0s autopkgtest [13:43:06]: starting date and time: 2026-01-24 13:43:06+0000 0s autopkgtest [13:43:06]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [13:43:06]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uf7eq1is/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-12.secgroup --name adt-resolute-amd64-python-biopython-20260124-134306-juju-7f2275-prod-proposed-migration-environment-15-ad478aa2-0cd4-4a65-b608-f711ad983b67 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-python-biopython-20260124-134306-juju-7f2275-prod-proposed-migration-environment-15-ad478aa2-0cd4-4a65-b608-f711ad983b67 from image adt/ubuntu-resolute-amd64-server-20260124.img (UUID 46811f22-3700-43f4-953b-ee3c613d71bb)... 74s autopkgtest [13:44:20]: testbed dpkg architecture: amd64 75s autopkgtest [13:44:21]: testbed apt version: 3.1.13 75s autopkgtest [13:44:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 75s autopkgtest [13:44:21]: testbed release detected to be: None 76s autopkgtest [13:44:22]: updating testbed package index (apt update) 76s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 76s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 76s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 76s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 76s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [92.3 kB] 76s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 76s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 76s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [998 kB] 76s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [115 kB] 76s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [98.2 kB] 76s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3712 B] 76s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 76s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 76s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 76s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [905 kB] 76s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [385 kB] 76s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.9 kB] 77s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.4 kB] 77s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 77s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [824 B] 77s Fetched 2806 kB in 1s (3115 kB/s) 78s Reading package lists... 78s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 78s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 79s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 79s The following packages were automatically installed and are no longer required: 79s python3.13 python3.13-minimal 79s Use 'sudo apt autoremove' to remove them. 79s The following NEW packages will be installed: 79s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 79s The following packages will be upgraded: 79s libpython3-stdlib python3 python3-gdbm python3-minimal rust-coreutils 79s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 10.4 MB of archives. 79s After this operation, 25.2 MB of additional disk space will be used. 79s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 80s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 80s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 80s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 80s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 80s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 80s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 80s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 rust-coreutils amd64 0.5.0-0ubuntu1 [3628 kB] 81s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 81s dpkg-preconfigure: unable to re-open stdin: No such file or directory 81s Fetched 10.4 MB in 1s (7782 kB/s) 81s Selecting previously unselected package libpython3.14-minimal:amd64. 81s (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 ... 124177 files and directories currently installed.) 81s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 81s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 81s Selecting previously unselected package python3.14-minimal. 81s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 81s Unpacking python3.14-minimal (3.14.2-1) ... 81s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 81s Setting up python3.14-minimal (3.14.2-1) ... 82s (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 ... 124519 files and directories currently installed.) 82s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 82s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 82s Setting up python3-minimal (3.14.2-1) ... 82s (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 ... 124519 files and directories currently installed.) 82s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 82s running python pre-rtupdate hooks for python3.14... 82s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 82s Selecting previously unselected package libpython3.14-stdlib:amd64. 82s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 82s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 82s Selecting previously unselected package python3.14. 82s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 82s Unpacking python3.14 (3.14.2-1) ... 82s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 82s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 82s Preparing to unpack .../rust-coreutils_0.5.0-0ubuntu1_amd64.deb ... 82s Unpacking rust-coreutils (0.5.0-0ubuntu1) over (0.2.2-0ubuntu2) ... 82s Setting up rust-coreutils (0.5.0-0ubuntu1) ... 82s (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 ... 124980 files and directories currently installed.) 82s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 82s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 82s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 82s Setting up python3.14 (3.14.2-1) ... 83s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 83s Setting up python3-gdbm (3.14.2-1) ... 83s Setting up python3 (3.14.2-1) ... 83s running python rtupdate hooks for python3.14... 83s running python post-rtupdate hooks for python3.14... 83s Processing triggers for man-db (2.13.1-1) ... 84s Processing triggers for systemd (259-1ubuntu2) ... 84s autopkgtest [13:44:30]: upgrading testbed (apt dist-upgrade and autopurge) 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Calculating upgrade... 84s The following packages were automatically installed and are no longer required: 84s python3.13 python3.13-minimal 84s Use 'sudo apt autoremove' to remove them. 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 85s The following packages will be REMOVED: 85s python3.13* python3.13-minimal* 85s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 85s After this operation, 7860 kB disk space will be freed. 85s (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 ... 124978 files and directories currently installed.) 85s Removing python3.13 (3.13.11-1) ... 85s Removing python3.13-minimal (3.13.11-1) ... 85s Processing triggers for man-db (2.13.1-1) ... 85s Processing triggers for systemd (259-1ubuntu2) ... 86s (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 ... 124951 files and directories currently installed.) 86s Purging configuration files for python3.13-minimal (3.13.11-1) ... 88s autopkgtest [13:44:34]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 88s autopkgtest [13:44:34]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 90s Get:1 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (dsc) [3562 B] 90s Get:2 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (tar) [14.5 MB] 90s Get:3 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (diff) [41.4 kB] 90s gpgv: Signature made Wed Oct 29 22:41:45 2025 UTC 90s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 90s gpgv: issuer "emollier@debian.org" 90s gpgv: Can't check signature: No public key 90s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.86+dfsg-1.dsc: no acceptable signature found 90s autopkgtest [13:44:36]: testing package python-biopython version 1.86+dfsg-1 91s autopkgtest [13:44:37]: build not needed 95s autopkgtest [13:44:41]: test dependencies: preparing testbed 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Solving dependencies... 96s The following NEW packages will be installed: 96s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 96s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 96s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 96s libjpeg-turbo8 libjpeg8 libjs-jquery liblapack3 liblcms2-2 liblerc4 96s libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 96s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 96s python-biopython-doc python3-all python3-biopython python3-biopython-sql 96s python3-cairo python3-charset-normalizer python3-freetype python3-numpy 96s python3-numpy-dev python3-pil python3-reportlab python3-rlpycairo python3.13 96s python3.13-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings 96s xfonts-utils xml-core 96s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 56.0 MB of archives. 96s After this operation, 162 MB of additional disk space will be used. 96s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-minimal amd64 3.13.11-1 [2408 kB] 96s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 96s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 96s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-11ubuntu1 [939 kB] 96s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 96s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 96s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13 amd64 3.13.11-1 [758 kB] 96s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 97s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 97s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 97s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 97s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 97s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7build1 [97.1 kB] 97s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8build1 [10.9 MB] 97s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.4ubuntu1 [38.1 kB] 97s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-extra all 2.37-8build1 [1944 kB] 97s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.4ubuntu1 [143 kB] 97s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 97s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 97s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 97s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 97s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 97s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 97s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-11ubuntu1 [151 kB] 97s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 97s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.0-4 [529 kB] 97s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 97s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 97s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 97s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 97s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 97s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 97s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 97s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 97s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 97s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 97s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 97s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1build1 [12.8 kB] 97s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1build1 [26.4 kB] 97s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 97s Get:41 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.14.2-1 [890 B] 97s Get:42 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-2 [173 kB] 97s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.4-1 [188 kB] 97s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 97s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 97s Get:46 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 97s Get:47 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 98s Get:48 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.9-1 [1149 kB] 98s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 98s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19build1 [20.3 kB] 98s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3build1 [278 kB] 98s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 98s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython-sql all 1.86+dfsg-1 [26.4 kB] 98s Fetched 56.0 MB in 2s (28.9 MB/s) 98s Selecting previously unselected package python3.13-minimal. 98s (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 ... 124953 files and directories currently installed.) 98s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_amd64.deb ... 98s Unpacking python3.13-minimal (3.13.11-1) ... 98s Selecting previously unselected package python3-numpy-dev:amd64. 98s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 98s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 98s Selecting previously unselected package libblas3:amd64. 98s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_amd64.deb ... 98s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 98s Selecting previously unselected package libgfortran5:amd64. 98s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_amd64.deb ... 98s Unpacking libgfortran5:amd64 (15.2.0-11ubuntu1) ... 98s Selecting previously unselected package liblapack3:amd64. 98s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 98s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 98s Selecting previously unselected package python3-numpy. 