0s autopkgtest [20:06:56]: starting date and time: 2024-11-15 20:06:56+0000 0s autopkgtest [20:06:56]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [20:06:56]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nxjaz9wn/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.232 lxd-armhf-10.145.243.232:autopkgtest/ubuntu/plucky/armhf 53s autopkgtest [20:07:49]: testbed dpkg architecture: armhf 54s autopkgtest [20:07:50]: testbed apt version: 2.9.8 54s autopkgtest [20:07:50]: @@@@@@@@@@@@@@@@@@@@ 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/restricted Sources [7016 B] 62s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [92.2 kB] 62s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1043 kB] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [143 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [747 kB] 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4428 B] 63s Fetched 2126 kB in 1s (2052 kB/s) 63s Reading package lists... 80s tee: /proc/self/fd/2: Permission denied 103s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 105s Reading package lists... 105s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Calculating upgrade... 107s The following NEW packages will be installed: 107s libassuan9 107s The following packages will be upgraded: 107s libgpgme11t64 libseccomp2 python3-cffi-backend python3-markupsafe 108s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 297 kB of archives. 108s After this operation, 224 kB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libseccomp2 armhf 2.5.5-1ubuntu5 [49.3 kB] 108s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cffi-backend armhf 1.17.1-2build1 [75.9 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libassuan9 armhf 3.0.1-2 [34.3 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgpgme11t64 armhf 1.24.0-2ubuntu1 [125 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-markupsafe armhf 2.1.5-1build3 [12.5 kB] 109s Fetched 297 kB in 0s (619 kB/s) 109s (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 ... 59566 files and directories currently installed.) 109s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu5_armhf.deb ... 109s Unpacking libseccomp2:armhf (2.5.5-1ubuntu5) over (2.5.5-1ubuntu4) ... 109s Setting up libseccomp2:armhf (2.5.5-1ubuntu5) ... 109s (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 ... 59566 files and directories currently installed.) 109s Preparing to unpack .../python3-cffi-backend_1.17.1-2build1_armhf.deb ... 109s Unpacking python3-cffi-backend:armhf (1.17.1-2build1) over (1.17.1-2) ... 109s Selecting previously unselected package libassuan9:armhf. 109s Preparing to unpack .../libassuan9_3.0.1-2_armhf.deb ... 109s Unpacking libassuan9:armhf (3.0.1-2) ... 109s Preparing to unpack .../libgpgme11t64_1.24.0-2ubuntu1_armhf.deb ... 109s Unpacking libgpgme11t64:armhf (1.24.0-2ubuntu1) over (1.23.2-5ubuntu4) ... 109s Preparing to unpack .../python3-markupsafe_2.1.5-1build3_armhf.deb ... 109s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ... 109s Setting up python3-markupsafe (2.1.5-1build3) ... 109s Setting up libassuan9:armhf (3.0.1-2) ... 109s Setting up libgpgme11t64:armhf (1.24.0-2ubuntu1) ... 109s Setting up python3-cffi-backend:armhf (1.17.1-2build1) ... 109s Processing triggers for libc-bin (2.40-1ubuntu3) ... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [20:08:50]: rebooting testbed after setup commands that affected boot 183s autopkgtest [20:09:59]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 209s autopkgtest [20:10:25]: @@@@@@@@@@@@@@@@@@@@ apt-source mirtop 224s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (dsc) [2340 B] 224s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (tar) [718 kB] 224s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (diff) [10.4 kB] 224s gpgv: Signature made Sat Oct 12 13:35:08 2024 UTC 224s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 224s gpgv: issuer "tchet@debian.org" 224s gpgv: Can't check signature: No public key 224s dpkg-source: warning: cannot verify inline signature for ./mirtop_0.4.28-1.dsc: no acceptable signature found 224s autopkgtest [20:10:40]: testing package mirtop version 0.4.28-1 226s autopkgtest [20:10:42]: build not needed 229s autopkgtest [20:10:45]: test run-unit-test: preparing testbed 239s Reading package lists... 240s Building dependency tree... 240s Reading state information... 240s Starting pkgProblemResolver with broken count: 0 240s Starting 2 pkgProblemResolver with broken count: 0 240s Done 241s The following additional packages will be installed: 241s bedtools fontconfig-config fonts-dejavu-core fonts-dejavu-mono 241s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 241s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 241s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 241s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 241s libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 241s libxrender1 mirtop python3-all python3-biopython python3-cairo 241s python3-dateutil python3-freetype python3-iniconfig python3-mirtop 241s python3-numpy python3-packaging python3-pandas python3-pandas-lib 242s python3-pil python3-pluggy python3-pybedtools python3-pysam python3-pytest 242s python3-reportlab python3-rlpycairo python3-six python3-tz samtools 242s seqan-apps sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils 242s xml-core 242s Suggested packages: 242s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 242s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 242s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 242s python3-rdflib python3-psycopg2 python3-scipy raxml t-coffee wise gcc 242s gfortran python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 242s python-pil-doc python-pybedtools-doc pdf-viewer python3-egenix-mxtexttools 242s python-reportlab-doc rl-accel rl-renderpm cwltool cwltool | cwl-runner 242s sgml-base-doc debhelper 242s Recommended packages: 242s python-biopython-doc ncbi-blast+ python3-scipy python3-matplotlib 242s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 242s python3-html5lib python3-lxml python3-tables python3-olefile 242s fonts-dejavu-extra 242s The following NEW packages will be installed: 242s autopkgtest-satdep bedtools fontconfig-config fonts-dejavu-core 242s fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 libdeflate0 242s libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 242s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 242s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 242s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 242s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mirtop python3-all 242s python3-biopython python3-cairo python3-dateutil python3-freetype 242s python3-iniconfig python3-mirtop python3-numpy python3-packaging 242s python3-pandas python3-pandas-lib python3-pil python3-pluggy 242s python3-pybedtools python3-pysam python3-pytest python3-reportlab 242s python3-rlpycairo python3-six python3-tz samtools seqan-apps sgml-base 242s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 242s 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded. 242s Need to get 61.1 MB/61.1 MB of archives. 