0s autopkgtest [20:02:12]: starting date and time: 2024-11-15 20:02:12+0000 0s autopkgtest [20:02:12]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [20:02:12]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lyrlfy4z/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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-20.secgroup --name adt-plucky-arm64-mirtop-20241115-200212-juju-7f2275-prod-proposed-migration-environment-15-0e187799-2915-4d36-8b7e-3fbb0e06aaab --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,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/ 64s autopkgtest [20:03:16]: testbed dpkg architecture: arm64 64s autopkgtest [20:03:16]: testbed apt version: 2.9.8 64s autopkgtest [20:03:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 65s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1043 kB] 65s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [92.2 kB] 65s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [168 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [789 kB] 65s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6404 B] 65s Fetched 2245 kB in 1s (2738 kB/s) 65s Reading package lists... 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 69s Calculating upgrade... 69s The following NEW packages will be installed: 69s libassuan9 69s The following packages will be upgraded: 69s libgpgme11t64 libseccomp2 python3-cffi-backend python3-markupsafe 69s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 69s Need to get 337 kB of archives. 69s After this operation, 447 kB of additional disk space will be used. 69s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libseccomp2 arm64 2.5.5-1ubuntu5 [51.4 kB] 70s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cffi-backend arm64 1.17.1-2build1 [89.9 kB] 70s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libassuan9 arm64 3.0.1-2 [40.6 kB] 70s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgpgme11t64 arm64 1.24.0-2ubuntu1 [142 kB] 70s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-markupsafe arm64 2.1.5-1build3 [13.0 kB] 70s Fetched 337 kB in 0s (686 kB/s) 71s (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 ... 79957 files and directories currently installed.) 71s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu5_arm64.deb ... 71s Unpacking libseccomp2:arm64 (2.5.5-1ubuntu5) over (2.5.5-1ubuntu4) ... 71s Setting up libseccomp2:arm64 (2.5.5-1ubuntu5) ... 71s (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 ... 79957 files and directories currently installed.) 71s Preparing to unpack .../python3-cffi-backend_1.17.1-2build1_arm64.deb ... 71s Unpacking python3-cffi-backend:arm64 (1.17.1-2build1) over (1.17.1-2) ... 71s Selecting previously unselected package libassuan9:arm64. 71s Preparing to unpack .../libassuan9_3.0.1-2_arm64.deb ... 71s Unpacking libassuan9:arm64 (3.0.1-2) ... 71s Preparing to unpack .../libgpgme11t64_1.24.0-2ubuntu1_arm64.deb ... 71s Unpacking libgpgme11t64:arm64 (1.24.0-2ubuntu1) over (1.23.2-5ubuntu4) ... 71s Preparing to unpack .../python3-markupsafe_2.1.5-1build3_arm64.deb ... 71s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ... 71s Setting up python3-markupsafe (2.1.5-1build3) ... 71s Setting up libassuan9:arm64 (3.0.1-2) ... 71s Setting up libgpgme11t64:arm64 (1.24.0-2ubuntu1) ... 71s Setting up python3-cffi-backend:arm64 (1.17.1-2build1) ... 71s Processing triggers for libc-bin (2.40-1ubuntu3) ... 71s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 73s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 73s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 74s Reading package lists... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 75s Calculating upgrade... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s autopkgtest [20:03:31]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 79s autopkgtest [20:03:31]: @@@@@@@@@@@@@@@@@@@@ apt-source mirtop 81s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (dsc) [2340 B] 81s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (tar) [718 kB] 81s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (diff) [10.4 kB] 81s gpgv: Signature made Sat Oct 12 13:35:08 2024 UTC 81s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 81s gpgv: issuer "tchet@debian.org" 81s gpgv: Can't check signature: No public key 81s dpkg-source: warning: cannot verify inline signature for ./mirtop_0.4.28-1.dsc: no acceptable signature found 81s autopkgtest [20:03:33]: testing package mirtop version 0.4.28-1 82s autopkgtest [20:03:34]: build not needed 83s autopkgtest [20:03:35]: test run-unit-test: preparing testbed 84s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Starting pkgProblemResolver with broken count: 0 85s Starting 2 pkgProblemResolver with broken count: 0 85s Done 86s The following additional packages will be installed: 86s bedtools fontconfig-config fonts-dejavu-core fonts-dejavu-mono 86s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 86s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 86s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 86s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 86s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mirtop 86s python3-all python3-biopython python3-cairo python3-dateutil 86s python3-freetype python3-iniconfig python3-mirtop python3-numpy 86s python3-packaging python3-pandas python3-pandas-lib python3-pil 86s python3-pluggy python3-pybedtools python3-pysam python3-pytest 86s python3-reportlab python3-rlpycairo python3-six python3-tz samtools 86s seqan-apps sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils 86s xml-core 86s Suggested packages: 86s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 86s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 86s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 86s python3-rdflib python3-psycopg2 python3-scipy raxml t-coffee wise gcc 86s gfortran python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 86s python-pil-doc python-pybedtools-doc pdf-viewer python3-egenix-mxtexttools 86s python-reportlab-doc rl-accel rl-renderpm cwltool cwltool | cwl-runner 86s sgml-base-doc debhelper 86s Recommended packages: 86s python-biopython-doc ncbi-blast+ python3-scipy python3-matplotlib 86s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 86s python3-html5lib python3-lxml python3-tables python3-olefile 86s fonts-dejavu-extra 86s The following NEW packages will be installed: 86s autopkgtest-satdep bedtools fontconfig-config fonts-dejavu-core 86s fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 libdeflate0 86s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 86s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 86s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 86s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 86s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mirtop python3-all 86s python3-biopython python3-cairo python3-dateutil python3-freetype 86s python3-iniconfig python3-mirtop python3-numpy python3-packaging 86s python3-pandas python3-pandas-lib python3-pil python3-pluggy 86s python3-pybedtools python3-pysam python3-pytest python3-reportlab 86s python3-rlpycairo python3-six python3-tz samtools seqan-apps sgml-base 86s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 86s 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. 