0s autopkgtest [21:42:23]: starting date and time: 2024-11-15 21:42:23+0000 0s autopkgtest [21:42:23]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [21:42:23]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2yzy_m9i/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-pybedtools --apt-upgrade mirtop --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-pybedtools/0.10.0-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-24.secgroup --name adt-plucky-i386-mirtop-20241115-203217-juju-7f2275-prod-proposed-migration-environment-20-c0a60c46-348d-4496-bec0-481eb19fa425 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 43s autopkgtest [21:43:06]: testbed dpkg architecture: amd64 44s autopkgtest [21:43:07]: testbed apt version: 2.9.8 44s autopkgtest [21:43:07]: test architecture: i386 44s autopkgtest [21:43:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 45s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 45s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 45s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 45s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1029 kB] 45s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [93.0 kB] 45s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB] 46s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [111 kB] 46s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 46s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [811 kB] 46s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [297 kB] 46s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 46s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 46s Fetched 2655 kB in 1s (3049 kB/s) 46s Reading package lists... 48s Reading package lists... 48s Building dependency tree... 48s Reading state information... 49s Calculating upgrade... 49s The following NEW packages will be installed: 49s libassuan9 49s The following packages will be upgraded: 49s libgpgme11t64 libseccomp2 python3-cffi-backend 49s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 49s Need to get 348 kB of archives. 49s After this operation, 361 kB of additional disk space will be used. 49s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu5 [53.3 kB] 49s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build1 [96.7 kB] 49s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.1-2 [42.9 kB] 49s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.0-2ubuntu1 [155 kB] 50s Fetched 348 kB in 0s (721 kB/s) 50s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75576 files and directories currently installed.) 50s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu5_amd64.deb ... 50s Unpacking libseccomp2:amd64 (2.5.5-1ubuntu5) over (2.5.5-1ubuntu4) ... 50s Setting up libseccomp2:amd64 (2.5.5-1ubuntu5) ... 50s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75576 files and directories currently installed.) 50s Preparing to unpack .../python3-cffi-backend_1.17.1-2build1_amd64.deb ... 50s Unpacking python3-cffi-backend:amd64 (1.17.1-2build1) over (1.17.1-2) ... 50s Selecting previously unselected package libassuan9:amd64. 50s Preparing to unpack .../libassuan9_3.0.1-2_amd64.deb ... 50s Unpacking libassuan9:amd64 (3.0.1-2) ... 50s Preparing to unpack .../libgpgme11t64_1.24.0-2ubuntu1_amd64.deb ... 50s Unpacking libgpgme11t64:amd64 (1.24.0-2ubuntu1) over (1.23.2-5ubuntu4) ... 50s Setting up libassuan9:amd64 (3.0.1-2) ... 50s Setting up libgpgme11t64:amd64 (1.24.0-2ubuntu1) ... 50s Setting up python3-cffi-backend:amd64 (1.17.1-2build1) ... 50s Processing triggers for libc-bin (2.40-1ubuntu3) ... 50s Reading package lists... 50s Building dependency tree... 51s Reading state information... 51s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 51s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 52s Reading package lists... 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 52s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s autopkgtest [21:43:18]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 56s autopkgtest [21:43:19]: @@@@@@@@@@@@@@@@@@@@ apt-source mirtop 58s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (dsc) [2340 B] 58s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (tar) [718 kB] 58s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mirtop 0.4.28-1 (diff) [10.4 kB] 58s gpgv: Signature made Sat Oct 12 13:35:08 2024 UTC 58s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 58s gpgv: issuer "tchet@debian.org" 58s gpgv: Can't check signature: No public key 58s dpkg-source: warning: cannot verify inline signature for ./mirtop_0.4.28-1.dsc: no acceptable signature found 58s autopkgtest [21:43:21]: testing package mirtop version 0.4.28-1 58s autopkgtest [21:43:21]: build not needed 59s autopkgtest [21:43:22]: test run-unit-test: preparing testbed 61s Note, using file '/tmp/autopkgtest.vGpgXD/1-autopkgtest-satdep.dsc' to get the build