98s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 98s Unpacking python3-numpy (1:2.3.5+ds-3) ... 98s Selecting previously unselected package python3.13. 98s Preparing to unpack .../06-python3.13_3.13.11-1_amd64.deb ... 98s Unpacking python3.13 (3.13.11-1) ... 98s Selecting previously unselected package fonts-dejavu-mono. 98s Preparing to unpack .../07-fonts-dejavu-mono_2.37-8build1_all.deb ... 98s Unpacking fonts-dejavu-mono (2.37-8build1) ... 98s Selecting previously unselected package fonts-dejavu-core. 98s Preparing to unpack .../08-fonts-dejavu-core_2.37-8build1_all.deb ... 98s Unpacking fonts-dejavu-core (2.37-8build1) ... 98s Selecting previously unselected package libfontenc1:amd64. 98s Preparing to unpack .../09-libfontenc1_1%3a1.1.8-1build2_amd64.deb ... 98s Unpacking libfontenc1:amd64 (1:1.1.8-1build2) ... 98s Selecting previously unselected package x11-common. 98s Preparing to unpack .../10-x11-common_1%3a7.7+24ubuntu1_all.deb ... 98s Unpacking x11-common (1:7.7+24ubuntu1) ... 98s Selecting previously unselected package xfonts-encodings. 98s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 98s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 98s Selecting previously unselected package xfonts-utils. 98s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7build1_amd64.deb ... 98s Unpacking xfonts-utils (1:7.7+7build1) ... 98s Selecting previously unselected package fonts-urw-base35. 98s Preparing to unpack .../13-fonts-urw-base35_20200910-8build1_all.deb ... 98s Unpacking fonts-urw-base35 (20200910-8build1) ... 98s Selecting previously unselected package fontconfig-config. 98s Preparing to unpack .../14-fontconfig-config_2.15.0-2.4ubuntu1_amd64.deb ... 98s Unpacking fontconfig-config (2.15.0-2.4ubuntu1) ... 98s Selecting previously unselected package fonts-dejavu-extra. 98s Preparing to unpack .../15-fonts-dejavu-extra_2.37-8build1_all.deb ... 98s Unpacking fonts-dejavu-extra (2.37-8build1) ... 99s Selecting previously unselected package libfontconfig1:amd64. 99s Preparing to unpack .../16-libfontconfig1_2.15.0-2.4ubuntu1_amd64.deb ... 99s Unpacking libfontconfig1:amd64 (2.15.0-2.4ubuntu1) ... 99s Selecting previously unselected package libpixman-1-0:amd64. 99s Preparing to unpack .../17-libpixman-1-0_0.46.4-1_amd64.deb ... 99s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 99s Selecting previously unselected package libxcb-render0:amd64. 99s Preparing to unpack .../18-libxcb-render0_1.17.0-2build1_amd64.deb ... 99s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 99s Selecting previously unselected package libxcb-shm0:amd64. 99s Preparing to unpack .../19-libxcb-shm0_1.17.0-2build1_amd64.deb ... 99s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 99s Selecting previously unselected package libxrender1:amd64. 99s Preparing to unpack .../20-libxrender1_1%3a0.9.12-1_amd64.deb ... 99s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 99s Selecting previously unselected package libcairo2:amd64. 99s Preparing to unpack .../21-libcairo2_1.18.4-3_amd64.deb ... 99s Unpacking libcairo2:amd64 (1.18.4-3) ... 99s Selecting previously unselected package libdeflate0:amd64. 99s Preparing to unpack .../22-libdeflate0_1.23-2_amd64.deb ... 99s Unpacking libdeflate0:amd64 (1.23-2) ... 99s Selecting previously unselected package libgomp1:amd64. 99s Preparing to unpack .../23-libgomp1_15.2.0-11ubuntu1_amd64.deb ... 99s Unpacking libgomp1:amd64 (15.2.0-11ubuntu1) ... 99s Selecting previously unselected package libgraphite2-3:amd64. 99s Preparing to unpack .../24-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 99s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 99s Selecting previously unselected package libharfbuzz0b:amd64. 99s Preparing to unpack .../25-libharfbuzz0b_12.3.0-4_amd64.deb ... 99s Unpacking libharfbuzz0b:amd64 (12.3.0-4) ... 99s Selecting previously unselected package libimagequant0:amd64. 99s Preparing to unpack .../26-libimagequant0_2.18.0-1build1_amd64.deb ... 99s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 99s Selecting previously unselected package libjpeg-turbo8:amd64. 99s Preparing to unpack .../27-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 99s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 99s Selecting previously unselected package libjpeg8:amd64. 99s Preparing to unpack .../28-libjpeg8_8c-2ubuntu11_amd64.deb ... 99s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 99s Selecting previously unselected package libjs-jquery. 99s Preparing to unpack .../29-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 99s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 99s Selecting previously unselected package liblcms2-2:amd64. 99s Preparing to unpack .../30-liblcms2-2_2.17-1_amd64.deb ... 99s Unpacking liblcms2-2:amd64 (2.17-1) ... 99s Selecting previously unselected package liblerc4:amd64. 99s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 99s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 99s Selecting previously unselected package libraqm0:amd64. 99s Preparing to unpack .../32-libraqm0_0.10.3-1_amd64.deb ... 99s Unpacking libraqm0:amd64 (0.10.3-1) ... 99s Selecting previously unselected package libsharpyuv0:amd64. 99s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1build1_amd64.deb ... 99s Unpacking libsharpyuv0:amd64 (1.5.0-0.1build1) ... 99s Selecting previously unselected package libjbig0:amd64. 99s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu3_amd64.deb ... 99s Unpacking libjbig0:amd64 (2.1-6.1ubuntu3) ... 99s Selecting previously unselected package libwebp7:amd64. 99s Preparing to unpack .../35-libwebp7_1.5.0-0.1build1_amd64.deb ... 99s Unpacking libwebp7:amd64 (1.5.0-0.1build1) ... 99s Selecting previously unselected package libtiff6:amd64. 99s Preparing to unpack .../36-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 99s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 99s Selecting previously unselected package libwebpdemux2:amd64. 99s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1build1_amd64.deb ... 99s Unpacking libwebpdemux2:amd64 (1.5.0-0.1build1) ... 99s Selecting previously unselected package libwebpmux3:amd64. 99s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1build1_amd64.deb ... 99s Unpacking libwebpmux3:amd64 (1.5.0-0.1build1) ... 99s Selecting previously unselected package python-biopython-doc. 99s Preparing to unpack .../39-python-biopython-doc_1.86+dfsg-1_all.deb ... 99s Unpacking python-biopython-doc (1.86+dfsg-1) ... 99s Selecting previously unselected package python3-all. 99s Preparing to unpack .../40-python3-all_3.14.2-1_amd64.deb ... 99s Unpacking python3-all (3.14.2-1) ... 99s Selecting previously unselected package python3-charset-normalizer. 99s Preparing to unpack .../41-python3-charset-normalizer_3.4.4-2_amd64.deb ... 99s Unpacking python3-charset-normalizer (3.4.4-2) ... 99s Selecting previously unselected package libopenjp2-7:amd64. 99s Preparing to unpack .../42-libopenjp2-7_2.5.4-1_amd64.deb ... 99s Unpacking libopenjp2-7:amd64 (2.5.4-1) ... 99s Selecting previously unselected package python3-pil:amd64. 99s Preparing to unpack .../43-python3-pil_12.0.0-1ubuntu1_amd64.deb ... 99s Unpacking python3-pil:amd64 (12.0.0-1ubuntu1) ... 99s Selecting previously unselected package python3-cairo. 99s Preparing to unpack .../44-python3-cairo_1.27.0-2build1_amd64.deb ... 99s Unpacking python3-cairo (1.27.0-2build1) ... 99s Selecting previously unselected package python3-freetype. 99s Preparing to unpack .../45-python3-freetype_2.5.1-2_all.deb ... 99s Unpacking python3-freetype (2.5.1-2) ... 99s Selecting previously unselected package python3-rlpycairo. 99s Preparing to unpack .../46-python3-rlpycairo_0.3.0-4_all.deb ... 99s Unpacking python3-rlpycairo (0.3.0-4) ... 99s Selecting previously unselected package python3-reportlab. 99s Preparing to unpack .../47-python3-reportlab_4.4.9-1_all.deb ... 99s Unpacking python3-reportlab (4.4.9-1) ... 99s Selecting previously unselected package sgml-base. 99s Preparing to unpack .../48-sgml-base_1.31+nmu1_all.deb ... 99s Unpacking sgml-base (1.31+nmu1) ... 99s Selecting previously unselected package xml-core. 99s Preparing to unpack .../49-xml-core_0.19build1_all.deb ... 99s Unpacking xml-core (0.19build1) ... 99s Selecting previously unselected package w3c-sgml-lib. 99s Preparing to unpack .../50-w3c-sgml-lib_1.3-3build1_all.deb ... 99s Unpacking w3c-sgml-lib (1.3-3build1) ... 99s Selecting previously unselected package python3-biopython. 99s Preparing to unpack .../51-python3-biopython_1.86+dfsg-1_amd64.deb ... 99s Unpacking python3-biopython (1.86+dfsg-1) ... 99s Selecting previously unselected package python3-biopython-sql. 99s Preparing to unpack .../52-python3-biopython-sql_1.86+dfsg-1_all.deb ... 99s Unpacking python3-biopython-sql (1.86+dfsg-1) ... 99s Setting up libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 99s Setting up liblcms2-2:amd64 (2.17-1) ... 99s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 99s Setting up libsharpyuv0:amd64 (1.5.0-0.1build1) ... 99s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 99s Setting up libxrender1:amd64 (1:0.9.12-1) ... 99s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 99s Setting up python3-charset-normalizer (3.4.4-2) ... 99s Setting up x11-common (1:7.7+24ubuntu1) ... 100s Setting up libdeflate0:amd64 (1.23-2) ... 100s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 100s Setting up libgomp1:amd64 (15.2.0-11ubuntu1) ... 100s Setting up python3-freetype (2.5.1-2) ... 100s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ... 100s Setting up libfontenc1:amd64 (1:1.1.8-1build2) ... 100s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 100s 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 100s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 100s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 100s Setting up fonts-dejavu-mono (2.37-8build1) ... 100s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 100s Setting up fonts-dejavu-core (2.37-8build1) ... 100s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 100s Setting up libgfortran5:amd64 (15.2.0-11ubuntu1) ... 100s Setting up libwebp7:amd64 (1.5.0-0.1build1) ... 100s Setting up fonts-dejavu-extra (2.37-8build1) ... 100s Setting up libopenjp2-7:amd64 (2.5.4-1) ... 100s Setting up python3.13-minimal (3.13.11-1) ... 100s Setting up libharfbuzz0b:amd64 (12.3.0-4) ... 100s Setting up sgml-base (1.31+nmu1) ... 100s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 100s Setting up libwebpmux3:amd64 (1.5.0-0.1build1) ... 100s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 100s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 100s 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 100s Setting up python3.13 (3.13.11-1) ... 101s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 101s Setting up libwebpdemux2:amd64 (1.5.0-0.1build1) ... 101s Setting up python3-all (3.14.2-1) ... 101s Setting up xfonts-utils (1:7.7+7build1) ... 101s Setting up libraqm0:amd64 (0.10.3-1) ... 101s Setting up python3-numpy (1:2.3.5+ds-3) ... 103s Setting up python-biopython-doc (1.86+dfsg-1) ... 103s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 103s Setting up xml-core (0.19build1) ... 103s Setting up libfontconfig1:amd64 (2.15.0-2.4ubuntu1) ... 103s Setting up fonts-urw-base35 (20200910-8build1) ... 103s Setting up libcairo2:amd64 (1.18.4-3) ... 103s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 104s Setting up python3-cairo (1.27.0-2build1) ... 104s Setting up python3-rlpycairo (0.3.0-4) ... 104s Setting up python3-reportlab (4.4.9-1) ... 105s Processing triggers for libc-bin (2.42-2ubuntu4) ... 105s Processing triggers for systemd (259-1ubuntu2) ... 105s Processing triggers for man-db (2.13.1-1) ... 106s Processing triggers for sgml-base (1.31+nmu1) ... 106s Setting up w3c-sgml-lib (1.3-3build1) ... 121s Setting up python3-biopython (1.86+dfsg-1) ... 122s Setting up python3-biopython-sql (1.86+dfsg-1) ... 