [ 24%] 170s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_descSummary_cmd PASSED [ 25%] 170s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_showColumns_cmd PASSED [ 27%] 171s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_showSchema_cmd PASSED [ 29%] 171s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_showTables_cmd PASSED [ 30%] 172s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_statIsomirsFile_cmd PASSED [ 32%] 172s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_statIsomirs_cmd PASSED [ 33%] 173s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_bam PASSED [ 35%] 174s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_bam_chunk PASSED [ 37%] 174s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_genomic_bam PASSED [ 38%] 175s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_genomic_bam_low_memory PASSED [ 40%] 175s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_stats PASSED [ 41%] 176s test/test_automated_analysis.py::AutomatedAnalysisTest::test_update_cmd PASSED [ 43%] 177s test/test_automated_analysis.py::AutomatedAnalysisTest::test_validate_cmd PASSED [ 45%] 177s test/test_functions.py::FunctionsTest::test_alignment PASSED [ 46%] 177s test/test_functions.py::FunctionsTest::test_alignment_genomic PASSED [ 48%] 177s test/test_functions.py::FunctionsTest::test_cigar PASSED [ 50%] 177s test/test_functions.py::FunctionsTest::test_class PASSED [ 51%] 177s test/test_functions.py::FunctionsTest::test_code PASSED [ 53%] 177s test/test_functions.py::FunctionsTest::test_code_convert PASSED [ 54%] 177s test/test_functions.py::FunctionsTest::test_collapse PASSED [ 56%] 177s test/test_functions.py::FunctionsTest::test_counts PASSED [ 58%] 177s test/test_functions.py::FunctionsTest::test_database PASSED [ 59%] 177s test/test_functions.py::FunctionsTest::test_error69 PASSED [ 61%] 177s test/test_functions.py::FunctionsTest::test_export_fasta PASSED [ 62%] 177s test/test_functions.py::FunctionsTest::test_gff PASSED [ 64%] 177s test/test_functions.py::FunctionsTest::test_is_sequence PASSED [ 66%] 177s test/test_functions.py::FunctionsTest::test_issue64 PASSED [ 67%] 177s test/test_functions.py::FunctionsTest::test_keep_name PASSED [ 69%] 177s test/test_functions.py::FunctionsTest::test_locala PASSED [ 70%] 177s test/test_functions.py::FunctionsTest::test_merge PASSED [ 72%] 178s test/test_functions.py::FunctionsTest::test_optimir PASSED [ 74%] 178s test/test_functions.py::FunctionsTest::test_prost PASSED [ 75%] 178s test/test_functions.py::FunctionsTest::test_read_hairpin PASSED [ 77%] 178s test/test_functions.py::FunctionsTest::test_read_hairpin_mirgenedb PASSED [ 79%] 178s test/test_functions.py::FunctionsTest::test_read_line PASSED [ 80%] 178s test/test_functions.py::FunctionsTest::test_read_mir2chr PASSED [ 82%] 178s test/test_functions.py::FunctionsTest::test_read_mir2genomic PASSED [ 83%] 178s test/test_functions.py::FunctionsTest::test_reverse PASSED [ 85%] 178s test/test_functions.py::FunctionsTest::test_seqbuster PASSED [ 87%] 178s test/test_functions.py::FunctionsTest::test_spikeins PASSED [ 88%] 178s test/test_functions.py::FunctionsTest::test_sql PASSED [ 90%] 178s test/test_functions.py::FunctionsTest::test_srnabench PASSED [ 91%] 178s test/test_functions.py::FunctionsTest::test_stats PASSED [ 93%] 178s test/test_functions.py::FunctionsTest::test_string_variant PASSED [ 95%] 178s test/test_functions.py::FunctionsTest::test_update PASSED [ 96%] 178s test/test_functions.py::FunctionsTest::test_validator PASSED [ 98%] 178s test/test_functions.py::FunctionsTest::test_variant PASSED [100%] 178s 178s =============================== warnings summary =============================== 178s test/test_functions.py::FunctionsTest::test_alignment 178s /usr/lib/python3/dist-packages/mirtop/libs/config.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 178s import pkg_resources 178s 178s test/test_functions.py::FunctionsTest::test_alignment 178s /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 178s warnings.warn( 178s 178s test/test_functions.py::FunctionsTest::test_collapse 178s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 178s return self.run(*args, **kwds) 178s 178s test/test_functions.py::FunctionsTest::test_counts 178s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 178s return self.run(*args, **kwds) 178s 178s test/test_functions.py::FunctionsTest::test_gff 178s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 178s return self.run(*args, **kwds) 178s 178s test/test_functions.py::FunctionsTest::test_read_hairpin 178s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 178s return self.run(*args, **kwds) 178s 178s test/test_functions.py::FunctionsTest::test_sql 178s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 178s return self.run(*args, **kwds) 178s 178s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 178s ======================= 62 passed, 7 warnings in 17.95s ======================== 179s autopkgtest [22:22:56]: test run-unit-test: -----------------------] 179s autopkgtest [22:22:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 179s run-unit-test PASS 179s autopkgtest [22:22:56]: test autodep8-python3: preparing testbed 545s autopkgtest [22:29:02]: testbed dpkg architecture: amd64 545s autopkgtest [22:29:02]: testbed apt version: 2.9.8 545s autopkgtest [22:29:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 546s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 546s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 546s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1029 kB] 546s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [93.0 kB] 546s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 546s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB] 546s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [111 kB] 546s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 546s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [297 kB] 546s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [811 kB] 546s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 546s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 546s Fetched 2655 kB in 1s (3097 kB/s) 547s Reading package lists... 