dependencies 61s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Starting pkgProblemResolver with broken count: 0 62s Starting 2 pkgProblemResolver with broken count: 0 62s Done 62s The following NEW packages will be installed: 62s bedtools build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu 62s cpp-x86-64-linux-gnu fontconfig-config fonts-dejavu-core fonts-dejavu-mono 62s fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 62s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libblas3 62s libcairo2 libcc1-0 libdeflate0 libfontconfig1 libfontenc1 libgcc-14-dev 62s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 62s libhwasan0 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 62s liblapack3 liblcms2-2 liblerc4 liblsan0 libmpc3 libopenjp2-7 libpixman-1-0 62s libquadmath0 libraqm0 libsharpyuv0 libstdc++-14-dev libtiff6 libtsan2 62s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 62s libxrender1 mirtop python3-all python3-biopython python3-cairo 62s python3-dateutil python3-freetype python3-iniconfig python3-mirtop 62s python3-numpy python3-packaging python3-pandas python3-pandas-lib 62s python3-pil python3-pluggy python3-pybedtools python3-pysam python3-pytest 62s python3-reportlab python3-rlpycairo python3-six python3-tz samtools 62s seqan-apps sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils 62s xml-core 63s 0 upgraded, 88 newly installed, 0 to remove and 0 not upgraded. 63s Need to get 133 MB of archives. 63s After this operation, 484 MB of additional disk space will be used. 63s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 bedtools amd64 2.31.1+dfsg-2 [674 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 63s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 63s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 63s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 63s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 63s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 63s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 63s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 63s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 63s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 63s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 64s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 64s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 64s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 64s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 64s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 64s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 64s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 64s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 64s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 65s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 65s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 65s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 65s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 65s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 65s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 65s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 65s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 65s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 65s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 65s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 65s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 65s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 65s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 65s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 65s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 65s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 65s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 65s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 65s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 65s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 65s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 65s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 65s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 65s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 65s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 65s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 65s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 65s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 65s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 65s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 65s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 65s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 65s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 65s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 65s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 65s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 