0s autopkgtest [13:05:27]: starting date and time: 2024-11-15 13:05:27+0000 0s autopkgtest [13:05:27]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [13:05:27]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dna1vtyx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-biopython --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-biopython/1.84+dfsg-4build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-23.secgroup --name adt-plucky-amd64-python-biopython-20241115-130527-juju-7f2275-prod-proposed-migration-environment-2-0126f230-f735-435e-81bd-6222c8f3fead --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 48s autopkgtest [13:06:15]: testbed dpkg architecture: amd64 48s autopkgtest [13:06:15]: testbed apt version: 2.9.8 48s autopkgtest [13:06:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 49s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 49s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1052 kB] 49s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 49s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.5 kB] 49s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 49s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [109 kB] 49s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 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 amd64 Packages [831 kB] 49s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [295 kB] 49s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 49s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 50s Fetched 2696 kB in 1s (3227 kB/s) 50s Reading package lists... 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 53s The following packages will be upgraded: 53s firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0 53s libexpat1 lxd-installer man-db pastebinit python3-markupsafe python3-systemd 53s xfsprogs 53s 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 53s Need to get 13.6 MB of archives. 53s After this operation, 493 kB of additional disk space will be used. 53s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 53s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 53s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 53s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 53s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB] 53s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB] 53s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB] 53s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB] 54s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 54s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 54s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build3 [13.0 kB] 54s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 54s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 54s Preconfiguring packages ... 54s Fetched 13.6 MB in 1s (12.6 MB/s) 54s (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 ... 75542 files and directories currently installed.) 54s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 54s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 54s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 54s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 54s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 54s (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 ... 75568 files and directories currently installed.) 54s Preparing to unpack .../00-libexpat1_2.6.4-1_amd64.deb ... 54s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 54s Preparing to unpack .../01-man-db_2.13.0-1_amd64.deb ... 54s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 55s Preparing to unpack .../02-grub2-common_2.12-5ubuntu7_amd64.deb ... 55s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 55s Preparing to unpack .../03-grub-pc_2.12-5ubuntu7_amd64.deb ... 55s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 55s Preparing to unpack .../04-grub-pc-bin_2.12-5ubuntu7_amd64.deb ... 55s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 55s Preparing to unpack .../05-grub-common_2.12-5ubuntu7_amd64.deb ... 55s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 55s Preparing to unpack .../06-lxd-installer_9_all.deb ... 55s Unpacking lxd-installer (9) over (8) ... 55s Preparing to unpack .../07-pastebinit_1.7.1-1_all.deb ... 55s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 55s Preparing to unpack .../08-python3-markupsafe_2.1.5-1build3_amd64.deb ... 55s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ... 55s Preparing to unpack .../09-python3-systemd_235-1build5_amd64.deb ... 55s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 55s Preparing to unpack .../10-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 55s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 55s Setting up libexpat1:amd64 (2.6.4-1) ... 55s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 55s Setting up pastebinit (1.7.1-1) ... 55s Setting up man-db (2.13.0-1) ... 55s Updating database of manual pages ... 57s man-db.service is a disabled or a static unit not running, not starting it. 57s Setting up python3-markupsafe (2.1.5-1build3) ... 57s Setting up grub-common (2.12-5ubuntu7) ... 57s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 58s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 58s update-initramfs: deferring update (trigger activated) 59s Setting up lxd-installer (9) ... 59s Setting up python3-systemd (235-1build5) ... 59s Setting up grub2-common (2.12-5ubuntu7) ... 59s Setting up grub-pc-bin (2.12-5ubuntu7) ... 59s Setting up grub-pc (2.12-5ubuntu7) ... 59s Installing for i386-pc platform. 60s Installation finished. No error reported. 60s Sourcing file `/etc/default/grub' 60s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 60s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 60s Generating grub configuration file ... 60s Found linux image: /boot/vmlinuz-6.11.0-8-generic 60s Found initrd image: /boot/initrd.img-6.11.0-8-generic 60s Warning: os-prober will not be executed to detect other bootable partitions. 60s Systems on them will not be added to the GRUB boot configuration. 60s Check GRUB_DISABLE_OS_PROBER documentation entry. 60s Adding boot menu entry for UEFI Firmware Settings ... 60s done 60s Processing triggers for libc-bin (2.40-1ubuntu3) ... 60s Processing triggers for install-info (7.1.1-1) ... 60s Processing triggers for initramfs-tools (0.142ubuntu34) ... 60s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 60s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 69s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 70s Reading package lists... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s Calculating upgrade... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s autopkgtest [13:06:38]: rebooting testbed after setup commands that affected boot 88s autopkgtest [13:06:55]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 90s autopkgtest [13:06:57]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 93s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe python-biopython 1.84+dfsg-4build1 (dsc) [3412 B] 93s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe python-biopython 1.84+dfsg-4build1 (tar) [14.6 MB] 93s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe python-biopython 1.84+dfsg-4build1 (diff) [42.9 kB] 93s gpgv: Signature made Thu Nov 14 18:31:06 2024 UTC 93s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 93s gpgv: Can't check signature: No public key 93s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.84+dfsg-4build1.dsc: no acceptable signature found 94s autopkgtest [13:07:01]: testing package python-biopython version 1.84+dfsg-4build1 95s autopkgtest [13:07:02]: build not needed 100s autopkgtest [13:07:07]: test dependencies: preparing testbed 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Starting pkgProblemResolver with broken count: 0 101s Starting 2 pkgProblemResolver with broken count: 0 101s Done 101s The following additional packages will be installed: 101s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 101s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 101s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 101s libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 101s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 101s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 101s python-biopython-doc python3-all python3-biopython python3-biopython-sql 101s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 101s python3-rlpycairo sgml-base w3c-sgml-lib x11-common xfonts-encodings 101s xfonts-utils xml-core 101s Suggested packages: 101s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 101s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 101s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 101s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 101s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 101s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 101s rl-renderpm sgml-base-doc debhelper 101s Recommended packages: 101s javascript-common ncbi-blast+ python3-olefile fonts-dejavu-extra 101s The following NEW packages will be installed: 101s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 101s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 101s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 101s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 101s liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 101s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 101s libxcb-shm0 libxrender1 python-biopython-doc python3-all python3-biopython 101s python3-biopython-sql python3-cairo python3-freetype python3-numpy 101s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 101s x11-common xfonts-encodings xfonts-utils xml-core 101s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 47.3 MB/47.3 MB of archives. 101s After this operation, 128 MB of additional disk space will be used. 101s Get:1 /tmp/autopkgtest.atMc0a/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [740 B] 101s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 102s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 102s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 102s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 102s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 102s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 102s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 102s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 102s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 102s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 102s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 102s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 102s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 102s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 102s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 102s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 102s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 102s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 102s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 102s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 102s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 102s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 102s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 102s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 102s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 103s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 103s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 103s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 103s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 103s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 103s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 103s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 103s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 103s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 103s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 103s Get:39 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python-biopython-doc all 1.84+dfsg-4build1 [18.1 MB] 103s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 103s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 103s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 103s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 103s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 103s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 103s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 103s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 103s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 103s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 103s Get:50 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB] 103s Get:51 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-biopython-sql all 1.84+dfsg-4build1 [26.4 kB] 104s Fetched 47.3 MB in 2s (23.5 MB/s) 104s Selecting previously unselected package sgml-base. 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75576 files and directories currently installed.) 104s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 104s Unpacking sgml-base (1.31) ... 104s Selecting previously unselected package fonts-dejavu-mono. 104s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 104s Unpacking fonts-dejavu-mono (2.37-8) ... 104s Selecting previously unselected package fonts-dejavu-core. 104s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 104s Unpacking fonts-dejavu-core (2.37-8) ... 104s Selecting previously unselected package libfontenc1:amd64. 104s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 104s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 104s Selecting previously unselected package x11-common. 104s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 104s Unpacking x11-common (1:7.7+23ubuntu3) ... 104s Selecting previously unselected package xfonts-encodings. 104s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 104s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 104s Selecting previously unselected package xfonts-utils. 104s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_amd64.deb ... 104s Unpacking xfonts-utils (1:7.7+7) ... 104s Selecting previously unselected package fonts-urw-base35. 104s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 104s Unpacking fonts-urw-base35 (20200910-8) ... 104s Selecting previously unselected package fontconfig-config. 104s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 104s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 104s Selecting previously unselected package libblas3:amd64. 104s Preparing to unpack .../09-libblas3_3.12.0-3build2_amd64.deb ... 104s Unpacking libblas3:amd64 (3.12.0-3build2) ... 104s Selecting previously unselected package libfontconfig1:amd64. 104s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 104s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 104s Selecting previously unselected package libpixman-1-0:amd64. 104s Preparing to unpack .../11-libpixman-1-0_0.44.0-3_amd64.deb ... 104s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 104s Selecting previously unselected package libxcb-render0:amd64. 104s Preparing to unpack .../12-libxcb-render0_1.17.0-2_amd64.deb ... 104s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 104s Selecting previously unselected package libxcb-shm0:amd64. 104s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_amd64.deb ... 104s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 104s Selecting previously unselected package libxrender1:amd64. 104s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 104s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 104s Selecting previously unselected package libcairo2:amd64. 105s Preparing to unpack .../15-libcairo2_1.18.2-2_amd64.deb ... 105s Unpacking libcairo2:amd64 (1.18.2-2) ... 105s Selecting previously unselected package libdeflate0:amd64. 105s Preparing to unpack .../16-libdeflate0_1.22-1_amd64.deb ... 105s Unpacking libdeflate0:amd64 (1.22-1) ... 105s Selecting previously unselected package libgfortran5:amd64. 105s Preparing to unpack .../17-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 105s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 105s Selecting previously unselected package libgomp1:amd64. 105s Preparing to unpack .../18-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 105s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 105s Selecting previously unselected package libgraphite2-3:amd64. 105s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 105s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 105s Selecting previously unselected package libharfbuzz0b:amd64. 105s Preparing to unpack .../20-libharfbuzz0b_10.0.1-1_amd64.deb ... 105s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 105s Selecting previously unselected package libimagequant0:amd64. 105s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_amd64.deb ... 105s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 105s Selecting previously unselected package libjpeg-turbo8:amd64. 105s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 105s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 105s Selecting previously unselected package libjpeg8:amd64. 105s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_amd64.deb ... 105s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 105s Selecting previously unselected package libjs-jquery. 