86s Need to get 63.6 MB/63.6 MB of archives. 86s After this operation, 246 MB of additional disk space will be used. 86s Get:1 /tmp/autopkgtest.eDKomo/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [748 B] 86s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 86s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 bedtools arm64 2.31.1+dfsg-2 [636 kB] 86s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 87s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 87s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 87s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 87s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 87s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 87s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 87s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 87s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 87s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 87s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 87s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 87s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 87s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 87s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 87s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 87s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 87s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 87s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 87s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 87s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 87s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 87s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 87s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 87s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 87s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 87s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 87s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 87s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 87s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 87s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 87s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 87s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 87s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 87s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 87s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 87s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 87s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 87s Get:42 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-pybedtools arm64 0.10.0-2 [12.4 MB] 88s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 88s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 88s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 88s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 88s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 88s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 88s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 88s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 88s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 88s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 88s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 88s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 88s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 88s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mirtop all 0.4.28-1 [61.9 kB] 88s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 mirtop all 0.4.28-1 [13.5 kB] 88s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 88s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 88s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 88s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 88s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 88s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.20-3 [590 kB] 88s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 seqan-apps arm64 2.4.0+dfsg-16 [11.8 MB] 89s Fetched 63.6 MB in 3s (24.2 MB/s) 89s Selecting previously unselected package sgml-base. 89s (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 ... 79964 files and directories currently installed.) 89s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 89s Unpacking sgml-base (1.31) ... 89s Selecting previously unselected package bedtools. 89s Preparing to unpack .../01-bedtools_2.31.1+dfsg-2_arm64.deb ... 89s Unpacking bedtools (2.31.1+dfsg-2) ... 89s Selecting previously unselected package fonts-dejavu-mono. 89s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 89s Unpacking fonts-dejavu-mono (2.37-8) ... 89s Selecting previously unselected package fonts-dejavu-core. 89s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 89s Unpacking fonts-dejavu-core (2.37-8) ... 89s Selecting previously unselected package libfontenc1:arm64. 89s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 89s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 89s Selecting previously unselected package x11-common. 89s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 89s Unpacking x11-common (1:7.7+23ubuntu3) ... 89s Selecting previously unselected package xfonts-encodings. 89s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 89s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 89s Selecting previously unselected package xfonts-utils. 89s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_arm64.deb ... 89s Unpacking xfonts-utils (1:7.7+7) ... 89s Selecting previously unselected package fonts-urw-base35. 89s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 90s Unpacking fonts-urw-base35 (20200910-8) ... 90s Selecting previously unselected package fontconfig-config. 90s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 90s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 90s Selecting previously unselected package libblas3:arm64. 90s Preparing to unpack .../10-libblas3_3.12.0-3build2_arm64.deb ... 90s Unpacking libblas3:arm64 (3.12.0-3build2) ... 90s Selecting previously unselected package libfontconfig1:arm64. 90s Preparing to unpack .../11-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 90s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 90s Selecting previously unselected package libpixman-1-0:arm64. 90s Preparing to unpack .../12-libpixman-1-0_0.44.0-3_arm64.deb ... 90s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 90s Selecting previously unselected package libxcb-render0:arm64. 