0s autopkgtest [08:09:31]: starting date and time: 2024-11-13 08:09:31+0000 0s autopkgtest [08:09:31]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [08:09:31]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.g5xuy1r7/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade busco --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-19.secgroup --name adt-plucky-amd64-busco-20241113-080931-juju-7f2275-prod-proposed-migration-environment-15-3995f192-8636-4674-b5d4-4285e2a8ce26 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 47s autopkgtest [08:10:18]: testbed dpkg architecture: amd64 47s autopkgtest [08:10:18]: testbed apt version: 2.9.8 47s autopkgtest [08:10:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 48s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 49s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 49s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 49s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [848 kB] 49s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 49s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 49s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 49s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 49s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 49s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 49s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 49s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 49s Fetched 2171 kB in 1s (2631 kB/s) 49s Reading package lists... 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 52s The following NEW packages will be installed: 52s python3.13-gdbm 52s The following packages will be upgraded: 52s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 52s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 52s Need to get 253 kB of archives. 52s After this operation, 147 kB of additional disk space will be used. 52s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 52s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 52s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 52s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 52s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 52s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 52s Fetched 253 kB in 0s (581 kB/s) 53s (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 ... 75541 files and directories currently installed.) 53s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 53s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 53s Setting up python3-minimal (3.12.7-1) ... 53s (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 ... 75541 files and directories currently installed.) 53s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 53s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 53s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 53s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 53s Selecting previously unselected package python3.13-gdbm. 53s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 53s Unpacking python3.13-gdbm (3.13.0-2) ... 53s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 53s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 53s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 53s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 53s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 53s Setting up python3.13-gdbm (3.13.0-2) ... 53s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 53s Setting up python3 (3.12.7-1) ... 53s Setting up python3-gdbm:amd64 (3.12.7-1) ... 53s Processing triggers for man-db (2.12.1-3) ... 54s Processing triggers for libc-bin (2.40-1ubuntu3) ... 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 55s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 56s Reading package lists... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s autopkgtest [08:10:30]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 59s autopkgtest [08:10:30]: @@@@@@@@@@@@@@@@@@@@ apt-source busco 61s Get:1 http://ftpmaster.internal/ubuntu plucky/universe busco 5.5.0-2 (dsc) [2079 B] 61s Get:2 http://ftpmaster.internal/ubuntu plucky/universe busco 5.5.0-2 (tar) [392 kB] 61s Get:3 http://ftpmaster.internal/ubuntu plucky/universe busco 5.5.0-2 (diff) [8244 B] 61s gpgv: Signature made Tue Dec 19 16:28:54 2023 UTC 61s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 61s gpgv: issuer "tille@debian.org" 61s gpgv: Can't check signature: No public key 61s dpkg-source: warning: cannot verify inline signature for ./busco_5.5.0-2.dsc: no acceptable signature found 61s autopkgtest [08:10:32]: testing package busco version 5.5.0-2 62s autopkgtest [08:10:33]: build not needed 62s autopkgtest [08:10:33]: test run-unit-test: preparing testbed 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 64s Starting pkgProblemResolver with broken count: 0 64s Starting 2 pkgProblemResolver with broken count: 0 64s Done 64s The following additional packages will be installed: 64s bbmap busco ca-certificates-java diffstat fontconfig-config 64s fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 gettext hmmer 64s java-common libapache-pom-java libblas3 libcairo2 libcommons-cli-java 64s libcommons-codec-java libcommons-io-java libcommons-parent-java libdeflate0 64s libdivsufsort3 libfontconfig1 libfontenc1 libgfortran5 libgomp1 64s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 64s liblapack3 liblcms2-2 liblerc4 liblog4j1.2-java libmpj-java libopenjp2-7 64s libpcsclite1 libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib 64s libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 64s libxcb-render0 libxcb-shm0 libxrender1 openjdk-17-jre-headless prodigal 64s python3-all python3-biopython python3-cairo python3-dateutil 64s python3-freetype python3-numpy python3-pandas python3-pandas-lib python3-pil 64s python3-reportlab python3-rlpycairo python3-six python3-tz python3.13 64s python3.13-minimal quilt sgml-base w3c-sgml-lib x11-common xfonts-encodings 64s xfonts-utils xml-core 64s Suggested packages: 64s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre autopoint gettext-doc 64s libasprintf-dev libgettextpo-dev hmmer-doc default-jre liblcms2-utils 64s liblog4j1.2-java-doc libmail-java pcscd libnss-mdns fonts-dejavu-extra 64s fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei 64s | fonts-wqy-zenhei fonts-indic python3-tk bwa clustalo clustalw dialign dssp 64s emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb 64s python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 64s python3-scipy raxml samtools t-coffee wise gcc gfortran python-numpy-doc 64s python3-dev python3-pytest python-pandas-doc python3-statsmodels 64s python-pil-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc 64s rl-accel rl-renderpm python3.13-venv python3.13-doc binfmt-support 64s default-mta | mail-transport-agent graphviz procmail sgml-base-doc debhelper 64s Recommended packages: 64s pigz libcups2t64 libasound2t64 python-biopython-doc ncbi-blast+ 64s python3-scipy python3-matplotlib python3-bottleneck python3-numexpr 64s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 64s python3-tables python3-numba python3-olefile fonts-dejavu-extra 64s The following NEW packages will be installed: 64s autopkgtest-satdep bbmap busco ca-certificates-java diffstat 64s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 64s gettext hmmer java-common libapache-pom-java libblas3 libcairo2 64s libcommons-cli-java libcommons-codec-java libcommons-io-java 64s libcommons-parent-java libdeflate0 libdivsufsort3 libfontconfig1 libfontenc1 64s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 64s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 liblog4j1.2-java 64s libmpj-java libopenjp2-7 libpcsclite1 libpixman-1-0 libpython3.13-minimal 64s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 64s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 openjdk-17-jre-headless 64s prodigal python3-all python3-biopython python3-cairo python3-dateutil 64s python3-freetype python3-numpy python3-pandas python3-pandas-lib python3-pil 64s python3-reportlab python3-rlpycairo python3-six python3-tz python3.13 64s python3.13-minimal quilt sgml-base w3c-sgml-lib x11-common xfonts-encodings 64s xfonts-utils xml-core 64s 0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded. 64s Need to get 106 MB/106 MB of archives. 64s After this operation, 391 MB of additional disk space will be used. 64s Get:1 /tmp/autopkgtest.Im7Mv4/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [724 B] 64s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 65s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 65s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 65s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 65s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.17.1-1 [302 kB] 65s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.17.0-1 [457 kB] 65s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblog4j1.2-java all 1.2.17-11 [439 kB] 65s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpj-java all 0.44+dfsg-4 [443 kB] 65s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB] 65s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B] 65s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 65s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 65s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 65s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.0-1 [23.9 kB] 65s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 openjdk-17-jre-headless amd64 17.0.13+11-2build1 [48.0 MB] 67s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 bbmap all 39.09+dfsg-1 [10.1 MB] 67s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 67s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 67s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 67s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 67s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 68s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 68s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 68s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 