65s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 65s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 65s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 65s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 65s Get:66 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-pybedtools amd64 0.10.0-2 [12.4 MB] 66s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 66s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 66s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 66s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 66s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 66s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 66s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 66s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 66s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 66s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 66s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 66s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 66s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 66s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mirtop all 0.4.28-1 [61.9 kB] 66s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 mirtop all 0.4.28-1 [13.5 kB] 66s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 66s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 66s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 66s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 66s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 66s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 66s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 seqan-apps amd64 2.4.0+dfsg-16 [12.3 MB] 67s Fetched 133 MB in 4s (31.8 MB/s) 67s Selecting previously unselected package sgml-base. 67s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75582 files and directories currently installed.) 67s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 67s Unpacking sgml-base (1.31) ... 67s Selecting previously unselected package bedtools. 67s Preparing to unpack .../01-bedtools_2.31.1+dfsg-2_amd64.deb ... 67s Unpacking bedtools (2.31.1+dfsg-2) ... 67s Selecting previously unselected package libisl23:amd64. 67s Preparing to unpack .../02-libisl23_0.27-1_amd64.deb ... 67s Unpacking libisl23:amd64 (0.27-1) ... 67s Selecting previously unselected package libmpc3:amd64. 67s Preparing to unpack .../03-libmpc3_1.3.1-1build2_amd64.deb ... 67s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 67s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 67s Preparing to unpack .../04-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 67s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 67s Selecting previously unselected package cpp-14. 67s Preparing to unpack .../05-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 67s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 67s Selecting previously unselected package cpp-x86-64-linux-gnu. 67s Preparing to unpack .../06-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 67s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 67s Selecting previously unselected package cpp. 67s Preparing to unpack .../07-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 67s Unpacking cpp (4:14.1.0-2ubuntu1) ... 67s Selecting previously unselected package libcc1-0:amd64. 67s 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(14.2.0-8ubuntu1) ... 68s Selecting previously unselected package libubsan1:amd64. 68s Preparing to unpack .../14-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package libhwasan0:amd64. 68s Preparing to unpack .../15-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package libquadmath0:amd64. 68s Preparing to unpack .../16-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package libgcc-14-dev:amd64. 68s Preparing to unpack .../17-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 68s Preparing to unpack .../18-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package gcc-14. 68s Preparing to unpack .../19-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package gcc-x86-64-linux-gnu. 68s Preparing to unpack .../20-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 68s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 68s Selecting previously unselected package gcc. 68s Preparing to unpack .../21-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 68s Unpacking gcc (4:14.1.0-2ubuntu1) ... 68s Selecting previously unselected package libstdc++-14-dev:amd64. 68s Preparing to unpack .../22-libstdc++-14-dev_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package g++-14-x86-64-linux-gnu. 69s Preparing to unpack .../23-g++-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package g++-14. 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fonts-dejavu-core (2.37-8) ... 69s Selecting previously unselected package libfontenc1:amd64. 