90s Preparing to unpack .../13-libxcb-render0_1.17.0-2_arm64.deb ... 90s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 90s Selecting previously unselected package libxcb-shm0:arm64. 90s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_arm64.deb ... 90s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 90s Selecting previously unselected package libxrender1:arm64. 90s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 90s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 90s Selecting previously unselected package libcairo2:arm64. 90s Preparing to unpack .../16-libcairo2_1.18.2-2_arm64.deb ... 90s Unpacking libcairo2:arm64 (1.18.2-2) ... 90s Selecting previously unselected package libdeflate0:arm64. 90s Preparing to unpack .../17-libdeflate0_1.22-1_arm64.deb ... 90s Unpacking libdeflate0:arm64 (1.22-1) ... 90s Selecting previously unselected package libgfortran5:arm64. 90s Preparing to unpack .../18-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 90s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 90s Selecting previously unselected package libgomp1:arm64. 90s Preparing to unpack .../19-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 90s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 90s Selecting previously unselected package libgraphite2-3:arm64. 90s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 90s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 90s Selecting previously unselected package libharfbuzz0b:arm64. 90s Preparing to unpack .../21-libharfbuzz0b_10.0.1-1_arm64.deb ... 90s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 90s Selecting previously unselected package libhtscodecs2:arm64. 90s Preparing to unpack .../22-libhtscodecs2_1.6.1-1_arm64.deb ... 90s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 90s Selecting previously unselected package libhts3t64:arm64. 90s Preparing to unpack .../23-libhts3t64_1.20+ds-1_arm64.deb ... 90s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 90s Selecting previously unselected package libimagequant0:arm64. 91s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_arm64.deb ... 91s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 91s Selecting previously unselected package libjpeg-turbo8:arm64. 91s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 91s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 91s Selecting previously unselected package libjpeg8:arm64. 91s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_arm64.deb ... 91s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 91s Selecting previously unselected package liblapack3:arm64. 91s Preparing to unpack .../27-liblapack3_3.12.0-3build2_arm64.deb ... 91s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 91s Selecting previously unselected package liblcms2-2:arm64. 91s Preparing to unpack .../28-liblcms2-2_2.16-2_arm64.deb ... 91s Unpacking liblcms2-2:arm64 (2.16-2) ... 91s Selecting previously unselected package liblerc4:arm64. 91s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 91s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 91s Selecting previously unselected package libraqm0:arm64. 91s Preparing to unpack .../30-libraqm0_0.10.1-1build1_arm64.deb ... 91s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 91s Selecting previously unselected package libsharpyuv0:arm64. 91s Preparing to unpack .../31-libsharpyuv0_1.4.0-0.1_arm64.deb ... 91s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 91s Selecting previously unselected package libjbig0:arm64. 91s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 91s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 91s Selecting previously unselected package libwebp7:arm64. 91s Preparing to unpack .../33-libwebp7_1.4.0-0.1_arm64.deb ... 91s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 91s Selecting previously unselected package libtiff6:arm64. 91s Preparing to unpack .../34-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 91s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 91s Selecting previously unselected package libwebpdemux2:arm64. 91s Preparing to unpack .../35-libwebpdemux2_1.4.0-0.1_arm64.deb ... 91s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 91s Selecting previously unselected package libwebpmux3:arm64. 91s Preparing to unpack .../36-libwebpmux3_1.4.0-0.1_arm64.deb ... 91s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 91s Selecting previously unselected package python3-six. 91s Preparing to unpack .../37-python3-six_1.16.0-7_all.deb ... 91s Unpacking python3-six (1.16.0-7) ... 91s Selecting previously unselected package python3-pysam. 91s Preparing to unpack .../38-python3-pysam_0.22.1+ds-2_arm64.deb ... 91s Unpacking python3-pysam (0.22.1+ds-2) ... 91s Selecting previously unselected package python3-numpy. 91s Preparing to unpack .../39-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 91s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 91s Selecting previously unselected package python3-pybedtools. 91s Preparing to unpack .../40-python3-pybedtools_0.10.0-2_arm64.deb ... 91s Unpacking python3-pybedtools (0.10.0-2) ... 92s Selecting previously unselected package python3-dateutil. 92s Preparing to unpack .../41-python3-dateutil_2.9.0-2_all.deb ... 92s Unpacking python3-dateutil (2.9.0-2) ... 92s Selecting previously unselected package python3-tz. 92s Preparing to unpack .../42-python3-tz_2024.1-2_all.deb ... 92s Unpacking python3-tz (2024.1-2) ... 92s Selecting previously unselected package python3-pandas-lib:arm64. 92s Preparing to unpack .../43-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 92s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 92s Selecting previously unselected package python3-pandas. 92s Preparing to unpack .../44-python3-pandas_2.2.3+dfsg-5_all.deb ... 92s Unpacking python3-pandas (2.2.3+dfsg-5) ... 92s Selecting previously unselected package libopenjp2-7:arm64. 92s Preparing to unpack .../45-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 92s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 92s Selecting previously unselected package python3-pil:arm64. 92s Preparing to unpack .../46-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 92s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 92s Selecting previously unselected package python3-cairo. 92s Preparing to unpack .../47-python3-cairo_1.26.1-2_arm64.deb ... 92s Unpacking python3-cairo (1.26.1-2) ... 92s Selecting previously unselected package python3-freetype. 92s Preparing to unpack .../48-python3-freetype_2.5.1-1_all.deb ... 92s Unpacking python3-freetype (2.5.1-1) ... 92s Selecting previously unselected package python3-rlpycairo. 92s Preparing to unpack .../49-python3-rlpycairo_0.3.0-3_all.deb ... 92s Unpacking python3-rlpycairo (0.3.0-3) ... 92s Selecting previously unselected package python3-reportlab. 