242s After this operation, 207 MB of additional disk space will be used. 242s Get:1 /tmp/autopkgtest.cO2vKi/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [748 B] 242s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 242s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf bedtools armhf 2.31.1+dfsg-2 [739 kB] 242s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 242s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 242s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 242s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 242s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 242s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 242s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 242s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 243s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 243s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 243s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 243s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 243s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 243s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 243s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 243s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 243s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 243s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 243s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 243s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 243s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 243s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-1 [67.9 kB] 243s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 243s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 243s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 243s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 243s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 243s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 243s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 243s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 243s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 243s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 243s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 243s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 243s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 243s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 243s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 243s Get:41 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.22.1+ds-2 [3383 kB] 243s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 243s Get:43 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-pybedtools armhf 0.10.0-2 [12.4 MB] 244s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-2 [80.3 kB] 244s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 244s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5 [4728 kB] 244s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5 [3112 kB] 244s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 244s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 244s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 244s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 244s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 244s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 244s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 244s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 244s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 244s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mirtop all 0.4.28-1 [61.9 kB] 244s Get:58 http://ftpmaster.internal/ubuntu plucky/universe armhf mirtop all 0.4.28-1 [13.5 kB] 244s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 244s Get:60 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 244s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 244s Get:62 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 244s Get:63 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.3-1 [251 kB] 244s Get:64 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.20-3 [607 kB] 244s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf seqan-apps armhf 2.4.0+dfsg-16 [9459 kB] 245s Fetched 61.1 MB in 3s (20.7 MB/s) 245s Selecting previously unselected package sgml-base. 245s (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 ... 59573 files and directories currently installed.) 245s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 245s Unpacking sgml-base (1.31) ... 245s Selecting previously unselected package bedtools. 245s Preparing to unpack .../01-bedtools_2.31.1+dfsg-2_armhf.deb ... 245s Unpacking bedtools (2.31.1+dfsg-2) ... 245s Selecting previously unselected package fonts-dejavu-mono. 245s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 245s Unpacking fonts-dejavu-mono (2.37-8) ... 246s Selecting previously unselected package fonts-dejavu-core. 246s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 246s Unpacking fonts-dejavu-core (2.37-8) ... 246s Selecting previously unselected package libfontenc1:armhf. 246s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 246s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 246s Selecting previously unselected package libfreetype6:armhf. 246s Preparing to unpack .../05-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 246s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 246s Selecting previously unselected package x11-common. 246s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ... 246s Unpacking x11-common (1:7.7+23ubuntu3) ... 246s Selecting previously unselected package xfonts-encodings. 246s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 246s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 246s Selecting previously unselected package xfonts-utils. 246s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_armhf.deb ... 246s Unpacking xfonts-utils (1:7.7+7) ... 246s Selecting previously unselected package fonts-urw-base35. 246s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 246s Unpacking fonts-urw-base35 (20200910-8) ... 246s Selecting previously unselected package fontconfig-config. 246s Preparing to unpack .../10-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 247s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 247s Selecting previously unselected package libblas3:armhf. 247s Preparing to unpack .../11-libblas3_3.12.0-3build2_armhf.deb ... 247s Unpacking libblas3:armhf (3.12.0-3build2) ... 247s Selecting previously unselected package libfontconfig1:armhf. 