105s Preparing to unpack .../24-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 105s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 105s Selecting previously unselected package libjs-underscore. 105s Preparing to unpack .../25-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 105s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 105s Selecting previously unselected package libjs-sphinxdoc. 105s Preparing to unpack .../26-libjs-sphinxdoc_7.4.7-4_all.deb ... 105s Unpacking libjs-sphinxdoc (7.4.7-4) ... 105s Selecting previously unselected package liblapack3:amd64. 105s Preparing to unpack .../27-liblapack3_3.12.0-3build2_amd64.deb ... 105s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 105s Selecting previously unselected package liblcms2-2:amd64. 105s Preparing to unpack .../28-liblcms2-2_2.16-2_amd64.deb ... 105s Unpacking liblcms2-2:amd64 (2.16-2) ... 105s Selecting previously unselected package liblerc4:amd64. 105s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 105s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 105s Selecting previously unselected package libraqm0:amd64. 105s Preparing to unpack .../30-libraqm0_0.10.1-1build1_amd64.deb ... 105s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 105s Selecting previously unselected package libsharpyuv0:amd64. 105s Preparing to unpack .../31-libsharpyuv0_1.4.0-0.1_amd64.deb ... 105s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 105s Selecting previously unselected package libjbig0:amd64. 105s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 105s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 105s Selecting previously unselected package libwebp7:amd64. 105s Preparing to unpack .../33-libwebp7_1.4.0-0.1_amd64.deb ... 105s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 105s Selecting previously unselected package libtiff6:amd64. 105s Preparing to unpack .../34-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 105s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 105s Selecting previously unselected package libwebpdemux2:amd64. 105s Preparing to unpack .../35-libwebpdemux2_1.4.0-0.1_amd64.deb ... 105s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 105s Selecting previously unselected package libwebpmux3:amd64. 105s Preparing to unpack .../36-libwebpmux3_1.4.0-0.1_amd64.deb ... 105s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 105s Selecting previously unselected package python-biopython-doc. 105s Preparing to unpack .../37-python-biopython-doc_1.84+dfsg-4build1_all.deb ... 105s Unpacking python-biopython-doc (1.84+dfsg-4build1) ... 105s Selecting previously unselected package python3-all. 105s Preparing to unpack .../38-python3-all_3.12.6-0ubuntu1_amd64.deb ... 105s Unpacking python3-all (3.12.6-0ubuntu1) ... 105s Selecting previously unselected package python3-numpy. 105s Preparing to unpack .../39-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 105s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 106s Selecting previously unselected package libopenjp2-7:amd64. 106s Preparing to unpack .../40-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 106s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 106s Selecting previously unselected package python3-pil:amd64. 106s Preparing to unpack .../41-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 106s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 106s Selecting previously unselected package python3-cairo. 106s Preparing to unpack .../42-python3-cairo_1.26.1-2_amd64.deb ... 106s Unpacking python3-cairo (1.26.1-2) ... 106s Selecting previously unselected package python3-freetype. 106s Preparing to unpack .../43-python3-freetype_2.5.1-1_all.deb ... 106s Unpacking python3-freetype (2.5.1-1) ... 106s Selecting previously unselected package python3-rlpycairo. 106s Preparing to unpack .../44-python3-rlpycairo_0.3.0-3_all.deb ... 106s Unpacking python3-rlpycairo (0.3.0-3) ... 106s Selecting previously unselected package python3-reportlab. 106s Preparing to unpack .../45-python3-reportlab_4.2.5-1_all.deb ... 106s Unpacking python3-reportlab (4.2.5-1) ... 106s Selecting previously unselected package xml-core. 106s Preparing to unpack .../46-xml-core_0.19_all.deb ... 106s Unpacking xml-core (0.19) ... 106s Selecting previously unselected package w3c-sgml-lib. 106s Preparing to unpack .../47-w3c-sgml-lib_1.3-3_all.deb ... 106s Unpacking w3c-sgml-lib (1.3-3) ... 106s Selecting previously unselected package python3-biopython. 106s Preparing to unpack .../48-python3-biopython_1.84+dfsg-4build1_amd64.deb ... 106s Unpacking python3-biopython (1.84+dfsg-4build1) ... 106s Selecting previously unselected package python3-biopython-sql. 106s Preparing to unpack .../49-python3-biopython-sql_1.84+dfsg-4build1_all.deb ... 106s Unpacking python3-biopython-sql (1.84+dfsg-4build1) ... 106s Selecting previously unselected package autopkgtest-satdep. 106s Preparing to unpack .../50-1-autopkgtest-satdep.deb ... 106s Unpacking autopkgtest-satdep (0) ... 106s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 106s Setting up liblcms2-2:amd64 (2.16-2) ... 106s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 106s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 106s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 106s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 106s Setting up libxcb-render0:amd64 (1.17.0-2) ... 106s Setting up x11-common (1:7.7+23ubuntu3) ... 106s Setting up libdeflate0:amd64 (1.22-1) ... 106s Setting up python3-all (3.12.6-0ubuntu1) ... 106s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 106s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 106s Setting up python3-freetype (2.5.1-1) ... 106s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 106s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 106s Setting up libblas3:amd64 (3.12.0-3build2) ... 106s 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 106s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 106s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 106s Setting up fonts-dejavu-mono (2.37-8) ... 106s Setting up fonts-dejavu-core (2.37-8) ... 107s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 107s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 107s Setting up libwebp7:amd64 (1.4.0-0.1) ... 107s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 107s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 107s Setting up sgml-base (1.31) ... 107s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 107s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 107s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 107s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 107s Setting up liblapack3:amd64 (3.12.0-3build2) ... 107s 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 107s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 107s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 107s Setting up xfonts-utils (1:7.7+7) ... 107s Setting up libraqm0:amd64 (0.10.1-1build1) ... 107s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 108s Setting up libjs-sphinxdoc (7.4.7-4) ... 108s Setting up python-biopython-doc (1.84+dfsg-4build1) ... 108s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 108s Setting up xml-core (0.19) ... 108s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 108s Setting up fonts-urw-base35 (20200910-8) ... 109s Setting up libcairo2:amd64 (1.18.2-2) ... 109s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 109s Setting up python3-cairo (1.26.1-2) ... 109s Setting up python3-rlpycairo (0.3.0-3) ... 109s Setting up python3-reportlab (4.2.5-1) ... 110s Processing triggers for libc-bin (2.40-1ubuntu3) ... 110s Processing triggers for man-db (2.13.0-1) ... 111s Processing triggers for sgml-base (1.31) ... 111s Setting up w3c-sgml-lib (1.3-3) ... 133s Setting up python3-biopython (1.84+dfsg-4build1) ... 134s Setting up python3-biopython-sql (1.84+dfsg-4build1) ... 134s Setting up autopkgtest-satdep (0) ... 137s (Reading database ... 80992 files and directories currently installed.) 137s Removing autopkgtest-satdep (0) ... 138s autopkgtest [13:07:45]: test dependencies: sh debian/tests/run-unit-test 138s autopkgtest [13:07:45]: test dependencies: [----------------------- 138s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 138s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 138s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 138s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 139s mkdir: created directory 'Bio' 139s mkdir: created directory 'Bio/Align' 139s mkdir: created directory 'Bio/Align/substitution_matrices' 139s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 139s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 139s Remove test test_Tutorial.py which is bound to fail 140s test_Ace ... ok 140s test_Affy ... ok 142s test_AlignIO ... ok 142s test_AlignIO_ClustalIO ... ok 142s test_AlignIO_EmbossIO ... ok 142s test_AlignIO_FastaIO ... ok 142s test_AlignIO_MauveIO ... ok 142s test_AlignIO_PhylipIO ... ok 142s test_AlignIO_convert ... ok 142s test_AlignInfo ... ok 142s test_Align_Alignment ... ok 142s test_Align_a2m ... ok 142s test_Align_bed ... ok 142s test_Align_bigbed ... ok 143s test_Align_bigmaf ... ok 143s test_Align_bigpsl ... ok 143s test_Align_chain ... ok 143s test_Align_clustal ... ok 146s test_Align_codonalign ... ok 146s test_Align_emboss ... ok 146s test_Align_exonerate ... ok 146s test_Align_fasta ... ok 146s test_Align_hhr ... ok 147s test_Align_maf ... ok 147s test_Align_mauve ... ok 147s test_Align_msf ... ok 147s test_Align_nexus ... ok 147s test_Align_phylip ... ok 147s test_Align_psl ... ok 147s test_Align_sam ... ok 148s test_Align_stockholm ... ok 149s test_Align_tabular ... ok 149s test_Application ... ok 149s test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython 149s test_BioSQL_MySQLdb_online ... skipping. internet not available 149s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 149s test_BioSQL_mysql_connector_online ... skipping. internet not available 149s test_BioSQL_psycopg2_online ... skipping. internet not available 152s test_BioSQL_sqlite3 ... ok 152s test_BioSQL_sqlite3_online ... skipping. internet not available 152s test_Blast_Record ... ok 153s test_Blast_parser ... ok 153s test_CAPS ... ok 153s test_Chi2 ... ok 153s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 153s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 153s test_Cluster ... ok 153s test_CodonTable ... ok 153s test_ColorSpiral ... ok 153s test_Compass ... ok 154s test_Consensus ... ok 154s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 154s test_EMBL_unittest ... ok 154s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 154s test_EmbossPrimer ... ok 158s test_Entrez ... ok 158s test_Entrez_online ... skipping. internet not available 159s test_Entrez_parser ... ok 159s test_Enzyme ... ok 159s test_ExPASy ... skipping. internet not available 159s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 159s test_File ... ok 159s test_GenBank ... ok 160s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 162s ok 162s test_GraphicsChromosome ... ok 162s test_GraphicsDistribution ... ok 163s test_GraphicsGeneral ... ok 163s test_HMMCasino ... ok 163s test_HMMGeneral ... ok 163s test_KEGG ... ok 163s test_KEGG_online ... skipping. internet not available 167s test_KGML_graphics ... ok 167s test_KGML_graphics_online ... skipping. internet not available 168s test_KGML_nographics ... ok 168s test_KeyWList ... ok 168s test_LogisticRegression ... ok 168s test_MafIO_index ... ok 168s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 168s test_MarkovModel ... ok 168s test_Medline ... ok 168s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 169s test_NCBIXML ... ok 169s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 169s test_NCBI_qblast ... ok 169s test_NMR ... ok 169s test_NaiveBayes ... ok 169s test_Nexus ... ok 169s test_PAML_baseml ... ok 170s test_PAML_codeml ... ok 170s test_PAML_yn00 ... ok 172s test_PDB_CEAligner ... ok 172s test_PDB_DSSP ... ok 172s test_PDB_Dice ... ok 172s test_PDB_Disordered ... ok 172s test_PDB_Exposure ... ok 172s test_PDB_FragmentMapper ... ok 173s test_PDB_KDTree ... ok 173s test_PDB_MMCIF2Dict ... ok 173s test_PDB_MMCIFIO ... ok 174s test_PDB_MMCIFParser ... ok 174s test_PDB_NACCESS ... ok 174s test_PDB_PDBIO ... ok 174s test_PDB_PDBList ... skipping. internet not available 179s test_PDB_PDBMLParser ... ok 180s test_PDB_PDBParser ... ok 180s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 180s test_PDB_Polypeptide ... ok 180s test_PDB_QCPSuperimposer ... ok 182s test_PDB_SASA ... ok 183s test_PDB_SMCRA ... ok 183s test_PDB_Selection ... ok 183s test_PDB_StructureAlignment ... ok 183s test_PDB_Superimposer ... ok 183s test_PDB_alphafold_db ... skipping. internet not available 183s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 183s 183s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 183s 183s test_PDB_parse_pdb_header ... ok 183s test_PDB_vectors ... ok 183s test_PQR ... ok 183s test_Pathway ... ok 183s test_Phd ... ok 183s test_Phylo ... ok 184s test_PhyloXML ... ok 184s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 184s test_Phylo_NeXML ... ok 184s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 184s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 184s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 184s test_PopGen_GenePop_nodepend ... ok 184s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 184s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 184s test_ProtParam ... ok 184s test_RCSBFormats ... ok 184s test_Restriction ... ok 184s test_SCOP_Astral ... ok 184s test_SCOP_Cla ... ok 184s test_SCOP_Des ... ok 184s test_SCOP_Dom ... ok 184s test_SCOP_Hie ... ok 185s test_SCOP_Raf ... ok 185s test_SCOP_Residues ... ok 185s test_SCOP_Scop ... ok 185s test_SVDSuperimposer ... ok 185s test_SearchIO_blast_tab ... ok 185s test_SearchIO_blast_tab_index ... ok 185s test_SearchIO_blast_xml ... ok 186s test_SearchIO_blast_xml_index ... ok 186s test_SearchIO_blat_psl ... ok 186s test_SearchIO_blat_psl_index ... ok 186s test_SearchIO_exonerate ... ok 186s test_SearchIO_exonerate_text_index ... ok 186s test_SearchIO_exonerate_vulgar_index ... ok 186s test_SearchIO_fasta_m10 ... ok 186s test_SearchIO_fasta_m10_index ... ok 186s test_SearchIO_hhsuite2_text ... ok 186s test_SearchIO_hmmer2_text ... ok 187s test_SearchIO_hmmer2_text_index ... ok 187s test_SearchIO_hmmer3_domtab ... ok 187s test_SearchIO_hmmer3_domtab_index ... ok 187s test_SearchIO_hmmer3_tab ... ok 187s test_SearchIO_hmmer3_tab_index ... ok 187s test_SearchIO_hmmer3_text ... ok 187s test_SearchIO_hmmer3_text_index ... ok 187s test_SearchIO_interproscan_xml ... ok 187s test_SearchIO_model ... ok 187s test_SearchIO_write ... ok 187s test_SeqFeature ... ok 198s test_SeqIO ... ok 199s test_SeqIO_AbiIO ... ok 199s test_SeqIO_FastaIO ... ok 199s test_SeqIO_Gck ... ok 199s test_SeqIO_Gfa ... ok 199s test_SeqIO_Insdc ... ok 199s test_SeqIO_NibIO ... ok 200s test_SeqIO_PdbIO ... ok 201s test_SeqIO_QualityIO ... ok 201s test_SeqIO_SeqXML ... ok 201s test_SeqIO_SnapGene ... ok 201s test_SeqIO_TwoBitIO ... ok 201s test_SeqIO_Xdna ... ok 202s test_SeqIO_features ... ok 213s test_SeqIO_index ... ok 213s test_SeqIO_online ... skipping. internet not available 213s test_SeqIO_write ... ok 213s test_SeqRecord ... ok 213s test_SeqUtils ... ok 214s test_Seq_objs ... ok 214s test_SffIO ... ok 214s test_SwissProt ... ok 214s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 214s test_TogoWS ... skipping. internet not available 214s test_TreeConstruction ... ok 215s test_UniGene ... ok 215s test_UniProt ... skipping. internet not available 215s test_UniProt_GOA ... ok 215s test_UniProt_Parser ... ok 215s test_align ... ok 215s test_align_substitution_matrices ... ok 217s test_bgzf ... ok 217s test_cellosaurus ... ok 220s test_codonalign ... ok 220s test_geo ... ok 220s test_kNN ... ok 220s test_motifs ... ok 220s test_motifs_online ... skipping. internet not available 220s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 220s warnings.warn( 220s ok 220s test_pairwise2_no_C ... ok 221s test_pairwise_aligner ... ok 221s test_pairwise_alignment_map ... ok 226s test_phenotype ... ok 226s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 226s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 226s test_prodoc ... ok 226s test_prosite ... ok 226s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 226s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 226s test_seq ... ok 226s test_translate ... ok 226s ---------------------------------------------------------------------- 226s Ran 218 tests in 86.522 seconds 226s 226s Skipping any tests requiring internet access 226s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 226s Operating system: posix linux 227s autopkgtest [13:09:14]: test dependencies: -----------------------] 227s autopkgtest [13:09:14]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 227s dependencies PASS 228s autopkgtest [13:09:15]: test full_suite: preparing testbed 268s autopkgtest [13:09:55]: testbed dpkg architecture: amd64 269s autopkgtest [13:09:56]: testbed apt version: 2.9.8 269s autopkgtest [13:09:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 269s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 270s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 270s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.5 kB] 270s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1052 kB] 270s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 270s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB] 270s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [109 kB] 270s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 270s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [295 kB] 270s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [831 kB] 270s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 270s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 270s Fetched 2696 kB in 1s (3292 kB/s) 270s Reading package lists... 