68s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 68s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 68s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 68s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 68s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 68s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 68s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 68s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 68s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 68s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 68s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 68s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 68s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 68s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 68s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 68s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 68s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 68s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 68s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 68s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 68s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 68s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 68s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 69s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 69s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 69s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 69s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 69s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 69s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 69s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 69s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 69s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 69s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 69s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 69s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 69s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 69s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 69s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdivsufsort3 amd64 2.0.1-6 [46.5 kB] 69s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 hmmer amd64 3.4+dfsg-2 [1147 kB] 69s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 prodigal amd64 1:2.6.3-6 [643 kB] 69s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 busco amd64 5.5.0-2 [295 kB] 69s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 diffstat amd64 1.66-1build1 [29.7 kB] 69s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 69s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 69s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 69s Get:73 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 69s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 quilt all 0.68-1 [439 kB] 70s Fetched 106 MB in 5s (19.7 MB/s) 70s Selecting previously unselected package libpython3.13-minimal:amd64. 70s (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 ... 75548 files and directories currently installed.) 70s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 70s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 70s Selecting previously unselected package python3.13-minimal. 70s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 70s Unpacking python3.13-minimal (3.13.0-2) ... 70s Selecting previously unselected package sgml-base. 70s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 70s Unpacking sgml-base (1.31) ... 70s Selecting previously unselected package libcommons-cli-java. 70s Preparing to unpack .../03-libcommons-cli-java_1.6.0-1_all.deb ... 70s Unpacking libcommons-cli-java (1.6.0-1) ... 70s Selecting previously unselected package libapache-pom-java. 70s Preparing to unpack .../04-libapache-pom-java_33-2_all.deb ... 70s Unpacking libapache-pom-java (33-2) ... 70s Selecting previously unselected package libcommons-parent-java. 70s Preparing to unpack .../05-libcommons-parent-java_56-1_all.deb ... 70s Unpacking libcommons-parent-java (56-1) ... 70s Selecting previously unselected package libcommons-codec-java. 70s Preparing to unpack .../06-libcommons-codec-java_1.17.1-1_all.deb ... 70s Unpacking libcommons-codec-java (1.17.1-1) ... 70s Selecting previously unselected package libcommons-io-java. 70s Preparing to unpack .../07-libcommons-io-java_2.17.0-1_all.deb ... 70s Unpacking libcommons-io-java (2.17.0-1) ... 70s Selecting previously unselected package liblog4j1.2-java. 70s Preparing to unpack .../08-liblog4j1.2-java_1.2.17-11_all.deb ... 70s Unpacking liblog4j1.2-java (1.2.17-11) ... 70s Selecting previously unselected package libmpj-java. 70s Preparing to unpack .../09-libmpj-java_0.44+dfsg-4_all.deb ... 70s Unpacking libmpj-java (0.44+dfsg-4) ... 70s Selecting previously unselected package ca-certificates-java. 70s Preparing to unpack .../10-ca-certificates-java_20240118_all.deb ... 70s Unpacking ca-certificates-java (20240118) ... 70s Selecting previously unselected package java-common. 70s Preparing to unpack .../11-java-common_0.76_all.deb ... 70s Unpacking java-common (0.76) ... 70s Selecting previously unselected package liblcms2-2:amd64. 70s Preparing to unpack .../12-liblcms2-2_2.16-2_amd64.deb ... 70s Unpacking liblcms2-2:amd64 (2.16-2) ... 70s Selecting previously unselected package libjpeg-turbo8:amd64. 70s Preparing to unpack .../13-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 .../14-libjpeg8_8c-2ubuntu11_amd64.deb ... 70s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 70s Selecting previously unselected package libpcsclite1:amd64. 70s Preparing to unpack .../15-libpcsclite1_2.3.0-1_amd64.deb ... 70s Unpacking libpcsclite1:amd64 (2.3.0-1) ... 70s Selecting previously unselected package openjdk-17-jre-headless:amd64. 70s Preparing to unpack .../16-openjdk-17-jre-headless_17.0.13+11-2build1_amd64.deb ... 70s Unpacking openjdk-17-jre-headless:amd64 (17.0.13+11-2build1) ... 71s Selecting previously unselected package bbmap. 71s Preparing to unpack .../17-bbmap_39.09+dfsg-1_all.deb ... 71s Unpacking bbmap (39.09+dfsg-1) ... 71s Selecting previously unselected package python3-six. 71s Preparing to unpack .../18-python3-six_1.16.0-7_all.deb ... 71s Unpacking python3-six (1.16.0-7) ... 71s Selecting previously unselected package python3-dateutil. 71s Preparing to unpack .../19-python3-dateutil_2.9.0-2_all.deb ... 71s Unpacking python3-dateutil (2.9.0-2) ... 71s Selecting previously unselected package libblas3:amd64. 71s Preparing to unpack .../20-libblas3_3.12.0-3build2_amd64.deb ... 71s Unpacking libblas3:amd64 (3.12.0-3build2) ... 71s Selecting previously unselected package libgfortran5:amd64. 71s Preparing to unpack .../21-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 71s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 71s Selecting previously unselected package liblapack3:amd64. 71s Preparing to unpack .../22-liblapack3_3.12.0-3build2_amd64.deb ... 71s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 71s Selecting previously unselected package python3-numpy. 71s Preparing to unpack .../23-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 71s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 71s Selecting previously unselected package python3-tz. 71s Preparing to unpack .../24-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 .../25-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 .../26-python3-pandas_2.2.3+dfsg-5_all.deb ... 71s Unpacking python3-pandas (2.2.3+dfsg-5) ... 72s Selecting previously unselected package libgomp1:amd64. 72s Preparing to unpack .../27-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 72s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 72s Selecting previously unselected package libimagequant0:amd64. 72s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_amd64.deb ... 72s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 72s Selecting previously unselected package libopenjp2-7:amd64. 72s Preparing to unpack .../29-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 72s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 72s Selecting previously unselected package libgraphite2-3:amd64. 72s Preparing to unpack .../30-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 72s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 72s Selecting previously unselected package libharfbuzz0b:amd64. 72s Preparing to unpack .../31-libharfbuzz0b_10.0.1-1_amd64.deb ... 72s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 72s Selecting previously unselected package libraqm0:amd64. 72s Preparing to unpack .../32-libraqm0_0.10.1-1build1_amd64.deb ... 72s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 72s Selecting previously unselected package libdeflate0:amd64. 72s Preparing to unpack .../33-libdeflate0_1.22-1_amd64.deb ... 72s Unpacking libdeflate0:amd64 (1.22-1) ... 72s Selecting previously unselected package libjbig0:amd64. 72s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 72s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 72s Selecting previously unselected package liblerc4:amd64. 72s Preparing to unpack .../35-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 72s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 72s Selecting previously unselected package libsharpyuv0:amd64. 72s Preparing to unpack .../36-libsharpyuv0_1.4.0-0.1_amd64.deb ... 72s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 72s Selecting previously unselected package libwebp7:amd64. 72s Preparing to unpack .../37-libwebp7_1.4.0-0.1_amd64.deb ... 72s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 72s Selecting previously unselected package libtiff6:amd64. 72s Preparing to unpack .../38-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 72s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 72s Selecting previously unselected package libwebpdemux2:amd64. 72s Preparing to unpack .../39-libwebpdemux2_1.4.0-0.1_amd64.deb ... 72s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 72s Selecting previously unselected package libwebpmux3:amd64. 