92s Preparing to unpack .../50-python3-reportlab_4.2.5-1_all.deb ... 92s Unpacking python3-reportlab (4.2.5-1) ... 93s Selecting previously unselected package xml-core. 93s Preparing to unpack .../51-xml-core_0.19_all.deb ... 93s Unpacking xml-core (0.19) ... 93s Selecting previously unselected package w3c-sgml-lib. 93s Preparing to unpack .../52-w3c-sgml-lib_1.3-3_all.deb ... 93s Unpacking w3c-sgml-lib (1.3-3) ... 93s Selecting previously unselected package python3-biopython. 93s Preparing to unpack .../53-python3-biopython_1.84+dfsg-4_arm64.deb ... 93s Unpacking python3-biopython (1.84+dfsg-4) ... 93s Selecting previously unselected package python3-mirtop. 93s Preparing to unpack .../54-python3-mirtop_0.4.28-1_all.deb ... 93s Unpacking python3-mirtop (0.4.28-1) ... 93s Selecting previously unselected package mirtop. 93s Preparing to unpack .../55-mirtop_0.4.28-1_all.deb ... 93s Unpacking mirtop (0.4.28-1) ... 93s Selecting previously unselected package python3-all. 93s Preparing to unpack .../56-python3-all_3.12.6-0ubuntu1_arm64.deb ... 93s Unpacking python3-all (3.12.6-0ubuntu1) ... 93s Selecting previously unselected package python3-iniconfig. 93s Preparing to unpack .../57-python3-iniconfig_1.1.1-2_all.deb ... 93s Unpacking python3-iniconfig (1.1.1-2) ... 93s Selecting previously unselected package python3-packaging. 93s Preparing to unpack .../58-python3-packaging_24.1-1_all.deb ... 93s Unpacking python3-packaging (24.1-1) ... 93s Selecting previously unselected package python3-pluggy. 93s Preparing to unpack .../59-python3-pluggy_1.5.0-1_all.deb ... 93s Unpacking python3-pluggy (1.5.0-1) ... 93s Selecting previously unselected package python3-pytest. 93s Preparing to unpack .../60-python3-pytest_8.3.3-1_all.deb ... 93s Unpacking python3-pytest (8.3.3-1) ... 93s Selecting previously unselected package samtools. 93s Preparing to unpack .../61-samtools_1.20-3_arm64.deb ... 93s Unpacking samtools (1.20-3) ... 93s Selecting previously unselected package seqan-apps. 93s Preparing to unpack .../62-seqan-apps_2.4.0+dfsg-16_arm64.deb ... 93s Unpacking seqan-apps (2.4.0+dfsg-16) ... 94s Selecting previously unselected package autopkgtest-satdep. 94s Preparing to unpack .../63-1-autopkgtest-satdep.deb ... 94s Unpacking autopkgtest-satdep (0) ... 94s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 94s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 94s Setting up liblcms2-2:arm64 (2.16-2) ... 94s Setting up python3-iniconfig (1.1.1-2) ... 94s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 94s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 94s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 94s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 94s Setting up libxcb-render0:arm64 (1.17.0-2) ... 94s Setting up x11-common (1:7.7+23ubuntu3) ... 94s Setting up libdeflate0:arm64 (1.22-1) ... 94s Setting up python3-all (3.12.6-0ubuntu1) ... 94s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 94s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 94s Setting up python3-freetype (2.5.1-1) ... 94s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 94s Setting up python3-tz (2024.1-2) ... 94s Setting up python3-six (1.16.0-7) ... 95s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 95s Setting up libblas3:arm64 (3.12.0-3build2) ... 95s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 95s Setting up python3-packaging (24.1-1) ... 95s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 95s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 95s Setting up seqan-apps (2.4.0+dfsg-16) ... 95s Setting up fonts-dejavu-mono (2.37-8) ... 95s Setting up fonts-dejavu-core (2.37-8) ... 95s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 95s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 95s Setting up python3-pluggy (1.5.0-1) ... 95s Setting up libwebp7:arm64 (1.4.0-0.1) ... 95s Setting up libhts3t64:arm64 (1.20+ds-1) ... 95s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 95s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 95s Setting up python3-dateutil (2.9.0-2) ... 95s Setting up sgml-base (1.31) ... 95s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 95s Setting up bedtools (2.31.1+dfsg-2) ... 95s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 95s Setting up liblapack3:arm64 (3.12.0-3build2) ... 95s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 95s Setting up python3-pysam (0.22.1+ds-2) ... 95s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 95s Setting up python3-pytest (8.3.3-1) ... 96s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 96s Setting up xfonts-utils (1:7.7+7) ... 96s Setting up samtools (1.20-3) ... 96s Setting up libraqm0:arm64 (0.10.1-1build1) ... 96s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 98s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 98s Setting up xml-core (0.19) ... 98s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 98s Setting up python3-pybedtools (0.10.0-2) ... 98s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 98s Setting up fonts-urw-base35 (20200910-8) ... 98s Setting up libcairo2:arm64 (1.18.2-2) ... 98s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 99s Setting up python3-pandas (2.2.3+dfsg-5) ... 105s Setting up python3-cairo (1.26.1-2) ... 105s Setting up python3-rlpycairo (0.3.0-3) ... 105s Setting up python3-reportlab (4.2.5-1) ... 106s Processing triggers for libc-bin (2.40-1ubuntu3) ... 106s Processing triggers for man-db (2.13.0-1) ... 107s Processing triggers for sgml-base (1.31) ... 107s Setting up w3c-sgml-lib (1.3-3) ... 134s Setting up python3-biopython (1.84+dfsg-4) ... 136s Setting up python3-mirtop (0.4.28-1) ... 136s /usr/lib/python3/dist-packages/mirtop/sql/sql.py:478: SyntaxWarning: invalid escape sequence '\(' 136s print("Usage: mirtop sql --create --gff --db \(Default: mirtop.db\)") 136s Setting up mirtop (0.4.28-1) ... 136s Setting up autopkgtest-satdep (0) ... 140s (Reading database ... 86141 files and directories currently installed.) 140s Removing autopkgtest-satdep (0) ... 