272s Reading package lists... 273s Building dependency tree... 273s Reading state information... 273s Calculating upgrade... 273s The following packages will be upgraded: 273s firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0 273s libexpat1 lxd-installer man-db pastebinit python3-markupsafe python3-systemd 273s xfsprogs 273s 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 273s Need to get 13.6 MB of archives. 273s After this operation, 493 kB of additional disk space will be used. 273s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 274s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 274s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 274s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 274s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB] 274s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB] 274s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB] 274s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB] 274s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 274s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 274s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build3 [13.0 kB] 274s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 274s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 274s Preconfiguring packages ... 274s Fetched 13.6 MB in 1s (14.1 MB/s) 274s (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 ... 75542 files and directories currently installed.) 274s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 274s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 275s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 275s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 275s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 275s (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 ... 75568 files and directories currently installed.) 275s Preparing to unpack .../00-libexpat1_2.6.4-1_amd64.deb ... 275s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 275s Preparing to unpack .../01-man-db_2.13.0-1_amd64.deb ... 275s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 275s Preparing to unpack .../02-grub2-common_2.12-5ubuntu7_amd64.deb ... 275s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 275s Preparing to unpack .../03-grub-pc_2.12-5ubuntu7_amd64.deb ... 275s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 275s Preparing to unpack .../04-grub-pc-bin_2.12-5ubuntu7_amd64.deb ... 275s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 275s Preparing to unpack .../05-grub-common_2.12-5ubuntu7_amd64.deb ... 275s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 275s Preparing to unpack .../06-lxd-installer_9_all.deb ... 275s Unpacking lxd-installer (9) over (8) ... 275s Preparing to unpack .../07-pastebinit_1.7.1-1_all.deb ... 275s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 275s Preparing to unpack .../08-python3-markupsafe_2.1.5-1build3_amd64.deb ... 275s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ... 275s Preparing to unpack .../09-python3-systemd_235-1build5_amd64.deb ... 275s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 275s Preparing to unpack .../10-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 275s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 275s Setting up libexpat1:amd64 (2.6.4-1) ... 275s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 275s Setting up pastebinit (1.7.1-1) ... 275s Setting up man-db (2.13.0-1) ... 276s Updating database of manual pages ... 277s man-db.service is a disabled or a static unit not running, not starting it. 277s Setting up python3-markupsafe (2.1.5-1build3) ... 277s Setting up grub-common (2.12-5ubuntu7) ... 277s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 278s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 278s update-initramfs: deferring update (trigger activated) 278s Setting up lxd-installer (9) ... 279s Setting up python3-systemd (235-1build5) ... 279s Setting up grub2-common (2.12-5ubuntu7) ... 279s Setting up grub-pc-bin (2.12-5ubuntu7) ... 279s Setting up grub-pc (2.12-5ubuntu7) ... 279s Installing for i386-pc platform. 279s Installation finished. No error reported. 280s Sourcing file `/etc/default/grub' 280s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 280s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 280s Generating grub configuration file ... 280s Found linux image: /boot/vmlinuz-6.11.0-8-generic 280s Found initrd image: /boot/initrd.img-6.11.0-8-generic 280s Warning: os-prober will not be executed to detect other bootable partitions. 280s Systems on them will not be added to the GRUB boot configuration. 280s Check GRUB_DISABLE_OS_PROBER documentation entry. 280s Adding boot menu entry for UEFI Firmware Settings ... 280s done 280s Processing triggers for libc-bin (2.40-1ubuntu3) ... 280s Processing triggers for install-info (7.1.1-1) ... 280s Processing triggers for initramfs-tools (0.142ubuntu34) ... 280s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 280s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 288s Reading package lists... 288s Building dependency tree... 288s Reading state information... 289s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 289s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 289s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 289s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 289s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 290s Reading package lists... 290s Reading package lists... 290s Building dependency tree... 290s Reading state information... 291s Calculating upgrade... 291s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 291s Reading package lists... 291s Building dependency tree... 291s Reading state information... 291s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 291s autopkgtest [13:10:18]: rebooting testbed after setup commands that affected boot 295s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 313s Reading package lists... 313s Building dependency tree... 313s Reading state information... 313s Starting pkgProblemResolver with broken count: 0 313s Starting 2 pkgProblemResolver with broken count: 0 313s Done 314s The following additional packages will be installed: 314s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 314s clustalw cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper 314s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 314s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 314s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 314s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 314s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 314s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext ghostscript hevea 314s hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 314s intltool-debian libamd-comgr2 libamdhip64-5 libaom3 libapache-pom-java 314s libarchive-zip-perl libargtable2-0 libasan8 libavahi-client3 314s libavahi-common-data libavahi-common3 libblas3 libcairo2 libcc1-0 314s libcifpp-data libcifpp7 libcommons-logging-java libcommons-parent-java 314s libcups2t64 libde265-0 libdebhelper-perl libdeflate0 libdrm-amdgpu1 314s libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfftw3-double3 314s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 314s libgcc-14-dev libgd3 libgfortran5 libgomp1 libgraphite2-3 libgs-common 314s libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 314s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhsakmt1 314s libhts3t64 libhtscodecs2 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 314s libibumad3 libice6 libidn12 libijs-0.35 libimagequant0 libisl23 libitm1 314s libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 314s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 314s liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblqr-1-0 liblsan0 libltdl7 314s libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmbedcrypto7t64 314s libmbedtls14t64 libmbedx509-1t64 libmpc3 libmpfi0 libmunge2 libmysqlclient21 314s libnetpbm11t64 libopenjp2-7 libopenmpi3t64 libpaper-utils libpaper1 314s libpciaccess0 libpdfbox-java libpixman-1-0 libpmix2t64 libpotrace0 libpq5 314s libpsm-infinipath1 libpsm2-2 libptexenc1 libpython3-all-dev libpython3-dev 314s libpython3.12-dev libqhull-r8.0 libquadmath0 libraqm0 libraw23t64 314s librdmacm1t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 314s libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 314s libucx0 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 314s libxcb-shm0 libxft2 libxi6 libxmu6 libxnvctrl0 libxpm4 libxrender1 314s libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft muscle3 mysql-common 314s ncbi-blast+ ncbi-data netpbm ocl-icd-libopencl1 openmpi-bin openmpi-common 314s phylip phyml po-debconf poppler-data prank preview-latex-style probcons 314s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 314s python3-all-dev python3-appdirs python3-biopython python3-biopython-sql 314s python3-brotli python3-cairo python3-contourpy python3-cycler 314s python3-dateutil python3-decorator python3-defusedxml python3-dev 314s python3-docutils python3-fonttools python3-freetype python3-fs 314s python3-imagesize python3-kiwisolver python3-lxml python3-lz4 314s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 314s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 314s python3-packaging python3-pil python3-pil.imagetk python3-psycopg2 314s python3-rdflib python3-reportlab python3-rlpycairo python3-roman 314s python3-scipy python3-six python3-snowballstemmer python3-sphinx 314s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 314s python3-tabulate python3-tk python3-tz python3-ufolib2 python3.12-dev 314s python3.12-tk raxml samtools sgml-base sphinx-common sphinx-rtd-theme-common 314s t-coffee t1utils tex-common texlive-base texlive-binaries 314s texlive-fonts-recommended texlive-latex-base texlive-latex-extra 314s texlive-latex-recommended texlive-pictures tk8.6-blt2.5 unicode-data 314s w3c-sgml-lib wise wise-data x11-common xdg-utils xfonts-encodings 314s xfonts-utils xml-core zlib1g-dev 314s Suggested packages: 314s autoconf-archive gnu-standards autoconf-doc blt-demo clustalx seaview 314s cpp-doc gcc-14-locales cpp-14-doc dh-make flit python3-build 314s python3-installer python3-wheel emboss-doc emboss-test embassy bison 314s flex-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre g++-multilib 314s g++-14-multilib gcc-14-doc gcc-multilib manpages-dev gdb gcc-doc 314s gcc-14-multilib gdb-x86-64-linux-gnu gettext-doc libasprintf-dev 314s libgettextpo-dev hevea-doc imagemagick-6-doc autotrace cups-bsd | lpr 314s | lprng enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin 314s mplayer povray radiance sane-utils transfig libraw-bin 314s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 314s cups-common libfftw3-bin libfftw3-dev libgd-tools libheif-plugin-x265 314s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 314s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar 314s libheif-plugin-rav1e libheif-plugin-svtenc libhwloc-contrib-plugins 314s libjs-jquery-ui-docs liblcms2-utils libmagickcore-6.q16-7-extra libmpfi-doc 314s libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler 314s gcj-jdk m4-doc opencl-icd gfortran | fortran-compiler phylip-doc 314s libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho 314s fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai 314s fonts-arphic-uming fonts-nanum probcons-extra python-cycler-doc docutils-doc 314s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 314s python-lxml-doc cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 314s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 314s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 314s texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server 314s | virtual-mysql-server python3-gdal python3-pydot python3-pygraphviz 314s gfortran python-numpy-doc python3-pytest python-pil-doc python-psycopg2-doc 314s python-rdflib-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc 314s rl-accel rl-renderpm python-scipy-doc python3-stemmer dvisvgm 314s fonts-freefont-otf latexmk libjs-mathjax sphinx-doc tex-gyre 314s texlive-fonts-extra texlive-plain-generic python-sympy-doc tix 314s python3-tk-dbg python3.13-tk cwltool sgml-base-doc boxshade 314s t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 314s hintview texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex 314s icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science 314s texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex 314s texlive-pictures-doc vprerex wise-doc 314s Recommended packages: 314s primer3 libfl-dev libmagickcore-6.q16-7-extra libarchive-cpio-perl 314s fonts-droid-fallback libheif-plugin-aomenc javascript-common libjson-xs-perl 314s libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 314s python3-cssselect python3-html5lib python3-olefile python3-html5rdf 314s python3-orjson fonts-dejavu-extra isympy-common amap-align dialign-tx fsa 314s kalign libsoap-lite-perl libxml-simple-perl muscle mustang poa proda 314s tm-align lmodern dvisvgm tex-gyre tipa default-jre 314s libspreadsheet-parseexcel-perl texlive-plain-generic tk 314s libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils 314s x11-xserver-utils 314s The following NEW packages will be installed: 314s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 314s build-essential bwa clustalo clustalw cpp cpp-14 cpp-14-x86-64-linux-gnu 314s cpp-x86-64-linux-gnu debhelper debugedit dh-autoreconf dh-python 314s dh-strip-nondeterminism dialign docutils-common dssp dwz emboss emboss-data 314s emboss-lib fasttree flex fontconfig-config fonts-dejavu-core 314s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 314s fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 314s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext ghostscript 314s hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 314s intltool-debian libamd-comgr2 libamdhip64-5 libaom3 libapache-pom-java 314s libarchive-zip-perl libargtable2-0 libasan8 libavahi-client3 314s libavahi-common-data libavahi-common3 libblas3 libcairo2 libcc1-0 314s libcifpp-data libcifpp7 libcommons-logging-java libcommons-parent-java 314s libcups2t64 libde265-0 libdebhelper-perl libdeflate0 libdrm-amdgpu1 314s libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfftw3-double3 314s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 314s libgcc-14-dev libgd3 libgfortran5 libgomp1 libgraphite2-3 libgs-common 314s libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 314s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhsakmt1 314s libhts3t64 libhtscodecs2 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 314s libibumad3 libice6 libidn12 libijs-0.35 libimagequant0 libisl23 libitm1 314s libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 314s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 314s liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblqr-1-0 liblsan0 libltdl7 314s libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmbedcrypto7t64 314s libmbedtls14t64 libmbedx509-1t64 libmpc3 libmpfi0 libmunge2 libmysqlclient21 314s libnetpbm11t64 libopenjp2-7 libopenmpi3t64 libpaper-utils libpaper1 314s libpciaccess0 libpdfbox-java libpixman-1-0 libpmix2t64 libpotrace0 libpq5 314s libpsm-infinipath1 libpsm2-2 libptexenc1 libpython3-all-dev libpython3-dev 314s libpython3.12-dev libqhull-r8.0 libquadmath0 libraqm0 libraw23t64 314s librdmacm1t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 314s libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 314s libucx0 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 314s libxcb-shm0 libxft2 libxi6 libxmu6 libxnvctrl0 libxpm4 libxrender1 314s libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft muscle3 mysql-common 314s ncbi-blast+ ncbi-data netpbm ocl-icd-libopencl1 openmpi-bin openmpi-common 314s phylip phyml po-debconf poppler-data prank preview-latex-style probcons 314s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 314s python3-all-dev python3-appdirs python3-biopython python3-biopython-sql 314s python3-brotli python3-cairo python3-contourpy python3-cycler 314s python3-dateutil python3-decorator python3-defusedxml python3-dev 314s python3-docutils python3-fonttools python3-freetype python3-fs 314s python3-imagesize python3-kiwisolver python3-lxml python3-lz4 314s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 314s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 314s python3-packaging python3-pil python3-pil.imagetk python3-psycopg2 314s python3-rdflib python3-reportlab python3-rlpycairo python3-roman 314s python3-scipy python3-six python3-snowballstemmer python3-sphinx 314s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 314s python3-tabulate python3-tk python3-tz python3-ufolib2 python3.12-dev 314s python3.12-tk raxml samtools sgml-base sphinx-common sphinx-rtd-theme-common 314s t-coffee t1utils tex-common texlive-base texlive-binaries 314s texlive-fonts-recommended texlive-latex-base texlive-latex-extra 314s texlive-latex-recommended texlive-pictures tk8.6-blt2.5 unicode-data 314s w3c-sgml-lib wise wise-data x11-common xdg-utils xfonts-encodings 314s xfonts-utils xml-core zlib1g-dev 314s 0 upgraded, 284 newly installed, 0 to remove and 0 not upgraded. 