72s Preparing to unpack .../40-libwebpmux3_1.4.0-0.1_amd64.deb ... 72s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 72s Selecting previously unselected package python3-pil:amd64. 72s Preparing to unpack .../41-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 72s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 72s Selecting previously unselected package fonts-dejavu-mono. 72s Preparing to unpack .../42-fonts-dejavu-mono_2.37-8_all.deb ... 72s Unpacking fonts-dejavu-mono (2.37-8) ... 72s Selecting previously unselected package fonts-dejavu-core. 72s Preparing to unpack .../43-fonts-dejavu-core_2.37-8_all.deb ... 72s Unpacking fonts-dejavu-core (2.37-8) ... 72s Selecting previously unselected package libfontenc1:amd64. 72s Preparing to unpack .../44-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 72s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 72s Selecting previously unselected package x11-common. 72s Preparing to unpack .../45-x11-common_1%3a7.7+23ubuntu3_all.deb ... 72s Unpacking x11-common (1:7.7+23ubuntu3) ... 72s Selecting previously unselected package xfonts-encodings. 72s Preparing to unpack .../46-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 72s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 72s Selecting previously unselected package xfonts-utils. 72s Preparing to unpack .../47-xfonts-utils_1%3a7.7+7_amd64.deb ... 72s Unpacking xfonts-utils (1:7.7+7) ... 72s Selecting previously unselected package fonts-urw-base35. 72s Preparing to unpack .../48-fonts-urw-base35_20200910-8_all.deb ... 72s Unpacking fonts-urw-base35 (20200910-8) ... 72s Selecting previously unselected package fontconfig-config. 72s Preparing to unpack .../49-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 72s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 72s Selecting previously unselected package libfontconfig1:amd64. 72s Preparing to unpack .../50-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 72s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 72s Selecting previously unselected package libpixman-1-0:amd64. 73s Preparing to unpack .../51-libpixman-1-0_0.44.0-3_amd64.deb ... 73s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 73s Selecting previously unselected package libxcb-render0:amd64. 73s Preparing to unpack .../52-libxcb-render0_1.17.0-2_amd64.deb ... 73s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 73s Selecting previously unselected package libxcb-shm0:amd64. 73s Preparing to unpack .../53-libxcb-shm0_1.17.0-2_amd64.deb ... 73s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 73s Selecting previously unselected package libxrender1:amd64. 73s Preparing to unpack .../54-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 73s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 73s Selecting previously unselected package libcairo2:amd64. 73s Preparing to unpack .../55-libcairo2_1.18.2-2_amd64.deb ... 73s Unpacking libcairo2:amd64 (1.18.2-2) ... 73s Selecting previously unselected package python3-cairo. 73s Preparing to unpack .../56-python3-cairo_1.26.1-2_amd64.deb ... 73s Unpacking python3-cairo (1.26.1-2) ... 73s Selecting previously unselected package python3-freetype. 73s Preparing to unpack .../57-python3-freetype_2.5.1-1_all.deb ... 73s Unpacking python3-freetype (2.5.1-1) ... 73s Selecting previously unselected package python3-rlpycairo. 73s Preparing to unpack .../58-python3-rlpycairo_0.3.0-3_all.deb ... 73s Unpacking python3-rlpycairo (0.3.0-3) ... 73s Selecting previously unselected package python3-reportlab. 73s Preparing to unpack .../59-python3-reportlab_4.2.5-1_all.deb ... 73s Unpacking python3-reportlab (4.2.5-1) ... 73s Selecting previously unselected package xml-core. 73s Preparing to unpack .../60-xml-core_0.19_all.deb ... 73s Unpacking xml-core (0.19) ... 73s Selecting previously unselected package w3c-sgml-lib. 73s Preparing to unpack .../61-w3c-sgml-lib_1.3-3_all.deb ... 73s Unpacking w3c-sgml-lib (1.3-3) ... 73s Selecting previously unselected package python3-biopython. 73s Preparing to unpack .../62-python3-biopython_1.84+dfsg-4_amd64.deb ... 73s Unpacking python3-biopython (1.84+dfsg-4) ... 73s Selecting previously unselected package libdivsufsort3:amd64. 73s Preparing to unpack .../63-libdivsufsort3_2.0.1-6_amd64.deb ... 73s Unpacking libdivsufsort3:amd64 (2.0.1-6) ... 73s Selecting previously unselected package hmmer. 73s Preparing to unpack .../64-hmmer_3.4+dfsg-2_amd64.deb ... 73s Unpacking hmmer (3.4+dfsg-2) ... 73s Selecting previously unselected package prodigal. 73s Preparing to unpack .../65-prodigal_1%3a2.6.3-6_amd64.deb ... 73s Unpacking prodigal (1:2.6.3-6) ... 73s Selecting previously unselected package busco. 73s Preparing to unpack .../66-busco_5.5.0-2_amd64.deb ... 73s Unpacking busco (5.5.0-2) ... 73s Selecting previously unselected package diffstat. 73s Preparing to unpack .../67-diffstat_1.66-1build1_amd64.deb ... 73s Unpacking diffstat (1.66-1build1) ... 73s Selecting previously unselected package gettext. 73s Preparing to unpack .../68-gettext_0.22.5-2_amd64.deb ... 73s Unpacking gettext (0.22.5-2) ... 73s Selecting previously unselected package libpython3.13-stdlib:amd64. 73s Preparing to unpack .../69-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 73s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 73s Selecting previously unselected package python3.13. 73s Preparing to unpack .../70-python3.13_3.13.0-2_amd64.deb ... 73s Unpacking python3.13 (3.13.0-2) ... 73s Selecting previously unselected package python3-all. 73s Preparing to unpack .../71-python3-all_3.12.7-1_amd64.deb ... 73s Unpacking python3-all (3.12.7-1) ... 73s Selecting previously unselected package quilt. 73s Preparing to unpack .../72-quilt_0.68-1_all.deb ... 73s Unpacking quilt (0.68-1) ... 73s Selecting previously unselected package autopkgtest-satdep. 73s Preparing to unpack .../73-1-autopkgtest-satdep.deb ... 73s Unpacking autopkgtest-satdep (0) ... 73s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 73s Setting up liblcms2-2:amd64 (2.16-2) ... 73s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 73s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 73s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 73s Setting up java-common (0.76) ... 73s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 73s Setting up libcommons-cli-java (1.6.0-1) ... 73s Setting up libxcb-render0:amd64 (1.17.0-2) ... 73s Setting up prodigal (1:2.6.3-6) ... 73s Setting up x11-common (1:7.7+23ubuntu3) ... 74s Setting up libdeflate0:amd64 (1.22-1) ... 74s Setting up liblog4j1.2-java (1.2.17-11) ... 74s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 74s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 74s Setting up python3-freetype (2.5.1-1) ... 74s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 74s Setting up python3-tz (2024.1-2) ... 74s Setting up python3-six (1.16.0-7) ... 74s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 74s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 74s Setting up libblas3:amd64 (3.12.0-3build2) ... 74s 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 74s Setting up libapache-pom-java (33-2) ... 74s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 74s Setting up diffstat (1.66-1build1) ... 74s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 74s Setting up fonts-dejavu-mono (2.37-8) ... 74s Setting up fonts-dejavu-core (2.37-8) ... 74s Setting up libpcsclite1:amd64 (2.3.0-1) ... 74s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 74s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 74s Setting up libwebp7:amd64 (1.4.0-0.1) ... 74s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 74s Setting up python3.13-minimal (3.13.0-2) ... 75s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 75s Setting up python3-dateutil (2.9.0-2) ... 75s Setting up sgml-base (1.31) ... 75s Setting up ca-certificates-java (20240118) ... 75s No JRE found. Skipping Java certificates setup. 75s Setting up libdivsufsort3:amd64 (2.0.1-6) ... 75s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 75s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 75s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 75s Setting up liblapack3:amd64 (3.12.0-3build2) ... 75s 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 75s Setting up gettext (0.22.5-2) ... 75s Setting up python3.13 (3.13.0-2) ... 76s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 76s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 76s Setting up libcommons-parent-java (56-1) ... 76s Setting up python3-all (3.12.7-1) ... 76s Setting up quilt (0.68-1) ... 76s Setting up xfonts-utils (1:7.7+7) ... 76s Setting up libraqm0:amd64 (0.10.1-1build1) ... 76s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 79s Setting up openjdk-17-jre-headless:amd64 (17.0.13+11-2build1) ... 79s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 79s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 79s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 79s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 79s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 79s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 79s Setting up xml-core (0.19) ... 79s Setting up hmmer (3.4+dfsg-2) ... 79s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 79s Setting up libcommons-codec-java (1.17.1-1) ... 79s Setting up libcommons-io-java (2.17.0-1) ... 79s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 79s Setting up fonts-urw-base35 (20200910-8) ... 79s Setting up libcairo2:amd64 (1.18.2-2) ... 79s Setting up libmpj-java (0.44+dfsg-4) ... 79s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 80s Setting up python3-pandas (2.2.3+dfsg-5) ... 87s Setting up python3-cairo (1.26.1-2) ... 87s Setting up python3-rlpycairo (0.3.0-3) ... 87s Setting up python3-reportlab (4.2.5-1) ... 89s Processing triggers for libc-bin (2.40-1ubuntu3) ... 89s Processing triggers for systemd (256.5-2ubuntu4) ... 89s Processing triggers for man-db (2.12.1-3) ... 