141s autopkgtest [20:04:33]: test run-unit-test: [----------------------- 141s Testing with python3.12 in /tmp/autopkgtest.eDKomo/autopkgtest_tmp: 142s ============================= test session starts ============================== 142s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 142s cachedir: .pytest_cache 142s rootdir: /tmp/autopkgtest.eDKomo/autopkgtest_tmp 142s plugins: typeguard-4.4.1 142s collecting ... collected 62 items 142s 143s test/test_automated_analysis.py::AutomatedAnalysisTest::test_count PASSED [ 1%] 144s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_fasta PASSED [ 3%] 145s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_seqbuster PASSED [ 4%] 145s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_vcf PASSED [ 6%] 146s test/test_automated_analysis.py::AutomatedAnalysisTest::test_merge_bam PASSED [ 8%] 146s 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test/test_functions.py::FunctionsTest::test_read_hairpin_mirgenedb PASSED [ 79%] 167s test/test_functions.py::FunctionsTest::test_read_line PASSED [ 80%] 167s test/test_functions.py::FunctionsTest::test_read_mir2chr PASSED [ 82%] 167s test/test_functions.py::FunctionsTest::test_read_mir2genomic PASSED [ 83%] 167s test/test_functions.py::FunctionsTest::test_reverse PASSED [ 85%] 167s test/test_functions.py::FunctionsTest::test_seqbuster PASSED [ 87%] 167s test/test_functions.py::FunctionsTest::test_spikeins PASSED [ 88%] 168s test/test_functions.py::FunctionsTest::test_sql PASSED [ 90%] 168s test/test_functions.py::FunctionsTest::test_srnabench PASSED [ 91%] 168s test/test_functions.py::FunctionsTest::test_stats PASSED [ 93%] 168s test/test_functions.py::FunctionsTest::test_string_variant PASSED [ 95%] 168s test/test_functions.py::FunctionsTest::test_update PASSED [ 96%] 168s test/test_functions.py::FunctionsTest::test_validator PASSED [ 98%] 168s test/test_functions.py::FunctionsTest::test_variant PASSED [100%] 168s 168s =============================== warnings summary =============================== 168s test/test_functions.py::FunctionsTest::test_alignment 168s /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 168s import pkg_resources 168s 168s test/test_functions.py::FunctionsTest::test_alignment 168s /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. 168s warnings.warn( 168s 168s test/test_functions.py::FunctionsTest::test_collapse 168s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 168s return self.run(*args, **kwds) 168s 168s test/test_functions.py::FunctionsTest::test_counts 168s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 168s return self.run(*args, **kwds) 168s 168s test/test_functions.py::FunctionsTest::test_gff 168s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 168s return self.run(*args, **kwds) 168s 168s test/test_functions.py::FunctionsTest::test_read_hairpin 168s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 168s return self.run(*args, **kwds) 168s 168s test/test_functions.py::FunctionsTest::test_sql 168s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 168s return self.run(*args, **kwds) 168s 168s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 168s ======================= 62 passed, 7 warnings in 26.28s ======================== 169s autopkgtest [20:05:01]: test run-unit-test: -----------------------] 169s run-unit-test PASS 169s autopkgtest [20:05:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 169s autopkgtest [20:05:01]: test autodep8-python3: preparing testbed 265s autopkgtest [20:06:37]: testbed dpkg architecture: arm64 265s autopkgtest [20:06:37]: testbed apt version: 2.9.8 265s autopkgtest [20:06:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 266s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 266s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [92.2 kB] 266s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 266s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1043 kB] 267s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 267s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [168 kB] 267s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 267s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [789 kB] 267s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6404 B] 267s Fetched 2245 kB in 1s (2561 kB/s) 267s Reading package lists... 269s Reading package lists... 270s Building dependency tree... 270s Reading state information... 271s Calculating upgrade... 271s The following NEW packages will be installed: 271s libassuan9 271s The following packages will be upgraded: 271s libgpgme11t64 libseccomp2 python3-cffi-backend python3-markupsafe 271s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 271s Need to get 337 kB of archives. 271s After this operation, 447 kB of additional disk space will be used. 271s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libseccomp2 arm64 2.5.5-1ubuntu5 [51.4 kB] 272s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cffi-backend arm64 1.17.1-2build1 [89.9 kB] 272s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libassuan9 arm64 3.0.1-2 [40.6 kB] 272s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgpgme11t64 arm64 1.24.0-2ubuntu1 [142 kB] 272s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-markupsafe arm64 2.1.5-1build3 [13.0 kB] 272s Fetched 337 kB in 0s (681 kB/s) 272s (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 ... 79957 files and directories currently installed.) 272s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu5_arm64.deb ... 272s Unpacking libseccomp2:arm64 (2.5.5-1ubuntu5) over (2.5.5-1ubuntu4) ... 273s Setting up libseccomp2:arm64 (2.5.5-1ubuntu5) ... 273s (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 ... 79957 files and directories currently installed.) 273s Preparing to unpack .../python3-cffi-backend_1.17.1-2build1_arm64.deb ... 273s Unpacking python3-cffi-backend:arm64 (1.17.1-2build1) over (1.17.1-2) ... 273s Selecting previously unselected package libassuan9:arm64. 273s Preparing to unpack .../libassuan9_3.0.1-2_arm64.deb ... 273s Unpacking libassuan9:arm64 (3.0.1-2) ... 273s Preparing to unpack .../libgpgme11t64_1.24.0-2ubuntu1_arm64.deb ... 273s Unpacking libgpgme11t64:arm64 (1.24.0-2ubuntu1) over (1.23.2-5ubuntu4) ... 273s Preparing to unpack .../python3-markupsafe_2.1.5-1build3_arm64.deb ... 273s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ... 273s Setting up python3-markupsafe (2.1.5-1build3) ... 273s Setting up libassuan9:arm64 (3.0.1-2) ... 273s Setting up libgpgme11t64:arm64 (1.24.0-2ubuntu1) ... 273s Setting up python3-cffi-backend:arm64 (1.17.1-2build1) ... 273s Processing triggers for libc-bin (2.40-1ubuntu3) ... 273s Reading package lists... 274s Building dependency tree... 274s Reading state information... 275s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 275s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 275s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 275s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 276s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 277s Reading package lists... 277s Reading package lists... 277s Building dependency tree... 277s Reading state information... 278s Calculating upgrade... 279s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 279s Reading package lists... 280s Building dependency tree... 280s Reading state information... 281s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 285s Reading package lists... 285s Building dependency tree... 285s Reading state information... 