314s Need to get 465 MB/465 MB of archives. 314s After this operation, 2008 MB of additional disk space will be used. 314s Get:1 /tmp/autopkgtest.atMc0a/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [1024 B] 314s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 315s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 flex amd64 2.6.4-8.2build1 [301 kB] 315s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 315s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 315s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu4 [839 kB] 315s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 315s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 315s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 315s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 315s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 315s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 315s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 315s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 315s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 315s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 315s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libaom3 amd64 3.11.0~rc1-1 [2762 kB] 315s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-aomdec amd64 1.19.3-1 [11.5 kB] 315s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libde265-0 amd64 1.0.15-1build4 [168 kB] 315s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-libde265 amd64 1.19.3-1 [8968 B] 315s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif1 amd64 1.19.3-1 [415 kB] 315s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 315s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 315s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 315s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 315s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblqr-1-0 amd64 0.4.2-2.1build2 [28.5 kB] 315s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.4.7-7build1 [40.3 kB] 315s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 315s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libraw23t64 amd64 0.21.3-1 [433 kB] 315s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 315s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 315s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 315s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 315s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 315s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 315s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick-6-common all 8:6.9.13.12+dfsg1-1build1 [69.6 kB] 315s Get:37 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmagickcore-6.q16-7t64 amd64 8:6.9.13.12+dfsg1-1build1 [1851 kB] 315s Get:38 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmagickwand-6.q16-7t64 amd64 8:6.9.13.12+dfsg1-1build1 [316 kB] 315s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-data all 0.4.12-1 [2060 kB] 315s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 315s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 315s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 315s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 316s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 316s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 316s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 316s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 316s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 316s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 316s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 316s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 316s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 316s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 316s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 316s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 316s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 316s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 316s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 316s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 316s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 316s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 316s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 316s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 316s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 316s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 316s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 316s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 317s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 317s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 317s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 317s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 317s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 317s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 317s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 317s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 317s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 317s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 bwa amd64 0.7.18-1 [204 kB] 317s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 libargtable2-0 amd64 13-2 [14.6 kB] 317s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 clustalo amd64 1.2.4-8build1 [202 kB] 317s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 clustalw amd64 2.1+lgpl-7 [275 kB] 317s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 317s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 317s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 317s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 317s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 317s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 317s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 317s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 317s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 317s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 317s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 317s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 317s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB] 317s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 dialign amd64 2.2.1-13 [154 kB] 317s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 317s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 317s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcifpp-data all 7.0.7-3 [480 kB] 317s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcifpp7 amd64 7.0.7-3 [1141 kB] 317s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 dssp amd64 4.4.10-1 [786 kB] 317s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 317s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 317s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 318s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 318s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB] 318s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libgd3 amd64 2.3.3-12ubuntu3 [127 kB] 318s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1build3 [432 kB] 318s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 mysql-common all 5.8+1.1.1 [6800 B] 318s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libmysqlclient21 amd64 8.0.40-1 [1250 kB] 318s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libpq5 amd64 17.0-1 [249 kB] 318s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss-lib amd64 6.6.0+dfsg-12ubuntu2 [2976 kB] 318s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss-data all 6.6.0+dfsg-12ubuntu2 [61.0 MB] 321s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss amd64 6.6.0+dfsg-12ubuntu2 [980 kB] 321s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 321s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lmodern all 2.005-1 [4799 kB] 321s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 321s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs-common all 10.03.1~dfsg1-0ubuntu3 [175 kB] 321s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs10-common all 10.03.1~dfsg1-0ubuntu3 [488 kB] 321s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-13ubuntu6 [29.7 kB] 321s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-13ubuntu6 [23.3 kB] 321s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-13ubuntu6 [26.8 kB] 321s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.10-1ubuntu2 [271 kB] 321s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libidn12 amd64 1.42-2 [55.9 kB] 321s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libijs-0.35 amd64 0.35-15.1build1 [15.3 kB] 321s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig2dec0 amd64 0.20-1build3 [65.0 kB] 321s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB] 321s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 321s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 321s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 321s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs10 amd64 10.03.1~dfsg1-0ubuntu3 [4579 kB] 321s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 ghostscript amd64 10.03.1~dfsg1-0ubuntu3 [43.5 kB] 321s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetpbm11t64 amd64 2:11.08.01-1 [125 kB] 321s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 netpbm amd64 2:11.08.01-1 [2282 kB] 321s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 tex-common all 6.18 [32.8 kB] 321s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B] 321s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5 [66.8 kB] 321s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5 [43.7 kB] 321s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5 [62.3 kB] 321s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5 [145 kB] 321s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 t1utils amd64 1.41-4build3 [61.3 kB] 321s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 321s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 321s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 321s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 321s Get:144 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] 321s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpotrace0 amd64 1.16-2build1 [17.7 kB] 321s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 libteckit0 amd64 2.5.12+ds1-1 [411 kB] 321s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB] 321s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libxaw7 amd64 2:1.0.16-1 [207 kB] 321s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 321s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2build1 [28.1 kB] 321s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-binaries amd64 2024.20240313.70630+ds-5 [9801 kB] 322s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 322s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-base all 2024.20241102-1 [22.5 MB] 322s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-1 [13.5 kB] 322s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick-6.q16 amd64 8:6.9.13.12+dfsg1-1build1 [254 kB] 322s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick amd64 8:6.9.13.12+dfsg1-1build1 [14.2 kB] 322s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 hevea amd64 2.36-2 [2023 kB] 322s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-18 [26.0 MB] 323s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 324s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [21.7 kB] 324s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 324s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 324s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 324s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 324s Get:165 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 324s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 324s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 324s Get:168 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 324s Get:169 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB] 324s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 324s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 324s Get:172 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 52.0-2ubuntu1 [70.8 kB] 324s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3ubuntu1 [658 kB] 324s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 324s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 324s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 324s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.11.2-1 [193 kB] 324s Get:178 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 324s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 324s Get:180 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 324s Get:181 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 324s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 324s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 325s Get:184 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 325s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto7t64 amd64 2.28.8-1 [209 kB] 325s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-1t64 amd64 2.28.8-1 [46.6 kB] 325s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls14t64 amd64 2.28.8-1 [82.2 kB] 325s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.15-4build1 [14.7 kB] 325s Get:189 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 325s Get:190 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 325s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 325s Get:192 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.11.2-1 [16.0 kB] 325s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.3-2 [697 kB] 325s Get:194 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 52.0-2ubuntu1 [29.0 kB] 325s Get:195 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 52.0-2ubuntu1 [42.6 kB] 325s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.17.0+ds-3build1 [1162 kB] 325s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi3t64 amd64 4.1.6-13.3ubuntu2 [2575 kB] 325s Get:198 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 325s Get:199 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.7-3 [5699 kB] 325s Get:200 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.12.6-0ubuntu1 [10.2 kB] 325s Get:201 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-all-dev amd64 3.12.6-0ubuntu1 [916 B] 325s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 325s Get:203 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 325s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 mafft amd64 7.505-1 [795 kB] 326s Get:205 http://ftpmaster.internal/ubuntu plucky/universe amd64 muscle3 amd64 3.8.1551-3 [198 kB] 326s Get:206 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 326s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] 326s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-common all 4.1.6-13.3ubuntu2 [170 kB] 326s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-bin amd64 4.1.6-13.3ubuntu2 [114 kB] 326s Get:210 http://ftpmaster.internal/ubuntu plucky/universe amd64 phylip amd64 1:3.697+dfsg-4build1 [874 kB] 326s Get:211 http://ftpmaster.internal/ubuntu plucky/universe amd64 phyml amd64 3:3.3.20220408-3build3 [965 kB] 326s Get:212 http://ftpmaster.internal/ubuntu plucky/universe amd64 prank amd64 0.0.170427+dfsg-3 [396 kB] 326s Get:213 http://ftpmaster.internal/ubuntu plucky/universe amd64 preview-latex-style all 13.2-1 [347 kB] 326s Get:214 http://ftpmaster.internal/ubuntu plucky/universe amd64 probcons amd64 1.12-14 [125 kB] 326s Get:215 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python-biopython-doc all 1.84+dfsg-4build1 [18.1 MB] 327s Get:216 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 327s Get:217 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 327s Get:218 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] 327s Get:219 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.12.6-0ubuntu1 [26.7 kB] 327s Get:220 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all-dev amd64 3.12.6-0ubuntu1 [908 B] 327s Get:221 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 327s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 327s Get:223 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 327s Get:224 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.6-1ubuntu1 [9806 B] 327s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 327s Get:226 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 327s Get:227 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 327s Get:228 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 327s Get:229 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 327s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 327s Get:231 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 327s Get:232 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB] 327s Get:233 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-biopython-sql