69s Preparing to unpack .../30-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 69s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 69s Selecting previously unselected package x11-common. 69s Preparing to unpack .../31-x11-common_1%3a7.7+23ubuntu3_all.deb ... 69s Unpacking x11-common (1:7.7+23ubuntu3) ... 69s Selecting previously unselected package xfonts-encodings. 69s Preparing to unpack .../32-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 69s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 69s Selecting previously unselected package xfonts-utils. 69s Preparing to unpack .../33-xfonts-utils_1%3a7.7+7_amd64.deb ... 69s Unpacking xfonts-utils (1:7.7+7) ... 69s Selecting previously unselected package fonts-urw-base35. 69s Preparing to unpack .../34-fonts-urw-base35_20200910-8_all.deb ... 69s Unpacking fonts-urw-base35 (20200910-8) ... 69s Selecting previously unselected package fontconfig-config. 69s Preparing to unpack .../35-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 69s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 69s Selecting previously unselected package libblas3:amd64. 69s Preparing to unpack .../36-libblas3_3.12.0-3build2_amd64.deb ... 69s Unpacking libblas3:amd64 (3.12.0-3build2) ... 69s Selecting previously unselected package libfontconfig1:amd64. 69s Preparing to unpack .../37-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 69s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 69s Selecting previously unselected package libpixman-1-0:amd64. 69s Preparing to unpack .../38-libpixman-1-0_0.44.0-3_amd64.deb ... 69s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 69s Selecting previously unselected package libxcb-render0:amd64. 69s Preparing to unpack .../39-libxcb-render0_1.17.0-2_amd64.deb ... 69s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 69s Selecting previously unselected package libxcb-shm0:amd64. 69s Preparing to unpack .../40-libxcb-shm0_1.17.0-2_amd64.deb ... 69s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 70s Selecting previously unselected package libxrender1:amd64. 70s Preparing to unpack .../41-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 70s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 70s Selecting previously unselected package libcairo2:amd64. 70s Preparing to unpack .../42-libcairo2_1.18.2-2_amd64.deb ... 70s Unpacking libcairo2:amd64 (1.18.2-2) ... 70s Selecting previously unselected package libdeflate0:amd64. 70s Preparing to unpack .../43-libdeflate0_1.22-1_amd64.deb ... 70s Unpacking libdeflate0:amd64 (1.22-1) ... 70s Selecting previously unselected package libgfortran5:amd64. 70s Preparing to unpack .../44-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 70s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 70s Selecting previously unselected package libgraphite2-3:amd64. 70s Preparing to unpack .../45-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 70s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 70s Selecting previously unselected package libharfbuzz0b:amd64. 70s Preparing to unpack .../46-libharfbuzz0b_10.0.1-1_amd64.deb ... 70s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 70s Selecting previously unselected package libhtscodecs2:amd64. 70s Preparing to unpack .../47-libhtscodecs2_1.6.1-1_amd64.deb ... 70s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 70s Selecting previously unselected package libhts3t64:amd64. 70s Preparing to unpack .../48-libhts3t64_1.20+ds-1_amd64.deb ... 70s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 70s Selecting previously unselected package libimagequant0:amd64. 70s Preparing to unpack .../49-libimagequant0_2.18.0-1build1_amd64.deb ... 70s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 70s Selecting previously unselected package libjpeg-turbo8:amd64. 70s Preparing to unpack .../50-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 70s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 70s Selecting previously unselected package libjpeg8:amd64. 70s Preparing to unpack .../51-libjpeg8_8c-2ubuntu11_amd64.deb ... 70s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 70s Selecting previously unselected package liblapack3:amd64. 70s Preparing to unpack .../52-liblapack3_3.12.0-3build2_amd64.deb ... 70s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 70s Selecting previously unselected package liblcms2-2:amd64. 70s Preparing to unpack .../53-liblcms2-2_2.16-2_amd64.deb ... 70s Unpacking liblcms2-2:amd64 (2.16-2) ... 70s Selecting previously unselected package liblerc4:amd64. 70s Preparing to unpack .../54-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 70s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 70s Selecting previously unselected package libraqm0:amd64. 70s Preparing to unpack .../55-libraqm0_0.10.1-1build1_amd64.deb ... 