89s Processing triggers for install-info (7.1.1-1) ... 89s Processing triggers for ca-certificates-java (20240118) ... 90s Adding debian:ACCVRAIZ1.pem 90s Adding debian:AC_RAIZ_FNMT-RCM.pem 90s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 90s Adding debian:ANF_Secure_Server_Root_CA.pem 90s Adding debian:Actalis_Authentication_Root_CA.pem 90s Adding debian:AffirmTrust_Commercial.pem 90s Adding debian:AffirmTrust_Networking.pem 90s Adding debian:AffirmTrust_Premium.pem 90s Adding debian:AffirmTrust_Premium_ECC.pem 90s Adding debian:Amazon_Root_CA_1.pem 90s Adding debian:Amazon_Root_CA_2.pem 90s Adding debian:Amazon_Root_CA_3.pem 90s Adding debian:Amazon_Root_CA_4.pem 90s Adding debian:Atos_TrustedRoot_2011.pem 90s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 90s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 90s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 90s Adding debian:BJCA_Global_Root_CA1.pem 90s Adding debian:BJCA_Global_Root_CA2.pem 90s Adding debian:Baltimore_CyberTrust_Root.pem 90s Adding debian:Buypass_Class_2_Root_CA.pem 90s Adding debian:Buypass_Class_3_Root_CA.pem 90s Adding debian:CA_Disig_Root_R2.pem 90s Adding debian:CFCA_EV_ROOT.pem 90s Adding debian:COMODO_Certification_Authority.pem 90s Adding debian:COMODO_ECC_Certification_Authority.pem 90s Adding debian:COMODO_RSA_Certification_Authority.pem 90s Adding debian:Certainly_Root_E1.pem 90s Adding debian:Certainly_Root_R1.pem 90s Adding debian:Certigna.pem 90s Adding debian:Certigna_Root_CA.pem 90s Adding debian:Certum_EC-384_CA.pem 90s Adding debian:Certum_Trusted_Network_CA.pem 90s Adding debian:Certum_Trusted_Network_CA_2.pem 90s Adding debian:Certum_Trusted_Root_CA.pem 90s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 90s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 90s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 90s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 90s Adding debian:Comodo_AAA_Services_root.pem 90s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 90s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 90s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 90s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 90s Adding debian:DigiCert_Assured_ID_Root_CA.pem 90s Adding debian:DigiCert_Assured_ID_Root_G2.pem 90s Adding debian:DigiCert_Assured_ID_Root_G3.pem 90s Adding debian:DigiCert_Global_Root_CA.pem 90s Adding debian:DigiCert_Global_Root_G2.pem 90s Adding debian:DigiCert_Global_Root_G3.pem 90s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 90s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 90s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 90s Adding debian:DigiCert_Trusted_Root_G4.pem 90s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 90s Adding debian:Entrust_Root_Certification_Authority.pem 90s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 90s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 90s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 90s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 90s Adding debian:GLOBALTRUST_2020.pem 90s Adding debian:GTS_Root_R1.pem 90s Adding debian:GTS_Root_R2.pem 90s Adding debian:GTS_Root_R3.pem 90s Adding debian:GTS_Root_R4.pem 90s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 90s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 90s Adding debian:GlobalSign_Root_CA.pem 90s Adding debian:GlobalSign_Root_CA_-_R3.pem 90s Adding debian:GlobalSign_Root_CA_-_R6.pem 90s Adding debian:GlobalSign_Root_E46.pem 90s Adding debian:GlobalSign_Root_R46.pem 90s Adding debian:Go_Daddy_Class_2_CA.pem 90s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 90s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 90s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 90s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 90s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 90s Adding debian:HiPKI_Root_CA_-_G1.pem 90s Adding debian:Hongkong_Post_Root_CA_3.pem 90s Adding debian:ISRG_Root_X1.pem 90s Adding debian:ISRG_Root_X2.pem 90s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 90s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 90s Adding debian:Izenpe.com.pem 90s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 90s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 90s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 90s Adding debian:NAVER_Global_Root_Certification_Authority.pem 90s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 90s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 90s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 90s Adding debian:QuoVadis_Root_CA_1_G3.pem 90s Adding debian:QuoVadis_Root_CA_2.pem 90s Adding debian:QuoVadis_Root_CA_2_G3.pem 90s Adding debian:QuoVadis_Root_CA_3.pem 90s Adding debian:QuoVadis_Root_CA_3_G3.pem 90s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 90s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 90s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 90s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 90s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 90s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 90s Adding debian:SZAFIR_ROOT_CA2.pem 90s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 90s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 90s Adding debian:SecureSign_RootCA11.pem 90s Adding debian:SecureTrust_CA.pem 90s Adding debian:Secure_Global_CA.pem 90s Adding debian:Security_Communication_ECC_RootCA1.pem 90s Adding debian:Security_Communication_RootCA2.pem 90s Adding debian:Security_Communication_RootCA3.pem 90s Adding debian:Security_Communication_Root_CA.pem 90s Adding debian:Starfield_Class_2_CA.pem 90s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 90s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 90s Adding debian:SwissSign_Gold_CA_-_G2.pem 90s Adding debian:SwissSign_Silver_CA_-_G2.pem 90s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 90s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 90s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 90s Adding debian:TWCA_Global_Root_CA.pem 90s Adding debian:TWCA_Root_Certification_Authority.pem 90s Adding debian:TeliaSonera_Root_CA_v1.pem 90s Adding debian:Telia_Root_CA_v2.pem 90s Adding debian:TrustAsia_Global_Root_CA_G3.pem 90s Adding debian:TrustAsia_Global_Root_CA_G4.pem 90s Adding debian:Trustwave_Global_Certification_Authority.pem 90s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 90s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 90s Adding debian:TunTrust_Root_CA.pem 90s Adding debian:UCA_Extended_Validation_Root.pem 90s Adding debian:UCA_Global_G2_Root.pem 90s Adding debian:USERTrust_ECC_Certification_Authority.pem 90s Adding debian:USERTrust_RSA_Certification_Authority.pem 90s Adding debian:XRamp_Global_CA_Root.pem 90s Adding debian:certSIGN_ROOT_CA.pem 90s Adding debian:certSIGN_Root_CA_G2.pem 90s Adding debian:e-Szigno_Root_CA_2017.pem 90s Adding debian:ePKI_Root_Certification_Authority.pem 90s Adding debian:emSign_ECC_Root_CA_-_C3.pem 90s Adding debian:emSign_ECC_Root_CA_-_G3.pem 90s Adding debian:emSign_Root_CA_-_C1.pem 90s Adding debian:emSign_Root_CA_-_G1.pem 90s Adding debian:vTrus_ECC_Root_CA.pem 90s Adding debian:vTrus_Root_CA.pem 90s done. 90s Setting up bbmap (39.09+dfsg-1) ... 90s Processing triggers for sgml-base (1.31) ... 90s Setting up w3c-sgml-lib (1.3-3) ... 113s Setting up python3-biopython (1.84+dfsg-4) ... 115s Setting up busco (5.5.0-2) ... 115s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' 115s "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]" 115s /usr/lib/python3/dist-packages/busco/busco_tools/miniprot.py:200: SyntaxWarning: invalid escape sequence '\*' 115s self.ata_seq = re.sub("\*", "", sta_seq.upper()) 115s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' 115s "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]" 115s /usr/lib/python3/dist-packages/busco/busco_tools/miniprot.py:200: SyntaxWarning: invalid escape sequence '\*' 115s self.ata_seq = re.sub("\*", "", sta_seq.upper()) 115s Setting up autopkgtest-satdep (0) ... 118s (Reading database ... 82385 files and directories currently installed.) 118s Removing autopkgtest-satdep (0) ... 119s autopkgtest [08:11:30]: test run-unit-test: [----------------------- 119s File series fully applied, ends at patch debian/patches/find-bbmap-instead-of-bbtools.patch 119s Testing with python3.13 in /tmp/autopkgtest.Im7Mv4/autopkgtest_tmp: 119s unittest_runner (unittest.loader._FailedTest.unittest_runner) ... ERROR 119s 119s ====================================================================== 119s ERROR: unittest_runner (unittest.loader._FailedTest.unittest_runner) 119s ---------------------------------------------------------------------- 119s ImportError: Failed to import test module: unittest_runner 119s Traceback (most recent call last): 119s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 119s module = __import__(module_name) 119s File "/tmp/autopkgtest.Im7Mv4/autopkgtest_tmp/tests/unittest_runner.py", line 2, in 119s from tests.unittests import run_BUSCO_unittests 119s File "/tmp/autopkgtest.Im7Mv4/autopkgtest_tmp/tests/unittests/run_BUSCO_unittests.py", line 2, in 119s from busco import run_BUSCO 119s File "/usr/lib/python3/dist-packages/busco/run_BUSCO.py", line 25, in 119s from busco.BuscoRunner import AnalysisRunner, BatchRunner, SingleRunner 119s File "/usr/lib/python3/dist-packages/busco/BuscoRunner.py", line 2, in 119s from busco.analysis.BuscoAnalysis import BuscoAnalysis 119s File "/usr/lib/python3/dist-packages/busco/analysis/BuscoAnalysis.py", line 14, in 119s from busco.BuscoConfig import BaseConfig, BuscoConfigAuto 119s File "/usr/lib/python3/dist-packages/busco/BuscoConfig.py", line 9, in 119s from busco.BuscoDownloadManager import BuscoDownloadManager 119s File "/usr/lib/python3/dist-packages/busco/BuscoDownloadManager.py", line 22, in 119s import pandas as pd 119s File "/usr/lib/python3/dist-packages/pandas/__init__.py", line 19, in 119s raise ImportError( 119s "Unable to import required dependencies:\n" + "\n".join(_missing_dependencies) 119s ) 119s ImportError: Unable to import required dependencies: 119s numpy: Error importing numpy: you should not try to import numpy from 119s its source directory; please exit the numpy source tree, and relaunch 119s your python interpreter from there. 