all 1.84+dfsg-4build1 [26.4 kB] 327s Get:234 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 327s Get:235 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 327s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 327s Get:237 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 327s Get:238 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 327s Get:239 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 327s Get:240 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-defusedxml all 0.7.1-2 [42.0 kB] 327s Get:241 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-roman all 4.2-1 [10.0 kB] 327s Get:242 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 328s Get:243 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 328s Get:244 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 328s Get:245 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 328s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 328s Get:247 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 328s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 328s Get:249 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 328s Get:250 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 328s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 329s Get:252 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 329s Get:253 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-imagesize all 1.4.1-1 [6844 B] 329s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 329s Get:255 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 329s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 329s Get:257 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-msgpack amd64 1.0.3-3build2 [80.1 kB] 329s Get:258 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mmtf all 1.1.3-1 [16.2 kB] 329s Get:259 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-mysqldb amd64 1.4.6-2build4 [49.3 kB] 329s Get:260 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 329s Get:261 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-common all 7.4.7-4 [775 kB] 329s Get:262 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 329s Get:263 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 329s Get:264 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sphinx all 7.4.7-4 [593 kB] 329s Get:265 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tabulate all 0.9.0-1 [45.3 kB] 329s Get:266 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numpydoc all 1.6.0-2 [50.5 kB] 329s Get:267 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psycopg2 amd64 2.9.9-2build1 [146 kB] 329s Get:268 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rdflib all 7.1.1-2 [426 kB] 329s Get:269 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 329s Get:270 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 329s Get:271 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 329s Get:272 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB] 329s Get:273 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 329s Get:274 http://ftpmaster.internal/ubuntu plucky/universe amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [929 kB] 330s Get:275 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-fonts-recommended all 2024.20241102-1 [4974 kB] 330s Get:276 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-base all 2024.20241102-1 [1260 kB] 330s Get:277 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfontbox-java all 1:1.8.16-5 [208 kB] 330s Get:278 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 330s Get:279 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-recommended all 2024.20241102-1 [8739 kB] 330s Get:280 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-pictures all 2024.20241102-1 [17.0 MB] 331s Get:281 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-extra all 2024.20241102-1 [24.2 MB] 332s Get:282 http://ftpmaster.internal/ubuntu plucky/universe amd64 wise-data all 2.4.1-25 [83.0 kB] 332s Get:283 http://ftpmaster.internal/ubuntu plucky/universe amd64 wise amd64 2.4.1-25 [843 kB] 332s Get:284 http://ftpmaster.internal/ubuntu plucky/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 332s Preconfiguring packages ... 332s Fetched 465 MB in 18s (26.4 MB/s) 332s Selecting previously unselected package m4. 333s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75576 files and directories currently installed.) 333s Preparing to unpack .../000-m4_1.4.19-4build1_amd64.deb ... 333s Unpacking m4 (1.4.19-4build1) ... 333s Selecting previously unselected package flex. 333s Preparing to unpack .../001-flex_2.6.4-8.2build1_amd64.deb ... 333s Unpacking flex (2.6.4-8.2build1) ... 333s Selecting previously unselected package fonts-lato. 333s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 333s Unpacking fonts-lato (2.015-1) ... 333s Selecting previously unselected package libgomp1:amd64. 333s Preparing to unpack .../003-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 333s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 333s Selecting previously unselected package libfftw3-double3:amd64. 333s Preparing to unpack .../004-libfftw3-double3_3.3.10-1ubuntu4_amd64.deb ... 333s Unpacking libfftw3-double3:amd64 (3.3.10-1ubuntu4) ... 333s Selecting previously unselected package fonts-dejavu-mono. 333s Preparing to unpack .../005-fonts-dejavu-mono_2.37-8_all.deb ... 333s Unpacking fonts-dejavu-mono (2.37-8) ... 333s Selecting previously unselected package fonts-dejavu-core. 333s Preparing to unpack .../006-fonts-dejavu-core_2.37-8_all.deb ... 333s Unpacking fonts-dejavu-core (2.37-8) ... 333s Selecting previously unselected package libfontenc1:amd64. 333s Preparing to unpack .../007-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 333s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 333s Selecting previously unselected package x11-common. 333s Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu3_all.deb ... 333s Unpacking x11-common (1:7.7+23ubuntu3) ... 333s Selecting previously unselected package xfonts-encodings. 333s Preparing to unpack .../009-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 333s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 333s Selecting previously unselected package xfonts-utils. 333s Preparing to unpack .../010-xfonts-utils_1%3a7.7+7_amd64.deb ... 333s Unpacking xfonts-utils (1:7.7+7) ... 333s Selecting previously unselected package fonts-urw-base35. 333s Preparing to unpack .../011-fonts-urw-base35_20200910-8_all.deb ... 333s Unpacking fonts-urw-base35 (20200910-8) ... 333s Selecting previously unselected package fontconfig-config. 333s Preparing to unpack .../012-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 333s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 333s Selecting previously unselected package libfontconfig1:amd64. 333s Preparing to unpack .../013-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 333s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 333s Selecting previously unselected package libsharpyuv0:amd64. 333s Preparing to unpack .../014-libsharpyuv0_1.4.0-0.1_amd64.deb ... 333s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 333s Selecting previously unselected package libaom3:amd64. 333s Preparing to unpack .../015-libaom3_3.11.0~rc1-1_amd64.deb ... 333s Unpacking libaom3:amd64 (3.11.0~rc1-1) ... 334s Selecting previously unselected package libheif-plugin-aomdec:amd64. 334s Preparing to unpack .../016-libheif-plugin-aomdec_1.19.3-1_amd64.deb ... 334s Unpacking libheif-plugin-aomdec:amd64 (1.19.3-1) ... 334s Selecting previously unselected package libde265-0:amd64. 334s Preparing to unpack .../017-libde265-0_1.0.15-1build4_amd64.deb ... 334s Unpacking libde265-0:amd64 (1.0.15-1build4) ... 334s Selecting previously unselected package libheif-plugin-libde265:amd64. 334s Preparing to unpack .../018-libheif-plugin-libde265_1.19.3-1_amd64.deb ... 334s Unpacking libheif-plugin-libde265:amd64 (1.19.3-1) ... 334s Selecting previously unselected package libheif1:amd64. 334s Preparing to unpack .../019-libheif1_1.19.3-1_amd64.deb ... 334s Unpacking libheif1:amd64 (1.19.3-1) ... 334s Selecting previously unselected package libjbig0:amd64. 334s Preparing to unpack .../020-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 334s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 334s Selecting previously unselected package libjpeg-turbo8:amd64. 334s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 334s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 334s Selecting previously unselected package libjpeg8:amd64. 334s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_amd64.deb ... 334s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 334s Selecting previously unselected package liblcms2-2:amd64. 334s Preparing to unpack .../023-liblcms2-2_2.16-2_amd64.deb ... 334s Unpacking liblcms2-2:amd64 (2.16-2) ... 334s Selecting previously unselected package liblqr-1-0:amd64. 334s Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1build2_amd64.deb ... 334s Unpacking liblqr-1-0:amd64 (0.4.2-2.1build2) ... 334s Selecting previously unselected package libltdl7:amd64. 334s Preparing to unpack .../025-libltdl7_2.4.7-7build1_amd64.deb ... 334s Unpacking libltdl7:amd64 (2.4.7-7build1) ... 334s Selecting previously unselected package libopenjp2-7:amd64. 334s Preparing to unpack .../026-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 334s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 334s Selecting previously unselected package libraw23t64:amd64. 334s Preparing to unpack .../027-libraw23t64_0.21.3-1_amd64.deb ... 334s Unpacking libraw23t64:amd64 (0.21.3-1) ... 334s Selecting previously unselected package libdeflate0:amd64. 334s Preparing to unpack .../028-libdeflate0_1.22-1_amd64.deb ... 334s Unpacking libdeflate0:amd64 (1.22-1) ... 334s Selecting previously unselected package liblerc4:amd64. 334s Preparing to unpack .../029-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 334s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 334s Selecting previously unselected package libwebp7:amd64. 334s Preparing to unpack .../030-libwebp7_1.4.0-0.1_amd64.deb ... 334s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 334s Selecting previously unselected package libtiff6:amd64. 334s Preparing to unpack .../031-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 334s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 334s Selecting previously unselected package libwebpdemux2:amd64. 334s Preparing to unpack .../032-libwebpdemux2_1.4.0-0.1_amd64.deb ... 334s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 334s Selecting previously unselected package libwebpmux3:amd64. 334s Preparing to unpack .../033-libwebpmux3_1.4.0-0.1_amd64.deb ... 334s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 334s Selecting previously unselected package imagemagick-6-common. 334s Preparing to unpack .../034-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1build1_all.deb ... 334s Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 334s Selecting previously unselected package libmagickcore-6.q16-7t64:amd64. 334s Preparing to unpack .../035-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 334s Unpacking libmagickcore-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 334s Selecting previously unselected package libmagickwand-6.q16-7t64:amd64. 334s Preparing to unpack .../036-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 334s Unpacking libmagickwand-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 334s Selecting previously unselected package poppler-data. 334s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 334s Unpacking poppler-data (0.4.12-1) ... 334s Selecting previously unselected package sgml-base. 334s Preparing to unpack .../038-sgml-base_1.31_all.deb ... 334s Unpacking sgml-base (1.31) ... 334s Selecting previously unselected package autoconf. 334s Preparing to unpack .../039-autoconf_2.72-3_all.deb ... 334s Unpacking autoconf (2.72-3) ... 334s Selecting previously unselected package autotools-dev. 334s Preparing to unpack .../040-autotools-dev_20220109.1_all.deb ... 334s Unpacking autotools-dev (20220109.1) ... 334s Selecting previously unselected package automake. 334s Preparing to unpack .../041-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 334s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 334s Selecting previously unselected package autopoint. 334s Preparing to unpack .../042-autopoint_0.22.5-2_all.deb ... 334s Unpacking autopoint (0.22.5-2) ... 334s Selecting previously unselected package libtcl8.6:amd64. 334s Preparing to unpack .../043-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 334s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 334s Selecting previously unselected package libxrender1:amd64. 334s Preparing to unpack .../044-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 334s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 335s Selecting previously unselected package libxft2:amd64. 335s Preparing to unpack .../045-libxft2_2.3.6-1build1_amd64.deb ... 335s Unpacking libxft2:amd64 (2.3.6-1build1) ... 335s Selecting previously unselected package libxss1:amd64. 335s Preparing to unpack .../046-libxss1_1%3a1.2.3-1build3_amd64.deb ... 335s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 335s Selecting previously unselected package libtk8.6:amd64. 335s Preparing to unpack .../047-libtk8.6_8.6.15-1_amd64.deb ... 335s Unpacking libtk8.6:amd64 (8.6.15-1) ... 335s Selecting previously unselected package tk8.6-blt2.5. 335s Preparing to unpack .../048-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 335s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 335s Selecting previously unselected package blt. 335s Preparing to unpack .../049-blt_2.5.3+dfsg-7build1_amd64.deb ... 335s Unpacking blt (2.5.3+dfsg-7build1) ... 335s Selecting previously unselected package libisl23:amd64. 335s Preparing to unpack .../050-libisl23_0.27-1_amd64.deb ... 335s Unpacking libisl23:amd64 (0.27-1) ... 335s Selecting previously unselected package libmpc3:amd64. 335s Preparing to unpack .../051-libmpc3_1.3.1-1build2_amd64.deb ... 335s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 335s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 335s Preparing to unpack .../052-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package cpp-14. 335s Preparing to unpack .../053-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package cpp-x86-64-linux-gnu. 335s Preparing to unpack .../054-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 335s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 335s Selecting previously unselected package cpp. 335s Preparing to unpack .../055-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 335s Unpacking cpp (4:14.1.0-2ubuntu1) ... 335s Selecting previously unselected package libcc1-0:amd64. 335s Preparing to unpack .../056-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package libitm1:amd64. 335s Preparing to unpack .../057-libitm1_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package libasan8:amd64. 335s Preparing to unpack .../058-libasan8_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package liblsan0:amd64. 335s Preparing to unpack .../059-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package libtsan2:amd64. 335s Preparing to unpack .../060-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package libubsan1:amd64. 335s Preparing to unpack .../061-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package libhwasan0:amd64. 335s Preparing to unpack .../062-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package libquadmath0:amd64. 335s Preparing to unpack .../063-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package libgcc-14-dev:amd64. 335s Preparing to unpack .../064-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 335s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 335s Preparing to unpack .../065-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 335s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 336s Selecting previously unselected package gcc-14. 336s Preparing to unpack .../066-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 336s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 336s Selecting previously unselected package gcc-x86-64-linux-gnu. 336s Preparing to unpack .../067-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 336s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 336s Selecting previously unselected package gcc. 336s Preparing to unpack .../068-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 336s Unpacking gcc (4:14.1.0-2ubuntu1) ... 336s Selecting previously unselected package libstdc++-14-dev:amd64. 336s Preparing to unpack .../069-libstdc++-14-dev_14.2.0-8ubuntu1_amd64.deb ... 336s Unpacking libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 336s Selecting previously unselected package g++-14-x86-64-linux-gnu. 336s Preparing to unpack .../070-g++-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 336s Unpacking g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 336s Selecting previously unselected package g++-14. 336s Preparing to unpack .../071-g++-14_14.2.0-8ubuntu1_amd64.deb ... 336s Unpacking g++-14 (14.2.0-8ubuntu1) ... 336s Selecting previously unselected package g++-x86-64-linux-gnu. 336s Preparing to unpack .../072-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 336s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 336s Selecting previously unselected package g++. 