70s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 70s Selecting previously unselected package libsharpyuv0:amd64. 70s Preparing to unpack .../56-libsharpyuv0_1.4.0-0.1_amd64.deb ... 70s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 70s Selecting previously unselected package libjbig0:amd64. 70s Preparing to unpack .../57-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 70s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 70s Selecting previously unselected package libwebp7:amd64. 70s Preparing to unpack .../58-libwebp7_1.4.0-0.1_amd64.deb ... 70s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 70s Selecting previously unselected package libtiff6:amd64. 70s Preparing to unpack .../59-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 70s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 70s Selecting previously unselected package libwebpdemux2:amd64. 70s Preparing to unpack .../60-libwebpdemux2_1.4.0-0.1_amd64.deb ... 70s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 70s Selecting previously unselected package libwebpmux3:amd64. 70s Preparing to unpack .../61-libwebpmux3_1.4.0-0.1_amd64.deb ... 70s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 70s Selecting previously unselected package python3-six. 70s Preparing to unpack .../62-python3-six_1.16.0-7_all.deb ... 70s Unpacking python3-six (1.16.0-7) ... 70s Selecting previously unselected package python3-pysam. 70s Preparing to unpack .../63-python3-pysam_0.22.1+ds-2_amd64.deb ... 70s Unpacking python3-pysam (0.22.1+ds-2) ... 70s Selecting previously unselected package python3-numpy. 70s Preparing to unpack .../64-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 70s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 71s Selecting previously unselected package python3-pybedtools. 71s Preparing to unpack .../65-python3-pybedtools_0.10.0-2_amd64.deb ... 71s Unpacking python3-pybedtools (0.10.0-2) ... 71s Selecting previously unselected package python3-dateutil. 71s Preparing to unpack .../66-python3-dateutil_2.9.0-2_all.deb ... 71s Unpacking python3-dateutil (2.9.0-2) ... 71s Selecting previously unselected package python3-tz. 71s Preparing to unpack .../67-python3-tz_2024.1-2_all.deb ... 71s Unpacking python3-tz (2024.1-2) ... 71s Selecting previously unselected package python3-pandas-lib:amd64. 71s Preparing to unpack .../68-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ... 71s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 71s Selecting previously unselected package python3-pandas. 71s Preparing to unpack .../69-python3-pandas_2.2.3+dfsg-5_all.deb ... 71s Unpacking python3-pandas (2.2.3+dfsg-5) ... 71s Selecting previously unselected package libopenjp2-7:amd64. 71s Preparing to unpack .../70-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 71s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 71s Selecting previously unselected package python3-pil:amd64. 71s Preparing to unpack .../71-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 71s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 71s Selecting previously unselected package python3-cairo. 71s Preparing to unpack .../72-python3-cairo_1.26.1-2_amd64.deb ... 71s Unpacking python3-cairo (1.26.1-2) ... 71s Selecting previously unselected package python3-freetype. 71s 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python3-mirtop. 72s Preparing to unpack .../79-python3-mirtop_0.4.28-1_all.deb ... 72s Unpacking python3-mirtop (0.4.28-1) ... 72s Selecting previously unselected package mirtop. 72s Preparing to unpack .../80-mirtop_0.4.28-1_all.deb ... 72s Unpacking mirtop (0.4.28-1) ... 72s Selecting previously unselected package python3-all. 72s Preparing to unpack .../81-python3-all_3.12.6-0ubuntu1_amd64.deb ... 72s Unpacking python3-all (3.12.6-0ubuntu1) ... 72s Selecting previously unselected package python3-iniconfig. 72s Preparing to unpack .../82-python3-iniconfig_1.1.1-2_all.deb ... 72s Unpacking python3-iniconfig (1.1.1-2) ... 72s Selecting previously unselected package python3-packaging. 72s Preparing to unpack .../83-python3-packaging_24.1-1_all.deb ... 72s Unpacking python3-packaging (24.1-1) ... 72s Selecting previously unselected package python3-pluggy. 72s Preparing to unpack .../84-python3-pluggy_1.5.0-1_all.deb ... 72s Unpacking python3-pluggy (1.5.0-1) ... 72s Selecting previously unselected package python3-pytest. 72s Preparing to unpack .../85-python3-pytest_8.3.3-1_all.deb ... 72s Unpacking python3-pytest (8.3.3-1) ... 72s Selecting previously unselected package samtools. 72s Preparing to unpack .../86-samtools_1.20-3_amd64.deb ... 72s Unpacking samtools (1.20-3) ... 72s Selecting previously unselected package seqan-apps. 72s Preparing to unpack .../87-seqan-apps_2.4.0+dfsg-16_amd64.deb ... 72s Unpacking seqan-apps (2.4.0+dfsg-16) ... 