549s Reading package lists... 549s Building dependency tree... 549s Reading state information... 549s Calculating upgrade... 550s The following NEW packages will be installed: 550s libassuan9 550s The following packages will be upgraded: 550s libgpgme11t64 libseccomp2 python3-cffi-backend 550s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 550s Need to get 348 kB of archives. 550s After this operation, 361 kB of additional disk space will be used. 550s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu5 [53.3 kB] 550s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build1 [96.7 kB] 550s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.1-2 [42.9 kB] 550s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.0-2ubuntu1 [155 kB] 550s Fetched 348 kB in 0s (721 kB/s) 551s (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 ... 75576 files and directories currently installed.) 551s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu5_amd64.deb ... 551s Unpacking libseccomp2:amd64 (2.5.5-1ubuntu5) over (2.5.5-1ubuntu4) ... 551s Setting up libseccomp2:amd64 (2.5.5-1ubuntu5) ... 551s (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 ... 75576 files and directories currently installed.) 551s Preparing to unpack .../python3-cffi-backend_1.17.1-2build1_amd64.deb ... 551s Unpacking python3-cffi-backend:amd64 (1.17.1-2build1) over (1.17.1-2) ... 551s Selecting previously unselected package libassuan9:amd64. 551s Preparing to unpack .../libassuan9_3.0.1-2_amd64.deb ... 551s Unpacking libassuan9:amd64 (3.0.1-2) ... 551s Preparing to unpack .../libgpgme11t64_1.24.0-2ubuntu1_amd64.deb ... 551s Unpacking libgpgme11t64:amd64 (1.24.0-2ubuntu1) over (1.23.2-5ubuntu4) ... 551s Setting up libassuan9:amd64 (3.0.1-2) ... 551s Setting up libgpgme11t64:amd64 (1.24.0-2ubuntu1) ... 551s Setting up python3-cffi-backend:amd64 (1.17.1-2build1) ... 551s Processing triggers for libc-bin (2.40-1ubuntu3) ... 551s Reading package lists... 551s Building dependency tree... 551s Reading state information... 552s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 552s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 552s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 552s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 552s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 553s Reading package lists... 553s Reading package lists... 554s Building dependency tree... 554s Reading state information... 554s Calculating upgrade... 554s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 554s Reading package lists... 555s Building dependency tree... 555s Reading state information... 555s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 561s Reading package lists... 561s Building dependency tree... 561s Reading state information... 561s Starting pkgProblemResolver with broken count: 0 562s Starting 2 pkgProblemResolver with broken count: 0 562s Done 562s The following additional packages will be installed: 562s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 562s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 562s libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 562s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 562s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 562s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-all 562s python3-biopython python3-cairo python3-dateutil python3-freetype 562s python3-mirtop python3-numpy python3-pandas python3-pandas-lib python3-pil 562s python3-pybedtools python3-pysam python3-reportlab python3-rlpycairo 562s python3-six python3-tz sgml-base w3c-sgml-lib x11-common xfonts-encodings 562s xfonts-utils xml-core 562s Suggested packages: 562s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 562s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 562s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 562s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 562s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 562s python3-statsmodels python-pil-doc python-pybedtools-doc pdf-viewer 562s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 562s sgml-base-doc debhelper 562s Recommended packages: 562s python-biopython-doc ncbi-blast+ python3-scipy python3-matplotlib 562s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 562s python3-html5lib python3-lxml python3-tables python3-numba python3-olefile 562s fonts-dejavu-extra 562s The following NEW packages will be installed: 562s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 562s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 562s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 562s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 562s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 562s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-all 562s python3-biopython python3-cairo python3-dateutil python3-freetype 562s python3-mirtop python3-numpy python3-pandas python3-pandas-lib python3-pil 562s python3-pybedtools python3-pysam python3-reportlab python3-rlpycairo 562s python3-six python3-tz sgml-base w3c-sgml-lib x11-common xfonts-encodings 562s xfonts-utils xml-core 562s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 562s Need to get 53.3 MB/53.3 MB of archives. 