336s Preparing to unpack .../073-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 336s Unpacking g++ (4:14.1.0-2ubuntu1) ... 336s Selecting previously unselected package build-essential. 336s Preparing to unpack .../074-build-essential_12.10ubuntu1_amd64.deb ... 336s Unpacking build-essential (12.10ubuntu1) ... 336s Selecting previously unselected package bwa. 336s Preparing to unpack .../075-bwa_0.7.18-1_amd64.deb ... 336s Unpacking bwa (0.7.18-1) ... 336s Selecting previously unselected package libargtable2-0. 336s Preparing to unpack .../076-libargtable2-0_13-2_amd64.deb ... 336s Unpacking libargtable2-0 (13-2) ... 336s Selecting previously unselected package clustalo. 336s Preparing to unpack .../077-clustalo_1.2.4-8build1_amd64.deb ... 336s Unpacking clustalo (1.2.4-8build1) ... 336s Selecting previously unselected package clustalw. 336s Preparing to unpack .../078-clustalw_2.1+lgpl-7_amd64.deb ... 336s Unpacking clustalw (2.1+lgpl-7) ... 336s Selecting previously unselected package libdebhelper-perl. 336s Preparing to unpack .../079-libdebhelper-perl_13.20ubuntu1_all.deb ... 336s Unpacking libdebhelper-perl (13.20ubuntu1) ... 336s Selecting previously unselected package libtool. 336s Preparing to unpack .../080-libtool_2.4.7-7build1_all.deb ... 336s Unpacking libtool (2.4.7-7build1) ... 336s Selecting previously unselected package dh-autoreconf. 336s Preparing to unpack .../081-dh-autoreconf_20_all.deb ... 336s Unpacking dh-autoreconf (20) ... 336s Selecting previously unselected package libarchive-zip-perl. 336s Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... 336s Unpacking libarchive-zip-perl (1.68-1) ... 337s Selecting previously unselected package libfile-stripnondeterminism-perl. 337s Preparing to unpack .../083-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 337s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 337s Selecting previously unselected package dh-strip-nondeterminism. 337s Preparing to unpack .../084-dh-strip-nondeterminism_1.14.0-1_all.deb ... 337s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 337s Selecting previously unselected package debugedit. 337s Preparing to unpack .../085-debugedit_1%3a5.1-1_amd64.deb ... 337s Unpacking debugedit (1:5.1-1) ... 337s Selecting previously unselected package dwz. 337s Preparing to unpack .../086-dwz_0.15-1build6_amd64.deb ... 337s Unpacking dwz (0.15-1build6) ... 337s Selecting previously unselected package gettext. 337s Preparing to unpack .../087-gettext_0.22.5-2_amd64.deb ... 337s Unpacking gettext (0.22.5-2) ... 337s Selecting previously unselected package intltool-debian. 337s Preparing to unpack .../088-intltool-debian_0.35.0+20060710.6_all.deb ... 337s Unpacking intltool-debian (0.35.0+20060710.6) ... 337s Selecting previously unselected package po-debconf. 337s Preparing to unpack .../089-po-debconf_1.0.21+nmu1_all.deb ... 337s Unpacking po-debconf (1.0.21+nmu1) ... 337s Selecting previously unselected package debhelper. 337s Preparing to unpack .../090-debhelper_13.20ubuntu1_all.deb ... 337s Unpacking debhelper (13.20ubuntu1) ... 337s Selecting previously unselected package dh-python. 337s Preparing to unpack .../091-dh-python_6.20241024_all.deb ... 337s Unpacking dh-python (6.20241024) ... 337s Selecting previously unselected package dialign. 337s Preparing to unpack .../092-dialign_2.2.1-13_amd64.deb ... 337s Unpacking dialign (2.2.1-13) ... 337s Selecting previously unselected package xml-core. 337s Preparing to unpack .../093-xml-core_0.19_all.deb ... 337s Unpacking xml-core (0.19) ... 337s Selecting previously unselected package docutils-common. 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(1.3.14-2ubuntu1) ... 337s Selecting previously unselected package libharfbuzz0b:amd64. 337s Preparing to unpack .../100-libharfbuzz0b_10.0.1-1_amd64.deb ... 337s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 337s Selecting previously unselected package libraqm0:amd64. 337s Preparing to unpack .../101-libraqm0_0.10.1-1build1_amd64.deb ... 337s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 337s Selecting previously unselected package libxpm4:amd64. 337s Preparing to unpack .../102-libxpm4_1%3a3.5.17-1build2_amd64.deb ... 337s Unpacking libxpm4:amd64 (1:3.5.17-1build2) ... 337s Selecting previously unselected package libgd3:amd64. 337s Preparing to unpack .../103-libgd3_2.3.3-12ubuntu3_amd64.deb ... 337s Unpacking libgd3:amd64 (2.3.3-12ubuntu3) ... 337s Selecting previously unselected package libhpdf-2.3.0:amd64. 337s Preparing to unpack .../104-libhpdf-2.3.0_2.3.0+dfsg-1build3_amd64.deb ... 337s Unpacking libhpdf-2.3.0:amd64 (2.3.0+dfsg-1build3) ... 337s Selecting previously unselected package mysql-common. 337s Preparing to unpack .../105-mysql-common_5.8+1.1.1_all.deb ... 337s Unpacking mysql-common (5.8+1.1.1) ... 337s Selecting previously unselected package libmysqlclient21:amd64. 337s Preparing to unpack .../106-libmysqlclient21_8.0.40-1_amd64.deb ... 337s Unpacking libmysqlclient21:amd64 (8.0.40-1) ... 337s Selecting previously unselected package libpq5:amd64. 337s Preparing to unpack .../107-libpq5_17.0-1_amd64.deb ... 337s Unpacking libpq5:amd64 (17.0-1) ... 337s Selecting previously unselected package emboss-lib. 337s Preparing to unpack .../108-emboss-lib_6.6.0+dfsg-12ubuntu2_amd64.deb ... 337s Unpacking emboss-lib (6.6.0+dfsg-12ubuntu2) ... 338s Selecting previously unselected package emboss-data. 338s Preparing to unpack .../109-emboss-data_6.6.0+dfsg-12ubuntu2_all.deb ... 338s Unpacking emboss-data (6.6.0+dfsg-12ubuntu2) ... 340s Selecting previously unselected package emboss. 340s Preparing to unpack .../110-emboss_6.6.0+dfsg-12ubuntu2_amd64.deb ... 340s Unpacking emboss (6.6.0+dfsg-12ubuntu2) ... 340s Selecting previously unselected package fonts-font-awesome. 340s Preparing to unpack .../111-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 340s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 340s Selecting previously unselected package fonts-lmodern. 340s Preparing to unpack .../112-fonts-lmodern_2.005-1_all.deb ... 340s Unpacking fonts-lmodern (2.005-1) ... 340s Selecting previously unselected package fonts-lyx. 340s Preparing to unpack .../113-fonts-lyx_2.4.2.1-1_all.deb ... 340s Unpacking fonts-lyx (2.4.2.1-1) ... 340s Selecting previously unselected package libgs-common. 340s Preparing to unpack .../114-libgs-common_10.03.1~dfsg1-0ubuntu3_all.deb ... 340s Unpacking libgs-common (10.03.1~dfsg1-0ubuntu3) ... 340s Selecting previously unselected package libgs10-common. 340s Preparing to unpack .../115-libgs10-common_10.03.1~dfsg1-0ubuntu3_all.deb ... 340s Unpacking libgs10-common (10.03.1~dfsg1-0ubuntu3) ... 340s Selecting previously unselected package libavahi-common-data:amd64. 340s Preparing to unpack .../116-libavahi-common-data_0.8-13ubuntu6_amd64.deb ... 340s Unpacking libavahi-common-data:amd64 (0.8-13ubuntu6) ... 340s Selecting previously unselected package libavahi-common3:amd64. 340s Preparing to unpack .../117-libavahi-common3_0.8-13ubuntu6_amd64.deb ... 340s Unpacking libavahi-common3:amd64 (0.8-13ubuntu6) ... 340s Selecting previously unselected package libavahi-client3:amd64. 340s Preparing to unpack .../118-libavahi-client3_0.8-13ubuntu6_amd64.deb ... 340s Unpacking libavahi-client3:amd64 (0.8-13ubuntu6) ... 340s Selecting previously unselected package libcups2t64:amd64. 340s Preparing to unpack .../119-libcups2t64_2.4.10-1ubuntu2_amd64.deb ... 340s Unpacking libcups2t64:amd64 (2.4.10-1ubuntu2) ... 340s Selecting previously unselected package libidn12:amd64. 340s Preparing to unpack .../120-libidn12_1.42-2_amd64.deb ... 340s Unpacking libidn12:amd64 (1.42-2) ... 340s Selecting previously unselected package libijs-0.35:amd64. 340s Preparing to unpack .../121-libijs-0.35_0.35-15.1build1_amd64.deb ... 340s Unpacking libijs-0.35:amd64 (0.35-15.1build1) ... 340s Selecting previously unselected package libjbig2dec0:amd64. 340s Preparing to unpack .../122-libjbig2dec0_0.20-1build3_amd64.deb ... 340s Unpacking libjbig2dec0:amd64 (0.20-1build3) ... 340s Selecting previously unselected package libpaper1:amd64. 340s Preparing to unpack .../123-libpaper1_1.1.29build1_amd64.deb ... 340s Unpacking libpaper1:amd64 (1.1.29build1) ... 340s Selecting previously unselected package libice6:amd64. 340s Preparing to unpack .../124-libice6_2%3a1.1.1-1_amd64.deb ... 340s Unpacking libice6:amd64 (2:1.1.1-1) ... 340s Selecting previously unselected package libsm6:amd64. 340s Preparing to unpack .../125-libsm6_2%3a1.2.4-1_amd64.deb ... 340s Unpacking libsm6:amd64 (2:1.2.4-1) ... 340s Selecting previously unselected package libxt6t64:amd64. 340s Preparing to unpack .../126-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 340s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 341s Selecting previously unselected package libgs10:amd64. 341s Preparing to unpack .../127-libgs10_10.03.1~dfsg1-0ubuntu3_amd64.deb ... 341s Unpacking libgs10:amd64 (10.03.1~dfsg1-0ubuntu3) ... 341s Selecting previously unselected package ghostscript. 341s Preparing to unpack .../128-ghostscript_10.03.1~dfsg1-0ubuntu3_amd64.deb ... 341s Unpacking ghostscript (10.03.1~dfsg1-0ubuntu3) ... 341s Selecting previously unselected package libnetpbm11t64:amd64. 341s Preparing to unpack .../129-libnetpbm11t64_2%3a11.08.01-1_amd64.deb ... 341s Unpacking libnetpbm11t64:amd64 (2:11.08.01-1) ... 341s Selecting previously unselected package netpbm. 341s Preparing to unpack .../130-netpbm_2%3a11.08.01-1_amd64.deb ... 341s Unpacking netpbm (2:11.08.01-1) ... 341s Selecting previously unselected package tex-common. 341s Preparing to unpack .../131-tex-common_6.18_all.deb 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.../136-libtexlua53-5_2024.20240313.70630+ds-5_amd64.deb ... 341s Unpacking libtexlua53-5:amd64 (2024.20240313.70630+ds-5) ... 341s Selecting previously unselected package t1utils. 341s Preparing to unpack .../137-t1utils_1.41-4build3_amd64.deb ... 341s Unpacking t1utils (1.41-4build3) ... 341s Selecting previously unselected package libpixman-1-0:amd64. 341s Preparing to unpack .../138-libpixman-1-0_0.44.0-3_amd64.deb ... 341s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 341s Selecting previously unselected package libxcb-render0:amd64. 341s Preparing to unpack .../139-libxcb-render0_1.17.0-2_amd64.deb ... 341s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 341s Selecting previously unselected package libxcb-shm0:amd64. 341s Preparing to unpack .../140-libxcb-shm0_1.17.0-2_amd64.deb ... 341s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 341s Selecting previously unselected package libcairo2:amd64. 341s Preparing to unpack .../141-libcairo2_1.18.2-2_amd64.deb ... 341s Unpacking libcairo2:amd64 (1.18.2-2) ... 341s Selecting previously unselected package libmpfi0:amd64. 341s Preparing to unpack .../142-libmpfi0_1.5.4+ds-4_amd64.deb ... 341s Unpacking libmpfi0:amd64 (1.5.4+ds-4) ... 341s Selecting previously unselected package libpotrace0:amd64. 341s Preparing to unpack .../143-libpotrace0_1.16-2build1_amd64.deb ... 341s Unpacking libpotrace0:amd64 (1.16-2build1) ... 341s Selecting previously unselected package libteckit0:amd64. 341s Preparing to unpack .../144-libteckit0_2.5.12+ds1-1_amd64.deb ... 341s Unpacking libteckit0:amd64 (2.5.12+ds1-1) ... 341s Selecting previously unselected package libxmu6:amd64. 341s Preparing to unpack .../145-libxmu6_2%3a1.1.3-3build2_amd64.deb ... 341s Unpacking libxmu6:amd64 (2:1.1.3-3build2) ... 341s Selecting previously unselected package libxaw7:amd64. 341s Preparing to unpack .../146-libxaw7_2%3a1.0.16-1_amd64.deb ... 341s Unpacking libxaw7:amd64 (2:1.0.16-1) ... 341s Selecting previously unselected package libxi6:amd64. 341s Preparing to unpack .../147-libxi6_2%3a1.8.2-1_amd64.deb ... 341s Unpacking libxi6:amd64 (2:1.8.2-1) ... 341s Selecting previously unselected package libzzip-0-13t64:amd64. 341s Preparing to unpack .../148-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_amd64.deb ... 341s Unpacking libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2build1) ... 341s Selecting previously unselected package texlive-binaries. 341s Preparing to unpack .../149-texlive-binaries_2024.20240313.70630+ds-5_amd64.deb ... 341s Unpacking texlive-binaries (2024.20240313.70630+ds-5) ... 341s Selecting previously unselected package xdg-utils. 341s Preparing to unpack .../150-xdg-utils_1.2.1-0ubuntu1_all.deb ... 341s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 341s Selecting previously unselected package texlive-base. 341s Preparing to unpack .../151-texlive-base_2024.20241102-1_all.deb ... 341s Unpacking texlive-base (2024.20241102-1) ... 342s Selecting previously unselected package hicolor-icon-theme. 342s Preparing to unpack .../152-hicolor-icon-theme_0.18-1_all.deb ... 342s Unpacking hicolor-icon-theme (0.18-1) ... 342s Selecting previously unselected package imagemagick-6.q16. 342s Preparing to unpack .../153-imagemagick-6.q16_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 342s Unpacking imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 342s Selecting previously unselected package imagemagick. 342s Preparing to unpack .../154-imagemagick_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 342s Unpacking imagemagick (8:6.9.13.12+dfsg1-1build1) ... 342s Selecting previously unselected package hevea. 342s Preparing to unpack .../155-hevea_2.36-2_amd64.deb ... 342s Unpacking hevea (2.36-2) ... 342s Selecting previously unselected package libllvm17t64:amd64. 342s Preparing to unpack .../156-libllvm17t64_1%3a17.0.6-18_amd64.deb ... 342s Unpacking libllvm17t64:amd64 (1:17.0.6-18) ... 343s Selecting previously unselected package libamd-comgr2:amd64. 343s Preparing to unpack .../157-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 343s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 343s Selecting previously unselected package libdrm-amdgpu1:amd64. 343s Preparing to unpack .../158-libdrm-amdgpu1_2.4.123-1_amd64.deb ... 343s Unpacking libdrm-amdgpu1:amd64 (2.4.123-1) ... 343s Selecting previously unselected package libhsakmt1:amd64. 343s Preparing to unpack .../159-libhsakmt1_5.7.0-1build1_amd64.deb ... 343s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 343s Selecting previously unselected package libhsa-runtime64-1. 343s Preparing to unpack .../160-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 343s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 343s Selecting previously unselected package libamdhip64-5. 343s Preparing to unpack .../161-libamdhip64-5_5.7.1-5_amd64.deb ... 343s Unpacking libamdhip64-5 (5.7.1-5) ... 343s Selecting previously unselected package libapache-pom-java. 343s Preparing to unpack .../162-libapache-pom-java_33-2_all.deb ... 343s Unpacking libapache-pom-java (33-2) ... 343s Selecting previously unselected package libblas3:amd64. 343s Preparing to unpack .../163-libblas3_3.12.0-3build2_amd64.deb ... 343s Unpacking libblas3:amd64 (3.12.0-3build2) ... 343s Selecting previously unselected package libcommons-parent-java. 343s Preparing to unpack .../164-libcommons-parent-java_56-1_all.deb ... 343s Unpacking libcommons-parent-java (56-1) ... 343s Selecting previously unselected package libcommons-logging-java. 343s Preparing to unpack .../165-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 343s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 344s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 344s Preparing to unpack .../166-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 344s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 344s Selecting previously unselected package libexpat1-dev:amd64. 344s Preparing to unpack .../167-libexpat1-dev_2.6.4-1_amd64.deb ... 344s Unpacking libexpat1-dev:amd64 (2.6.4-1) ... 344s Selecting previously unselected package libpsm-infinipath1. 344s Preparing to unpack .../168-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 344s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 344s Selecting previously unselected package libpsm2-2. 344s Preparing to unpack .../169-libpsm2-2_11.2.185-2.1_amd64.deb ... 344s Unpacking libpsm2-2 (11.2.185-2.1) ... 344s Selecting previously unselected package librdmacm1t64:amd64. 344s Preparing to unpack .../170-librdmacm1t64_52.0-2ubuntu1_amd64.deb ... 344s Unpacking librdmacm1t64:amd64 (52.0-2ubuntu1) ... 344s Selecting previously unselected package libfabric1:amd64. 344s Preparing to unpack .../171-libfabric1_1.17.0-3ubuntu1_amd64.deb ... 344s Unpacking libfabric1:amd64 (1.17.0-3ubuntu1) ... 344s Selecting previously unselected package libgfortran5:amd64. 344s Preparing to unpack .../172-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 344s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 344s Selecting previously unselected package libhtscodecs2:amd64. 344s Preparing to unpack .../173-libhtscodecs2_1.6.1-1_amd64.deb ... 344s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 344s Selecting previously unselected package libhts3t64:amd64. 344s Preparing to unpack .../174-libhts3t64_1.20+ds-1_amd64.deb ... 344s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 344s Selecting previously unselected package libhwloc15:amd64. 344s Preparing to unpack .../175-libhwloc15_2.11.2-1_amd64.deb ... 344s Unpacking libhwloc15:amd64 (2.11.2-1) ... 344s Selecting previously unselected package libjs-jquery. 