72s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 72s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 72s Setting up liblcms2-2:amd64 (2.16-2) ... 72s Setting up python3-iniconfig (1.1.1-2) ... 72s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 72s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 72s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 72s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 72s Setting up libxcb-render0:amd64 (1.17.0-2) ... 72s Setting up x11-common (1:7.7+23ubuntu3) ... 73s Setting up libdeflate0:amd64 (1.22-1) ... 73s Setting up python3-all (3.12.6-0ubuntu1) ... 73s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 73s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 73s Setting up python3-freetype (2.5.1-1) ... 73s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 73s Setting up python3-tz (2024.1-2) ... 73s Setting up python3-six (1.16.0-7) ... 73s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 73s Setting up libblas3:amd64 (3.12.0-3build2) ... 73s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 73s Setting up python3-packaging (24.1-1) ... 73s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 73s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ... 73s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 73s Setting up seqan-apps (2.4.0+dfsg-16) ... 73s Setting up fonts-dejavu-mono (2.37-8) ... 73s Setting up libmpc3:amd64 (1.3.1-1build2) ... 73s Setting up fonts-dejavu-core (2.37-8) ... 73s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 73s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 73s Setting up python3-pluggy (1.5.0-1) ... 73s Setting up libwebp7:amd64 (1.4.0-0.1) ... 73s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 73s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 73s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 73s Setting up libhts3t64:amd64 (1.20+ds-1) ... 73s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 73s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 73s Setting up python3-dateutil (2.9.0-2) ... 73s Setting up sgml-base (1.31) ... 73s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 73s Setting up libisl23:amd64 (0.27-1) ... 73s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 73s Setting up bedtools (2.31.1+dfsg-2) ... 73s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 73s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 73s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 73s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 73s Setting up liblapack3:amd64 (3.12.0-3build2) ... 73s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 73s Setting up python3-pysam (0.22.1+ds-2) ... 73s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 74s Setting up python3-pytest (8.3.3-1) ... 74s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 74s Setting up xfonts-utils (1:7.7+7) ... 74s Setting up samtools (1.20-3) ... 74s Setting up libraqm0:amd64 (0.10.1-1build1) ... 74s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 74s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 75s Setting up cpp-14 (14.2.0-8ubuntu1) ... 75s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 75s Setting up xml-core (0.19) ... 76s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 76s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 76s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 76s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 76s Setting up python3-pybedtools (0.10.0-2) ... 76s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 76s Setting up fonts-urw-base35 (20200910-8) ... 76s Setting up libcairo2:amd64 (1.18.2-2) ... 76s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 76s Setting up python3-pandas (2.2.3+dfsg-5) ... 80s Setting up cpp (4:14.1.0-2ubuntu1) ... 80s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 80s Setting up python3-cairo (1.26.1-2) ... 80s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 80s Setting up gcc-14 (14.2.0-8ubuntu1) ... 80s Setting up python3-rlpycairo (0.3.0-3) ... 80s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 80s Setting up python3-reportlab (4.2.5-1) ... 81s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 81s Setting up g++-14 (14.2.0-8ubuntu1) ... 81s Setting up gcc (4:14.1.0-2ubuntu1) ... 81s Setting up g++ (4:14.1.0-2ubuntu1) ... 81s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 81s Setting up build-essential (12.10ubuntu1) ... 81s Processing triggers for libc-bin (2.40-1ubuntu3) ... 81s Processing triggers for man-db (2.13.0-1) ... 82s Processing triggers for sgml-base (1.31) ... 82s Setting up w3c-sgml-lib (1.3-3) ... 104s Setting up python3-biopython (1.84+dfsg-4) ... 108s Setting up python3-mirtop (0.4.28-1) ... 108s /usr/lib/python3/dist-packages/mirtop/sql/sql.py:478: SyntaxWarning: invalid escape sequence '\(' 108s print("Usage: mirtop sql --create --gff --db \(Default: mirtop.db\)") 108s Setting up mirtop (0.4.28-1) ... 