119s 119s 119s ---------------------------------------------------------------------- 119s Ran 1 test in 0.000s 119s 119s FAILED (errors=1) 120s autopkgtest [08:11:31]: test run-unit-test: -----------------------] 120s run-unit-test FAIL non-zero exit status 1 120s autopkgtest [08:11:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 120s autopkgtest [08:11:31]: test run-busco-analysis: preparing testbed 168s autopkgtest [08:12:19]: testbed dpkg architecture: amd64 168s autopkgtest [08:12:19]: testbed apt version: 2.9.8 168s autopkgtest [08:12:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 169s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 170s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 170s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 170s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 170s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [848 kB] 171s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 171s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 171s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 171s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 171s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 171s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 171s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 171s Fetched 2171 kB in 2s (1289 kB/s) 171s Reading package lists... 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Calculating upgrade... 174s The following NEW packages will be installed: 174s python3.13-gdbm 174s The following packages will be upgraded: 174s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 174s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 253 kB of archives. 174s After this operation, 147 kB of additional disk space will be used. 174s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 174s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 174s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 174s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 174s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 174s Fetched 253 kB in 0s (609 kB/s) 175s (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 ... 75541 files and directories currently installed.) 175s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 175s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 175s Setting up python3-minimal (3.12.7-1) ... 175s (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 ... 75541 files and directories currently installed.) 175s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 175s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 175s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 175s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 175s Selecting previously unselected package python3.13-gdbm. 175s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 175s Unpacking python3.13-gdbm (3.13.0-2) ... 175s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 175s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 175s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 175s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 175s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 175s Setting up python3.13-gdbm (3.13.0-2) ... 175s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 175s Setting up python3 (3.12.7-1) ... 175s Setting up python3-gdbm:amd64 (3.12.7-1) ... 175s Processing triggers for man-db (2.12.1-3) ... 176s Processing triggers for libc-bin (2.40-1ubuntu3) ... 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 177s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 177s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 177s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 178s Reading package lists... 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Calculating upgrade... 179s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 179s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 186s Starting pkgProblemResolver with broken count: 0 186s Starting 2 pkgProblemResolver with broken count: 0 186s Done 186s The following additional packages will be installed: 186s bbmap busco ca-certificates-java fontconfig-config fonts-dejavu-core 186s fonts-dejavu-mono fonts-urw-base35 hmmer java-common libapache-pom-java 186s libblas3 libcairo2 libcommons-cli-java libcommons-codec-java 186s libcommons-io-java libcommons-parent-java libdeflate0 libdivsufsort3 186s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 186s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 186s liblcms2-2 liblerc4 liblog4j1.2-java libmpj-java libopenjp2-7 libpcsclite1 186s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0 186s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 186s libxcb-shm0 libxrender1 openjdk-17-jre-headless prodigal python3-all 186s python3-biopython python3-cairo python3-dateutil python3-freetype 186s python3-numpy python3-pandas python3-pandas-lib python3-pil 186s python3-reportlab python3-rlpycairo python3-six python3-tz python3.13 186s python3.13-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings 186s xfonts-utils xml-core 186s Suggested packages: 186s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre hmmer-doc default-jre 186s liblcms2-utils liblog4j1.2-java-doc libmail-java pcscd libnss-mdns 186s fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho 186s fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic python3-tk bwa clustalo 186s clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank 186s probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib 186s python3-psycopg2 python3-scipy raxml samtools t-coffee wise gcc gfortran 186s python-numpy-doc python3-dev python3-pytest python-pandas-doc 186s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 186s python-reportlab-doc rl-accel rl-renderpm python3.13-venv python3.13-doc 186s binfmt-support sgml-base-doc debhelper 186s Recommended packages: 186s pigz libcups2t64 libasound2t64 python-biopython-doc ncbi-blast+ 186s python3-scipy python3-matplotlib python3-bottleneck python3-numexpr 186s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 186s python3-tables python3-numba python3-olefile fonts-dejavu-extra 186s The following NEW packages will be installed: 186s autopkgtest-satdep bbmap busco ca-certificates-java fontconfig-config 186s fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 hmmer java-common 186s libapache-pom-java libblas3 libcairo2 libcommons-cli-java 186s libcommons-codec-java libcommons-io-java libcommons-parent-java libdeflate0 186s libdivsufsort3 libfontconfig1 libfontenc1 libgfortran5 libgomp1 186s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 186s liblapack3 liblcms2-2 liblerc4 liblog4j1.2-java libmpj-java libopenjp2-7 186s libpcsclite1 libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib 186s libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 186s libxcb-render0 libxcb-shm0 libxrender1 openjdk-17-jre-headless prodigal 186s python3-all python3-biopython python3-cairo python3-dateutil 186s python3-freetype python3-numpy python3-pandas python3-pandas-lib python3-pil 186s python3-reportlab python3-rlpycairo python3-six python3-tz python3.13 186s python3.13-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings 186s xfonts-utils xml-core 186s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 186s Need to get 105 MB/105 MB of archives. 186s After this operation, 387 MB of additional disk space will be used. 186s Get:1 /tmp/autopkgtest.Im7Mv4/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 186s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 187s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 187s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 187s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-cli-java all 1.6.0-1 [59.9 kB] 187s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 187s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 187s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.17.1-1 [302 kB] 187s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.17.0-1 [457 kB] 187s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblog4j1.2-java all 1.2.17-11 [439 kB] 187s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpj-java all 0.44+dfsg-4 [443 kB] 187s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB] 187s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B] 187s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 187s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 187s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 187s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.0-1 [23.9 kB] 187s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 openjdk-17-jre-headless amd64 17.0.13+11-2build1 [48.0 MB] 188s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 bbmap all 39.09+dfsg-1 [10.1 MB] 189s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 189s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 189s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 189s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 189s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 189s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 189s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 189s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 189s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 189s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 189s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 189s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 189s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 189s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 189s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 189s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 189s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 