344s Preparing to unpack .../176-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 344s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 344s Selecting previously unselected package libjs-jquery-ui. 344s Preparing to unpack .../177-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 344s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 344s Selecting previously unselected package libjs-underscore. 344s Preparing to unpack .../178-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 344s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 344s Selecting previously unselected package libjs-sphinxdoc. 344s Preparing to unpack .../179-libjs-sphinxdoc_7.4.7-4_all.deb ... 344s Unpacking libjs-sphinxdoc (7.4.7-4) ... 344s Selecting previously unselected package libjson-perl. 344s Preparing to unpack .../180-libjson-perl_4.10000-1_all.deb ... 344s Unpacking libjson-perl (4.10000-1) ... 344s Selecting previously unselected package liblapack3:amd64. 344s Preparing to unpack .../181-liblapack3_3.12.0-3build2_amd64.deb ... 344s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 344s Selecting previously unselected package liblbfgsb0:amd64. 344s Preparing to unpack .../182-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 344s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 344s Selecting previously unselected package libmbedcrypto7t64:amd64. 344s Preparing to unpack .../183-libmbedcrypto7t64_2.28.8-1_amd64.deb ... 344s Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ... 344s Selecting previously unselected package libmbedx509-1t64:amd64. 344s Preparing to unpack .../184-libmbedx509-1t64_2.28.8-1_amd64.deb ... 344s Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ... 344s Selecting previously unselected package libmbedtls14t64:amd64. 344s Preparing to unpack .../185-libmbedtls14t64_2.28.8-1_amd64.deb ... 344s Unpacking libmbedtls14t64:amd64 (2.28.8-1) ... 344s Selecting previously unselected package libmunge2:amd64. 344s Preparing to unpack .../186-libmunge2_0.5.15-4build1_amd64.deb ... 344s Unpacking libmunge2:amd64 (0.5.15-4build1) ... 344s Selecting previously unselected package libpciaccess0:amd64. 344s Preparing to unpack .../187-libpciaccess0_0.17-3build1_amd64.deb ... 344s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 344s Selecting previously unselected package libxnvctrl0:amd64. 344s Preparing to unpack .../188-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 344s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 344s Selecting previously unselected package ocl-icd-libopencl1:amd64. 344s Preparing to unpack .../189-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 344s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 344s Selecting previously unselected package libhwloc-plugins:amd64. 344s Preparing to unpack .../190-libhwloc-plugins_2.11.2-1_amd64.deb ... 344s Unpacking libhwloc-plugins:amd64 (2.11.2-1) ... 344s Selecting previously unselected package libpmix2t64:amd64. 344s Preparing to unpack .../191-libpmix2t64_5.0.3-2_amd64.deb ... 344s Unpacking libpmix2t64:amd64 (5.0.3-2) ... 344s Selecting previously unselected package libibumad3:amd64. 344s Preparing to unpack .../192-libibumad3_52.0-2ubuntu1_amd64.deb ... 344s Unpacking libibumad3:amd64 (52.0-2ubuntu1) ... 344s Selecting previously unselected package libibmad5:amd64. 344s Preparing to unpack .../193-libibmad5_52.0-2ubuntu1_amd64.deb ... 344s Unpacking libibmad5:amd64 (52.0-2ubuntu1) ... 344s Selecting previously unselected package libucx0:amd64. 344s Preparing to unpack .../194-libucx0_1.17.0+ds-3build1_amd64.deb ... 344s Unpacking libucx0:amd64 (1.17.0+ds-3build1) ... 344s Selecting previously unselected package libopenmpi3t64:amd64. 345s Preparing to unpack .../195-libopenmpi3t64_4.1.6-13.3ubuntu2_amd64.deb ... 345s Unpacking libopenmpi3t64:amd64 (4.1.6-13.3ubuntu2) ... 345s Selecting previously unselected package zlib1g-dev:amd64. 345s Preparing to unpack .../196-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 345s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 345s Selecting previously unselected package libpython3.12-dev:amd64. 345s Preparing to unpack .../197-libpython3.12-dev_3.12.7-3_amd64.deb ... 345s Unpacking libpython3.12-dev:amd64 (3.12.7-3) ... 345s Selecting previously unselected package libpython3-dev:amd64. 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345s Selecting previously unselected package phyml. 345s Preparing to unpack .../209-phyml_3%3a3.3.20220408-3build3_amd64.deb ... 345s Unpacking phyml (3:3.3.20220408-3build3) ... 346s Selecting previously unselected package prank. 346s Preparing to unpack .../210-prank_0.0.170427+dfsg-3_amd64.deb ... 346s Unpacking prank (0.0.170427+dfsg-3) ... 346s Selecting previously unselected package preview-latex-style. 346s Preparing to unpack .../211-preview-latex-style_13.2-1_all.deb ... 346s Unpacking preview-latex-style (13.2-1) ... 346s Selecting previously unselected package probcons. 346s Preparing to unpack .../212-probcons_1.12-14_amd64.deb ... 346s Unpacking probcons (1.12-14) ... 346s Selecting previously unselected package python-biopython-doc. 346s Preparing to unpack .../213-python-biopython-doc_1.84+dfsg-4build1_all.deb ... 346s Unpacking python-biopython-doc (1.84+dfsg-4build1) ... 346s Selecting previously unselected package python-matplotlib-data. 346s Preparing to unpack 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Selecting previously unselected package python3-cairo. 346s Preparing to unpack .../225-python3-cairo_1.26.1-2_amd64.deb ... 346s Unpacking python3-cairo (1.26.1-2) ... 347s Selecting previously unselected package python3-freetype. 347s Preparing to unpack .../226-python3-freetype_2.5.1-1_all.deb ... 347s Unpacking python3-freetype (2.5.1-1) ... 347s Selecting previously unselected package python3-rlpycairo. 347s Preparing to unpack .../227-python3-rlpycairo_0.3.0-3_all.deb ... 347s Unpacking python3-rlpycairo (0.3.0-3) ... 347s Selecting previously unselected package python3-reportlab. 347s Preparing to unpack .../228-python3-reportlab_4.2.5-1_all.deb ... 347s Unpacking python3-reportlab (4.2.5-1) ... 347s Selecting previously unselected package w3c-sgml-lib. 347s Preparing to unpack .../229-w3c-sgml-lib_1.3-3_all.deb ... 347s Unpacking w3c-sgml-lib (1.3-3) ... 347s Selecting previously unselected package python3-biopython. 347s Preparing to unpack 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347s Unpacking python3-six (1.16.0-7) ... 347s Selecting previously unselected package python3-dateutil. 347s Preparing to unpack .../236-python3-dateutil_2.9.0-2_all.deb ... 347s Unpacking python3-dateutil (2.9.0-2) ... 347s Selecting previously unselected package python3-decorator. 347s Preparing to unpack .../237-python3-decorator_5.1.1-5_all.deb ... 347s Unpacking python3-decorator (5.1.1-5) ... 347s Selecting previously unselected package python3-defusedxml. 347s Preparing to unpack .../238-python3-defusedxml_0.7.1-2_all.deb ... 347s Unpacking python3-defusedxml (0.7.1-2) ... 347s Selecting previously unselected package python3-roman. 347s Preparing to unpack .../239-python3-roman_4.2-1_all.deb ... 347s Unpacking python3-roman (4.2-1) ... 347s Selecting previously unselected package python3-docutils. 347s Preparing to unpack .../240-python3-docutils_0.21.2+dfsg-2_all.deb ... 347s Unpacking python3-docutils (0.21.2+dfsg-2) ... 347s Selecting previously unselected package python3-scipy. 347s Preparing to unpack .../241-python3-scipy_1.13.1-5_amd64.deb ... 347s Unpacking python3-scipy (1.13.1-5) ... 348s Selecting previously unselected package python3-ufolib2. 348s Preparing to unpack .../242-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 348s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 348s Selecting previously unselected package python3-mpmath. 348s Preparing to unpack .../243-python3-mpmath_1.3.0-1_all.deb ... 348s Unpacking python3-mpmath (1.3.0-1) ... 348s Selecting previously unselected package python3-sympy. 348s Preparing to unpack .../244-python3-sympy_1.13.3-1_all.deb ... 348s Unpacking python3-sympy (1.13.3-1) ... 348s Selecting previously unselected package python3-tz. 348s Preparing to unpack .../245-python3-tz_2024.1-2_all.deb ... 348s Unpacking python3-tz (2024.1-2) ... 348s Selecting previously unselected package python3-fs. 348s Preparing to unpack .../246-python3-fs_2.4.16-4_all.deb ... 348s Unpacking python3-fs (2.4.16-4) ... 348s 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... 354s Setting up libpq5:amd64 (17.0-1) ... 354s Setting up libibumad3:amd64 (52.0-2ubuntu1) ... 354s Setting up libdeflate0:amd64 (1.22-1) ... 354s Setting up python3-tabulate (0.9.0-1) ... 355s Setting up m4 (1.4.19-4build1) ... 355s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 355s Setting up python3-all (3.12.6-0ubuntu1) ... 355s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 355s Setting up libibmad5:amd64 (52.0-2ubuntu1) ... 355s Setting up libpaper-utils (1.1.29build1) ... 355s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 355s Setting up python3-freetype (2.5.1-1) ... 355s Setting up emboss-data (6.6.0+dfsg-12ubuntu2) ... 355s Setting up python3-networkx (3.2.1-4ubuntu1) ... 356s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 356s Setting up libnetpbm11t64:amd64 (2:11.08.01-1) ... 356s Setting up python3-tz (2024.1-2) ... 356s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 356s Setting up poppler-data (0.4.12-1) ... 356s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 356s Setting up unicode-data (15.1.0-1) ... 356s Setting up python3-mysqldb (1.4.6-2build4) ... 356s Setting up python3-six (1.16.0-7) ... 356s Setting up tex-common (6.18) ... 356s update-language: texlive-base not installed and configured, doing nothing! 356s Setting up python3-roman (4.2-1) ... 356s Setting up python3-decorator (5.1.1-5) ... 356s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 356s Setting up autotools-dev (20220109.1) ... 356s Setting up libblas3:amd64 (3.12.0-3build2) ... 356s 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 356s Setting up python3-packaging (24.1-1) ... 356s Setting up libmunge2:amd64 (0.5.15-4build1) ... 356s Setting up libllvm17t64:amd64 (1:17.0.6-18) ... 356s Setting up libexpat1-dev:amd64 (2.6.4-1) ... 356s Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2build1) ... 356s Setting up libjbig2dec0:amd64 (0.20-1build3) ... 356s Setting up python3-snowballstemmer (2.2.0-4build1) ... 357s Setting up libteckit0:amd64 (2.5.12+ds1-1) ... 357s Setting up python3-brotli (1.1.0-2build2) ... 357s Setting up libapache-pom-java (33-2) ... 357s Setting up libavahi-common-data:amd64 (0.8-13ubuntu6) ... 357s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 357s Setting up muscle3 (3.8.1551-3) ... 357s Setting up t1utils (1.41-4build3) ... 357s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ... 357s Setting up python3-cycler (0.12.1-1) ... 357s Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-5) ... 357s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 357s Setting up fonts-dejavu-mono (2.37-8) ... 357s Setting up python3-kiwisolver (1.4.7-2build1) ... 357s Setting up libhwloc15:amd64 (2.11.2-1) ... 357s Setting up libmpc3:amd64 (1.3.1-1build2) ... 357s Setting up libidn12:amd64 (1.42-2) ... 357s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 357s Setting up autopoint (0.22.5-2) ... 357s Setting up libmpfi0:amd64 (1.5.4+ds-4) ... 357s Setting up python3-psycopg2 (2.9.9-2build1) ... 357s Setting up fonts-dejavu-core (2.37-8) ... 357s Setting up wise-data (2.4.1-25) ... 357s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 357s Setting up libltdl7:amd64 (2.4.7-7build1) ... 357s Setting up libfftw3-double3:amd64 (3.3.10-1ubuntu4) ... 357s Setting up libcifpp-data (7.0.7-3) ... 357s Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-5) ... 357s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 357s Setting up autoconf (2.72-3) ... 357s Setting up libwebp7:amd64 (1.4.0-0.1) ... 357s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 357s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 357s Setting up dwz (0.15-1build6) ... 357s Setting up liblqr-1-0:amd64 (0.4.2-2.1build2) ... 357s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 357s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 357s Setting up python3-rdflib (7.1.1-2) ... 357s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 357s Setting up libjson-perl (4.10000-1) ... 357s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 357s Setting up libpsm2-2 (11.2.185-2.1) ... 357s Setting up openmpi-common (4.1.6-13.3ubuntu2) ... 357s Setting up clustalw (2.1+lgpl-7) ... 358s Setting up debugedit (1:5.1-1) ... 358s Setting up libhts3t64:amd64 (1.20+ds-1) ... 358s Setting up fonts-lmodern (2.005-1) ... 358s Setting up librdmacm1t64:amd64 (52.0-2ubuntu1) ... 358s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 358s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 358s Setting up python3-dateutil (2.9.0-2) ... 358s Setting up fasttree (2.1.11-2) ... 358s Setting up sgml-base (1.31) ... 358s Setting up python3-msgpack (1.0.3-3build2) ... 358s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 358s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 358s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 358s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 358s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 358s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 358s Setting up python3-mpmath (1.3.0-1) ... 358s Setting up libisl23:amd64 (0.27-1) ... 358s Setting up libde265-0:amd64 (1.0.15-1build4) ... 358s Setting up python-matplotlib-data (3.8.3-3) ... 358s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 358s Setting up python3-appdirs (1.4.4-4) ... 358s Setting up dialign (2.2.1-13) ... 358s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 358s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 358s Setting up xdg-utils (1.2.1-0ubuntu1) ... 358s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 358s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 358s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 358s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 358s Setting up libsynctex2:amd64 (2024.20240313.70630+ds-5) ... 358s Setting up prank (0.0.170427+dfsg-3) ... 358s Setting up libargtable2-0 (13-2) ... 358s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 358s Setting up raxml (8.2.13+dfsg-1) ... 358s Setting up python3-imagesize (1.4.1-1) ... 358s Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... 358s Setting up libpotrace0:amd64 (1.16-2build1) ... 358s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 358s Setting up automake (1:1.16.5-1.3ubuntu1) ... 358s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 358s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 358s Setting up libfabric1:amd64 (1.17.0-3ubuntu1) ... 358s Setting up python3-sympy (1.13.3-1) ... 363s Setting up libice6:amd64 (2:1.1.1-1) ... 363s Setting up flex (2.6.4-8.2build1) ... 363s Setting up liblapack3:amd64 (3.12.0-3build2) ... 363s 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 363s Setting up gettext (0.22.5-2) ... 363s Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... 363s Setting up libpdfbox-java (1:1.8.16-5) ... 363s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 363s Setting up wise (2.4.1-25) ... 363s Setting up preview-latex-style (13.2-1) ... 363s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 363s Setting up libcommons-parent-java (56-1) ... 363s Setting up libavahi-common3:amd64 (0.8-13ubuntu6) ... 363s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 363s Setting up libcifpp7:amd64 (7.0.7-3) ... 363s Setting up libpython3.12-dev:amd64 (3.12.7-3) ... 363s Setting up clustalo (1.2.4-8build1) ... 363s Setting up dssp (4.4.10-1) ... 363s Setting up xfonts-utils (1:7.7+7) ... 363s Setting up libhwloc-plugins:amd64 (2.11.2-1) ... 363s Setting up samtools (1.20-3) ... 363s Setting up intltool-debian (0.35.0+20060710.6) ... 363s Setting up python3-fs (2.4.16-4) ... 363s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 363s Setting up libptexenc1:amd64 (2024.20240313.70630+ds-5) ... 363s Setting up libraqm0:amd64 (0.10.1-1build1) ... 363s Setting up python3.12-dev (3.12.7-3) ... 363s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 363s Setting up libpmix2t64:amd64 (5.0.3-2) ... 363s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 365s Setting up libjs-sphinxdoc (7.4.7-4) ... 365s Setting up libraw23t64:amd64 (0.21.3-1) ... 365s Setting up cpp-14 (14.2.0-8ubuntu1) ... 365s Setting up dh-strip-nondeterminism (1.14.0-1) ... 365s Setting up libmbedtls14t64:amd64 (2.28.8-1) ... 365s Setting up python3-lxml:amd64 (5.3.0-1) ... 365s Setting up python-biopython-doc (1.84+dfsg-4build1) ... 365s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 365s Setting up xml-core (0.19) ... 365s Setting up python3-contourpy (1.3.0-2) ... 365s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 365s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 365s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 365s Setting up libsm6:amd64 (2:1.2.4-1) ... 365s Setting up libavahi-client3:amd64 (0.8-13ubuntu6) ... 365s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 365s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 365s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 365s Setting up libxft2:amd64 (2.3.6-1build1) ... 