123s autopkgtest [13:45:09]: test dependencies: sh debian/tests/run-unit-test 123s autopkgtest [13:45:09]: test dependencies: [----------------------- 123s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 123s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 124s mkdir: created directory 'Bio' 124s mkdir: created directory 'Bio/Align' 124s mkdir: created directory 'Bio/Align/substitution_matrices' 124s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 124s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 125s test_Ace ... ok 125s test_Affy ... ok 125s test_AlignIO ... ok 125s test_AlignIO_ClustalIO ... ok 125s test_AlignIO_EmbossIO ... ok 125s test_AlignIO_FastaIO ... ok 125s test_AlignIO_MauveIO ... ok 125s test_AlignIO_PhylipIO ... ok 125s test_AlignIO_convert ... ok 125s test_Align_Alignment ... ok 125s test_Align_a2m ... ok 125s test_Align_bed ... ok 125s test_Align_bigbed ... ok 126s test_Align_bigmaf ... ok 126s test_Align_bigpsl ... ok 126s test_Align_chain ... ok 126s test_Align_clustal ... ok 128s test_Align_codonalign ... ok 128s test_Align_emboss ... ok 128s test_Align_exonerate ... ok 128s test_Align_fasta ... ok 128s test_Align_format_matrix ... ok 128s test_Align_hhr ... ok 129s test_Align_maf ... ok 129s test_Align_mauve ... ok 129s test_Align_msf ... ok 129s test_Align_nexus ... ok 129s test_Align_phylip ... ok 129s test_Align_psl ... ok 130s test_Align_sam ... ok 130s test_Align_stockholm ... ok 131s test_Align_tabular ... ok 131s test_BioSQL_MySQLdb_online ... skipping. internet not available 131s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 131s test_BioSQL_mysql_connector_online ... skipping. internet not available 131s test_BioSQL_psycopg2_online ... skipping. internet not available 133s test_BioSQL_sqlite3 ... ok 133s test_BioSQL_sqlite3_online ... skipping. internet not available 133s test_Blast_Record ... ok 133s test_Blast_parser ... ok 133s test_CAPS ... ok 133s test_Chi2 ... ok 133s test_Cluster ... ok 133s test_CodonTable ... ok 133s test_ColorSpiral ... ok 133s test_Compass ... ok 134s test_Consensus ... ok 134s test_EMBL_unittest ... ok 134s test_EmbossPrimer ... ok 138s test_Entrez ... ok 138s test_Entrez_online ... skipping. internet not available 138s test_Entrez_parser ... ok 138s test_Enzyme ... ok 138s test_ExPASy ... skipping. internet not available 138s test_File ... ok 138s test_GenBank ... ok 139s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 140s ok 141s test_GraphicsChromosome ... ok 141s test_GraphicsDistribution ... ok 141s test_GraphicsGeneral ... ok 141s test_KEGG ... ok 141s test_KEGG_online ... skipping. internet not available 144s test_KGML_graphics ... ok 144s test_KGML_graphics_online ... skipping. internet not available 144s test_KGML_nographics ... ok 144s test_KeyWList ... ok 144s test_MafIO_index ... ok 144s test_Medline ... ok 145s test_NCBIXML ... Exception ignored in: 145s Traceback (most recent call last): 145s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 145s expat_parser.Parse(NULL, True) 145s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 145s ok 145s test_NCBI_qblast ... ok 145s test_NMR ... ok 145s test_Nexus ... ok 145s test_PAML_baseml ... ok 145s test_PAML_codeml ... ok 145s test_PAML_yn00 ... ok 148s test_PDB_CEAligner ... ok 148s test_PDB_DSSP ... ok 148s test_PDB_Dice ... ok 148s test_PDB_Disordered ... ok 148s test_PDB_Exposure ... ok 148s test_PDB_FragmentMapper ... ok 149s test_PDB_KDTree ... ok 149s test_PDB_MMCIF2Dict ... ok 149s test_PDB_MMCIFIO ... ok 150s test_PDB_MMCIFParser ... ok 150s test_PDB_NACCESS ... ok 150s test_PDB_PDBIO ... ok 150s test_PDB_PDBList ... skipping. internet not available 153s test_PDB_PDBMLParser ... ok 153s test_PDB_PDBParser ... ok 153s 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 154s test_PDB_Polypeptide ... ok 154s test_PDB_QCPSuperimposer ... ok 155s test_PDB_SASA ... ok 156s test_PDB_SMCRA ... ok 156s test_PDB_Selection ... ok 156s test_PDB_StructureAlignment ... ok 156s test_PDB_Superimposer ... ok 156s test_PDB_alphafold_db ... skipping. internet not available 156s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 156s 156s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 156s 156s test_PDB_parse_pdb_header ... ok 156s test_PDB_vectors ... ok 156s test_PQR ... ok 156s test_Pathway ... ok 156s test_Phd ... ok 157s test_Phylo ... ok 157s test_PhyloXML ... ok 157s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 157s test_Phylo_NeXML ... ok 157s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 157s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 157s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 157s test_PopGen_GenePop_nodepend ... ok 157s test_ProtParam ... ok 157s test_RCSBFormats ... ok 157s test_Restriction ... ok 157s test_SCOP_Astral ... ok 157s test_SCOP_Cla ... ok 157s test_SCOP_Des ... ok 157s test_SCOP_Dom ... ok 157s test_SCOP_Hie ... ok 157s test_SCOP_Raf ... ok 157s test_SCOP_Residues ... ok 157s test_SCOP_Scop ... ok 157s test_SVDSuperimposer ... ok 158s test_SearchIO_blast_tab ... ok 158s test_SearchIO_blast_tab_index ... ok 158s test_SearchIO_blast_xml ... ok 158s test_SearchIO_blast_xml_index ... ok 158s test_SearchIO_blat_psl ... ok 159s test_SearchIO_blat_psl_index ... ok 159s test_SearchIO_exonerate ... ok 159s test_SearchIO_exonerate_text_index ... ok 159s test_SearchIO_exonerate_vulgar_index ... ok 159s test_SearchIO_fasta_m10 ... ok 159s test_SearchIO_fasta_m10_index ... ok 159s test_SearchIO_hhsuite2_text ... ok 159s test_SearchIO_hmmer2_text ... ok 159s test_SearchIO_hmmer2_text_index ... ok 159s test_SearchIO_hmmer3_domtab ... ok 159s test_SearchIO_hmmer3_domtab_index ... ok 159s test_SearchIO_hmmer3_tab ... ok 159s test_SearchIO_hmmer3_tab_index ... ok 159s test_SearchIO_hmmer3_text ... ok 159s test_SearchIO_hmmer3_text_index ... ok 159s test_SearchIO_infernal_tab ... ok 159s test_SearchIO_infernal_tab_index ... ok 159s test_SearchIO_infernal_text ... ok 159s test_SearchIO_infernal_text_index ... ok 159s test_SearchIO_interproscan_xml ... ok 159s test_SearchIO_model ... ok 160s test_SearchIO_write ... ok 160s test_SeqFeature ... ok 169s test_SeqIO ... ok 169s test_SeqIO_AbiIO ... ok 169s test_SeqIO_FastaIO ... ok 169s test_SeqIO_Gck ... ok 169s test_SeqIO_Gfa ... ok 169s test_SeqIO_Insdc ... ok 169s test_SeqIO_NibIO ... ok 170s test_SeqIO_PdbIO ... ok 170s test_SeqIO_QualityIO ... ok 170s test_SeqIO_SeqXML ... ok 170s test_SeqIO_SffIO ... ok 171s test_SeqIO_SnapGene ... ok 171s test_SeqIO_TwoBitIO ... ok 171s test_SeqIO_UniprotIO ... ok 171s test_SeqIO_Xdna ... ok 171s test_SeqIO_features ... ok 179s test_SeqIO_index ... ok 179s test_SeqIO_online ... skipping. internet not available 179s test_SeqIO_write ... ok 179s test_SeqRecord ... ok 179s test_SeqUtils ... ok 179s test_Seq_objs ... ok 180s test_SwissProt ... ok 180s test_TogoWS ... skipping. internet not available 180s test_TreeConstruction ... ok 180s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 180s test_UniGene ... ok 180s test_UniProt ... skipping. internet not available 180s test_UniProt_GOA ... ok 180s test_align ... ok 180s test_align_substitution_matrices ... ok 181s test_bgzf ... ok 181s test_cellosaurus ... ok 184s test_codonalign ... ok 184s test_geo ... ok 184s test_motifs ... ok 184s test_motifs_online ... skipping. internet not available 184s 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. 184s warnings.warn( 184s ok 184s test_pairwise2_no_C ... ok 184s test_pairwise_aligner ... ok 185s test_pairwise_alignment_map ... ok 188s test_phenotype ... ok 188s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 188s test_prodoc ... ok 188s test_prosite ... ok 188s test_seq ... ok 188s test_translate ... ok 188s Skipping any tests requiring internet access 188s Python version: 3.13.11 (main, Dec 6 2025, 13:15:20) [GCC 15.2.0] 188s Operating system: posix linux 188s ---------------------------------------------------------------------- 188s Ran 201 tests in 63.822 seconds 188s 189s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 189s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 189s test_Ace ... ok 189s test_Affy ... ok 189s test_AlignIO ... ok 189s test_AlignIO_ClustalIO ... ok 189s test_AlignIO_EmbossIO ... ok 189s test_AlignIO_FastaIO ... ok 189s test_AlignIO_MauveIO ... ok 189s test_AlignIO_PhylipIO ... ok 189s test_AlignIO_convert ... ok 189s test_Align_Alignment ... ok 189s test_Align_a2m ... ok 189s test_Align_bed ... ok 189s test_Align_bigbed ... ok 190s test_Align_bigmaf ... ok 190s test_Align_bigpsl ... ok 190s test_Align_chain ... ok 190s test_Align_clustal ... ok 192s test_Align_codonalign ... ok 192s test_Align_emboss ... ok 192s test_Align_exonerate ... ok 192s test_Align_fasta ... ok 192s test_Align_format_matrix ... ok 193s test_Align_hhr ... ok 193s test_Align_maf ... ok 193s test_Align_mauve ... ok 193s test_Align_msf ... ok 193s test_Align_nexus ... ok 193s test_Align_phylip ... ok 194s test_Align_psl ... ok 194s test_Align_sam ... ok 196s test_Align_stockholm ... ok 196s test_Align_tabular ... ok 196s test_BioSQL_MySQLdb_online ... skipping. internet not available 196s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 196s test_BioSQL_mysql_connector_online ... skipping. internet not available 196s test_BioSQL_psycopg2_online ... skipping. internet not available 197s test_BioSQL_sqlite3 ... ok 197s test_BioSQL_sqlite3_online ... skipping. internet not available 197s test_Blast_Record ... ok 197s test_Blast_parser ... ok 197s test_CAPS ... ok 197s test_Chi2 ... ok 197s test_Cluster ... ok 198s test_CodonTable ... ok 198s test_ColorSpiral ... ok 198s test_Compass ... ok 198s test_Consensus ... ok 198s test_EMBL_unittest ... ok 198s test_EmbossPrimer ... ok 202s test_Entrez ... ok 202s test_Entrez_online ... skipping. internet not available 203s test_Entrez_parser ... ok 203s test_Enzyme ... ok 203s test_ExPASy ... skipping. internet not available 203s test_File ... ok 203s test_GenBank ... ok 204s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 205s ok 205s test_GraphicsChromosome ... ok 205s test_GraphicsDistribution ... ok 206s test_GraphicsGeneral ... ok 206s test_KEGG ... ok 206s test_KEGG_online ... skipping. internet not available 208s test_KGML_graphics ... ok 208s test_KGML_graphics_online ... skipping. internet not available 208s test_KGML_nographics ... ok 208s test_KeyWList ... ok 209s test_MafIO_index ... ok 209s test_Medline ... ok 209s test_NCBIXML ... Exception ignored while closing generator : 209s Traceback (most recent call last): 209s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 209s expat_parser.Parse(NULL, True) 209s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 209s ok 209s test_NCBI_qblast ... ok 209s test_NMR ... ok 209s test_Nexus ... ok 209s test_PAML_baseml ... ok 210s test_PAML_codeml ... ok 210s test_PAML_yn00 ... ok 212s test_PDB_CEAligner ... ok 212s test_PDB_DSSP ... ok 212s test_PDB_Dice ... ok 212s test_PDB_Disordered ... ok 212s test_PDB_Exposure ... ok 212s test_PDB_FragmentMapper ... ok 213s test_PDB_KDTree ... ok 213s test_PDB_MMCIF2Dict ... ok 213s test_PDB_MMCIFIO ... ok 214s test_PDB_MMCIFParser ... ok 214s test_PDB_NACCESS ... ok 214s test_PDB_PDBIO ... ok 214s test_PDB_PDBList ... skipping. internet not available 217s test_PDB_PDBMLParser ... ok 217s test_PDB_PDBParser ... ok 217s 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 217s test_PDB_Polypeptide ... ok 217s test_PDB_QCPSuperimposer ... ok 219s test_PDB_SASA ... ok 219s test_PDB_SMCRA ... ok 219s test_PDB_Selection ... ok 219s test_PDB_StructureAlignment ... ok 220s test_PDB_Superimposer ... ok 220s test_PDB_alphafold_db ... skipping. internet not available 220s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 220s 220s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 220s 220s test_PDB_parse_pdb_header ... ok 220s test_PDB_vectors ... ok 220s test_PQR ... ok 220s test_Pathway ... ok 220s test_Phd ... ok 220s test_Phylo ... ok 220s test_PhyloXML ... ok 220s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 220s test_Phylo_NeXML ... ok 220s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 220s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 220s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 220s test_PopGen_GenePop_nodepend ... ok 221s test_ProtParam ... ok 221s test_RCSBFormats ... ok 221s test_Restriction ... ok 221s test_SCOP_Astral ... ok 221s test_SCOP_Cla ... ok 221s test_SCOP_Des ... ok 221s test_SCOP_Dom ... ok 221s test_SCOP_Hie ... ok 221s test_SCOP_Raf ... ok 221s test_SCOP_Residues ... ok 221s test_SCOP_Scop ... ok 221s test_SVDSuperimposer ... ok 221s test_SearchIO_blast_tab ... ok 221s test_SearchIO_blast_tab_index ... ok 221s test_SearchIO_blast_xml ... ok 222s test_SearchIO_blast_xml_index ... ok 222s test_SearchIO_blat_psl ... ok 222s test_SearchIO_blat_psl_index ... ok 222s test_SearchIO_exonerate ... ok 222s test_SearchIO_exonerate_text_index ... ok 222s test_SearchIO_exonerate_vulgar_index ... ok 222s test_SearchIO_fasta_m10 ... ok 222s test_SearchIO_fasta_m10_index ... ok 223s test_SearchIO_hhsuite2_text ... ok 223s test_SearchIO_hmmer2_text ... ok 223s test_SearchIO_hmmer2_text_index ... ok 223s test_SearchIO_hmmer3_domtab ... ok 223s test_SearchIO_hmmer3_domtab_index ... ok 223s test_SearchIO_hmmer3_tab ... ok 223s test_SearchIO_hmmer3_tab_index ... ok 223s test_SearchIO_hmmer3_text ... ok 223s test_SearchIO_hmmer3_text_index ... ok 223s test_SearchIO_infernal_tab ... ok 223s test_SearchIO_infernal_tab_index ... ok 223s test_SearchIO_infernal_text ... ok 223s test_SearchIO_infernal_text_index ... ok 223s test_SearchIO_interproscan_xml ... ok 223s test_SearchIO_model ... ok 223s test_SearchIO_write ... ok 223s test_SeqFeature ... ok 231s test_SeqIO ... ok 231s test_SeqIO_AbiIO ... ok 231s test_SeqIO_FastaIO ... ok 231s test_SeqIO_Gck ... ok 231s test_SeqIO_Gfa ... ok 231s test_SeqIO_Insdc ... ok 231s test_SeqIO_NibIO ... ok 232s test_SeqIO_PdbIO ... ok 232s test_SeqIO_QualityIO ... ok 232s test_SeqIO_SeqXML ... ok 232s test_SeqIO_SffIO ... ok 232s test_SeqIO_SnapGene ... ok 233s test_SeqIO_TwoBitIO ... ok 233s test_SeqIO_UniprotIO ... ok 233s test_SeqIO_Xdna ... ok 233s test_SeqIO_features ... ok 240s test_SeqIO_index ... ok 240s test_SeqIO_online ... skipping. internet not available 240s test_SeqIO_write ... ok 240s test_SeqRecord ... ok 241s test_SeqUtils ... ok 241s test_Seq_objs ... ok 241s test_SwissProt ... ok 241s test_TogoWS ... skipping. internet not available 242s test_TreeConstruction ... ok 242s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 242s test_UniGene ... ok 242s test_UniProt ... skipping. internet not available 242s test_UniProt_GOA ... ok 242s test_align ... ok 242s test_align_substitution_matrices ... ok 243s test_bgzf ... ok 243s test_cellosaurus ... ok 245s test_codonalign ... ok 245s test_geo ... ok 246s test_motifs ... ok 246s test_motifs_online ... skipping. internet not available 246s 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. 