189s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 189s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 189s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 189s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 189s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 189s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 189s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 189s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 189s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 189s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 189s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 189s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 189s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 189s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 190s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 190s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 190s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 190s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 190s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 190s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 190s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 190s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 190s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 190s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 190s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 190s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 190s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 190s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 190s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdivsufsort3 amd64 2.0.1-6 [46.5 kB] 190s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 hmmer amd64 3.4+dfsg-2 [1147 kB] 190s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 prodigal amd64 1:2.6.3-6 [643 kB] 190s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 busco amd64 5.5.0-2 [295 kB] 190s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 190s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 190s Get:71 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 190s Fetched 105 MB in 4s (27.0 MB/s) 190s Selecting previously unselected package libpython3.13-minimal:amd64. 190s (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 ... 75548 files and directories currently installed.) 190s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 190s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 191s Selecting previously unselected package python3.13-minimal. 191s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 191s Unpacking python3.13-minimal (3.13.0-2) ... 191s Selecting previously unselected package sgml-base. 191s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 191s Unpacking sgml-base (1.31) ... 191s Selecting previously unselected package libcommons-cli-java. 191s Preparing to unpack .../03-libcommons-cli-java_1.6.0-1_all.deb ... 191s Unpacking libcommons-cli-java (1.6.0-1) ... 191s Selecting previously unselected package libapache-pom-java. 191s Preparing to unpack .../04-libapache-pom-java_33-2_all.deb ... 191s Unpacking libapache-pom-java (33-2) ... 191s Selecting previously unselected package libcommons-parent-java. 191s Preparing to unpack .../05-libcommons-parent-java_56-1_all.deb ... 191s Unpacking libcommons-parent-java (56-1) ... 191s Selecting previously unselected package libcommons-codec-java. 191s Preparing to unpack .../06-libcommons-codec-java_1.17.1-1_all.deb ... 191s Unpacking libcommons-codec-java (1.17.1-1) ... 191s Selecting previously unselected package libcommons-io-java. 191s Preparing to unpack .../07-libcommons-io-java_2.17.0-1_all.deb ... 191s Unpacking libcommons-io-java (2.17.0-1) ... 191s Selecting previously unselected package liblog4j1.2-java. 191s Preparing to unpack .../08-liblog4j1.2-java_1.2.17-11_all.deb ... 191s Unpacking liblog4j1.2-java (1.2.17-11) ... 191s Selecting previously unselected package libmpj-java. 191s Preparing to unpack .../09-libmpj-java_0.44+dfsg-4_all.deb ... 191s Unpacking libmpj-java (0.44+dfsg-4) ... 191s Selecting previously unselected package ca-certificates-java. 191s Preparing to unpack .../10-ca-certificates-java_20240118_all.deb ... 191s Unpacking ca-certificates-java (20240118) ... 191s Selecting previously unselected package java-common. 191s Preparing to unpack .../11-java-common_0.76_all.deb ... 191s Unpacking java-common (0.76) ... 191s Selecting previously unselected package liblcms2-2:amd64. 191s Preparing to unpack .../12-liblcms2-2_2.16-2_amd64.deb ... 191s Unpacking liblcms2-2:amd64 (2.16-2) ... 191s Selecting previously unselected package libjpeg-turbo8:amd64. 191s Preparing to unpack .../13-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 191s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 191s Selecting previously unselected package libjpeg8:amd64. 191s Preparing to unpack .../14-libjpeg8_8c-2ubuntu11_amd64.deb ... 191s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 191s Selecting previously unselected package libpcsclite1:amd64. 191s Preparing to unpack .../15-libpcsclite1_2.3.0-1_amd64.deb ... 191s Unpacking libpcsclite1:amd64 (2.3.0-1) ... 191s Selecting previously unselected package openjdk-17-jre-headless:amd64. 191s Preparing to unpack .../16-openjdk-17-jre-headless_17.0.13+11-2build1_amd64.deb ... 191s Unpacking openjdk-17-jre-headless:amd64 (17.0.13+11-2build1) ... 192s Selecting previously unselected package bbmap. 192s Preparing to unpack .../17-bbmap_39.09+dfsg-1_all.deb ... 192s Unpacking bbmap (39.09+dfsg-1) ... 192s Selecting previously unselected package python3-six. 192s Preparing to unpack .../18-python3-six_1.16.0-7_all.deb ... 192s Unpacking python3-six (1.16.0-7) ... 192s Selecting previously unselected package python3-dateutil. 192s Preparing to unpack .../19-python3-dateutil_2.9.0-2_all.deb ... 192s Unpacking python3-dateutil (2.9.0-2) ... 192s Selecting previously unselected package libblas3:amd64. 192s Preparing to unpack .../20-libblas3_3.12.0-3build2_amd64.deb ... 192s Unpacking libblas3:amd64 (3.12.0-3build2) ... 192s Selecting previously unselected package libgfortran5:amd64. 192s Preparing to unpack .../21-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 192s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 192s Selecting previously unselected package liblapack3:amd64. 192s Preparing to unpack .../22-liblapack3_3.12.0-3build2_amd64.deb ... 192s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 192s Selecting previously unselected package python3-numpy. 192s Preparing to unpack .../23-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 192s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 192s Selecting previously unselected package python3-tz. 192s Preparing to unpack .../24-python3-tz_2024.1-2_all.deb ... 192s Unpacking python3-tz (2024.1-2) ... 192s Selecting previously unselected package python3-pandas-lib:amd64. 192s Preparing to unpack .../25-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ... 192s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 192s Selecting previously unselected package python3-pandas. 192s Preparing to unpack .../26-python3-pandas_2.2.3+dfsg-5_all.deb ... 192s Unpacking python3-pandas (2.2.3+dfsg-5) ... 193s Selecting previously unselected package libgomp1:amd64. 193s Preparing to unpack .../27-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 193s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 193s Selecting previously unselected package libimagequant0:amd64. 193s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_amd64.deb ... 193s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 193s Selecting previously unselected package libopenjp2-7:amd64. 193s Preparing to unpack .../29-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 193s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 193s Selecting previously unselected package libgraphite2-3:amd64. 193s Preparing to unpack .../30-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 193s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 193s Selecting previously unselected package libharfbuzz0b:amd64. 193s Preparing to unpack .../31-libharfbuzz0b_10.0.1-1_amd64.deb ... 193s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 193s Selecting previously unselected package libraqm0:amd64. 193s Preparing to unpack .../32-libraqm0_0.10.1-1build1_amd64.deb ... 193s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 193s Selecting previously unselected package libdeflate0:amd64. 193s Preparing to unpack .../33-libdeflate0_1.22-1_amd64.deb ... 193s Unpacking libdeflate0:amd64 (1.22-1) ... 193s Selecting previously unselected package libjbig0:amd64. 193s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 193s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 193s Selecting previously unselected package liblerc4:amd64. 193s Preparing to unpack .../35-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 193s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 193s Selecting previously unselected package libsharpyuv0:amd64. 193s Preparing to unpack .../36-libsharpyuv0_1.4.0-0.1_amd64.deb ... 193s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 193s Selecting previously unselected package libwebp7:amd64. 193s Preparing to unpack .../37-libwebp7_1.4.0-0.1_amd64.deb ... 193s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 193s Selecting previously unselected package libtiff6:amd64. 193s Preparing to unpack .../38-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 193s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 193s Selecting previously unselected package libwebpdemux2:amd64. 193s Preparing to unpack .../39-libwebpdemux2_1.4.0-0.1_amd64.deb ... 193s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 193s Selecting previously unselected package libwebpmux3:amd64. 193s Preparing to unpack .../40-libwebpmux3_1.4.0-0.1_amd64.deb ... 193s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 193s Selecting previously unselected package python3-pil:amd64. 