562s After this operation, 193 MB of additional disk space will be used. 562s Get:1 /tmp/autopkgtest.wOu7bp/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 562s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 562s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 562s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 562s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 562s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 562s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 563s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 563s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 563s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 563s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 563s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 563s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 563s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 563s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 563s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 563s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 563s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 563s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 563s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 563s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 563s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 563s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 563s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 563s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 563s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 563s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 563s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 563s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 563s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 563s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 563s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 563s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 563s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 563s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 563s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 563s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 563s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 563s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 563s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 563s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 563s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 563s Get:43 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 563s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 563s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 563s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 563s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 563s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 563s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 563s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 563s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 564s Get:52 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-pybedtools amd64 0.10.0-2 [12.4 MB] 564s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 564s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 564s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 564s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mirtop all 0.4.28-1 [61.9 kB] 564s Fetched 53.3 MB in 2s (24.1 MB/s) 564s Selecting previously unselected package sgml-base. 564s (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 ... 75582 files and directories currently installed.) 564s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 564s Unpacking sgml-base (1.31) ... 564s Selecting previously unselected package fonts-dejavu-mono. 565s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 565s Unpacking fonts-dejavu-mono (2.37-8) ... 565s Selecting previously unselected package fonts-dejavu-core. 565s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 565s Unpacking fonts-dejavu-core (2.37-8) ... 565s Selecting previously unselected package libfontenc1:amd64. 565s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 565s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 565s Selecting previously unselected package x11-common. 565s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 565s Unpacking x11-common (1:7.7+23ubuntu3) ... 565s Selecting previously unselected package xfonts-encodings. 565s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 565s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 565s Selecting previously unselected package xfonts-utils. 565s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_amd64.deb ... 565s Unpacking xfonts-utils (1:7.7+7) ... 565s Selecting previously unselected package fonts-urw-base35. 565s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 565s Unpacking fonts-urw-base35 (20200910-8) ... 565s Selecting previously unselected package fontconfig-config. 565s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 565s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 565s Selecting previously unselected package libblas3:amd64. 565s Preparing to unpack .../09-libblas3_3.12.0-3build2_amd64.deb ... 565s Unpacking libblas3:amd64 (3.12.0-3build2) ... 565s Selecting previously unselected package libfontconfig1:amd64. 565s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 565s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 565s Selecting previously unselected package libpixman-1-0:amd64. 565s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_amd64.deb ... 565s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 565s Selecting previously unselected package libxcb-render0:amd64. 565s Preparing to unpack .../12-libxcb-render0_1.17.0-2_amd64.deb ... 565s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 565s Selecting previously unselected package libxcb-shm0:amd64. 