247s Preparing to unpack .../12-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 247s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 247s Selecting previously unselected package libpixman-1-0:armhf. 247s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_armhf.deb ... 247s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 247s Selecting previously unselected package libxcb-render0:armhf. 247s Preparing to unpack .../14-libxcb-render0_1.17.0-2_armhf.deb ... 247s Unpacking libxcb-render0:armhf (1.17.0-2) ... 247s Selecting previously unselected package libxcb-shm0:armhf. 247s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_armhf.deb ... 247s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 247s Selecting previously unselected package libxrender1:armhf. 247s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 247s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 247s Selecting previously unselected package libcairo2:armhf. 247s Preparing to unpack .../17-libcairo2_1.18.2-2_armhf.deb ... 247s Unpacking libcairo2:armhf (1.18.2-2) ... 247s Selecting previously unselected package libdeflate0:armhf. 247s Preparing to unpack .../18-libdeflate0_1.22-1_armhf.deb ... 247s Unpacking libdeflate0:armhf (1.22-1) ... 247s Selecting previously unselected package libgfortran5:armhf. 247s Preparing to unpack .../19-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 247s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 247s Selecting previously unselected package libgomp1:armhf. 247s Preparing to unpack .../20-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 247s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 247s Selecting previously unselected package libgraphite2-3:armhf. 247s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 247s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 247s Selecting previously unselected package libharfbuzz0b:armhf. 247s Preparing to unpack .../22-libharfbuzz0b_10.0.1-1_armhf.deb ... 247s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 247s Selecting previously unselected package libhtscodecs2:armhf. 247s Preparing to unpack .../23-libhtscodecs2_1.6.1-1_armhf.deb ... 247s Unpacking libhtscodecs2:armhf (1.6.1-1) ... 247s Selecting previously unselected package libhts3t64:armhf. 247s Preparing to unpack .../24-libhts3t64_1.20+ds-1_armhf.deb ... 247s Unpacking libhts3t64:armhf (1.20+ds-1) ... 247s Selecting previously unselected package libimagequant0:armhf. 248s Preparing to unpack .../25-libimagequant0_2.18.0-1build1_armhf.deb ... 248s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 248s Selecting previously unselected package libjpeg-turbo8:armhf. 248s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 248s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 248s Selecting previously unselected package libjpeg8:armhf. 248s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_armhf.deb ... 248s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 248s Selecting previously unselected package liblapack3:armhf. 248s Preparing to unpack .../28-liblapack3_3.12.0-3build2_armhf.deb ... 248s Unpacking liblapack3:armhf (3.12.0-3build2) ... 248s Selecting previously unselected package liblcms2-2:armhf. 248s Preparing to unpack .../29-liblcms2-2_2.16-2_armhf.deb ... 248s Unpacking liblcms2-2:armhf (2.16-2) ... 248s Selecting previously unselected package liblerc4:armhf. 248s Preparing to unpack .../30-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 248s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 248s Selecting previously unselected package libraqm0:armhf. 248s Preparing to unpack .../31-libraqm0_0.10.1-1build1_armhf.deb ... 248s Unpacking libraqm0:armhf (0.10.1-1build1) ... 248s Selecting previously unselected package libsharpyuv0:armhf. 248s Preparing to unpack .../32-libsharpyuv0_1.4.0-0.1_armhf.deb ... 248s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 248s Selecting previously unselected package libjbig0:armhf. 248s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 248s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 248s Selecting previously unselected package libwebp7:armhf. 248s Preparing to unpack .../34-libwebp7_1.4.0-0.1_armhf.deb ... 248s Unpacking libwebp7:armhf (1.4.0-0.1) ... 248s Selecting previously unselected package libtiff6:armhf. 248s Preparing to unpack .../35-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 248s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 248s Selecting previously unselected package libwebpdemux2:armhf. 248s Preparing to unpack .../36-libwebpdemux2_1.4.0-0.1_armhf.deb ... 248s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 248s Selecting previously unselected package libwebpmux3:armhf. 248s Preparing to unpack .../37-libwebpmux3_1.4.0-0.1_armhf.deb ... 248s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 248s Selecting previously unselected package python3-six. 248s Preparing to unpack .../38-python3-six_1.16.0-7_all.deb ... 248s Unpacking python3-six (1.16.0-7) ... 248s Selecting previously unselected package python3-pysam. 248s Preparing to unpack .../39-python3-pysam_0.22.1+ds-2_armhf.deb ... 248s Unpacking python3-pysam (0.22.1+ds-2) ... 249s Selecting previously unselected package python3-numpy. 249s Preparing to unpack .../40-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 249s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 249s Selecting previously unselected package python3-pybedtools. 249s Preparing to unpack .../41-python3-pybedtools_0.10.0-2_armhf.deb ... 249s Unpacking python3-pybedtools (0.10.0-2) ... 249s Selecting previously unselected package python3-dateutil. 249s Preparing to unpack .../42-python3-dateutil_2.9.0-2_all.deb ... 249s Unpacking python3-dateutil (2.9.0-2) ... 249s Selecting previously unselected package python3-tz. 249s Preparing to unpack .../43-python3-tz_2024.1-2_all.deb ... 249s Unpacking python3-tz (2024.1-2) ... 249s Selecting previously unselected package python3-pandas-lib:armhf. 249s Preparing to unpack .../44-python3-pandas-lib_2.2.3+dfsg-5_armhf.deb ... 249s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5) ... 249s Selecting previously unselected package python3-pandas. 249s Preparing to unpack .../45-python3-pandas_2.2.3+dfsg-5_all.deb ... 249s Unpacking python3-pandas (2.2.3+dfsg-5) ... 250s Selecting previously unselected package libopenjp2-7:armhf. 250s Preparing to unpack .../46-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 250s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 250s Selecting previously unselected package python3-pil:armhf. 250s Preparing to unpack .../47-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 250s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 250s Selecting previously unselected package python3-cairo. 250s Preparing to unpack .../48-python3-cairo_1.26.1-2_armhf.deb ... 250s Unpacking python3-cairo (1.26.1-2) ... 