246s warnings.warn( 246s ok 246s test_pairwise2_no_C ... ok 246s test_pairwise_aligner ... ok 246s test_pairwise_alignment_map ... ok 250s test_phenotype ... ok 250s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 250s test_prodoc ... ok 250s test_prosite ... ok 250s test_seq ... ok 250s test_translate ... ok 250s Skipping any tests requiring internet access 250s Python version: 3.14.2 (main, Dec 6 2025, 13:20:08) [GCC 15.2.0] 250s Operating system: posix linux 250s ---------------------------------------------------------------------- 250s Ran 201 tests in 61.394 seconds 250s 250s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 250s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 251s autopkgtest [13:47:17]: test dependencies: -----------------------] 251s autopkgtest [13:47:17]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 251s dependencies PASS 251s autopkgtest [13:47:17]: test full_suite: preparing testbed 269s Creating nova instance adt-resolute-amd64-python-biopython-20260124-134306-juju-7f2275-prod-proposed-migration-environment-15-ad478aa2-0cd4-4a65-b608-f711ad983b67 from image adt/ubuntu-resolute-amd64-server-20260124.img (UUID 46811f22-3700-43f4-953b-ee3c613d71bb)... 352s autopkgtest [13:48:58]: testbed dpkg architecture: amd64 353s autopkgtest [13:48:59]: testbed apt version: 3.1.13 353s autopkgtest [13:48:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 353s autopkgtest [13:48:59]: testbed release detected to be: resolute 354s autopkgtest [13:49:00]: updating testbed package index (apt update) 354s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 354s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 354s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 354s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 354s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [92.3 kB] 354s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [998 kB] 355s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 355s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 355s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [115 kB] 355s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [98.2 kB] 355s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3712 B] 355s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 355s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 355s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 355s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [385 kB] 355s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [905 kB] 355s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.9 kB] 355s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.4 kB] 355s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 355s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [824 B] 356s Fetched 2806 kB in 1s (2030 kB/s) 357s Reading package lists... 358s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 358s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 358s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 358s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 359s Reading package lists... 359s Reading package lists... 359s Building dependency tree... 359s Reading state information... 360s Calculating upgrade... 360s The following packages were automatically installed and are no longer required: 360s python3.13 python3.13-minimal 360s Use 'sudo apt autoremove' to remove them. 360s The following NEW packages will be installed: 360s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 360s The following packages will be upgraded: 360s libpython3-stdlib python3 python3-gdbm python3-minimal rust-coreutils 360s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 360s Need to get 10.4 MB of archives. 360s After this operation, 25.2 MB of additional disk space will be used. 360s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 360s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 360s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 360s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 360s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 360s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 360s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 360s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 rust-coreutils amd64 0.5.0-0ubuntu1 [3628 kB] 360s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 361s dpkg-preconfigure: unable to re-open stdin: No such file or directory 361s Fetched 10.4 MB in 1s (16.4 MB/s) 361s Selecting previously unselected package libpython3.14-minimal:amd64. 361s (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 ... 124177 files and directories currently installed.) 361s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 361s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 361s Selecting previously unselected package python3.14-minimal. 361s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 361s Unpacking python3.14-minimal (3.14.2-1) ... 361s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 361s Setting up python3.14-minimal (3.14.2-1) ... 363s (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 ... 124519 files and directories currently installed.) 363s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 363s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 363s Setting up python3-minimal (3.14.2-1) ... 363s (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 ... 124519 files and directories currently installed.) 363s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 363s running python pre-rtupdate hooks for python3.14... 363s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 363s Selecting previously unselected package libpython3.14-stdlib:amd64. 363s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 363s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 363s Selecting previously unselected package python3.14. 363s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 363s Unpacking python3.14 (3.14.2-1) ... 363s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 363s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 363s Preparing to unpack .../rust-coreutils_0.5.0-0ubuntu1_amd64.deb ... 363s Unpacking rust-coreutils (0.5.0-0ubuntu1) over (0.2.2-0ubuntu2) ... 364s Setting up rust-coreutils (0.5.0-0ubuntu1) ... 364s (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 ... 124980 files and directories currently installed.) 364s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 364s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 364s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 364s Setting up python3.14 (3.14.2-1) ... 365s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 365s Setting up python3-gdbm (3.14.2-1) ... 365s Setting up python3 (3.14.2-1) ... 365s running python rtupdate hooks for python3.14... 365s running python post-rtupdate hooks for python3.14... 365s Processing triggers for man-db (2.13.1-1) ... 366s Processing triggers for systemd (259-1ubuntu2) ... 366s autopkgtest [13:49:12]: upgrading testbed (apt dist-upgrade and autopurge) 366s Reading package lists... 366s Building dependency tree... 366s Reading state information... 367s Calculating upgrade... 367s The following packages were automatically installed and are no longer required: 367s python3.13 python3.13-minimal 367s Use 'sudo apt autoremove' to remove them. 367s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 367s Reading package lists... 367s Building dependency tree... 367s Reading state information... 367s Solving dependencies... 367s The following packages will be REMOVED: 367s python3.13* python3.13-minimal* 368s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 368s After this operation, 7860 kB disk space will be freed. 368s (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 ... 124978 files and directories currently installed.) 368s Removing python3.13 (3.13.11-1) ... 368s Removing python3.13-minimal (3.13.11-1) ... 369s Processing triggers for man-db (2.13.1-1) ... 369s Processing triggers for systemd (259-1ubuntu2) ... 369s (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 ... 124951 files and directories currently installed.) 369s Purging configuration files for python3.13-minimal (3.13.11-1) ... 372s Reading package lists... 372s Building dependency tree... 372s Reading state information... 372s Solving dependencies... 372s The following NEW packages will be installed: 372s autoconf automake autopoint autotools-dev build-essential bwa clustalo 372s clustalw cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper 372s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 372s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 372s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 372s fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ 372s g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15 372s gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext ghostscript hevea 372s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 372s intltool-debian libamd-comgr3 libamd3 libamdhip64-6 libaom3 372s libapache-pom-java libarchive-zip-perl libargtable2-0 libarpack2t64 libasan8 372s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libcairo2 372s libcc1-0 libcifpp-data libcifpp9 libcolamd3 libcommons-logging-java 372s libcommons-parent-java libcups2t64 libde265-0 libdebhelper-perl libdeflate0 372s libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfftw3-double3 372s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 372s libgcc-15-dev libgd3 libgfortran5 libglpk40 libgomp1 libgraphite2-3 372s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 372s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhsakmt1 372s libhts3t64 libhtscodecs2 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 372s libibumad3 libice6 libidn12 libigraph4 libijs-0.35 libimagequant0 libisl23 372s libitm1 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery 372s libjson-perl libkpathsea6 liblapack3 liblcms2-2 liblerc4 liblqr-1-0 liblsan0 372s libltdl7 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 372s libmbedtls21 libmbedx509-7 libmpc3 libmpfi0 libmysqlclient24 libncbi-vdb3 372s libnetpbm11t64 libopenjp2-7 libopenmpi40 libpaper-utils libpaper2 372s libpciaccess0 libpdfbox-java libpixman-1-0 libplfit0 libpotrace0 libpq5 372s libpsm2-2 libptexenc1 libpython3-all-dev libpython3-dev libpython3.13-dev 372s libpython3.14 libpython3.14-dev libqhull-r8.0 libquadmath0 libraqm0 372s libraw23t64 librdmacm1t64 libsharpyuv0 libsm6 libstdc++-15-dev 372s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 372s libtiff6 libtk8.6 libtool libtsan2 libubsan1 libucx0 libwebp7 libwebpdemux2 372s libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 372s libxnvctrl0 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 libze1 372s libzopfli1 libzzip-0-13t64 lmodern m4 mafft mpi-default-bin muscle3 372s mysql-common ncbi-blast+ ncbi-data ncbi-vdb-data netpbm ocl-icd-libopencl1 372s openmpi-bin openmpi-common phylip phyml po-debconf poppler-data prank 372s preview-latex-style probcons python-biopython-doc python-matplotlib-data 372s python3-alabaster python3-all python3-all-dev python3-biopython 372s python3-biopython-sql python3-brotli python3-cairo 372s python3-charset-normalizer python3-contourpy python3-cycler 372s python3-decorator python3-defusedxml python3-dev python3-docutils 372s python3-fonttools python3-freetype python3-igraph python3-imagesize 372s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 372s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 372s python3-numpy python3-numpy-dev python3-numpydoc python3-pil 372s python3-pil.imagetk python3-psycopg2 python3-rdflib python3-reportlab 372s python3-rlpycairo python3-roman-numerals python3-scipy 372s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 372s python3-sphinxcontrib.jquery python3-sympy python3-texttable python3-tk 372s python3-ufolib2 python3-zopfli python3.13 python3.13-dev python3.13-minimal 372s python3.13-tk python3.14-dev python3.14-tk raxml samtools sgml-base 372s sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 372s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 372s texlive-latex-extra texlive-latex-recommended texlive-luatex 372s texlive-pictures unicode-data w3c-sgml-lib wise wise-data x11-common 372s xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 373s 0 upgraded, 291 newly installed, 0 to remove and 0 not upgraded. 373s Need to get 541 MB of archives. 