565s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_amd64.deb ... 565s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 565s Selecting previously unselected package libxrender1:amd64. 565s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 565s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 565s Selecting previously unselected package libcairo2:amd64. 565s Preparing to unpack .../15-libcairo2_1.18.2-2_amd64.deb ... 565s Unpacking libcairo2:amd64 (1.18.2-2) ... 565s Selecting previously unselected package libdeflate0:amd64. 565s Preparing to unpack .../16-libdeflate0_1.22-1_amd64.deb ... 565s Unpacking libdeflate0:amd64 (1.22-1) ... 565s Selecting previously unselected package libgfortran5:amd64. 565s Preparing to unpack .../17-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 565s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 565s Selecting previously unselected package libgomp1:amd64. 565s Preparing to unpack .../18-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 565s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 565s Selecting previously unselected package libgraphite2-3:amd64. 565s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 565s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 565s Selecting previously unselected package libharfbuzz0b:amd64. 565s Preparing to unpack .../20-libharfbuzz0b_10.0.1-1_amd64.deb ... 565s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 565s Selecting previously unselected package libhtscodecs2:amd64. 566s Preparing to unpack .../21-libhtscodecs2_1.6.1-1_amd64.deb ... 566s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 566s Selecting previously unselected package libhts3t64:amd64. 566s Preparing to unpack .../22-libhts3t64_1.20+ds-1_amd64.deb ... 566s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 566s Selecting previously unselected package libimagequant0:amd64. 566s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_amd64.deb ... 566s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 566s Selecting previously unselected package libjpeg-turbo8:amd64. 566s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 566s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 566s Selecting previously unselected package libjpeg8:amd64. 566s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_amd64.deb ... 566s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 566s Selecting previously unselected package liblapack3:amd64. 566s Preparing to unpack .../26-liblapack3_3.12.0-3build2_amd64.deb ... 566s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 566s Selecting previously unselected package liblcms2-2:amd64. 566s Preparing to unpack .../27-liblcms2-2_2.16-2_amd64.deb ... 566s Unpacking liblcms2-2:amd64 (2.16-2) ... 566s Selecting previously unselected package liblerc4:amd64. 566s Preparing to unpack .../28-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 566s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 566s Selecting previously unselected package libraqm0:amd64. 566s Preparing to unpack .../29-libraqm0_0.10.1-1build1_amd64.deb ... 566s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 566s Selecting previously unselected package libsharpyuv0:amd64. 566s Preparing to unpack .../30-libsharpyuv0_1.4.0-0.1_amd64.deb ... 566s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 566s Selecting previously unselected package libjbig0:amd64. 566s Preparing to unpack .../31-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 566s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 566s Selecting previously unselected package libwebp7:amd64. 566s Preparing to unpack .../32-libwebp7_1.4.0-0.1_amd64.deb ... 566s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 566s Selecting previously unselected package libtiff6:amd64. 566s Preparing to unpack .../33-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 566s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 566s Selecting previously unselected package libwebpdemux2:amd64. 566s Preparing to unpack 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Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 566s Selecting previously unselected package python3-cairo. 566s Preparing to unpack .../40-python3-cairo_1.26.1-2_amd64.deb ... 566s Unpacking python3-cairo (1.26.1-2) ... 566s Selecting previously unselected package python3-freetype. 566s Preparing to unpack .../41-python3-freetype_2.5.1-1_all.deb ... 566s Unpacking python3-freetype (2.5.1-1) ... 566s Selecting previously unselected package python3-rlpycairo. 566s Preparing to unpack .../42-python3-rlpycairo_0.3.0-3_all.deb ... 566s Unpacking python3-rlpycairo (0.3.0-3) ... 566s Selecting previously unselected package python3-reportlab. 566s Preparing to unpack .../43-python3-reportlab_4.2.5-1_all.deb ... 566s Unpacking python3-reportlab (4.2.5-1) ... 566s Selecting previously unselected package xml-core. 566s Preparing to unpack .../44-xml-core_0.19_all.deb ... 566s Unpacking xml-core (0.19) ... 566s Selecting previously unselected package w3c-sgml-lib. 566s Preparing to unpack .../45-w3c-sgml-lib_1.3-3_all.deb ... 566s Unpacking w3c-sgml-lib (1.3-3) ... 566s Selecting previously unselected package python3-biopython. 566s Preparing to unpack .../46-python3-biopython_1.84+dfsg-4_amd64.deb ... 566s Unpacking python3-biopython (1.84+dfsg-4) ... 567s Selecting previously unselected package python3-six. 567s Preparing to unpack .../47-python3-six_1.16.0-7_all.deb ... 567s Unpacking python3-six (1.16.0-7) ... 567s Selecting previously unselected package python3-dateutil. 567s Preparing to unpack .../48-python3-dateutil_2.9.0-2_all.deb ... 567s Unpacking python3-dateutil (2.9.0-2) ... 567s Selecting previously unselected package python3-pysam. 567s Preparing to unpack .../49-python3-pysam_0.22.1+ds-2_amd64.deb ... 