250s Selecting previously unselected package python3-freetype. 250s Preparing to unpack .../49-python3-freetype_2.5.1-1_all.deb ... 250s Unpacking python3-freetype (2.5.1-1) ... 250s Selecting previously unselected package python3-rlpycairo. 250s Preparing to unpack .../50-python3-rlpycairo_0.3.0-3_all.deb ... 250s Unpacking python3-rlpycairo (0.3.0-3) ... 250s Selecting previously unselected package python3-reportlab. 250s Preparing to unpack .../51-python3-reportlab_4.2.5-1_all.deb ... 250s Unpacking python3-reportlab (4.2.5-1) ... 251s Selecting previously unselected package xml-core. 251s Preparing to unpack .../52-xml-core_0.19_all.deb ... 251s Unpacking xml-core (0.19) ... 251s Selecting previously unselected package w3c-sgml-lib. 251s Preparing to unpack .../53-w3c-sgml-lib_1.3-3_all.deb ... 251s Unpacking w3c-sgml-lib (1.3-3) ... 251s Selecting previously unselected package python3-biopython. 251s Preparing to unpack .../54-python3-biopython_1.84+dfsg-4_armhf.deb ... 251s Unpacking python3-biopython (1.84+dfsg-4) ... 251s Selecting previously unselected package python3-mirtop. 251s Preparing to unpack .../55-python3-mirtop_0.4.28-1_all.deb ... 251s Unpacking python3-mirtop (0.4.28-1) ... 251s Selecting previously unselected package mirtop. 251s Preparing to unpack .../56-mirtop_0.4.28-1_all.deb ... 251s Unpacking mirtop (0.4.28-1) ... 251s Selecting previously unselected package python3-all. 251s Preparing to unpack .../57-python3-all_3.12.6-0ubuntu1_armhf.deb ... 251s Unpacking python3-all (3.12.6-0ubuntu1) ... 251s Selecting previously unselected package python3-iniconfig. 251s Preparing to unpack .../58-python3-iniconfig_1.1.1-2_all.deb ... 251s Unpacking python3-iniconfig (1.1.1-2) ... 251s Selecting previously unselected package python3-packaging. 251s Preparing to unpack .../59-python3-packaging_24.1-1_all.deb ... 251s Unpacking python3-packaging (24.1-1) ... 251s Selecting previously unselected package python3-pluggy. 251s Preparing to unpack .../60-python3-pluggy_1.5.0-1_all.deb ... 251s Unpacking python3-pluggy (1.5.0-1) ... 251s Selecting previously unselected package python3-pytest. 251s Preparing to unpack .../61-python3-pytest_8.3.3-1_all.deb ... 251s Unpacking python3-pytest (8.3.3-1) ... 252s Selecting previously unselected package samtools. 252s Preparing to unpack .../62-samtools_1.20-3_armhf.deb ... 252s Unpacking samtools (1.20-3) ... 252s Selecting previously unselected package seqan-apps. 252s Preparing to unpack .../63-seqan-apps_2.4.0+dfsg-16_armhf.deb ... 252s Unpacking seqan-apps (2.4.0+dfsg-16) ... 252s Selecting previously unselected package autopkgtest-satdep. 252s Preparing to unpack .../64-1-autopkgtest-satdep.deb ... 252s Unpacking autopkgtest-satdep (0) ... 252s Setting up libhtscodecs2:armhf (1.6.1-1) ... 252s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 252s Setting up liblcms2-2:armhf (2.16-2) ... 252s Setting up python3-iniconfig (1.1.1-2) ... 252s Setting up libpixman-1-0:armhf (0.44.0-3) ... 252s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 252s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 252s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 252s Setting up libxcb-render0:armhf (1.17.0-2) ... 252s Setting up x11-common (1:7.7+23ubuntu3) ... 253s Setting up libdeflate0:armhf (1.22-1) ... 253s Setting up python3-all (3.12.6-0ubuntu1) ... 253s Setting up libxcb-shm0:armhf (1.17.0-2) ... 253s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 253s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 253s Setting up python3-tz (2024.1-2) ... 253s Setting up python3-six (1.16.0-7) ... 253s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 253s Setting up libblas3:armhf (3.12.0-3build2) ... 253s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 253s Setting up python3-packaging (24.1-1) ... 254s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 254s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 254s Setting up libimagequant0:armhf (2.18.0-1build1) ... 254s Setting up seqan-apps (2.4.0+dfsg-16) ... 254s Setting up fonts-dejavu-mono (2.37-8) ... 254s Setting up fonts-dejavu-core (2.37-8) ... 254s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 254s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 254s Setting up python3-pluggy (1.5.0-1) ... 254s Setting up libwebp7:armhf (1.4.0-0.1) ... 254s Setting up libhts3t64:armhf (1.20+ds-1) ... 254s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 254s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 254s Setting up python3-dateutil (2.9.0-2) ... 254s Setting up sgml-base (1.31) ... 254s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 254s Setting up bedtools (2.31.1+dfsg-2) ... 254s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 254s Setting up liblapack3:armhf (3.12.0-3build2) ... 254s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 254s Setting up python3-pysam (0.22.1+ds-2) ... 254s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 255s Setting up python3-pytest (8.3.3-1) ... 256s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 256s Setting up python3-freetype (2.5.1-1) ... 256s Setting up xfonts-utils (1:7.7+7) ... 256s Setting up samtools (1.20-3) ... 256s Setting up libraqm0:armhf (0.10.1-1build1) ... 256s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 259s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 259s Setting up xml-core (0.19) ... 259s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 259s Setting up python3-pybedtools (0.10.0-2) ... 259s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5) ... 259s Setting up fonts-urw-base35 (20200910-8) ... 260s Setting up libcairo2:armhf (1.18.2-2) ... 260s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 260s Setting up python3-pandas (2.2.3+dfsg-5) ... 269s Setting up python3-cairo (1.26.1-2) ... 269s Setting up python3-rlpycairo (0.3.0-3) ... 269s Setting up python3-reportlab (4.2.5-1) ... 270s Processing triggers for libc-bin (2.40-1ubuntu3) ... 270s Processing triggers for man-db (2.13.0-1) ... 272s Processing triggers for sgml-base (1.31) ... 272s Setting up w3c-sgml-lib (1.3-3) ... 309s Setting up python3-biopython (1.84+dfsg-4) ... 311s Setting up python3-mirtop (0.4.28-1) ... 311s /usr/lib/python3/dist-packages/mirtop/sql/sql.py:478: SyntaxWarning: invalid escape sequence '\(' 311s print("Usage: mirtop sql --create --gff --db \(Default: mirtop.db\)") 311s Setting up mirtop (0.4.28-1) ... 311s Setting up autopkgtest-satdep (0) ... 333s (Reading database ... 65733 files and directories currently installed.) 333s Removing autopkgtest-satdep (0) ... 