373s After this operation, 2216 MB of additional disk space will be used. 373s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-minimal amd64 3.13.11-1 [2408 kB] 373s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 m4 amd64 1.4.20-2 [217 kB] 373s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 flex amd64 2.6.4-8.2build2 [300 kB] 373s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-lato all 2.015-1build1 [2779 kB] 373s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-11ubuntu1 [151 kB] 373s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libfftw3-double3 amd64 3.3.10-2fakesync1build2 [860 kB] 373s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 373s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 373s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build2 [14.1 kB] 373s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 373s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 373s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7build1 [97.1 kB] 373s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8build1 [10.9 MB] 373s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.4ubuntu1 [38.1 kB] 373s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.4ubuntu1 [143 kB] 373s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 373s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libaom3 amd64 3.13.1-2 [1970 kB] 373s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libheif-plugin-aomdec amd64 1.21.2-1 [14.2 kB] 373s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libde265-0 amd64 1.0.16-1build1 [172 kB] 373s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libheif-plugin-libde265 amd64 1.21.2-1 [9978 B] 373s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libheif1 amd64 1.21.2-1 [544 kB] 373s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 373s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 373s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 373s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 373s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblqr-1-0 amd64 0.4.2-2.2 [29.4 kB] 373s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libltdl7 amd64 2.5.4-9 [43.7 kB] 373s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.4-1 [188 kB] 374s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libraw23t64 amd64 0.21.4-2 [376 kB] 374s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 374s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 374s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 374s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 374s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1build1 [12.8 kB] 374s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1build1 [26.4 kB] 374s Get:36 http://ftpmaster.internal/ubuntu resolute/universe amd64 imagemagick-7-common all 8:7.1.2.12+dfsg1-1 [71.8 kB] 374s Get:37 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmagickcore-7.q16-10 amd64 8:7.1.2.12+dfsg1-1 [1966 kB] 374s Get:38 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmagickwand-7.q16-10 amd64 8:7.1.2.12+dfsg1-1 [344 kB] 374s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 poppler-data all 0.4.12-1build1 [2000 kB] 374s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 374s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 374s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-11ubuntu1 [939 kB] 374s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 374s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 374s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13 amd64 3.13.11-1 [758 kB] 374s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 autoconf all 2.72-3.1ubuntu1 [384 kB] 374s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 autotools-dev all 20240727.1 [43.4 kB] 374s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 automake all 1:1.18.1-3build1 [582 kB] 374s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 autopoint all 0.23.2-1 [620 kB] 374s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 374s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 374s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [12.9 MB] 374s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-11ubuntu1 [1030 B] 374s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 374s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 374s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-11ubuntu1 [47.4 kB] 374s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-11ubuntu1 [29.5 kB] 374s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-11ubuntu1 [3070 kB] 374s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-11ubuntu1 [1360 kB] 374s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-11ubuntu1 [2757 kB] 375s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-11ubuntu1 [1210 kB] 375s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-11ubuntu1 [1685 kB] 375s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-11ubuntu1 [153 kB] 375s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-11ubuntu1 [2863 kB] 375s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [25.4 MB] 375s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-11ubuntu1 [528 kB] 375s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 375s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 375s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-11ubuntu1 [2574 kB] 376s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [14.4 MB] 376s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-11ubuntu1 [24.6 kB] 376s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 376s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 376s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 376s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 bwa amd64 0.7.19-1 [200 kB] 376s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 libargtable2-0 amd64 13-4 [15.4 kB] 376s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 clustalo amd64 1.2.4-8build2 [203 kB] 376s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 clustalw amd64 2.1+lgpl-7build1 [254 kB] 376s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 376s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libtool all 2.5.4-9 [169 kB] 376s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-autoreconf all 21 [12.5 kB] 376s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 376s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 376s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 376s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 debugedit amd64 1:5.2-3 [49.9 kB] 376s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 dwz amd64 0.16-2 [115 kB] 376s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 gettext amd64 0.23.2-1 [1019 kB] 376s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 376s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 po-debconf all 1.0.22 [215 kB] 376s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 debhelper all 13.28ubuntu1 [916 kB] 376s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 dh-python all 7.20251231 [122 kB] 376s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 dialign amd64 2.2.1-13build1 [154 kB] 376s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 376s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19build1 [20.3 kB] 376s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 docutils-common all 0.22.4+dfsg-1 [130 kB] 376s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcifpp-data all 9.0.5-2 [483 kB] 376s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcifpp9 amd64 9.0.5-2 [1089 kB] 376s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 dssp amd64 4.5.7-1 [645 kB] 376s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 376s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libxpm4 amd64 1:3.5.17-1build3 [37.3 kB] 376s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libgd3 amd64 2.3.3-13ubuntu1 [130 kB] 376s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1build4 [432 kB] 376s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 mysql-common all 5.8+1.1.1ubuntu2 [7002 B] 376s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 libmysqlclient24 amd64 8.4.7-0ubuntu3 [1258 kB] 376s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 libpq5 amd64 18.1-2 [155 kB] 376s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 emboss-lib amd64 6.6.0+dfsg-15ubuntu3 [3001 kB] 376s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 emboss-data all 6.6.0+dfsg-15ubuntu3 [61.0 MB] 378s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 emboss amd64 6.6.0+dfsg-15ubuntu3 [977 kB] 378s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-extra all 2.37-8build1 [1944 kB] 378s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 378s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lmodern all 2.005-1build1 [4788 kB] 378s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.5.0~RC2-3 [171 kB] 378s Get:113 http://ftpmaster.internal/ubuntu resolute/main amd64 libgs-common all 10.05.0dfsg1-0ubuntu4 [176 kB] 378s Get:114 http://ftpmaster.internal/ubuntu resolute/main amd64 libgs10-common all 10.05.0dfsg1-0ubuntu4 [490 kB] 378s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-common-data amd64 0.8-17ubuntu2 [31.5 kB] 378s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-common3 amd64 0.8-17ubuntu2 [23.7 kB] 378s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 libavahi-client3 amd64 0.8-17ubuntu2 [27.3 kB] 378s Get:118 http://ftpmaster.internal/ubuntu resolute/main amd64 libcups2t64 amd64 2.4.16-1ubuntu1 [273 kB] 378s Get:119 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn12 amd64 1.43-2 [60.1 kB] 378s Get:120 http://ftpmaster.internal/ubuntu resolute/main amd64 libijs-0.35 amd64 0.35-16 [15.6 kB] 378s Get:121 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig2dec0 amd64 0.20-1build4 [65.6 kB] 378s Get:122 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 378s Get:123 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 378s Get:124 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1 [16.4 kB] 378s Get:125 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 378s Get:126 http://ftpmaster.internal/ubuntu resolute/main amd64 libgs10 amd64 10.05.0dfsg1-0ubuntu4 [3777 kB] 378s Get:127 http://ftpmaster.internal/ubuntu resolute/main amd64 ghostscript amd64 10.05.0dfsg1-0ubuntu4 [42.8 kB] 378s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnetpbm11t64 amd64 2:11.10.02-1build1 [114 kB] 378s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 netpbm amd64 2:11.10.02-1build1 [2096 kB] 378s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 tex-common all 6.20 [30.0 kB] 378s Get:131 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 378s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 libkpathsea6 amd64 2025.20250727.75242+ds-5build1 [66.0 kB] 378s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 libptexenc1 amd64 2025.20250727.75242+ds-5build1 [46.4 kB] 378s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsynctex2 amd64 2025.20250727.75242+ds-5build1 [62.1 kB] 378s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-5build1 [125 kB] 378s Get:136 http://ftpmaster.internal/ubuntu resolute/main amd64 t1utils amd64 1.41-4build4 [62.7 kB] 378s Get:137 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 378s Get:138 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 378s Get:139 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 378s Get:140 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 378s Get:141 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 379s Get:142 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 379s Get:143 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.0-4 [529 kB] 379s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] 379s Get:145 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpotrace0 amd64 1.16-2build2 [17.9 kB] 379s Get:146 http://ftpmaster.internal/ubuntu resolute/universe amd64 libteckit0 amd64 2.5.13+ds-1 [431 kB] 379s Get:147 http://ftpmaster.internal/ubuntu resolute/main amd64 libxmu6 amd64 2:1.1.3-4 [48.9 kB] 379s Get:148 http://ftpmaster.internal/ubuntu resolute/main amd64 libxaw7 amd64 2:1.0.16-1build1 [190 kB] 379s Get:149 http://ftpmaster.internal/ubuntu resolute/main amd64 libxi6 amd64 2:1.8.2-2 [33.1 kB] 379s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.2 [30.1 kB] 379s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-binaries amd64 2025.20250727.75242+ds-5build1 [8747 kB] 379s Get:152 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 379s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-base all 2025.20251127-1 [22.8 MB] 379s Get:154 http://ftpmaster.internal/ubuntu resolute/main amd64 hicolor-icon-theme all 0.18-2build1 [13.2 kB] 379s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 imagemagick-7.q16 amd64 8:7.1.2.12+dfsg1-1 [703 kB] 379s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 imagemagick amd64 8:7.1.2.12+dfsg1-1 [14.1 kB] 379s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 hevea amd64 2.36-2build3 [2276 kB] 379s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd-comgr3 amd64 7.1.0+dfsg-0ubuntu2 [15.2 MB] 379s Get:159 http://ftpmaster.internal/ubuntu resolute/main amd64 libsuitesparseconfig7 amd64 1:7.12.1+dfsg-1 [22.0 kB] 379s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd3 amd64 1:7.12.1+dfsg-1 [35.8 kB] 379s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsakmt1 amd64 6.4.3+dfsg-3 [67.5 kB] 379s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-3 [630 kB] 379s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamdhip64-6 amd64 6.4.3-4 [10.3 MB] 380s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 libapache-pom-java all 33-2build1 [5976 B] 380s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 libarpack2t64 amd64 3.9.1-6 [108 kB] 380s Get:166 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolamd3 amd64 1:7.12.1+dfsg-1 [27.4 kB] 380s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-parent-java all 56-1build1 [11.1 kB] 380s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 380s Get:169 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10build1 [8360 B] 380s Get:170 http://ftpmaster.internal/ubuntu resolute/main amd64 libexpat1-dev amd64 2.7.3-1 [143 kB] 380s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 380s Get:172 http://ftpmaster.internal/ubuntu resolute/main amd64 librdmacm1t64 amd64 61.0-2ubuntu1 [73.7 kB] 380s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfabric1 amd64 2.1.0-1.1 [697 kB] 380s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 libglpk40 amd64 5.0-2 [380 kB] 380s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2build1 [108 kB] 380s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.22.1+ds2-1 [461 kB] 380s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc15 amd64 2.12.2-1 [181 kB] 380s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 libplfit0 amd64 0.9.6+ds-2ubuntu1 [31.9 kB] 380s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 libigraph4 amd64 1.0.1+ds-3 [1325 kB] 380s Get:180 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 380s Get:181 http://ftpmaster.internal/ubuntu