286s Starting pkgProblemResolver with broken count: 0 286s Starting 2 pkgProblemResolver with broken count: 0 286s Done 287s The following additional packages will be installed: 287s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 287s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 287s libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 287s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 287s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 287s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-all 287s python3-biopython python3-cairo python3-dateutil python3-freetype 287s python3-mirtop python3-numpy python3-pandas python3-pandas-lib python3-pil 287s python3-pybedtools python3-pysam python3-reportlab python3-rlpycairo 287s python3-six python3-tz sgml-base w3c-sgml-lib x11-common xfonts-encodings 287s xfonts-utils xml-core 287s Suggested packages: 287s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 287s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 287s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 287s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 287s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 287s python3-statsmodels python-pil-doc python-pybedtools-doc pdf-viewer 287s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 287s sgml-base-doc debhelper 287s Recommended packages: 287s python-biopython-doc ncbi-blast+ python3-scipy python3-matplotlib 287s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 287s python3-html5lib python3-lxml python3-tables python3-olefile 287s fonts-dejavu-extra 287s The following NEW packages will be installed: 287s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 287s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 287s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 287s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 287s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 287s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-all 287s python3-biopython python3-cairo python3-dateutil python3-freetype 287s python3-mirtop python3-numpy python3-pandas python3-pandas-lib python3-pil 287s python3-pybedtools python3-pysam python3-reportlab python3-rlpycairo 287s python3-six python3-tz sgml-base w3c-sgml-lib x11-common xfonts-encodings 287s xfonts-utils xml-core 287s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 287s Need to get 50.3 MB/50.3 MB of archives. 287s After this operation, 180 MB of additional disk space will be used. 287s Get:1 /tmp/autopkgtest.eDKomo/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 287s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 287s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 287s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 288s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 288s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 288s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 288s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 288s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 288s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 288s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 288s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 288s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 288s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 288s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 288s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 288s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 288s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 288s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 288s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 288s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 288s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 288s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 288s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 288s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 288s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 288s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 288s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 288s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 288s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 288s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 288s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 288s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 288s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 288s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 288s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 288s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 288s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 288s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 288s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 288s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 288s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 288s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 288s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 288s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 288s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 288s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 288s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 289s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 289s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 289s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 289s Get:52 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-pybedtools arm64 0.10.0-2 [12.4 MB] 289s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 289s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 289s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 289s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mirtop all 0.4.28-1 [61.9 kB] 290s Fetched 50.3 MB in 2s (21.3 MB/s) 290s Selecting previously unselected package sgml-base. 290s (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 ... 79964 files and directories currently installed.) 290s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 290s Unpacking sgml-base (1.31) ... 290s Selecting previously unselected package fonts-dejavu-mono. 290s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 290s Unpacking fonts-dejavu-mono (2.37-8) ... 290s Selecting previously unselected package fonts-dejavu-core. 290s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 290s Unpacking fonts-dejavu-core (2.37-8) ... 290s Selecting previously unselected package libfontenc1:arm64. 290s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 290s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 290s Selecting previously unselected package x11-common. 290s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 290s Unpacking x11-common (1:7.7+23ubuntu3) ... 290s Selecting previously unselected package xfonts-encodings. 290s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 290s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 290s Selecting previously unselected package xfonts-utils. 290s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_arm64.deb ... 