339s autopkgtest [20:12:35]: test run-unit-test: [----------------------- 342s Testing with python3.12 in /tmp/autopkgtest.cO2vKi/autopkgtest_tmp: 342s ============================= test session starts ============================== 342s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 342s cachedir: .pytest_cache 342s rootdir: /tmp/autopkgtest.cO2vKi/autopkgtest_tmp 342s plugins: typeguard-4.4.1 342s collecting ... collected 62 items 342s 344s test/test_automated_analysis.py::AutomatedAnalysisTest::test_count PASSED [ 1%] 345s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_fasta PASSED [ 3%] 347s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_seqbuster PASSED [ 4%] 348s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_vcf PASSED [ 6%] 350s test/test_automated_analysis.py::AutomatedAnalysisTest::test_merge_bam PASSED [ 8%] 350s test/test_automated_analysis.py::AutomatedAnalysisTest::test_simulate PASSED [ 9%] 352s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_create_1_cmd PASSED [ 11%] 354s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_create_2_cmd PASSED [ 12%] 355s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectColumns_cmd PASSED [ 14%] 356s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectCount_cmd PASSED [ 16%] 358s 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test/test_functions.py::FunctionsTest::test_sql PASSED [ 90%] 381s test/test_functions.py::FunctionsTest::test_srnabench PASSED [ 91%] 381s test/test_functions.py::FunctionsTest::test_stats PASSED [ 93%] 381s test/test_functions.py::FunctionsTest::test_string_variant PASSED [ 95%] 381s test/test_functions.py::FunctionsTest::test_update PASSED [ 96%] 381s test/test_functions.py::FunctionsTest::test_validator PASSED [ 98%] 381s test/test_functions.py::FunctionsTest::test_variant PASSED [100%] 381s 381s =============================== warnings summary =============================== 381s test/test_functions.py::FunctionsTest::test_alignment 381s /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 381s import pkg_resources 381s 381s test/test_functions.py::FunctionsTest::test_alignment 381s /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. 381s warnings.warn( 381s 381s test/test_functions.py::FunctionsTest::test_collapse 381s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 381s return self.run(*args, **kwds) 381s 381s test/test_functions.py::FunctionsTest::test_counts 381s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 381s return self.run(*args, **kwds) 381s 381s test/test_functions.py::FunctionsTest::test_gff 381s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 381s return self.run(*args, **kwds) 381s 381s test/test_functions.py::FunctionsTest::test_read_hairpin 381s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 381s return self.run(*args, **kwds) 381s 381s test/test_functions.py::FunctionsTest::test_sql 381s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 381s return self.run(*args, **kwds) 381s 381s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 381s ======================= 62 passed, 7 warnings in 39.43s ======================== 382s autopkgtest [20:13:18]: test run-unit-test: -----------------------] 386s autopkgtest [20:13:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 386s run-unit-test PASS 390s autopkgtest [20:13:26]: test autodep8-python3: preparing testbed 445s autopkgtest [20:14:21]: testbed dpkg architecture: armhf 448s autopkgtest [20:14:24]: testbed apt version: 2.9.8 448s autopkgtest [20:14:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 455s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 456s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1043 kB] 456s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [92.2 kB] 456s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 456s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 456s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [143 kB] 456s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [747 kB] 456s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4428 B] 456s Fetched 2126 kB in 1s (2122 kB/s) 456s Reading package lists... 472s tee: /proc/self/fd/2: Permission denied 494s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 494s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 494s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 494s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 496s Reading package lists... 496s Reading package lists... 496s Building dependency tree... 496s Reading state information... 497s Calculating upgrade... 498s The following NEW packages will be installed: 498s libassuan9 498s The following packages will be upgraded: 498s libgpgme11t64 libseccomp2 python3-cffi-backend python3-markupsafe 498s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 498s Need to get 297 kB of archives. 498s After this operation, 224 kB of additional disk space will be used. 498s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libseccomp2 armhf 2.5.5-1ubuntu5 [49.3 kB] 498s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cffi-backend armhf 1.17.1-2build1 [75.9 kB] 498s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libassuan9 armhf 3.0.1-2 [34.3 kB] 498s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgpgme11t64 armhf 1.24.0-2ubuntu1 [125 kB] 498s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-markupsafe armhf 2.1.5-1build3 [12.5 kB] 499s Fetched 297 kB in 0s (623 kB/s) 499s (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 ... 59566 files and directories currently installed.) 499s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu5_armhf.deb ... 499s Unpacking libseccomp2:armhf (2.5.5-1ubuntu5) over (2.5.5-1ubuntu4) ... 499s Setting up libseccomp2:armhf (2.5.5-1ubuntu5) ... 499s (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 ... 59566 files and directories currently installed.) 499s Preparing to unpack .../python3-cffi-backend_1.17.1-2build1_armhf.deb ... 499s Unpacking python3-cffi-backend:armhf (1.17.1-2build1) over (1.17.1-2) ... 499s Selecting previously unselected package libassuan9:armhf. 499s Preparing to unpack .../libassuan9_3.0.1-2_armhf.deb ... 499s Unpacking libassuan9:armhf (3.0.1-2) ... 499s Preparing to unpack .../libgpgme11t64_1.24.0-2ubuntu1_armhf.deb ... 499s Unpacking libgpgme11t64:armhf (1.24.0-2ubuntu1) over (1.23.2-5ubuntu4) ... 499s Preparing to unpack .../python3-markupsafe_2.1.5-1build3_armhf.deb ... 499s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ... 499s Setting up python3-markupsafe (2.1.5-1build3) ... 499s Setting up libassuan9:armhf (3.0.1-2) ... 499s Setting up libgpgme11t64:armhf (1.24.0-2ubuntu1) ... 499s Setting up python3-cffi-backend:armhf (1.17.1-2build1) ... 499s Processing triggers for libc-bin (2.40-1ubuntu3) ... 500s Reading package lists... 500s Building dependency tree... 500s Reading state information... 501s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 503s autopkgtest [20:15:19]: rebooting testbed after setup commands that affected boot 605s Reading package lists... 606s Building dependency tree... 606s Reading state information... 