resolute/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 380s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedcrypto16 amd64 3.6.5-0.1ubuntu2 [259 kB] 380s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedx509-7 amd64 3.6.5-0.1ubuntu2 [35.4 kB] 380s Get:184 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmbedtls21 amd64 3.6.5-0.1ubuntu2 [130 kB] 380s Get:185 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [81.3 kB] 380s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1376 kB] 380s Get:187 http://ftpmaster.internal/ubuntu resolute/main amd64 libibumad3 amd64 61.0-2ubuntu1 [31.5 kB] 380s Get:188 http://ftpmaster.internal/ubuntu resolute/main amd64 libibmad5 amd64 61.0-2ubuntu1 [44.2 kB] 380s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 libucx0 amd64 1.20.0+ds-4 [951 kB] 380s Get:190 http://ftpmaster.internal/ubuntu resolute/main amd64 libpciaccess0 amd64 0.18.1-1ubuntu2 [19.0 kB] 380s Get:191 http://ftpmaster.internal/ubuntu resolute/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu6 [13.0 kB] 380s Get:192 http://ftpmaster.internal/ubuntu resolute/universe amd64 libze1 amd64 1.27.0-1 [630 kB] 380s Get:193 http://ftpmaster.internal/ubuntu resolute/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1 [40.9 kB] 380s Get:194 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc-plugins amd64 2.12.2-1 [22.2 kB] 380s Get:195 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenmpi40 amd64 5.0.8-8ubuntu1 [3384 kB] 380s Get:196 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 380s Get:197 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB] 380s Get:198 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-dev amd64 3.14.2-1 [5963 kB] 380s Get:199 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-dev amd64 3.14.2-1 [11.2 kB] 380s Get:200 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.13-dev amd64 3.13.11-1 [5798 kB] 380s Get:201 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-all-dev amd64 3.14.2-1 [916 B] 380s Get:202 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-8 [197 kB] 380s Get:203 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 380s Get:204 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 380s Get:205 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 380s Get:206 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 380s Get:207 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 380s Get:208 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 380s Get:209 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 380s Get:210 http://ftpmaster.internal/ubuntu resolute/universe amd64 lmodern all 2.005-1build1 [9538 kB] 381s Get:211 http://ftpmaster.internal/ubuntu resolute/universe amd64 mafft amd64 7.525-1 [841 kB] 381s Get:212 http://ftpmaster.internal/ubuntu resolute/universe amd64 muscle3 amd64 3.8.1551-3build1 [216 kB] 381s Get:213 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-data all 6.1.20170106+dfsg2-7 [3969 kB] 381s Get:214 http://ftpmaster.internal/ubuntu resolute/universe amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] 381s Get:215 http://ftpmaster.internal/ubuntu resolute/universe amd64 openmpi-common all 5.0.8-8ubuntu1 [108 kB] 381s Get:216 http://ftpmaster.internal/ubuntu resolute/universe amd64 openmpi-bin amd64 5.0.8-8ubuntu1 [201 kB] 381s Get:217 http://ftpmaster.internal/ubuntu resolute/universe amd64 phylip amd64 1:3.697+dfsg-4build2 [879 kB] 381s Get:218 http://ftpmaster.internal/ubuntu resolute/universe amd64 mpi-default-bin amd64 1.20 [2658 B] 381s Get:219 http://ftpmaster.internal/ubuntu resolute/universe amd64 phyml amd64 3:3.3.20220408-4build1 [1081 kB] 381s Get:220 http://ftpmaster.internal/ubuntu resolute/universe amd64 prank amd64 250331-1 [346 kB] 381s Get:221 http://ftpmaster.internal/ubuntu resolute/universe amd64 preview-latex-style all 13.2-1.1 [347 kB] 381s Get:222 http://ftpmaster.internal/ubuntu resolute/universe amd64 probcons amd64 1.12-15 [138 kB] 381s Get:223 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 382s Get:224 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 382s Get:225 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.14.2-1 [890 B] 382s Get:226 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-dev amd64 3.14.2-1 [510 kB] 382s Get:227 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-dev amd64 3.14.2-1 [26.6 kB] 382s Get:228 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-dev amd64 3.13.11-1 [508 kB] 382s Get:229 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all-dev amd64 3.14.2-1 [914 B] 382s Get:230 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.4-2 [173 kB] 382s Get:231 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.11-1 [108 kB] 382s Get:232 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.2-1 [109 kB] 382s Get:233 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-tk amd64 3.14.2-1 [11.2 kB] 382s Get:234 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 12.0.0-1ubuntu1 [9700 B] 382s Get:235 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 12.0.0-1ubuntu1 [494 kB] 382s Get:236 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 382s Get:237 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 382s Get:238 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 382s Get:239 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.9-1 [1149 kB] 382s Get:240 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3build1 [278 kB] 382s Get:241 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.86+dfsg-1 [1682 kB] 382s Get:242 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython-sql all 1.86+dfsg-1 [26.4 kB] 382s Get:243 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 382s Get:244 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.3-1 [255 kB] 382s Get:245 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 382s Get:246 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 382s Get:247 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-defusedxml all 0.7.1-3build1 [42.4 kB] 382s Get:248 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-roman-numerals all 4.1.0-1 [8660 B] 382s Get:249 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-docutils all 0.22.4+dfsg-1 [439 kB] 382s Get:250 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 382s Get:251 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.5+dfsg-1 [27.7 kB] 382s Get:252 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.16.3-3 [18.8 MB] 382s Get:253 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 382s Get:254 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 382s Get:255 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.18.1+dfsg1-1 [33.7 kB] 382s Get:256 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 382s Get:257 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1build1 [9543 kB] 382s Get:258 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.61.1-3 [1742 kB] 382s Get:259 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-imagesize all 1.4.1-1build1 [6900 B] 382s Get:260 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 382s Get:261 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 383s Get:262 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-msgpack amd64 1.1.2-1 [107 kB] 383s Get:263 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mmtf all 1.1.3-1build1 [16.4 kB] 383s Get:264 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-mysqldb amd64 1.4.6-2build7 [51.4 kB] 383s Get:265 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-networkx all 3.2.1-4ubuntu2 [11.8 MB] 383s Get:266 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-common all 8.2.3-12 [657 kB] 383s Get:267 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 383s Get:268 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-snowballstemmer all 3.0.1-1 [65.9 kB] 383s Get:269 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-sphinx all 8.2.3-12 [483 kB] 383s Get:270 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-numpydoc all 1.9.0-1 [53.2 kB] 383s Get:271 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-psycopg2 amd64 2.9.11-1 [164 kB] 383s Get:272 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rdflib all 7.1.1-3 [427 kB] 383s Get:273 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 383s Get:274 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 383s Get:275 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 383s Get:276 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-texttable all 1.7.0-1 [11.2 kB] 383s Get:277 http://ftpmaster.internal/ubuntu resolute/universe amd64 raxml amd64 8.2.13+dfsg-3 [1715 kB] 383s Get:278 http://ftpmaster.internal/ubuntu resolute/universe amd64 samtools amd64 1.22.1-1 [645 kB] 383s Get:279 http://ftpmaster.internal/ubuntu resolute/universe amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1build1 [934 kB] 383s Get:280 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-fonts-recommended all 2025.20251127-1 [4972 kB] 383s Get:281 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-luatex all 2025.20251127-1 [36.0 MB] 384s Get:282 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-latex-base all 2025.20251127-1 [1309 kB] 384s Get:283 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfontbox-java all 1:1.8.16-5 [208 kB] 384s Get:284 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 384s Get:285 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-latex-recommended all 2025.20251127-1 [8494 kB] 384s Get:286 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-pictures all 2025.20251127-1 [23.5 MB] 384s Get:287 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-latex-extra all 2025.20251127-2 [32.5 MB] 385s Get:288 http://ftpmaster.internal/ubuntu resolute/universe amd64 wise-data all 2.4.1-27 [83.2 kB] 385s Get:289 http://ftpmaster.internal/ubuntu resolute/universe amd64 wise amd64 2.4.1-27 [838 kB] 385s Get:290 http://ftpmaster.internal/ubuntu resolute/universe amd64 fasttree amd64 2.1.11-2build1 [188 kB] 385s Get:291 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-igraph amd64 1.0.0+ds-1 [349 kB] 386s Preconfiguring packages ... 386s Fetched 541 MB in 13s (43.1 MB/s) 386s Selecting previously unselected package python3.13-minimal. 386s (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 ... 124953 files and directories currently installed.) 386s Preparing to unpack .../000-python3.13-minimal_3.13.11-1_amd64.deb ... 386s Unpacking python3.13-minimal (3.13.11-1) ... 386s Selecting previously unselected package m4. 386s Preparing to unpack .../001-m4_1.4.20-2_amd64.deb ... 386s Unpacking m4 (1.4.20-2) ... 386s Selecting previously unselected package flex. 386s Preparing to unpack .../002-flex_2.6.4-8.2build2_amd64.deb ... 386s Unpacking flex (2.6.4-8.2build2) ... 386s Selecting previously unselected package fonts-lato. 386s Preparing to unpack .../003-fonts-lato_2.015-1build1_all.deb ... 386s Unpacking fonts-lato (2.015-1build1) ... 386s Selecting previously unselected package libgomp1:amd64. 386s Preparing to unpack .../004-libgomp1_15.2.0-11ubuntu1_amd64.deb ... 386s Unpacking libgomp1:amd64 (15.2.0-11ubuntu1) ... 386s Selecting previously unselected package libfftw3-double3:amd64. 386s Preparing to unpack .../005-libfftw3-double3_3.3.10-2fakesync1build2_amd64.deb ... 386s Unpacking libfftw3-double3:amd64 (3.3.10-2fakesync1build2) ... 386s Selecting previously unselected package fonts-dejavu-mono. 386s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8build1_all.deb ... 386s Unpacking fonts-dejavu-mono (2.37-8build1) ... 386s Selecting previously unselected package fonts-dejavu-core. 386s Preparing to unpack .../007-fonts-dejavu-core_2.37-8build1_all.deb ... 386s Unpacking fonts-dejavu-core (2.37-8build1) ... 386s Selecting previously unselected package libfontenc1:amd64. 386s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build2_amd64.deb ... 386s Unpacking libfontenc1:amd64 (1:1.1.8-1build2) ... 386s Selecting previously unselected package x11-common. 386s Preparing to unpack .../009-x11-common_1%3a7.7+24ubuntu1_all.deb ... 386s Unpacking x11-common (1:7.7+24ubuntu1) ... 386s Selecting previously unselected package xfonts-encodings. 386s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 386s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 386s Selecting previously unselected package xfonts-utils. 386s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7build1_amd64.deb ... 386s Unpacking xfonts-utils (1:7.7+7build1) ... 386s Selecting previously unselected package fonts-urw-base35. 386s Preparing to unpack .../012-fonts-urw-base35_20200910-8build1_all.deb ... 386s Unpacking fonts-urw-base35 (20200910-8build1) ... 387s Selecting previously unselected package fontconfig-config. 387s Preparing to unpack .../013-fontconfig-config_2.15.0-2.4ubuntu1_amd64.deb ... 387s Unpacking fontconfig-config (2.15.0-2.4ubuntu1) ... 387s Selecting previously unselected package libfontconfig1:amd64. 387s Preparing to unpack .../014-libfontconfig1_2.15.0-2.4ubuntu1_amd64.deb ... 387s Unpacking libfontconfig1:amd64 (2.15.0-2.4ubuntu1) ... 387s Selecting previously unselected package libsharpyuv0:amd64. 387s Preparing to unpack .../015-libsharpyuv0_1.5.0-0.1build1_amd64.deb ... 387s Unpacking libsharpyuv0:amd64 (1.5.0-0.1build1) ... 387s Selecting previously unselected package libaom3:amd64. 387s Preparing to unpack .../016-libaom3_3.13.1-2_amd64.deb ... 387s Unpacking libaom3:amd64 (3.13.1-2) ... 387s Selecting previously unselected package libheif-plugin-aomdec:amd64. 387s Preparing to unpack .../017-libheif-plugin-aomdec_1.21.2-1_amd64.deb ... 387s Unpacking libheif-plugin-aomdec:amd64 (1.21.2-1) ... 