109s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Starting pkgProblemResolver with broken count: 0 110s Starting 2 pkgProblemResolver with broken count: 0 110s Done 110s The following NEW packages will be installed: 110s autopkgtest-satdep 110s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 110s Need to get 0 B/700 B of archives. 110s After this operation, 0 B of additional disk space will be used. 110s Get:1 /tmp/autopkgtest.vGpgXD/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B] 111s Selecting previously unselected package autopkgtest-satdep. 111s (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 ... 83016 files and directories currently installed.) 111s Preparing to unpack .../2-autopkgtest-satdep.deb ... 111s Unpacking autopkgtest-satdep (0) ... 111s Setting up autopkgtest-satdep (0) ... 113s (Reading database ... 83016 files and directories currently installed.) 113s Removing autopkgtest-satdep (0) ... 113s autopkgtest [21:44:16]: test run-unit-test: [----------------------- 113s Testing with python3.12 in /tmp/autopkgtest.vGpgXD/autopkgtest_tmp: 114s ============================= test session starts ============================== 114s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 114s cachedir: .pytest_cache 114s rootdir: /tmp/autopkgtest.vGpgXD/autopkgtest_tmp 114s plugins: typeguard-4.4.1 114s collecting ... collected 62 items 114s 114s test/test_automated_analysis.py::AutomatedAnalysisTest::test_count PASSED [ 1%] 115s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_fasta PASSED [ 3%] 115s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_seqbuster PASSED [ 4%] 116s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_vcf PASSED [ 6%] 117s test/test_automated_analysis.py::AutomatedAnalysisTest::test_merge_bam PASSED [ 8%] 117s test/test_automated_analysis.py::AutomatedAnalysisTest::test_simulate PASSED [ 9%] 117s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_create_1_cmd PASSED [ 11%] 118s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_create_2_cmd PASSED [ 12%] 119s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectColumns_cmd PASSED [ 14%] 119s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectCount_cmd PASSED [ 16%] 120s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectFilter_cmd PASSED [ 17%] 120s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectLimit_cmd PASSED [ 19%] 121s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectMirna_cmd PASSED [ 20%] 121s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectTextOut_cmd PASSED [ 22%] 122s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectiVariant_cmd PASSED [ 24%] 122s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_descSummary_cmd PASSED [ 25%] 123s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_showColumns_cmd PASSED [ 27%] 123s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_showSchema_cmd PASSED [ 29%] 124s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_showTables_cmd PASSED [ 30%] 125s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_statIsomirsFile_cmd PASSED [ 32%] 125s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_statIsomirs_cmd PASSED [ 33%] 126s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_bam PASSED [ 35%] 126s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_bam_chunk PASSED [ 37%] 127s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_genomic_bam PASSED [ 38%] 127s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_genomic_bam_low_memory PASSED [ 40%] 128s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_stats PASSED [ 41%] 128s test/test_automated_analysis.py::AutomatedAnalysisTest::test_update_cmd PASSED [ 43%] 129s test/test_automated_analysis.py::AutomatedAnalysisTest::test_validate_cmd PASSED [ 45%] 129s test/test_functions.py::FunctionsTest::test_alignment PASSED [ 46%] 129s test/test_functions.py::FunctionsTest::test_alignment_genomic PASSED [ 48%] 129s test/test_functions.py::FunctionsTest::test_cigar PASSED [ 50%] 129s test/test_functions.py::FunctionsTest::test_class PASSED [ 51%] 129s test/test_functions.py::FunctionsTest::test_code PASSED [ 53%] 129s test/test_functions.py::FunctionsTest::test_code_convert PASSED [ 54%] 129s test/test_functions.py::FunctionsTest::test_collapse PASSED [ 56%] 130s test/test_functions.py::FunctionsTest::test_counts PASSED [ 58%] 130s test/test_functions.py::FunctionsTest::test_database PASSED [ 59%] 130s test/test_functions.py::FunctionsTest::test_error69 PASSED [ 61%] 130s test/test_functions.py::FunctionsTest::test_export_fasta PASSED [ 62%] 130s test/test_functions.py::FunctionsTest::test_gff PASSED [ 64%] 130s test/test_functions.py::FunctionsTest::test_is_sequence PASSED [ 66%] 130s test/test_functions.py::FunctionsTest::test_issue64 PASSED [ 67%] 130s