606s Starting pkgProblemResolver with broken count: 0 607s Starting 2 pkgProblemResolver with broken count: 0 607s Done 608s The following additional packages will be installed: 608s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 608s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 608s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 608s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 608s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 608s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-all 608s python3-biopython python3-cairo python3-dateutil python3-freetype 608s python3-mirtop python3-numpy python3-pandas python3-pandas-lib python3-pil 608s python3-pybedtools python3-pysam python3-reportlab python3-rlpycairo 608s python3-six python3-tz sgml-base w3c-sgml-lib x11-common xfonts-encodings 608s xfonts-utils xml-core 608s Suggested packages: 608s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 608s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 608s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 608s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 608s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 608s python3-statsmodels python-pil-doc python-pybedtools-doc pdf-viewer 608s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 608s sgml-base-doc debhelper 608s Recommended packages: 608s python-biopython-doc ncbi-blast+ python3-scipy python3-matplotlib 608s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 608s python3-html5lib python3-lxml python3-tables python3-olefile 608s fonts-dejavu-extra 608s The following NEW packages will be installed: 608s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 608s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 608s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 608s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 608s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 608s libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 608s libxrender1 python3-all python3-biopython python3-cairo python3-dateutil 608s python3-freetype python3-mirtop python3-numpy python3-pandas 608s python3-pandas-lib python3-pil python3-pybedtools python3-pysam 608s python3-reportlab python3-rlpycairo python3-six python3-tz sgml-base 608s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 608s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 608s Need to get 50.0 MB/50.0 MB of archives. 608s After this operation, 162 MB of additional disk space will be used. 608s Get:1 /tmp/autopkgtest.cO2vKi/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [712 B] 608s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 608s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 608s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 608s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 608s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 609s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 609s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 609s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 609s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 609s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 609s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 609s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 609s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 609s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 609s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 609s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 609s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 609s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 609s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 609s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 609s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 609s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 609s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-1 [67.9 kB] 609s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 609s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 609s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 609s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 609s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 609s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 609s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 609s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 609s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 609s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 609s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 609s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 609s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 609s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 609s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 609s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 609s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 609s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 609s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 609s Get:44 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 609s Get:45 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 609s Get:46 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 609s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 609s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 609s Get:49 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 609s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 609s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-2 [80.3 kB] 609s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.22.1+ds-2 [3383 kB] 610s Get:53 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-pybedtools armhf 0.10.0-2 [12.4 MB] 610s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 610s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5 [4728 kB] 610s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5 [3112 kB] 610s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mirtop all 0.4.28-1 [61.9 kB] 611s Fetched 50.0 MB in 2s (21.5 MB/s) 611s Selecting previously unselected package sgml-base. 611s (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 ... 59573 files and directories currently installed.) 611s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 611s Unpacking sgml-base (1.31) ... 611s Selecting previously unselected package fonts-dejavu-mono. 611s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 611s Unpacking fonts-dejavu-mono (2.37-8) ... 611s Selecting previously unselected package fonts-dejavu-core. 611s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 611s Unpacking fonts-dejavu-core (2.37-8) ... 611s Selecting previously unselected package libfontenc1:armhf. 611s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 611s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 611s Selecting previously unselected package libfreetype6:armhf. 