387s Selecting previously unselected package libde265-0:amd64. 387s Preparing to unpack .../018-libde265-0_1.0.16-1build1_amd64.deb ... 387s Unpacking libde265-0:amd64 (1.0.16-1build1) ... 387s Selecting previously unselected package libheif-plugin-libde265:amd64. 387s Preparing to unpack .../019-libheif-plugin-libde265_1.21.2-1_amd64.deb ... 387s Unpacking libheif-plugin-libde265:amd64 (1.21.2-1) ... 387s Selecting previously unselected package libheif1:amd64. 387s Preparing to unpack .../020-libheif1_1.21.2-1_amd64.deb ... 387s Unpacking libheif1:amd64 (1.21.2-1) ... 387s Selecting previously unselected package libjbig0:amd64. 387s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu3_amd64.deb ... 387s Unpacking libjbig0:amd64 (2.1-6.1ubuntu3) ... 387s Selecting previously unselected package libjpeg-turbo8:amd64. 387s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 387s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 387s Selecting previously unselected package libjpeg8:amd64. 387s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_amd64.deb ... 387s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 387s Selecting previously unselected package liblcms2-2:amd64. 387s Preparing to unpack .../024-liblcms2-2_2.17-1_amd64.deb ... 387s Unpacking liblcms2-2:amd64 (2.17-1) ... 387s Selecting previously unselected package liblqr-1-0:amd64. 387s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.2_amd64.deb ... 387s Unpacking liblqr-1-0:amd64 (0.4.2-2.2) ... 387s Selecting previously unselected package libltdl7:amd64. 387s Preparing to unpack .../026-libltdl7_2.5.4-9_amd64.deb ... 387s Unpacking libltdl7:amd64 (2.5.4-9) ... 387s Selecting previously unselected package libopenjp2-7:amd64. 387s Preparing to unpack .../027-libopenjp2-7_2.5.4-1_amd64.deb ... 387s Unpacking libopenjp2-7:amd64 (2.5.4-1) ... 387s Selecting previously unselected package libraw23t64:amd64. 387s Preparing to unpack .../028-libraw23t64_0.21.4-2_amd64.deb ... 387s Unpacking libraw23t64:amd64 (0.21.4-2) ... 387s Selecting previously unselected package libdeflate0:amd64. 387s Preparing to unpack .../029-libdeflate0_1.23-2_amd64.deb ... 387s Unpacking libdeflate0:amd64 (1.23-2) ... 387s Selecting previously unselected package liblerc4:amd64. 387s Preparing to unpack .../030-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ... 387s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 387s Selecting previously unselected package libwebp7:amd64. 387s Preparing to unpack .../031-libwebp7_1.5.0-0.1build1_amd64.deb ... 387s Unpacking libwebp7:amd64 (1.5.0-0.1build1) ... 387s Selecting previously unselected package libtiff6:amd64. 387s Preparing to unpack .../032-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 387s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 387s Selecting previously unselected package libwebpdemux2:amd64. 387s Preparing to unpack .../033-libwebpdemux2_1.5.0-0.1build1_amd64.deb ... 387s Unpacking libwebpdemux2:amd64 (1.5.0-0.1build1) ... 387s Selecting previously unselected package libwebpmux3:amd64. 387s Preparing to unpack .../034-libwebpmux3_1.5.0-0.1build1_amd64.deb ... 387s Unpacking libwebpmux3:amd64 (1.5.0-0.1build1) ... 387s Selecting previously unselected package imagemagick-7-common. 387s Preparing to unpack .../035-imagemagick-7-common_8%3a7.1.2.12+dfsg1-1_all.deb ... 387s Unpacking imagemagick-7-common (8:7.1.2.12+dfsg1-1) ... 387s Selecting previously unselected package libmagickcore-7.q16-10:amd64. 387s Preparing to unpack .../036-libmagickcore-7.q16-10_8%3a7.1.2.12+dfsg1-1_amd64.deb ... 387s Unpacking libmagickcore-7.q16-10:amd64 (8:7.1.2.12+dfsg1-1) ... 387s Selecting previously unselected package libmagickwand-7.q16-10:amd64. 387s Preparing to unpack .../037-libmagickwand-7.q16-10_8%3a7.1.2.12+dfsg1-1_amd64.deb ... 387s Unpacking libmagickwand-7.q16-10:amd64 (8:7.1.2.12+dfsg1-1) ... 387s Selecting previously unselected package poppler-data. 387s Preparing to unpack .../038-poppler-data_0.4.12-1build1_all.deb ... 387s Unpacking poppler-data (0.4.12-1build1) ... 388s Selecting previously unselected package python3-numpy-dev:amd64. 388s Preparing to unpack .../039-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 388s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 388s Selecting previously unselected package libblas3:amd64. 388s Preparing to unpack .../040-libblas3_3.12.1-7ubuntu1_amd64.deb ... 388s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 388s Selecting previously unselected package libgfortran5:amd64. 388s Preparing to unpack .../041-libgfortran5_15.2.0-11ubuntu1_amd64.deb ... 388s Unpacking libgfortran5:amd64 (15.2.0-11ubuntu1) ... 388s Selecting previously unselected package liblapack3:amd64. 388s Preparing to unpack .../042-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 388s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 388s Selecting previously unselected package python3-numpy. 388s Preparing to unpack .../043-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 388s Unpacking python3-numpy (1:2.3.5+ds-3) ... 388s Selecting previously unselected package python3.13. 388s Preparing to unpack .../044-python3.13_3.13.11-1_amd64.deb ... 388s Unpacking python3.13 (3.13.11-1) ... 388s Selecting previously unselected package autoconf. 388s Preparing to unpack .../045-autoconf_2.72-3.1ubuntu1_all.deb ... 388s Unpacking autoconf (2.72-3.1ubuntu1) ... 388s Selecting previously unselected package autotools-dev. 388s Preparing to unpack .../046-autotools-dev_20240727.1_all.deb ... 388s Unpacking autotools-dev (20240727.1) ... 388s Selecting previously unselected package automake. 388s Preparing to unpack .../047-automake_1%3a1.18.1-3build1_all.deb ... 388s Unpacking automake (1:1.18.1-3build1) ... 388s Selecting previously unselected package autopoint. 388s Preparing to unpack .../048-autopoint_0.23.2-1_all.deb ... 388s Unpacking autopoint (0.23.2-1) ... 388s Selecting previously unselected package libisl23:amd64. 388s Preparing to unpack .../049-libisl23_0.27-1build1_amd64.deb ... 388s Unpacking libisl23:amd64 (0.27-1build1) ... 388s Selecting previously unselected package libmpc3:amd64. 388s Preparing to unpack .../050-libmpc3_1.3.1-2_amd64.deb ... 388s Unpacking libmpc3:amd64 (1.3.1-2) ... 388s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 388s Preparing to unpack .../051-cpp-15-x86-64-linux-gnu_15.2.0-11ubuntu1_amd64.deb ... 388s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 388s Selecting previously unselected package cpp-15. 388s Preparing to unpack .../052-cpp-15_15.2.0-11ubuntu1_amd64.deb ... 388s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 388s Selecting previously unselected package cpp-x86-64-linux-gnu. 388s Preparing to unpack .../053-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 388s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 388s Selecting previously unselected package cpp. 388s Preparing to unpack .../054-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 388s Unpacking cpp (4:15.2.0-4ubuntu1) ... 388s Selecting previously unselected package libcc1-0:amd64. 388s Preparing to unpack .../055-libcc1-0_15.2.0-11ubuntu1_amd64.deb ... 388s Unpacking libcc1-0:amd64 (15.2.0-11ubuntu1) ... 388s Selecting previously unselected package libitm1:amd64. 388s Preparing to unpack .../056-libitm1_15.2.0-11ubuntu1_amd64.deb ... 388s Unpacking libitm1:amd64 (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package libasan8:amd64. 389s Preparing to unpack .../057-libasan8_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking libasan8:amd64 (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package liblsan0:amd64. 389s Preparing to unpack .../058-liblsan0_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking liblsan0:amd64 (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package libtsan2:amd64. 389s Preparing to unpack .../059-libtsan2_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking libtsan2:amd64 (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package libubsan1:amd64. 389s Preparing to unpack .../060-libubsan1_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking libubsan1:amd64 (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package libhwasan0:amd64. 389s Preparing to unpack .../061-libhwasan0_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking libhwasan0:amd64 (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package libquadmath0:amd64. 389s Preparing to unpack .../062-libquadmath0_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking libquadmath0:amd64 (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package libgcc-15-dev:amd64. 389s Preparing to unpack .../063-libgcc-15-dev_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking libgcc-15-dev:amd64 (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 389s Preparing to unpack .../064-gcc-15-x86-64-linux-gnu_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package gcc-15. 389s Preparing to unpack .../065-gcc-15_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking gcc-15 (15.2.0-11ubuntu1) ... 389s Selecting previously unselected package gcc-x86-64-linux-gnu. 389s Preparing to unpack .../066-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 389s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 389s Selecting previously unselected package gcc. 389s Preparing to unpack .../067-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 389s Unpacking gcc (4:15.2.0-4ubuntu1) ... 389s Selecting previously unselected package libstdc++-15-dev:amd64. 389s Preparing to unpack .../068-libstdc++-15-dev_15.2.0-11ubuntu1_amd64.deb ... 389s Unpacking libstdc++-15-dev:amd64 (15.2.0-11ubuntu1) ... 390s Selecting previously unselected package g++-15-x86-64-linux-gnu. 390s Preparing to unpack .../069-g++-15-x86-64-linux-gnu_15.2.0-11ubuntu1_amd64.deb ... 390s Unpacking g++-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 390s Selecting previously unselected package g++-15. 390s Preparing to unpack .../070-g++-15_15.2.0-11ubuntu1_amd64.deb ... 390s Unpacking g++-15 (15.2.0-11ubuntu1) ... 390s Selecting previously unselected package g++-x86-64-linux-gnu. 390s Preparing to unpack .../071-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 390s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 390s Selecting previously unselected package g++. 390s Preparing to unpack .../072-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 390s Unpacking g++ (4:15.2.0-4ubuntu1) ... 390s Selecting previously unselected package build-essential. 390s Preparing to unpack .../073-build-essential_12.12ubuntu2_amd64.deb ... 390s Unpacking build-essential (12.12ubuntu2) ... 390s Selecting previously unselected package bwa. 390s Preparing to unpack .../074-bwa_0.7.19-1_amd64.deb ... 390s Unpacking bwa (0.7.19-1) ... 390s Selecting previously unselected package libargtable2-0:amd64. 390s Preparing to unpack .../075-libargtable2-0_13-4_amd64.deb ... 390s Unpacking libargtable2-0:amd64 (13-4) ... 390s Selecting previously unselected package clustalo. 390s Preparing to unpack .../076-clustalo_1.2.4-8build2_amd64.deb ... 390s Unpacking clustalo (1.2.4-8build2) ... 390s Selecting previously unselected package clustalw. 390s Preparing to unpack .../077-clustalw_2.1+lgpl-7build1_amd64.deb ... 390s Unpacking clustalw (2.1+lgpl-7build1) ... 390s Selecting previously unselected package libdebhelper-perl. 390s Preparing to unpack .../078-libdebhelper-perl_13.28ubuntu1_all.deb ... 390s Unpacking libdebhelper-perl (13.28ubuntu1) ... 390s Selecting previously unselected package libtool. 390s Preparing to unpack .../079-libtool_2.5.4-9_all.deb ... 390s Unpacking libtool (2.5.4-9) ... 390s Selecting previously unselected package dh-autoreconf. 390s Preparing to unpack .../080-dh-autoreconf_21_all.deb ... 390s Unpacking dh-autoreconf (21) ... 390s Selecting previously unselected package libarchive-zip-perl. 390s Preparing to unpack .../081-libarchive-zip-perl_1.68-1_all.deb ... 390s Unpacking libarchive-zip-perl (1.68-1) ... 390s Selecting previously unselected package libfile-stripnondeterminism-perl. 390s Preparing to unpack .../082-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 390s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 390s Selecting previously unselected package dh-strip-nondeterminism. 390s Preparing to unpack .../083-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 390s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 390s Selecting previously unselected package debugedit. 390s Preparing to unpack .../084-debugedit_1%3a5.2-3_amd64.deb ... 390s Unpacking debugedit (1:5.2-3) ... 390s Selecting previously unselected package dwz. 390s Preparing to unpack .../085-dwz_0.16-2_amd64.deb ... 390s Unpacking dwz (0.16-2) ... 390s Selecting previously unselected package gettext. 390s Preparing to unpack .../086-gettext_0.23.2-1_amd64.deb ... 390s Unpacking gettext (0.23.2-1) ... 390s Selecting previously unselected package intltool-debian. 390s Preparing to unpack .../087-intltool-debian_0.35.0+20060710.6build1_all.deb ... 390s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 390s Selecting previously unselected package po-debconf. 390s Preparing to unpack .../088-po-debconf_1.0.22_all.deb ... 390s Unpacking po-debconf (1.0.22) ... 390s Selecting previously unselected package debhelper. 390s Preparing to unpack .../089-debhelper_13.28ubuntu1_all.deb ... 390s Unpacking debhelper (13.28ubuntu1) ... 390s Selecting previously unselected package dh-python. 390s Preparing to unpack .../090-dh-python_7.20251231_all.deb ... 390s Unpacking dh-python (7.20251231) ... 390s Selecting previously unselected package dialign. 