567s Unpacking python3-pysam (0.22.1+ds-2) ... 567s Selecting previously unselected package python3-pybedtools. 567s Preparing to unpack .../50-python3-pybedtools_0.10.0-2_amd64.deb ... 567s Unpacking python3-pybedtools (0.10.0-2) ... 567s Selecting previously unselected package python3-tz. 567s Preparing to unpack .../51-python3-tz_2024.1-2_all.deb ... 567s Unpacking python3-tz (2024.1-2) ... 567s Selecting previously unselected package python3-pandas-lib:amd64. 567s Preparing to unpack .../52-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ... 567s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 567s Selecting previously unselected package python3-pandas. 567s Preparing to unpack .../53-python3-pandas_2.2.3+dfsg-5_all.deb ... 567s Unpacking python3-pandas (2.2.3+dfsg-5) ... 567s Selecting previously unselected package python3-mirtop. 567s Preparing to unpack .../54-python3-mirtop_0.4.28-1_all.deb ... 567s Unpacking python3-mirtop (0.4.28-1) ... 567s Selecting previously unselected package autopkgtest-satdep. 567s Preparing to unpack .../55-2-autopkgtest-satdep.deb ... 567s Unpacking autopkgtest-satdep (0) ... 567s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 567s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 567s Setting up liblcms2-2:amd64 (2.16-2) ... 567s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 567s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 567s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 567s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 567s Setting up libxcb-render0:amd64 (1.17.0-2) ... 567s Setting up x11-common (1:7.7+23ubuntu3) ... 568s Setting up libdeflate0:amd64 (1.22-1) ... 568s Setting up python3-all (3.12.6-0ubuntu1) ... 568s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 568s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 568s Setting up python3-freetype (2.5.1-1) ... 568s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 568s Setting up python3-tz (2024.1-2) ... 568s Setting up python3-six (1.16.0-7) ... 568s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 568s Setting up libblas3:amd64 (3.12.0-3build2) ... 568s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 568s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 568s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 568s Setting up fonts-dejavu-mono (2.37-8) ... 568s Setting up fonts-dejavu-core (2.37-8) ... 568s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 568s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 568s Setting up libwebp7:amd64 (1.4.0-0.1) ... 568s Setting up libhts3t64:amd64 (1.20+ds-1) ... 568s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 568s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 568s Setting up python3-dateutil (2.9.0-2) ... 568s Setting up sgml-base (1.31) ... 568s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 568s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 568s Setting up liblapack3:amd64 (3.12.0-3build2) ... 568s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 568s Setting up python3-pysam (0.22.1+ds-2) ... 568s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 569s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 569s Setting up xfonts-utils (1:7.7+7) ... 569s Setting up libraqm0:amd64 (0.10.1-1build1) ... 569s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 570s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 570s Setting up xml-core (0.19) ... 570s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 570s Setting up python3-pybedtools (0.10.0-2) ... 571s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 571s Setting up fonts-urw-base35 (20200910-8) ... 571s Setting up libcairo2:amd64 (1.18.2-2) ... 571s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 571s Setting up python3-pandas (2.2.3+dfsg-5) ... 575s Setting up python3-cairo (1.26.1-2) ... 575s Setting up python3-rlpycairo (0.3.0-3) ... 575s Setting up python3-reportlab (4.2.5-1) ... 576s Processing triggers for libc-bin (2.40-1ubuntu3) ... 576s Processing triggers for man-db (2.13.0-1) ... 577s Processing triggers for sgml-base (1.31) ... 577s Setting up w3c-sgml-lib (1.3-3) ... 600s Setting up python3-biopython (1.84+dfsg-4) ... 600s Setting up python3-mirtop (0.4.28-1) ... 601s /usr/lib/python3/dist-packages/mirtop/sql/sql.py:478: SyntaxWarning: invalid escape sequence '\(' 601s print("Usage: mirtop sql --create --gff --db \(Default: mirtop.db\)") 601s Setting up autopkgtest-satdep (0) ... 604s (Reading database ... 81224 files and directories currently installed.) 604s Removing autopkgtest-satdep (0) ... 606s autopkgtest [22:30:03]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import mirtop; print(mirtop)" ; done 606s autopkgtest [22:30:03]: test autodep8-python3: [----------------------- 606s Testing with python3.12: 606s 606s autopkgtest [22:30:03]: test autodep8-python3: -----------------------] 607s autopkgtest [22:30:04]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 607s autodep8-python3 PASS (superficial) 607s autopkgtest [22:30:04]: @@@@@@@@@@@@@@@@@@@@ summary 607s run-unit-test PASS 607s autodep8-python3 PASS (superficial) 619s nova [W] Skipping flock for amd64 619s Creating nova instance adt-plucky-amd64-mirtop-20241115-221957-juju-7f2275-prod-proposed-migration-environment-15-59115e38-3907-45c3-ade5-f9b9868cbba7 from image adt/ubuntu-plucky-amd64-server-20241115.img (UUID 9bb4dd9c-454f-45da-a125-77b9d27ed145)... 619s nova [W] Skipping flock for amd64 619s Creating nova instance adt-plucky-amd64-mirtop-20241115-221957-juju-7f2275-prod-proposed-migration-environment-15-59115e38-3907-45c3-ade5-f9b9868cbba7 from image adt/ubuntu-plucky-amd64-server-20241115.img (UUID 9bb4dd9c-454f-45da-a125-77b9d27ed145)... 619s nova [W] nova quota exceeded (attempt #0)