611s Preparing to unpack .../04-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 611s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 611s Selecting previously unselected package x11-common. 611s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 611s Unpacking x11-common (1:7.7+23ubuntu3) ... 611s Selecting previously unselected package xfonts-encodings. 611s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 611s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 611s Selecting previously unselected package xfonts-utils. 611s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_armhf.deb ... 611s Unpacking xfonts-utils (1:7.7+7) ... 611s Selecting previously unselected package fonts-urw-base35. 611s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 611s Unpacking fonts-urw-base35 (20200910-8) ... 612s Selecting previously unselected package fontconfig-config. 612s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 612s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 612s Selecting previously unselected package libblas3:armhf. 612s Preparing to unpack .../10-libblas3_3.12.0-3build2_armhf.deb ... 612s Unpacking libblas3:armhf (3.12.0-3build2) ... 612s Selecting previously unselected package libfontconfig1:armhf. 612s Preparing to unpack .../11-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 612s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 612s Selecting previously unselected package libpixman-1-0:armhf. 612s Preparing to unpack .../12-libpixman-1-0_0.44.0-3_armhf.deb ... 612s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 612s Selecting previously unselected package libxcb-render0:armhf. 612s Preparing to unpack .../13-libxcb-render0_1.17.0-2_armhf.deb ... 612s Unpacking libxcb-render0:armhf (1.17.0-2) ... 612s Selecting previously unselected package libxcb-shm0:armhf. 612s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_armhf.deb ... 612s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 612s Selecting previously unselected package libxrender1:armhf. 612s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 612s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 612s Selecting previously unselected package libcairo2:armhf. 612s Preparing to unpack .../16-libcairo2_1.18.2-2_armhf.deb ... 612s Unpacking libcairo2:armhf (1.18.2-2) ... 612s Selecting previously unselected package libdeflate0:armhf. 612s Preparing to unpack .../17-libdeflate0_1.22-1_armhf.deb ... 612s Unpacking libdeflate0:armhf (1.22-1) ... 612s Selecting previously unselected package libgfortran5:armhf. 612s Preparing to unpack .../18-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 612s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 612s Selecting previously unselected package libgomp1:armhf. 612s Preparing to unpack .../19-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 612s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 612s Selecting previously unselected package libgraphite2-3:armhf. 612s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 612s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 612s Selecting previously unselected package libharfbuzz0b:armhf. 612s Preparing to unpack .../21-libharfbuzz0b_10.0.1-1_armhf.deb ... 612s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 612s Selecting previously unselected package libhtscodecs2:armhf. 612s Preparing to unpack .../22-libhtscodecs2_1.6.1-1_armhf.deb ... 612s Unpacking libhtscodecs2:armhf (1.6.1-1) ... 612s Selecting previously unselected package libhts3t64:armhf. 613s Preparing to unpack .../23-libhts3t64_1.20+ds-1_armhf.deb ... 613s Unpacking libhts3t64:armhf (1.20+ds-1) ... 613s Selecting previously unselected package libimagequant0:armhf. 613s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_armhf.deb ... 613s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 613s Selecting previously unselected package libjpeg-turbo8:armhf. 613s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 613s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 613s Selecting previously unselected package libjpeg8:armhf. 613s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_armhf.deb ... 613s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 613s Selecting previously unselected package liblapack3:armhf. 613s Preparing to unpack .../27-liblapack3_3.12.0-3build2_armhf.deb ... 613s Unpacking liblapack3:armhf (3.12.0-3build2) ... 613s Selecting previously unselected package liblcms2-2:armhf. 613s Preparing to unpack .../28-liblcms2-2_2.16-2_armhf.deb ... 613s Unpacking liblcms2-2:armhf (2.16-2) ... 613s Selecting previously unselected package liblerc4:armhf. 613s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 613s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 613s Selecting previously unselected package libraqm0:armhf. 613s Preparing to unpack .../30-libraqm0_0.10.1-1build1_armhf.deb ... 613s Unpacking libraqm0:armhf (0.10.1-1build1) ... 613s Selecting previously unselected package libsharpyuv0:armhf. 613s Preparing to unpack .../31-libsharpyuv0_1.4.0-0.1_armhf.deb ... 613s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 613s Selecting previously unselected package libjbig0:armhf. 613s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 613s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 613s Selecting previously unselected package libwebp7:armhf. 613s Preparing to unpack .../33-libwebp7_1.4.0-0.1_armhf.deb ... 613s Unpacking libwebp7:armhf (1.4.0-0.1) ... 613s Selecting previously unselected package libtiff6:armhf. 613s Preparing to unpack .../34-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 613s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 613s Selecting previously unselected package libwebpdemux2:armhf. 613s Preparing to unpack .../35-libwebpdemux2_1.4.0-0.1_armhf.deb ... 613s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 613s Selecting previously unselected package libwebpmux3:armhf. 613s Preparing to unpack .../36-libwebpmux3_1.4.0-0.1_armhf.deb ... 613s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 613s Selecting previously unselected package python3-all. 613s Preparing to unpack .../37-python3-all_3.12.6-0ubuntu1_armhf.deb ... 613s Unpacking python3-all (3.12.6-0ubuntu1) ... 613s Selecting previously unselected package python3-numpy. 613s Preparing to unpack .../38-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 613s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 613s Selecting previously unselected package libopenjp2-7:armhf. 613s Preparing to unpack .../39-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 613s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 613s Selecting previously unselected package python3-pil:armhf. 613s Preparing to unpack .../40-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 613s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 614s Selecting previously unselected package python3-cairo. 