365s Setting up python3-scipy (1.13.1-5) ... 368s Setting up libpython3-dev:amd64 (3.12.6-0ubuntu1) ... 368s Setting up po-debconf (1.0.21+nmu1) ... 368s Setting up libtk8.6:amd64 (8.6.15-1) ... 368s Setting up python3.12-tk (3.12.7-3) ... 368s Setting up python3-mmtf (1.1.3-1) ... 368s Setting up fonts-urw-base35 (20200910-8) ... 368s Setting up libcairo2:amd64 (1.18.2-2) ... 368s Setting up ncbi-blast+ (2.16.0+ds-6) ... 368s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 368s Setting up libpython3-all-dev:amd64 (3.12.6-0ubuntu1) ... 368s Setting up sphinx-common (7.4.7-4) ... 368s Setting up python3-dev (3.12.6-0ubuntu1) ... 368s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 368s Setting up netpbm (2:11.08.01-1) ... 368s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 368s Setting up cpp (4:14.1.0-2ubuntu1) ... 368s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 368s Setting up libcups2t64:amd64 (2.4.10-1ubuntu2) ... 368s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 368s Setting up libgs10-common (10.03.1~dfsg1-0ubuntu3) ... 368s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 368s Setting up libxmu6:amd64 (2:1.1.3-3build2) ... 368s Setting up python3-cairo (1.26.1-2) ... 368s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 368s Setting up blt (2.5.3+dfsg-7build1) ... 368s Setting up python3-tk:amd64 (3.12.6-1ubuntu1) ... 368s Setting up libxaw7:amd64 (2:1.0.16-1) ... 368s Setting up gcc-14 (14.2.0-8ubuntu1) ... 368s Setting up libamdhip64-5 (5.7.1-5) ... 368s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 368s Setting up python3-rlpycairo (0.3.0-3) ... 369s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 369s Setting up python3-reportlab (4.2.5-1) ... 369s Setting up texlive-binaries (2024.20240313.70630+ds-5) ... 369s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 369s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 369s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 369s Setting up g++-14 (14.2.0-8ubuntu1) ... 369s Setting up texlive-base (2024.20241102-1) ... 370s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 370s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 370s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 370s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 371s Setting up libgs10:amd64 (10.03.1~dfsg1-0ubuntu3) ... 371s Setting up libucx0:amd64 (1.17.0+ds-3build1) ... 371s Setting up libtool (2.4.7-7build1) ... 371s Setting up ghostscript (10.03.1~dfsg1-0ubuntu3) ... 371s Setting up gcc (4:14.1.0-2ubuntu1) ... 371s Setting up dh-autoreconf (20) ... 371s Setting up texlive-latex-base (2024.20241102-1) ... 371s Setting up texlive-latex-recommended (2024.20241102-1) ... 371s Setting up texlive-pictures (2024.20241102-1) ... 371s Setting up libopenmpi3t64:amd64 (4.1.6-13.3ubuntu2) ... 371s Setting up g++ (4:14.1.0-2ubuntu1) ... 371s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 371s Setting up texlive-fonts-recommended (2024.20241102-1) ... 371s Setting up build-essential (12.10ubuntu1) ... 371s Setting up openmpi-bin (4.1.6-13.3ubuntu2) ... 371s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 371s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 371s Setting up phyml (3:3.3.20220408-3build3) ... 371s Setting up debhelper (13.20ubuntu1) ... 371s Setting up texlive-latex-extra (2024.20241102-1) ... 371s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 371s Setting up libheif-plugin-aomdec:amd64 (1.19.3-1) ... 371s Setting up libheif-plugin-libde265:amd64 (1.19.3-1) ... 371s Setting up libheif1:amd64 (1.19.3-1) ... 371s Setting up libmagickcore-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 371s Setting up python3-fonttools (4.46.0-1build2) ... 372s Setting up libmagickwand-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 372s Setting up libgd3:amd64 (2.3.3-12ubuntu3) ... 372s Setting up imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 372s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode 372s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode 372s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode 372s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode 372s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode 372s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode 372s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode 372s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode 372s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode 372s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode 372s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode 372s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode 372s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode 372s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode 372s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode 372s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode 372s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode 372s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode 372s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode 372s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode 372s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 372s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode 372s Setting up emboss-lib (6.6.0+dfsg-12ubuntu2) ... 372s Setting up python3-matplotlib (3.8.3-3) ... 373s Setting up emboss (6.6.0+dfsg-12ubuntu2) ... 373s Setting up hevea (2.36-2) ... 373s Setting up imagemagick (8:6.9.13.12+dfsg1-1build1) ... 373s Processing triggers for install-info (7.1.1-1) ... 373s Processing triggers for libc-bin (2.40-1ubuntu3) ... 373s Processing triggers for man-db (2.13.0-1) ... 375s Processing triggers for shared-mime-info (2.4-5) ... 375s Processing triggers for sgml-base (1.31) ... 375s Setting up w3c-sgml-lib (1.3-3) ... 398s Setting up docutils-common (0.21.2+dfsg-2) ... 398s Setting up python3-biopython (1.84+dfsg-4build1) ... 399s Setting up python3-biopython-sql (1.84+dfsg-4build1) ... 399s Processing triggers for sgml-base (1.31) ... 399s Setting up python3-docutils (0.21.2+dfsg-2) ... 399s Setting up python3-sphinx (7.4.7-4) ... 400s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 400s Setting up python3-numpydoc (1.6.0-2) ... 400s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 400s Setting up autopkgtest-satdep (0) ... 400s Processing triggers for tex-common (6.18) ... 401s Running updmap-sys. This may take some time... done. 401s Running mktexlsr /var/lib/texmf ... done. 401s Building format(s) --all. 438s This may take some time... done. 444s (Reading database ... 123335 files and directories currently installed.) 444s Removing autopkgtest-satdep (0) ... 452s autopkgtest [13:12:59]: test full_suite: sh debian/tests/run-unit-test 452s autopkgtest [13:12:59]: test full_suite: [----------------------- 452s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 452s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 454s mkdir: created directory 'Bio' 454s mkdir: created directory 'Bio/Align' 454s mkdir: created directory 'Bio/Align/substitution_matrices' 454s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 454s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 454s Remove test test_Tutorial.py which is bound to fail 454s test_Ace ... ok 454s test_Affy ... ok 456s test_AlignIO ... ok 456s test_AlignIO_ClustalIO ... ok 456s test_AlignIO_EmbossIO ... ok 456s test_AlignIO_FastaIO ... ok 456s test_AlignIO_MauveIO ... ok 456s test_AlignIO_PhylipIO ... ok 456s test_AlignIO_convert ... ok 456s test_AlignInfo ... ok 456s test_Align_Alignment ... ok 456s test_Align_a2m ... ok 457s test_Align_bed ... ok 457s test_Align_bigbed ... ok 457s test_Align_bigmaf ... ok 457s test_Align_bigpsl ... ok 458s test_Align_chain ... ok 458s test_Align_clustal ... ok 461s test_Align_codonalign ... ok 461s test_Align_emboss ... ok 462s test_Align_exonerate ... ok 462s test_Align_fasta ... ok 462s test_Align_hhr ... ok 462s test_Align_maf ... ok 462s test_Align_mauve ... ok 463s test_Align_msf ... ok 463s test_Align_nexus ... ok 463s test_Align_phylip ... ok 463s test_Align_psl ... ok 463s test_Align_sam ... ok 464s test_Align_stockholm ... ok 465s test_Align_tabular ... ok 465s test_Application ... ok 465s test_BWA_tool ... ok 465s test_BioSQL_MySQLdb_online ... skipping. internet not available 465s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 465s test_BioSQL_mysql_connector_online ... skipping. internet not available 465s test_BioSQL_psycopg2_online ... skipping. internet not available 469s test_BioSQL_sqlite3 ... ok 469s test_BioSQL_sqlite3_online ... skipping. internet not available 469s test_Blast_Record ... ok 469s test_Blast_parser ... ok 469s test_CAPS ... ok 469s test_Chi2 ... ok 470s test_ClustalOmega_tool ... ok 471s test_Clustalw_tool ... ok 471s test_Cluster ... ok 471s test_CodonTable ... ok 471s test_ColorSpiral ... ok 471s test_Compass ... ok 472s test_Consensus ... ok 473s test_Dialign_tool ... ok 473s test_EMBL_unittest ... ok 478s test_Emboss ... ok 478s test_EmbossPrimer ... ok 482s test_Entrez ... ok 482s test_Entrez_online ... skipping. internet not available 482s test_Entrez_parser ... ok 482s test_Enzyme ... ok 482s test_ExPASy ... skipping. internet not available 483s test_Fasttree_tool ... ok 483s test_File ... ok 483s test_GenBank ... ok 484s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 486s ok 486s test_GraphicsChromosome ... ok 486s test_GraphicsDistribution ... ok 487s test_GraphicsGeneral ... ok 487s test_HMMCasino ... ok 487s test_HMMGeneral ... ok 487s test_KEGG ... ok 487s test_KEGG_online ... skipping. internet not available 491s test_KGML_graphics ... ok 491s test_KGML_graphics_online ... skipping. internet not available 492s test_KGML_nographics ... ok 492s test_KeyWList ... ok 492s test_LogisticRegression ... ok 492s test_MafIO_index ... ok 494s test_Mafft_tool ... ok 494s test_MarkovModel ... ok 494s test_Medline ... ok 494s test_Muscle_tool ... ok 495s test_NCBIXML ... ok 496s test_NCBI_BLAST_tools ... ok 496s test_NCBI_qblast ... ok 496s test_NMR ... ok 496s test_NaiveBayes ... ok 496s test_Nexus ... ok 496s test_PAML_baseml ... ok 497s test_PAML_codeml ... ok 497s test_PAML_yn00 ... ok 499s test_PDB_CEAligner ... ok 500s test_PDB_DSSP ... /usr/lib/python3/dist-packages/Bio/PDB/DSSP.py:199: UserWarning: 500s Configuration error: 500s 500s The attempt to retrieve compound information for "SO4" failed. 500s 500s This information is searched for in a CCD file called components.cif or 500s components.cif.gz which should be located in one of the following directories: 500s 500s "/usr/share/libcifpp" 500s "/var/cache/libcifpp" 500s "/tmp/autopkgtest.atMc0a/autopkgtest_tmp/libcifpp-data" 500s "/usr/share/libcifpp" 500s "/usr/share/libcifpp" 500s 500s (Note that you can add a directory to the search paths by setting the 500s LIBCIFPP_DATA_DIR environmental variable) 500s 500s On Linux an optional cron script might have been installed that automatically updates 500s components.cif and mmCIF dictionary files. This script only works when the file 500s libcifpp.conf contains an uncommented line with the text: 500s 500s update=true 500s 500s If you do not have a working cron script, you can manually update the files 500s in /var/cache/libcifpp using the following commands: 500s 500s curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif 500s curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic 500s curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic 500s 500s The current order of compound factory objects is: 500s 500s CCD components.cif resource 500s CCD components.cif resource 500s Unknown compound: SO4 500s Missing compound information for SO4 500s 500s warnings.warn(err) 500s ok 500s test_PDB_Dice ... ok 500s test_PDB_Disordered ... ok 500s test_PDB_Exposure ... ok 500s test_PDB_FragmentMapper ... ok 501s test_PDB_KDTree ... ok 501s test_PDB_MMCIF2Dict ... ok 502s test_PDB_MMCIFIO ... ok 502s test_PDB_MMCIFParser ... ok 503s test_PDB_NACCESS ... ok 503s test_PDB_PDBIO ... ok 503s test_PDB_PDBList ... skipping. internet not available 508s test_PDB_PDBMLParser ... ok 508s test_PDB_PDBParser ... ok 508s test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path 508s test_PDB_Polypeptide ... ok 508s test_PDB_QCPSuperimposer ... ok 511s test_PDB_SASA ... ok 512s test_PDB_SMCRA ... ok 512s test_PDB_Selection ... ok 512s test_PDB_StructureAlignment ... ok 512s test_PDB_Superimposer ... ok 512s test_PDB_alphafold_db ... skipping. internet not available 514s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 514s warnings.warn( 514s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 514s warnings.warn( 514s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 514s warnings.warn( 514s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 514s warnings.warn( 514s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 514s warnings.warn( 515s ok 521s test_PDB_internal_coords ... ok 522s test_PDB_parse_pdb_header ... ok 522s test_PDB_vectors ... ok 522s test_PQR ... ok 522s test_Pathway ... ok 522s test_Phd ... ok 523s test_Phylo ... ok 523s test_PhyloXML ... ok 524s test_Phylo_CDAO ... ok 524s test_Phylo_NeXML ... ok 524s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 527s test_Phylo_matplotlib ... ok 528s test_Phylo_networkx ... ok 528s test_PopGen_GenePop_nodepend ... ok 529s test_Prank_tool ... ok 530s test_Probcons_tool ... ok 530s test_ProtParam ... ok 531s test_RCSBFormats ... ok 531s test_Restriction ... ok 532s test_SCOP_Astral ... ok 532s test_SCOP_Cla ... ok 533s test_SCOP_Des ... ok 533s test_SCOP_Dom ... ok 533s test_SCOP_Hie ... ok 534s test_SCOP_Raf ... ok 534s test_SCOP_Residues ... ok 535s test_SCOP_Scop ... ok 535s test_SVDSuperimposer ... ok 536s test_SearchIO_blast_tab ... ok 536s test_SearchIO_blast_tab_index ... ok 536s test_SearchIO_blast_xml ... ok 538s test_SearchIO_blast_xml_index ... ok 538s test_SearchIO_blat_psl ... ok 539s test_SearchIO_blat_psl_index ... ok 539s test_SearchIO_exonerate ... ok 539s test_SearchIO_exonerate_text_index ... ok 540s test_SearchIO_exonerate_vulgar_index ... ok 540s test_SearchIO_fasta_m10 ... ok 541s test_SearchIO_fasta_m10_index ... ok 541s test_SearchIO_hhsuite2_text ... ok 542s test_SearchIO_hmmer2_text ... ok 542s test_SearchIO_hmmer2_text_index ... ok 542s test_SearchIO_hmmer3_domtab ... ok 543s test_SearchIO_hmmer3_domtab_index ... ok 543s test_SearchIO_hmmer3_tab ... ok 544s test_SearchIO_hmmer3_tab_index ... ok 544s test_SearchIO_hmmer3_text ... ok 545s test_SearchIO_hmmer3_text_index ... ok 545s test_SearchIO_interproscan_xml ... ok 545s test_SearchIO_model ... ok 546s test_SearchIO_write ... ok 546s test_SeqFeature ... ok 558s test_SeqIO ... ok 558s test_SeqIO_AbiIO ... ok 559s test_SeqIO_FastaIO ... ok 559s test_SeqIO_Gck ... ok 560s test_SeqIO_Gfa ... ok 560s test_SeqIO_Insdc ... ok 561s test_SeqIO_NibIO ... ok 562s test_SeqIO_PdbIO ... ok 563s test_SeqIO_QualityIO ... ok 563s test_SeqIO_SeqXML ... ok 564s test_SeqIO_SnapGene ... ok 565s test_SeqIO_TwoBitIO ... ok 565s test_SeqIO_Xdna ... ok 566s test_SeqIO_features ... ok 577s test_SeqIO_index ... ok 578s test_SeqIO_online ... skipping. internet not available 578s test_SeqIO_write ... ok 579s test_SeqRecord ... ok 579s test_SeqUtils ... ok 580s test_Seq_objs ... ok 581s test_SffIO ... ok 581s test_SwissProt ... ok 584s test_TCoffee_tool ... ok 584s test_TogoWS ... skipping. internet not available 585s test_TreeConstruction ... ok 585s test_UniGene ... ok 586s test_UniProt ... skipping. internet not available 586s test_UniProt_GOA ... ok 587s test_UniProt_Parser ... ok 587s test_align ... ok 588s test_align_substitution_matrices ... ok 590s test_bgzf ... ok 590s test_cellosaurus ... ok 594s test_codonalign ... ok 595s test_geo ... ok 595s test_kNN ... ok 596s test_motifs ... ok 596s test_motifs_online ... skipping. internet not available 597s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 597s warnings.warn( 597s ok 597s test_pairwise2_no_C ... ok 598s test_pairwise_aligner ... ok 598s test_pairwise_alignment_map ... ok 604s test_phenotype ... ok 604s test_phenotype_fit ... ok 605s test_phyml_tool ... ok 605s test_prodoc ... ok 605s test_prosite ... ok 606s test_raxml_tool ... ok 606s test_samtools_tool ... ok 607s test_seq ... ok 607s test_translate ... ok 607s ---------------------------------------------------------------------- 607s Ran 218 tests in 153.524 seconds 607s 607s Skipping any tests requiring internet access 607s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 607s Operating system: posix linux 609s autopkgtest [13:15:36]: test full_suite: -----------------------] 609s autopkgtest [13:15:36]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 609s full_suite PASS 610s autopkgtest [13:15:37]: @@@@@@@@@@@@@@@@@@@@ summary 610s dependencies PASS 610s full_suite PASS 621s virt: nova [W] Skipping flock for amd64 621s virt: Creating nova instance adt-plucky-amd64-python-biopython-20241115-130527-juju-7f2275-prod-proposed-migration-environment-2-0126f230-f735-435e-81bd-6222c8f3fead from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)... 621s virt: nova [W] Skipping flock for amd64 621s virt: Creating nova instance adt-plucky-amd64-python-biopython-20241115-130527-juju-7f2275-prod-proposed-migration-environment-2-0126f230-f735-435e-81bd-6222c8f3fead from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...