290s Unpacking xfonts-utils (1:7.7+7) ... 290s Selecting previously unselected package fonts-urw-base35. 290s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 290s Unpacking fonts-urw-base35 (20200910-8) ... 291s Selecting previously unselected package fontconfig-config. 291s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 291s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 291s Selecting previously unselected package libblas3:arm64. 291s Preparing to unpack .../09-libblas3_3.12.0-3build2_arm64.deb ... 291s Unpacking libblas3:arm64 (3.12.0-3build2) ... 291s Selecting previously unselected package libfontconfig1:arm64. 291s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 291s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 291s Selecting previously unselected package libpixman-1-0:arm64. 291s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_arm64.deb ... 291s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 291s Selecting previously unselected package libxcb-render0:arm64. 291s Preparing to unpack .../12-libxcb-render0_1.17.0-2_arm64.deb ... 291s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 291s Selecting previously unselected package libxcb-shm0:arm64. 291s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_arm64.deb ... 291s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 291s Selecting previously unselected package libxrender1:arm64. 291s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 291s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 291s Selecting previously unselected package libcairo2:arm64. 291s Preparing to unpack .../15-libcairo2_1.18.2-2_arm64.deb ... 291s Unpacking libcairo2:arm64 (1.18.2-2) ... 291s Selecting previously unselected package libdeflate0:arm64. 291s Preparing to unpack .../16-libdeflate0_1.22-1_arm64.deb ... 291s Unpacking libdeflate0:arm64 (1.22-1) ... 291s Selecting previously unselected package libgfortran5:arm64. 291s Preparing to unpack .../17-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 291s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 291s Selecting previously unselected package libgomp1:arm64. 291s Preparing to unpack .../18-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 291s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 291s Selecting previously unselected package libgraphite2-3:arm64. 291s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 291s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 291s Selecting previously unselected package libharfbuzz0b:arm64. 291s Preparing to unpack .../20-libharfbuzz0b_10.0.1-1_arm64.deb ... 291s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 291s Selecting previously unselected package libhtscodecs2:arm64. 291s Preparing to unpack .../21-libhtscodecs2_1.6.1-1_arm64.deb ... 291s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 291s Selecting previously unselected package libhts3t64:arm64. 291s Preparing to unpack .../22-libhts3t64_1.20+ds-1_arm64.deb ... 291s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 291s Selecting previously unselected package libimagequant0:arm64. 291s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_arm64.deb ... 291s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 291s Selecting previously unselected package libjpeg-turbo8:arm64. 291s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 291s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 291s Selecting previously unselected package libjpeg8:arm64. 291s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_arm64.deb ... 291s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 291s Selecting previously unselected package liblapack3:arm64. 291s Preparing to unpack .../26-liblapack3_3.12.0-3build2_arm64.deb ... 291s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 292s Selecting previously unselected package liblcms2-2:arm64. 292s Preparing to unpack .../27-liblcms2-2_2.16-2_arm64.deb ... 292s Unpacking liblcms2-2:arm64 (2.16-2) ... 292s Selecting previously unselected package liblerc4:arm64. 292s Preparing to unpack .../28-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 292s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 292s Selecting previously unselected package libraqm0:arm64. 292s Preparing to unpack .../29-libraqm0_0.10.1-1build1_arm64.deb ... 292s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 292s Selecting previously unselected package libsharpyuv0:arm64. 292s Preparing to unpack .../30-libsharpyuv0_1.4.0-0.1_arm64.deb ... 292s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 292s Selecting previously unselected package libjbig0:arm64. 292s Preparing to unpack .../31-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 292s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 292s Selecting previously unselected package libwebp7:arm64. 292s Preparing to unpack .../32-libwebp7_1.4.0-0.1_arm64.deb ... 292s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 292s Selecting previously unselected package libtiff6:arm64. 292s Preparing to unpack .../33-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 292s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 292s Selecting previously unselected package libwebpdemux2:arm64. 292s Preparing to unpack .../34-libwebpdemux2_1.4.0-0.1_arm64.deb ... 292s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 292s Selecting previously unselected package libwebpmux3:arm64. 292s Preparing to unpack .../35-libwebpmux3_1.4.0-0.1_arm64.deb ... 292s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 292s Selecting previously unselected package python3-all. 292s Preparing to unpack .../36-python3-all_3.12.6-0ubuntu1_arm64.deb ... 292s Unpacking python3-all (3.12.6-0ubuntu1) ... 292s Selecting previously unselected package python3-numpy. 292s Preparing to unpack .../37-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 292s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 292s Selecting previously unselected package libopenjp2-7:arm64. 292s Preparing to unpack .../38-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 292s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 292s Selecting previously unselected package python3-pil:arm64. 292s Preparing to unpack .../39-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 292s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 292s Selecting previously unselected package python3-cairo. 292s Preparing to unpack .../40-python3-cairo_1.26.1-2_arm64.deb ... 292s Unpacking python3-cairo (1.26.1-2) ... 292s Selecting previously unselected package python3-freetype. 292s Preparing to unpack .../41-python3-freetype_2.5.1-1_all.deb ... 292s Unpacking python3-freetype (2.5.1-1) ... 292s Selecting previously unselected package python3-rlpycairo. 292s Preparing to unpack .../42-python3-rlpycairo_0.3.0-3_all.deb ... 292s Unpacking python3-rlpycairo (0.3.0-3) ... 