614s Preparing to unpack .../41-python3-cairo_1.26.1-2_armhf.deb ... 614s Unpacking python3-cairo (1.26.1-2) ... 614s Selecting previously unselected package python3-freetype. 614s Preparing to unpack .../42-python3-freetype_2.5.1-1_all.deb ... 614s Unpacking python3-freetype (2.5.1-1) ... 614s Selecting previously unselected package python3-rlpycairo. 614s Preparing to unpack .../43-python3-rlpycairo_0.3.0-3_all.deb ... 614s Unpacking python3-rlpycairo (0.3.0-3) ... 614s Selecting previously unselected package python3-reportlab. 614s Preparing to unpack .../44-python3-reportlab_4.2.5-1_all.deb ... 614s Unpacking python3-reportlab (4.2.5-1) ... 614s Selecting previously unselected package xml-core. 614s Preparing to unpack .../45-xml-core_0.19_all.deb ... 614s Unpacking xml-core (0.19) ... 614s Selecting previously unselected package w3c-sgml-lib. 614s Preparing to unpack .../46-w3c-sgml-lib_1.3-3_all.deb ... 614s Unpacking w3c-sgml-lib (1.3-3) ... 614s Selecting previously unselected package python3-biopython. 614s Preparing to unpack .../47-python3-biopython_1.84+dfsg-4_armhf.deb ... 614s Unpacking python3-biopython (1.84+dfsg-4) ... 614s Selecting previously unselected package python3-six. 614s Preparing to unpack .../48-python3-six_1.16.0-7_all.deb ... 614s Unpacking python3-six (1.16.0-7) ... 614s Selecting previously unselected package python3-dateutil. 614s Preparing to unpack .../49-python3-dateutil_2.9.0-2_all.deb ... 614s Unpacking python3-dateutil (2.9.0-2) ... 614s Selecting previously unselected package python3-pysam. 614s Preparing to unpack .../50-python3-pysam_0.22.1+ds-2_armhf.deb ... 614s Unpacking python3-pysam (0.22.1+ds-2) ... 615s Selecting previously unselected package python3-pybedtools. 615s Preparing to unpack .../51-python3-pybedtools_0.10.0-2_armhf.deb ... 615s Unpacking python3-pybedtools (0.10.0-2) ... 615s Selecting previously unselected package python3-tz. 615s Preparing to unpack .../52-python3-tz_2024.1-2_all.deb ... 615s Unpacking python3-tz (2024.1-2) ... 615s Selecting previously unselected package python3-pandas-lib:armhf. 615s Preparing to unpack .../53-python3-pandas-lib_2.2.3+dfsg-5_armhf.deb ... 615s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5) ... 615s Selecting previously unselected package python3-pandas. 615s Preparing to unpack .../54-python3-pandas_2.2.3+dfsg-5_all.deb ... 615s Unpacking python3-pandas (2.2.3+dfsg-5) ... 616s Selecting previously unselected package python3-mirtop. 616s Preparing to unpack .../55-python3-mirtop_0.4.28-1_all.deb ... 616s Unpacking python3-mirtop (0.4.28-1) ... 616s Selecting previously unselected package autopkgtest-satdep. 616s Preparing to unpack .../56-2-autopkgtest-satdep.deb ... 616s Unpacking autopkgtest-satdep (0) ... 616s Setting up libhtscodecs2:armhf (1.6.1-1) ... 616s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 616s Setting up liblcms2-2:armhf (2.16-2) ... 616s Setting up libpixman-1-0:armhf (0.44.0-3) ... 616s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 616s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 616s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 616s Setting up libxcb-render0:armhf (1.17.0-2) ... 616s Setting up x11-common (1:7.7+23ubuntu3) ... 616s Setting up libdeflate0:armhf (1.22-1) ... 616s Setting up python3-all (3.12.6-0ubuntu1) ... 616s Setting up libxcb-shm0:armhf (1.17.0-2) ... 616s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 616s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 616s Setting up python3-tz (2024.1-2) ... 616s Setting up python3-six (1.16.0-7) ... 616s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 616s Setting up libblas3:armhf (3.12.0-3build2) ... 616s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 616s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 616s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 616s Setting up libimagequant0:armhf (2.18.0-1build1) ... 616s Setting up fonts-dejavu-mono (2.37-8) ... 616s Setting up fonts-dejavu-core (2.37-8) ... 616s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 616s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 616s Setting up libwebp7:armhf (1.4.0-0.1) ... 616s Setting up libhts3t64:armhf (1.20+ds-1) ... 616s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 616s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 617s Setting up python3-dateutil (2.9.0-2) ... 617s Setting up sgml-base (1.31) ... 617s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 617s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 617s Setting up liblapack3:armhf (3.12.0-3build2) ... 617s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 617s Setting up python3-pysam (0.22.1+ds-2) ... 617s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 617s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 617s Setting up python3-freetype (2.5.1-1) ... 617s Setting up xfonts-utils (1:7.7+7) ... 617s Setting up libraqm0:armhf (0.10.1-1build1) ... 617s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 620s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 620s Setting up xml-core (0.19) ... 620s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 620s Setting up python3-pybedtools (0.10.0-2) ... 620s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5) ... 620s Setting up fonts-urw-base35 (20200910-8) ... 621s Setting up libcairo2:armhf (1.18.2-2) ... 621s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 621s Setting up python3-pandas (2.2.3+dfsg-5) ... 628s Setting up python3-cairo (1.26.1-2) ... 628s Setting up python3-rlpycairo (0.3.0-3) ... 628s Setting up python3-reportlab (4.2.5-1) ... 629s Processing triggers for libc-bin (2.40-1ubuntu3) ... 629s Processing triggers for man-db (2.13.0-1) ... 631s Processing triggers for sgml-base (1.31) ... 631s Setting up w3c-sgml-lib (1.3-3) ... 664s Setting up python3-biopython (1.84+dfsg-4) ... 665s Setting up python3-mirtop (0.4.28-1) ... 666s /usr/lib/python3/dist-packages/mirtop/sql/sql.py:478: SyntaxWarning: invalid escape sequence '\(' 666s print("Usage: mirtop sql --create --gff --db \(Default: mirtop.db\)") 666s Setting up autopkgtest-satdep (0) ... 684s (Reading database ... 65222 files and directories currently installed.) 684s Removing autopkgtest-satdep (0) ... 696s autopkgtest [20:18:32]: 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 696s autopkgtest [20:18:32]: test autodep8-python3: [----------------------- 698s Testing with python3.12: 698s 698s autopkgtest [20:18:34]: test autodep8-python3: -----------------------] 702s autopkgtest [20:18:38]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 702s autodep8-python3 PASS (superficial) 706s autopkgtest [20:18:42]: @@@@@@@@@@@@@@@@@@@@ summary 706s run-unit-test PASS 706s autodep8-python3 PASS (superficial)