test/test_functions.py::FunctionsTest::test_keep_name PASSED [ 69%] 130s test/test_functions.py::FunctionsTest::test_locala PASSED [ 70%] 130s test/test_functions.py::FunctionsTest::test_merge PASSED [ 72%] 130s test/test_functions.py::FunctionsTest::test_optimir PASSED [ 74%] 130s test/test_functions.py::FunctionsTest::test_prost PASSED [ 75%] 130s test/test_functions.py::FunctionsTest::test_read_hairpin PASSED [ 77%] 130s test/test_functions.py::FunctionsTest::test_read_hairpin_mirgenedb PASSED [ 79%] 130s test/test_functions.py::FunctionsTest::test_read_line PASSED [ 80%] 130s test/test_functions.py::FunctionsTest::test_read_mir2chr PASSED [ 82%] 130s test/test_functions.py::FunctionsTest::test_read_mir2genomic PASSED [ 83%] 130s test/test_functions.py::FunctionsTest::test_reverse PASSED [ 85%] 130s test/test_functions.py::FunctionsTest::test_seqbuster PASSED [ 87%] 130s test/test_functions.py::FunctionsTest::test_spikeins PASSED [ 88%] 130s test/test_functions.py::FunctionsTest::test_sql PASSED [ 90%] 130s test/test_functions.py::FunctionsTest::test_srnabench PASSED [ 91%] 130s test/test_functions.py::FunctionsTest::test_stats PASSED [ 93%] 130s test/test_functions.py::FunctionsTest::test_string_variant PASSED [ 95%] 130s test/test_functions.py::FunctionsTest::test_update PASSED [ 96%] 130s test/test_functions.py::FunctionsTest::test_validator PASSED [ 98%] 130s test/test_functions.py::FunctionsTest::test_variant PASSED [100%] 130s 130s =============================== warnings summary =============================== 130s test/test_functions.py::FunctionsTest::test_alignment 130s /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 130s import pkg_resources 130s 130s test/test_functions.py::FunctionsTest::test_alignment 130s /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. 130s warnings.warn( 130s 130s test/test_functions.py::FunctionsTest::test_collapse 130s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 130s return self.run(*args, **kwds) 130s 130s test/test_functions.py::FunctionsTest::test_counts 130s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 130s return self.run(*args, **kwds) 130s 130s test/test_functions.py::FunctionsTest::test_gff 130s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 130s return self.run(*args, **kwds) 130s 130s test/test_functions.py::FunctionsTest::test_read_hairpin 130s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 130s return self.run(*args, **kwds) 130s 130s test/test_functions.py::FunctionsTest::test_sql 130s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 130s return self.run(*args, **kwds) 130s 130s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 130s ======================= 62 passed, 7 warnings in 16.67s ======================== 131s autopkgtest [21:44:34]: test run-unit-test: -----------------------] 131s autopkgtest [21:44:34]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 131s run-unit-test PASS 131s autopkgtest [21:44:34]: test autodep8-python3: preparing testbed 4555s nova [W] Skipping flock for amd64 4555s Creating nova instance adt-plucky-i386-mirtop-20241115-203217-juju-7f2275-prod-proposed-migration-environment-20-c0a60c46-348d-4496-bec0-481eb19fa425 from image adt/ubuntu-plucky-amd64-server-20241115.img (UUID 9bb4dd9c-454f-45da-a125-77b9d27ed145)... 4555s ERROR (CommandError): Unable to delete the specified server(s). 4555s Unexpected error: 4555s Traceback (most recent call last): 4555s File "/home/ubuntu/autopkgtest/lib/VirtSubproc.py", line 830, in mainloop 4555s command() 4555s File "/home/ubuntu/autopkgtest/lib/VirtSubproc.py", line 759, in command 4555s r = f(c, ce) 4555s File "/home/ubuntu/autopkgtest/lib/VirtSubproc.py", line 392, in cmd_revert 4555s caller.hook_revert() 4555s File "/home/ubuntu/autopkgtest/virt/autopkgtest-virt-ssh", line 444, in hook_revert 4555s host_setup('revert') 4555s File "/home/ubuntu/autopkgtest/virt/autopkgtest-virt-ssh", line 263, in host_setup 4555s execute_setup_script(command) 4555s File "/home/ubuntu/autopkgtest/virt/autopkgtest-virt-ssh", line 202, in execute_setup_script 4555s (status, out, err) = VirtSubproc.execute_timeout( 4555s File "/home/ubuntu/autopkgtest/lib/VirtSubproc.py", line 155, in execute_timeout 4555s (out, err) = sp.communicate(instr) 4555s File "/usr/lib/python3.8/subprocess.py", line 1028, in communicate 4555s stdout, stderr = self._communicate(input, endtime, timeout) 4555s File "/usr/lib/python3.8/subprocess.py", line 1868, in _communicate 4555s ready = selector.select(timeout) 4555s File "/usr/lib/python3.8/selectors.py", line 415, in select 4555s fd_event_list = self._selector.poll(timeout) 4555s File "/home/ubuntu/autopkgtest/lib/VirtSubproc.py", line 75, in alarm_handler 4555s raise Timeout(to) 4555s VirtSubproc.Timeout: 1800 4555s autopkgtest [22:58:18]: ERROR: testbed failure: unexpected eof from the testbed