193s Preparing to unpack .../41-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 193s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 193s Selecting previously unselected package fonts-dejavu-mono. 193s Preparing to unpack .../42-fonts-dejavu-mono_2.37-8_all.deb ... 193s Unpacking fonts-dejavu-mono (2.37-8) ... 193s Selecting previously unselected package fonts-dejavu-core. 193s Preparing to unpack .../43-fonts-dejavu-core_2.37-8_all.deb ... 193s Unpacking fonts-dejavu-core (2.37-8) ... 193s Selecting previously unselected package libfontenc1:amd64. 193s Preparing to unpack .../44-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 193s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 193s Selecting previously unselected package x11-common. 193s Preparing to unpack .../45-x11-common_1%3a7.7+23ubuntu3_all.deb ... 193s Unpacking x11-common (1:7.7+23ubuntu3) ... 193s Selecting previously unselected package xfonts-encodings. 193s Preparing to unpack .../46-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 193s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 193s Selecting previously unselected package xfonts-utils. 193s Preparing to unpack .../47-xfonts-utils_1%3a7.7+7_amd64.deb ... 193s Unpacking xfonts-utils (1:7.7+7) ... 193s Selecting previously unselected package fonts-urw-base35. 193s Preparing to unpack .../48-fonts-urw-base35_20200910-8_all.deb ... 193s Unpacking fonts-urw-base35 (20200910-8) ... 193s Selecting previously unselected package fontconfig-config. 193s Preparing to unpack .../49-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 194s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 194s Selecting previously unselected package libfontconfig1:amd64. 194s Preparing to unpack .../50-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 194s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 194s Selecting previously unselected package libpixman-1-0:amd64. 194s Preparing to unpack .../51-libpixman-1-0_0.44.0-3_amd64.deb ... 194s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 194s Selecting previously unselected package libxcb-render0:amd64. 194s Preparing to unpack .../52-libxcb-render0_1.17.0-2_amd64.deb ... 194s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 194s Selecting previously unselected package libxcb-shm0:amd64. 194s Preparing to unpack .../53-libxcb-shm0_1.17.0-2_amd64.deb ... 194s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 194s Selecting previously unselected package libxrender1:amd64. 194s Preparing to unpack .../54-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 194s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 194s Selecting previously unselected package libcairo2:amd64. 194s Preparing to unpack .../55-libcairo2_1.18.2-2_amd64.deb ... 194s Unpacking libcairo2:amd64 (1.18.2-2) ... 194s Selecting previously unselected package python3-cairo. 194s Preparing to unpack .../56-python3-cairo_1.26.1-2_amd64.deb ... 194s Unpacking python3-cairo (1.26.1-2) ... 194s Selecting previously unselected package python3-freetype. 194s Preparing to unpack .../57-python3-freetype_2.5.1-1_all.deb ... 194s Unpacking python3-freetype (2.5.1-1) ... 194s Selecting previously unselected package python3-rlpycairo. 194s Preparing to unpack .../58-python3-rlpycairo_0.3.0-3_all.deb ... 194s Unpacking python3-rlpycairo (0.3.0-3) ... 194s Selecting previously unselected package python3-reportlab. 194s Preparing to unpack .../59-python3-reportlab_4.2.5-1_all.deb ... 194s Unpacking python3-reportlab (4.2.5-1) ... 194s Selecting previously unselected package xml-core. 194s Preparing to unpack .../60-xml-core_0.19_all.deb ... 194s Unpacking xml-core (0.19) ... 194s Selecting previously unselected package w3c-sgml-lib. 194s Preparing to unpack .../61-w3c-sgml-lib_1.3-3_all.deb ... 194s Unpacking w3c-sgml-lib (1.3-3) ... 194s Selecting previously unselected package python3-biopython. 194s Preparing to unpack .../62-python3-biopython_1.84+dfsg-4_amd64.deb ... 194s Unpacking python3-biopython (1.84+dfsg-4) ... 194s Selecting previously unselected package libdivsufsort3:amd64. 194s Preparing to unpack .../63-libdivsufsort3_2.0.1-6_amd64.deb ... 194s Unpacking libdivsufsort3:amd64 (2.0.1-6) ... 194s Selecting previously unselected package hmmer. 194s Preparing to unpack .../64-hmmer_3.4+dfsg-2_amd64.deb ... 194s Unpacking hmmer (3.4+dfsg-2) ... 194s Selecting previously unselected package prodigal. 194s Preparing to unpack .../65-prodigal_1%3a2.6.3-6_amd64.deb ... 194s Unpacking prodigal (1:2.6.3-6) ... 194s Selecting previously unselected package busco. 194s Preparing to unpack .../66-busco_5.5.0-2_amd64.deb ... 194s Unpacking busco (5.5.0-2) ... 194s Selecting previously unselected package libpython3.13-stdlib:amd64. 194s Preparing to unpack .../67-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 194s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 194s Selecting previously unselected package python3.13. 195s Preparing to unpack .../68-python3.13_3.13.0-2_amd64.deb ... 195s Unpacking python3.13 (3.13.0-2) ... 195s Selecting previously unselected package python3-all. 195s Preparing to unpack .../69-python3-all_3.12.7-1_amd64.deb ... 195s Unpacking python3-all (3.12.7-1) ... 195s Selecting previously unselected package autopkgtest-satdep. 195s Preparing to unpack .../70-2-autopkgtest-satdep.deb ... 195s Unpacking autopkgtest-satdep (0) ... 195s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 195s Setting up liblcms2-2:amd64 (2.16-2) ... 195s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 195s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 195s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 195s Setting up java-common (0.76) ... 195s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 195s Setting up libcommons-cli-java (1.6.0-1) ... 195s Setting up libxcb-render0:amd64 (1.17.0-2) ... 195s Setting up prodigal (1:2.6.3-6) ... 195s Setting up x11-common (1:7.7+23ubuntu3) ... 195s Setting up libdeflate0:amd64 (1.22-1) ... 195s Setting up liblog4j1.2-java (1.2.17-11) ... 195s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 195s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 195s Setting up python3-freetype (2.5.1-1) ... 195s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 195s Setting up python3-tz (2024.1-2) ... 195s Setting up python3-six (1.16.0-7) ... 195s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 195s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 195s Setting up libblas3:amd64 (3.12.0-3build2) ... 195s 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 195s Setting up libapache-pom-java (33-2) ... 195s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 195s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 195s Setting up fonts-dejavu-mono (2.37-8) ... 195s Setting up fonts-dejavu-core (2.37-8) ... 196s Setting up libpcsclite1:amd64 (2.3.0-1) ... 196s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 196s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 196s Setting up libwebp7:amd64 (1.4.0-0.1) ... 196s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 196s Setting up python3.13-minimal (3.13.0-2) ... 196s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 196s Setting up python3-dateutil (2.9.0-2) ... 196s Setting up sgml-base (1.31) ... 196s Setting up ca-certificates-java (20240118) ... 196s No JRE found. Skipping Java certificates setup. 196s Setting up libdivsufsort3:amd64 (2.0.1-6) ... 196s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 196s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 196s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 196s Setting up liblapack3:amd64 (3.12.0-3build2) ... 196s 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 196s Setting up python3.13 (3.13.0-2) ... 197s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 197s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 197s Setting up libcommons-parent-java (56-1) ... 197s Setting up python3-all (3.12.7-1) ... 197s Setting up xfonts-utils (1:7.7+7) ... 197s Setting up libraqm0:amd64 (0.10.1-1build1) ... 197s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 200s Setting up openjdk-17-jre-headless:amd64 (17.0.13+11-2build1) ... 200s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode 200s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode 200s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode 200s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode 200s update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 200s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 200s Setting up xml-core (0.19) ... 200s Setting up hmmer (3.4+dfsg-2) ... 200s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 200s Setting up libcommons-codec-java (1.17.1-1) ... 200s Setting up libcommons-io-java (2.17.0-1) ... 200s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 200s Setting up fonts-urw-base35 (20200910-8) ... 200s Setting up libcairo2:amd64 (1.18.2-2) ... 200s Setting up libmpj-java (0.44+dfsg-4) ... 200s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 201s Setting up python3-pandas (2.2.3+dfsg-5) ... 208s Setting up python3-cairo (1.26.1-2) ... 208s Setting up python3-rlpycairo (0.3.0-3) ... 209s Setting up python3-reportlab (4.2.5-1) ... 210s Processing triggers for libc-bin (2.40-1ubuntu3) ... 210s Processing triggers for systemd (256.5-2ubuntu4) ... 210s Processing triggers for man-db (2.12.1-3) ... 211s Processing triggers for ca-certificates-java (20240118) ... 