292s Selecting previously unselected package python3-reportlab. 292s Preparing to unpack .../43-python3-reportlab_4.2.5-1_all.deb ... 292s Unpacking python3-reportlab (4.2.5-1) ... 292s Selecting previously unselected package xml-core. 292s Preparing to unpack .../44-xml-core_0.19_all.deb ... 292s Unpacking xml-core (0.19) ... 292s Selecting previously unselected package w3c-sgml-lib. 293s Preparing to unpack .../45-w3c-sgml-lib_1.3-3_all.deb ... 293s Unpacking w3c-sgml-lib (1.3-3) ... 293s Selecting previously unselected package python3-biopython. 293s Preparing to unpack .../46-python3-biopython_1.84+dfsg-4_arm64.deb ... 293s Unpacking python3-biopython (1.84+dfsg-4) ... 293s Selecting previously unselected package python3-six. 293s Preparing to unpack .../47-python3-six_1.16.0-7_all.deb ... 293s Unpacking python3-six (1.16.0-7) ... 293s Selecting previously unselected package python3-dateutil. 293s Preparing to unpack .../48-python3-dateutil_2.9.0-2_all.deb ... 293s Unpacking python3-dateutil (2.9.0-2) ... 293s Selecting previously unselected package python3-pysam. 293s Preparing to unpack .../49-python3-pysam_0.22.1+ds-2_arm64.deb ... 293s Unpacking python3-pysam (0.22.1+ds-2) ... 293s Selecting previously unselected package python3-pybedtools. 293s Preparing to unpack .../50-python3-pybedtools_0.10.0-2_arm64.deb ... 293s Unpacking python3-pybedtools (0.10.0-2) ... 293s Selecting previously unselected package python3-tz. 293s Preparing to unpack .../51-python3-tz_2024.1-2_all.deb ... 293s Unpacking python3-tz (2024.1-2) ... 293s Selecting previously unselected package python3-pandas-lib:arm64. 293s Preparing to unpack .../52-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 293s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 293s Selecting previously unselected package python3-pandas. 293s Preparing to unpack .../53-python3-pandas_2.2.3+dfsg-5_all.deb ... 293s Unpacking python3-pandas (2.2.3+dfsg-5) ... 294s Selecting previously unselected package python3-mirtop. 294s Preparing to unpack .../54-python3-mirtop_0.4.28-1_all.deb ... 294s Unpacking python3-mirtop (0.4.28-1) ... 294s Selecting previously unselected package autopkgtest-satdep. 294s Preparing to unpack .../55-2-autopkgtest-satdep.deb ... 294s Unpacking autopkgtest-satdep (0) ... 294s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 294s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 294s Setting up liblcms2-2:arm64 (2.16-2) ... 294s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 294s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 294s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 294s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 294s Setting up libxcb-render0:arm64 (1.17.0-2) ... 294s Setting up x11-common (1:7.7+23ubuntu3) ... 294s Setting up libdeflate0:arm64 (1.22-1) ... 294s Setting up python3-all (3.12.6-0ubuntu1) ... 294s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 294s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 294s Setting up python3-freetype (2.5.1-1) ... 294s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 294s Setting up python3-tz (2024.1-2) ... 294s Setting up python3-six (1.16.0-7) ... 294s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 294s Setting up libblas3:arm64 (3.12.0-3build2) ... 295s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 295s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 295s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 295s Setting up fonts-dejavu-mono (2.37-8) ... 295s Setting up fonts-dejavu-core (2.37-8) ... 295s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 295s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 295s Setting up libwebp7:arm64 (1.4.0-0.1) ... 295s Setting up libhts3t64:arm64 (1.20+ds-1) ... 295s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 295s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 295s Setting up python3-dateutil (2.9.0-2) ... 295s Setting up sgml-base (1.31) ... 295s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 295s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 295s Setting up liblapack3:arm64 (3.12.0-3build2) ... 295s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 295s Setting up python3-pysam (0.22.1+ds-2) ... 295s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 295s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 295s Setting up xfonts-utils (1:7.7+7) ... 295s Setting up libraqm0:arm64 (0.10.1-1build1) ... 295s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 297s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 297s Setting up xml-core (0.19) ... 298s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 298s Setting up python3-pybedtools (0.10.0-2) ... 298s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 298s Setting up fonts-urw-base35 (20200910-8) ... 298s Setting up libcairo2:arm64 (1.18.2-2) ... 298s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 298s Setting up python3-pandas (2.2.3+dfsg-5) ... 304s Setting up python3-cairo (1.26.1-2) ... 304s Setting up python3-rlpycairo (0.3.0-3) ... 304s Setting up python3-reportlab (4.2.5-1) ... 305s Processing triggers for libc-bin (2.40-1ubuntu3) ... 305s Processing triggers for man-db (2.13.0-1) ... 307s Processing triggers for sgml-base (1.31) ... 307s Setting up w3c-sgml-lib (1.3-3) ... 336s Setting up python3-biopython (1.84+dfsg-4) ... 337s Setting up python3-mirtop (0.4.28-1) ... 338s /usr/lib/python3/dist-packages/mirtop/sql/sql.py:478: SyntaxWarning: invalid escape sequence '\(' 338s print("Usage: mirtop sql --create --gff --db \(Default: mirtop.db\)") 338s Setting up autopkgtest-satdep (0) ... 342s (Reading database ... 85606 files and directories currently installed.) 342s Removing autopkgtest-satdep (0) ... 344s autopkgtest [20:07:56]: 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 344s autopkgtest [20:07:56]: test autodep8-python3: [----------------------- 344s Testing with python3.12: 344s 345s autopkgtest [20:07:57]: test autodep8-python3: -----------------------] 345s autodep8-python3 PASS (superficial) 345s autopkgtest [20:07:57]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 345s autopkgtest [20:07:57]: @@@@@@@@@@@@@@@@@@@@ summary 345s run-unit-test PASS 345s autodep8-python3 PASS (superficial) 357s nova [W] Skipping flock in bos03-arm64 357s Creating nova instance adt-plucky-arm64-mirtop-20241115-200212-juju-7f2275-prod-proposed-migration-environment-15-0e187799-2915-4d36-8b7e-3fbb0e06aaab from image adt/ubuntu-plucky-arm64-server-20241115.img (UUID bf337bb2-b8c9-4fc7-87ba-f6e99408dba6)... 357s nova [W] Skipping flock in bos03-arm64 357s Creating nova instance adt-plucky-arm64-mirtop-20241115-200212-juju-7f2275-prod-proposed-migration-environment-15-0e187799-2915-4d36-8b7e-3fbb0e06aaab from image adt/ubuntu-plucky-arm64-server-20241115.img (UUID bf337bb2-b8c9-4fc7-87ba-f6e99408dba6)...