211s Adding debian:ACCVRAIZ1.pem 211s Adding debian:AC_RAIZ_FNMT-RCM.pem 211s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem 211s Adding debian:ANF_Secure_Server_Root_CA.pem 211s Adding debian:Actalis_Authentication_Root_CA.pem 211s Adding debian:AffirmTrust_Commercial.pem 211s Adding debian:AffirmTrust_Networking.pem 211s Adding debian:AffirmTrust_Premium.pem 211s Adding debian:AffirmTrust_Premium_ECC.pem 211s Adding debian:Amazon_Root_CA_1.pem 211s Adding debian:Amazon_Root_CA_2.pem 211s Adding debian:Amazon_Root_CA_3.pem 211s Adding debian:Amazon_Root_CA_4.pem 211s Adding debian:Atos_TrustedRoot_2011.pem 211s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem 211s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem 211s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem 211s Adding debian:BJCA_Global_Root_CA1.pem 211s Adding debian:BJCA_Global_Root_CA2.pem 211s Adding debian:Baltimore_CyberTrust_Root.pem 211s Adding debian:Buypass_Class_2_Root_CA.pem 211s Adding debian:Buypass_Class_3_Root_CA.pem 211s Adding debian:CA_Disig_Root_R2.pem 211s Adding debian:CFCA_EV_ROOT.pem 211s Adding debian:COMODO_Certification_Authority.pem 211s Adding debian:COMODO_ECC_Certification_Authority.pem 211s Adding debian:COMODO_RSA_Certification_Authority.pem 211s Adding debian:Certainly_Root_E1.pem 211s Adding debian:Certainly_Root_R1.pem 211s Adding debian:Certigna.pem 211s Adding debian:Certigna_Root_CA.pem 211s Adding debian:Certum_EC-384_CA.pem 211s Adding debian:Certum_Trusted_Network_CA.pem 211s Adding debian:Certum_Trusted_Network_CA_2.pem 211s Adding debian:Certum_Trusted_Root_CA.pem 211s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem 211s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem 211s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem 211s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem 211s Adding debian:Comodo_AAA_Services_root.pem 211s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem 211s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem 211s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem 211s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem 211s Adding debian:DigiCert_Assured_ID_Root_CA.pem 211s Adding debian:DigiCert_Assured_ID_Root_G2.pem 211s Adding debian:DigiCert_Assured_ID_Root_G3.pem 211s Adding debian:DigiCert_Global_Root_CA.pem 211s Adding debian:DigiCert_Global_Root_G2.pem 211s Adding debian:DigiCert_Global_Root_G3.pem 211s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem 211s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem 211s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem 211s Adding debian:DigiCert_Trusted_Root_G4.pem 211s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem 211s Adding debian:Entrust_Root_Certification_Authority.pem 211s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem 211s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem 211s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem 211s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem 211s Adding debian:GLOBALTRUST_2020.pem 211s Adding debian:GTS_Root_R1.pem 211s Adding debian:GTS_Root_R2.pem 211s Adding debian:GTS_Root_R3.pem 211s Adding debian:GTS_Root_R4.pem 211s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem 211s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem 211s Adding debian:GlobalSign_Root_CA.pem 211s Adding debian:GlobalSign_Root_CA_-_R3.pem 211s Adding debian:GlobalSign_Root_CA_-_R6.pem 211s Adding debian:GlobalSign_Root_E46.pem 211s Adding debian:GlobalSign_Root_R46.pem 211s Adding debian:Go_Daddy_Class_2_CA.pem 211s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem 211s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem 211s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem 211s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem 211s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem 211s Adding debian:HiPKI_Root_CA_-_G1.pem 211s Adding debian:Hongkong_Post_Root_CA_3.pem 211s Adding debian:ISRG_Root_X1.pem 211s Adding debian:ISRG_Root_X2.pem 211s Adding debian:IdenTrust_Commercial_Root_CA_1.pem 211s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem 211s Adding debian:Izenpe.com.pem 211s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem 211s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem 211s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem 211s Adding debian:NAVER_Global_Root_Certification_Authority.pem 211s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem 211s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem 211s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem 211s Adding debian:QuoVadis_Root_CA_1_G3.pem 211s Adding debian:QuoVadis_Root_CA_2.pem 211s Adding debian:QuoVadis_Root_CA_2_G3.pem 211s Adding debian:QuoVadis_Root_CA_3.pem 211s Adding debian:QuoVadis_Root_CA_3_G3.pem 211s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem 211s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem 211s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem 211s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem 211s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem 211s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem 211s Adding debian:SZAFIR_ROOT_CA2.pem 211s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem 211s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem 211s Adding debian:SecureSign_RootCA11.pem 211s Adding debian:SecureTrust_CA.pem 211s Adding debian:Secure_Global_CA.pem 211s Adding debian:Security_Communication_ECC_RootCA1.pem 211s Adding debian:Security_Communication_RootCA2.pem 211s Adding debian:Security_Communication_RootCA3.pem 211s Adding debian:Security_Communication_Root_CA.pem 211s Adding debian:Starfield_Class_2_CA.pem 211s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem 211s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem 211s Adding debian:SwissSign_Gold_CA_-_G2.pem 211s Adding debian:SwissSign_Silver_CA_-_G2.pem 211s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem 211s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem 211s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem 211s Adding debian:TWCA_Global_Root_CA.pem 211s Adding debian:TWCA_Root_Certification_Authority.pem 211s Adding debian:TeliaSonera_Root_CA_v1.pem 211s Adding debian:Telia_Root_CA_v2.pem 211s Adding debian:TrustAsia_Global_Root_CA_G3.pem 211s Adding debian:TrustAsia_Global_Root_CA_G4.pem 211s Adding debian:Trustwave_Global_Certification_Authority.pem 211s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem 211s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem 211s Adding debian:TunTrust_Root_CA.pem 211s Adding debian:UCA_Extended_Validation_Root.pem 211s Adding debian:UCA_Global_G2_Root.pem 211s Adding debian:USERTrust_ECC_Certification_Authority.pem 211s Adding debian:USERTrust_RSA_Certification_Authority.pem 211s Adding debian:XRamp_Global_CA_Root.pem 211s Adding debian:certSIGN_ROOT_CA.pem 211s Adding debian:certSIGN_Root_CA_G2.pem 211s Adding debian:e-Szigno_Root_CA_2017.pem 211s Adding debian:ePKI_Root_Certification_Authority.pem 211s Adding debian:emSign_ECC_Root_CA_-_C3.pem 211s Adding debian:emSign_ECC_Root_CA_-_G3.pem 211s Adding debian:emSign_Root_CA_-_C1.pem 211s Adding debian:emSign_Root_CA_-_G1.pem 211s Adding debian:vTrus_ECC_Root_CA.pem 211s Adding debian:vTrus_Root_CA.pem 211s done. 211s Setting up bbmap (39.09+dfsg-1) ... 211s Processing triggers for sgml-base (1.31) ... 211s Setting up w3c-sgml-lib (1.3-3) ... 234s Setting up python3-biopython (1.84+dfsg-4) ... 236s Setting up busco (5.5.0-2) ... 236s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' 236s "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]" 236s /usr/lib/python3/dist-packages/busco/busco_tools/miniprot.py:200: SyntaxWarning: invalid escape sequence '\*' 236s self.ata_seq = re.sub("\*", "", sta_seq.upper()) 236s /usr/lib/python3/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' 236s "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]" 236s /usr/lib/python3/dist-packages/busco/busco_tools/miniprot.py:200: SyntaxWarning: invalid escape sequence '\*' 236s self.ata_seq = re.sub("\*", "", sta_seq.upper()) 236s Setting up autopkgtest-satdep (0) ... 239s (Reading database ... 82186 files and directories currently installed.) 239s Removing autopkgtest-satdep (0) ... 241s autopkgtest [08:13:32]: test run-busco-analysis: [----------------------- 241s /usr/bin/busco:13: SyntaxWarning: invalid escape sequence '\w' 241s "cannot import name '(?P[\w]+)", err.msg 241s 2024-11-13 08:13:32 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 11/13/2024 08:13:32 ***** 241s 2024-11-13 08:13:32 INFO: Configuring BUSCO with local environment 241s 2024-11-13 08:13:32 INFO: Mode is genome 241s 2024-11-13 08:13:32 INFO: Downloading information on latest versions of BUSCO data... 241s 2024-11-13 08:13:32 INFO: Download connection problem. Retrying in 10 seconds 252s 2024-11-13 08:13:42 INFO: Download connection problem. Retrying in 100 seconds 352s 2024-11-13 08:15:23 INFO: Cannot reach https://busco-data.ezlab.org/v5/data/file_versions.tsv. Retrying with backup url https://busco-data2.ezlab.org/v5/data/ 352s 2024-11-13 08:15:23 INFO: Downloading information on latest versions of BUSCO data... 352s 2024-11-13 08:15:23 INFO: Download connection problem. Retrying in 10 seconds 362s 2024-11-13 08:15:33 INFO: Download connection problem. Retrying in 100 seconds 462s 2024-11-13 08:17:13 ERROR: Cannot reach https://busco-data2.ezlab.org/v5/data/file_versions.tsv 462s 2024-11-13 08:17:13 ERROR: BUSCO analysis failed! 462s 2024-11-13 08:17:13 ERROR: Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues 462s 463s autopkgtest [08:17:14]: test run-busco-analysis: -----------------------] 463s autopkgtest [08:17:14]: test run-busco-analysis: - - - - - - - - - - results - - - - - - - - - - 463s run-busco-analysis FAIL non-zero exit status 1 463s autopkgtest [08:17:14]: @@@@@@@@@@@@@@@@@@@@ summary 463s run-unit-test FAIL non-zero exit status 1 463s run-busco-analysis FAIL non-zero exit status 1 469s nova [W] Skipping flock for amd64 469s Creating nova instance adt-plucky-amd64-busco-20241113-080931-juju-7f2275-prod-proposed-migration-environment-15-3995f192-8636-4674-b5d4-4285e2a8ce26 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)... 469s nova [W] Skipping flock for amd64 469s Creating nova instance adt-plucky-amd64-busco-20241113-080931-juju-7f2275-prod-proposed-migration-environment-15-3995f192-8636-4674-b5d4-4285e2a8ce26 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...