390s Preparing to unpack .../091-dialign_2.2.1-13build1_amd64.deb ... 390s Unpacking dialign (2.2.1-13build1) ... 390s Selecting previously unselected package sgml-base. 390s Preparing to unpack .../092-sgml-base_1.31+nmu1_all.deb ... 390s Unpacking sgml-base (1.31+nmu1) ... 390s Selecting previously unselected package xml-core. 390s Preparing to unpack .../093-xml-core_0.19build1_all.deb ... 391s Unpacking xml-core (0.19build1) ... 391s Selecting previously unselected package docutils-common. 391s Preparing to unpack .../094-docutils-common_0.22.4+dfsg-1_all.deb ... 391s Unpacking docutils-common (0.22.4+dfsg-1) ... 391s Selecting previously unselected package libcifpp-data. 391s Preparing to unpack .../095-libcifpp-data_9.0.5-2_all.deb ... 391s Unpacking libcifpp-data (9.0.5-2) ... 391s Selecting previously unselected package libcifpp9:amd64. 391s Preparing to unpack .../096-libcifpp9_9.0.5-2_amd64.deb ... 391s Unpacking libcifpp9:amd64 (9.0.5-2) ... 391s Selecting previously unselected package dssp. 391s Preparing to unpack .../097-dssp_4.5.7-1_amd64.deb ... 391s Unpacking dssp (4.5.7-1) ... 391s Selecting previously unselected package libimagequant0:amd64. 391s Preparing to unpack .../098-libimagequant0_2.18.0-1build1_amd64.deb ... 391s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 391s Selecting previously unselected package libxpm4:amd64. 391s Preparing to unpack .../099-libxpm4_1%3a3.5.17-1build3_amd64.deb ... 391s Unpacking libxpm4:amd64 (1:3.5.17-1build3) ... 391s Selecting previously unselected package libgd3:amd64. 391s Preparing to unpack .../100-libgd3_2.3.3-13ubuntu1_amd64.deb ... 391s Unpacking libgd3:amd64 (2.3.3-13ubuntu1) ... 391s Selecting previously unselected package libhpdf-2.3.0:amd64. 391s Preparing to unpack .../101-libhpdf-2.3.0_2.3.0+dfsg-1build4_amd64.deb ... 391s Unpacking libhpdf-2.3.0:amd64 (2.3.0+dfsg-1build4) ... 391s Selecting previously unselected package mysql-common. 391s Preparing to unpack .../102-mysql-common_5.8+1.1.1ubuntu2_all.deb ... 391s Unpacking mysql-common (5.8+1.1.1ubuntu2) ... 391s Selecting previously unselected package libmysqlclient24:amd64. 391s Preparing to unpack .../103-libmysqlclient24_8.4.7-0ubuntu3_amd64.deb ... 391s Unpacking libmysqlclient24:amd64 (8.4.7-0ubuntu3) ... 391s Selecting previously unselected package libpq5:amd64. 391s Preparing to unpack .../104-libpq5_18.1-2_amd64.deb ... 391s Unpacking libpq5:amd64 (18.1-2) ... 391s Selecting previously unselected package emboss-lib. 391s Preparing to unpack .../105-emboss-lib_6.6.0+dfsg-15ubuntu3_amd64.deb ... 391s Unpacking emboss-lib (6.6.0+dfsg-15ubuntu3) ... 391s Selecting previously unselected package emboss-data. 391s Preparing to unpack .../106-emboss-data_6.6.0+dfsg-15ubuntu3_all.deb ... 391s Unpacking emboss-data (6.6.0+dfsg-15ubuntu3) ... 394s Selecting previously unselected package emboss. 394s Preparing to unpack .../107-emboss_6.6.0+dfsg-15ubuntu3_amd64.deb ... 394s Unpacking emboss (6.6.0+dfsg-15ubuntu3) ... 395s Selecting previously unselected package fonts-dejavu-extra. 395s Preparing to unpack .../108-fonts-dejavu-extra_2.37-8build1_all.deb ... 395s Unpacking fonts-dejavu-extra (2.37-8build1) ... 395s Selecting previously unselected package fonts-font-awesome. 395s Preparing to unpack .../109-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ... 395s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 395s Selecting previously unselected package fonts-lmodern. 395s Preparing to unpack .../110-fonts-lmodern_2.005-1build1_all.deb ... 395s Unpacking fonts-lmodern (2.005-1build1) ... 395s Selecting previously unselected package fonts-lyx. 395s Preparing to unpack .../111-fonts-lyx_2.5.0~RC2-3_all.deb ... 395s Unpacking fonts-lyx (2.5.0~RC2-3) ... 395s Selecting previously unselected package libgs-common. 395s Preparing to unpack .../112-libgs-common_10.05.0dfsg1-0ubuntu4_all.deb ... 395s Unpacking libgs-common (10.05.0dfsg1-0ubuntu4) ... 395s Selecting previously unselected package libgs10-common. 395s Preparing to unpack .../113-libgs10-common_10.05.0dfsg1-0ubuntu4_all.deb ... 395s Unpacking libgs10-common (10.05.0dfsg1-0ubuntu4) ... 395s Selecting previously unselected package libavahi-common-data:amd64. 395s Preparing to unpack .../114-libavahi-common-data_0.8-17ubuntu2_amd64.deb ... 395s Unpacking libavahi-common-data:amd64 (0.8-17ubuntu2) ... 395s Selecting previously unselected package libavahi-common3:amd64. 395s Preparing to unpack .../115-libavahi-common3_0.8-17ubuntu2_amd64.deb ... 395s Unpacking libavahi-common3:amd64 (0.8-17ubuntu2) ... 395s Selecting previously unselected package libavahi-client3:amd64. 395s Preparing to unpack .../116-libavahi-client3_0.8-17ubuntu2_amd64.deb ... 395s Unpacking libavahi-client3:amd64 (0.8-17ubuntu2) ... 395s Selecting previously unselected package libcups2t64:amd64. 395s Preparing to unpack .../117-libcups2t64_2.4.16-1ubuntu1_amd64.deb ... 395s Unpacking libcups2t64:amd64 (2.4.16-1ubuntu1) ... 395s Selecting previously unselected package libidn12:amd64. 395s Preparing to unpack .../118-libidn12_1.43-2_amd64.deb ... 395s Unpacking libidn12:amd64 (1.43-2) ... 395s Selecting previously unselected package libijs-0.35:amd64. 395s Preparing to unpack .../119-libijs-0.35_0.35-16_amd64.deb ... 395s Unpacking libijs-0.35:amd64 (0.35-16) ... 395s Selecting previously unselected package libjbig2dec0:amd64. 395s Preparing to unpack .../120-libjbig2dec0_0.20-1build4_amd64.deb ... 395s Unpacking libjbig2dec0:amd64 (0.20-1build4) ... 395s Selecting previously unselected package libpaper2:amd64. 395s Preparing to unpack .../121-libpaper2_2.2.5-0.3build1_amd64.deb ... 395s Unpacking libpaper2:amd64 (2.2.5-0.3build1) ... 395s Selecting previously unselected package libice6:amd64. 395s Preparing to unpack .../122-libice6_2%3a1.1.1-1build1_amd64.deb ... 395s Unpacking libice6:amd64 (2:1.1.1-1build1) ... 395s Selecting previously unselected package libsm6:amd64. 395s Preparing to unpack .../123-libsm6_2%3a1.2.6-1_amd64.deb ... 395s Unpacking libsm6:amd64 (2:1.2.6-1) ... 395s Selecting previously unselected package libxt6t64:amd64. 395s Preparing to unpack .../124-libxt6t64_1%3a1.2.1-1.3_amd64.deb ... 395s Unpacking libxt6t64:amd64 (1:1.2.1-1.3) ... 395s Selecting previously unselected package libgs10:amd64. 395s Preparing to unpack .../125-libgs10_10.05.0dfsg1-0ubuntu4_amd64.deb ... 395s Unpacking libgs10:amd64 (10.05.0dfsg1-0ubuntu4) ... 395s Selecting previously unselected package ghostscript. 395s Preparing to unpack .../126-ghostscript_10.05.0dfsg1-0ubuntu4_amd64.deb ... 395s Unpacking ghostscript (10.05.0dfsg1-0ubuntu4) ... 395s Selecting previously unselected package libnetpbm11t64:amd64. 395s Preparing to unpack .../127-libnetpbm11t64_2%3a11.10.02-1build1_amd64.deb ... 395s Unpacking libnetpbm11t64:amd64 (2:11.10.02-1build1) ... 395s Selecting previously unselected package netpbm. 395s Preparing to unpack .../128-netpbm_2%3a11.10.02-1build1_amd64.deb ... 395s Unpacking netpbm (2:11.10.02-1build1) ... 395s Selecting previously unselected package tex-common. 395s Preparing to unpack .../129-tex-common_6.20_all.deb ... 395s Unpacking tex-common (6.20) ... 395s Selecting previously unselected package libpaper-utils. 395s Preparing to unpack .../130-libpaper-utils_2.2.5-0.3build1_amd64.deb ... 395s Unpacking libpaper-utils (2.2.5-0.3build1) ... 396s Selecting previously unselected package libkpathsea6:amd64. 396s Preparing to unpack .../131-libkpathsea6_2025.20250727.75242+ds-5build1_amd64.deb ... 396s Unpacking libkpathsea6:amd64 (2025.20250727.75242+ds-5build1) ... 396s Selecting previously unselected package libptexenc1:amd64. 396s Preparing to unpack .../132-libptexenc1_2025.20250727.75242+ds-5build1_amd64.deb ... 396s Unpacking libptexenc1:amd64 (2025.20250727.75242+ds-5build1) ... 396s Selecting previously unselected package libsynctex2:amd64. 396s Preparing to unpack .../133-libsynctex2_2025.20250727.75242+ds-5build1_amd64.deb ... 396s Unpacking libsynctex2:amd64 (2025.20250727.75242+ds-5build1) ... 396s Selecting previously unselected package libtexlua53-5:amd64. 396s Preparing to unpack .../134-libtexlua53-5_2025.20250727.75242+ds-5build1_amd64.deb ... 396s Unpacking libtexlua53-5:amd64 (2025.20250727.75242+ds-5build1) ... 396s Selecting previously unselected package t1utils. 396s Preparing to unpack .../135-t1utils_1.41-4build4_amd64.deb ... 396s Unpacking t1utils (1.41-4build4) ... 396s Selecting previously unselected package libpixman-1-0:amd64. 396s Preparing to unpack .../136-libpixman-1-0_0.46.4-1_amd64.deb ... 396s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 396s Selecting previously unselected package libxcb-render0:amd64. 396s Preparing to unpack .../137-libxcb-render0_1.17.0-2build1_amd64.deb ... 396s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 396s Selecting previously unselected package libxcb-shm0:amd64. 396s Preparing to unpack .../138-libxcb-shm0_1.17.0-2build1_amd64.deb ... 396s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 396s Selecting previously unselected package libxrender1:amd64. 396s Preparing to unpack .../139-libxrender1_1%3a0.9.12-1_amd64.deb ... 396s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 396s Selecting previously unselected package libcairo2:amd64. 396s Preparing to unpack .../140-libcairo2_1.18.4-3_amd64.deb ... 396s Unpacking libcairo2:amd64 (1.18.4-3) ... 396s Selecting previously unselected package libgraphite2-3:amd64. 396s Preparing to unpack .../141-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 396s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 396s Selecting previously unselected package libharfbuzz0b:amd64. 396s Preparing to unpack .../142-libharfbuzz0b_12.3.0-4_amd64.deb ... 396s Unpacking libharfbuzz0b:amd64 (12.3.0-4) ... 396s Selecting previously unselected package libmpfi0:amd64. 396s Preparing to unpack .../143-libmpfi0_1.5.4+ds-4_amd64.deb ... 396s Unpacking libmpfi0:amd64 (1.5.4+ds-4) ... 396s Selecting previously unselected package libpotrace0:amd64. 396s Preparing to unpack .../144-libpotrace0_1.16-2build2_amd64.deb ... 396s Unpacking libpotrace0:amd64 (1.16-2build2) ... 396s Selecting previously unselected package libteckit0:amd64. 396s Preparing to unpack .../145-libteckit0_2.5.13+ds-1_amd64.deb ... 396s Unpacking libteckit0:amd64 (2.5.13+ds-1) ... 396s Selecting previously unselected package libxmu6:amd64. 396s Preparing to unpack .../146-libxmu6_2%3a1.1.3-4_amd64.deb ... 396s Unpacking libxmu6:amd64 (2:1.1.3-4) ... 396s Selecting previously unselected package libxaw7:amd64. 396s Preparing to unpack .../147-libxaw7_2%3a1.0.16-1build1_amd64.deb ... 396s Unpacking libxaw7:amd64 (2:1.0.16-1build1) ... 396s Selecting previously unselected package libxi6:amd64. 396s Preparing to unpack .../148-libxi6_2%3a1.8.2-2_amd64.deb ... 396s Unpacking libxi6:amd64 (2:1.8.2-2) ... 396s Selecting previously unselected package libzzip-0-13t64:amd64. 396s Preparing to unpack .../149-libzzip-0-13t64_0.13.78+dfsg.1-0.2_amd64.deb ... 396s Unpacking libzzip-0-13t64:amd64 (0.13.78+dfsg.1-0.2) ... 396s Selecting previously unselected package texlive-binaries. 396s Preparing to unpack .../150-texlive-binaries_2025.20250727.75242+ds-5build1_amd64.deb ... 396s Unpacking texlive-binaries (2025.20250727.75242+ds-5build1) ... 396s Selecting previously unselected package xdg-utils. 396s Preparing to unpack .../151-xdg-utils_1.2.1-2ubuntu2_all.deb ... 396s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 396s Selecting previously unselected package texlive-base. 396s Preparing to unpack .../152-texlive-base_2025.20251127-1_all.deb ... 396s Unpacking texlive-base (2025.20251127-1) ... 397s Selecting previously unselected package hicolor-icon-theme. 397s Preparing to unpack .../153-hicolor-icon-theme_0.18-2build1_all.deb ... 397s Unpacking hicolor-icon-theme (0.18-2build1) ... 397s Selecting previously unselected package imagemagick-7.q16. 397s Preparing to unpack .../154-imagemagick-7.q16_8%3a7.1.2.12+dfsg1-1_amd64.deb ... 397s Unpacking imagemagick-7.q16 (8:7.1.2.12+dfsg1-1) ... 397s Selecting previously unselected package imagemagick. 397s Preparing to unpack .../155-imagemagick_8%3a7.1.2.12+dfsg1-1_amd64.deb ... 397s Unpacking imagemagick (8:7.1.2.12+dfsg1-1) ... 397s Selecting previously unselected package hevea. 397s Preparing to unpack .../156-hevea_2.36-2build3_amd64.deb ... 397s Unpacking hevea (2.36-2build3) ... 397s Selecting previously unselected package libamd-comgr3:amd64. 397s Preparing to unpack .../157-libamd-comgr3_7.1.0+dfsg-0ubuntu2_amd64.deb ... 397s Unpacking libamd-comgr3:amd64 (7.1.0+dfsg-0ubuntu2) ... 398s Selecting previously unselected package libsuitesparseconfig7:amd64. 398s Preparing to unpack .../158-libsuitesparseconfig7_1%3a7.12.1+dfsg-1_amd64.deb ... 398s Unpacking libsuitesparseconfig7:amd64 (1:7.12.1+dfsg-1) ... 398s Selecting previously unselected package libamd3:amd64. 398s Preparing to unpack .../159-libamd3_1%3a7.12.1+dfsg-1_amd64.deb ... 398s Unpacking libamd3:amd64 (1:7.12.1+dfsg-1) ... 398s Selecting previously unselected package libhsakmt1:amd64. 398s Preparing to unpack .../160-libhsakmt1_6.4.3+dfsg-3_amd64.deb ... 398s Unpacking libhsakmt1:amd64 (6.4.3+dfsg-3) ... 398s Selecting previously unselected package libhsa-runtime64-1:amd64. 398s Preparing to unpack .../161-libhsa-runtime64-1_6.4.3+dfsg-3_amd64.deb ... 398s Unpacking libhsa-runtime64-1:amd64 (6.4.3+dfsg-3) ... 398s Selecting previously unselected package libamdhip64-6:amd64. 398s Preparing to unpack .../162-libamdhip64-6_6.4.3-4_amd64.deb ... 398s Unpacking libamdhip64-6:amd64 (6.4.3-4) ... 398s Selecting previously unselected package libapache-pom-java. 398s Preparing to unpack .../163-libapache-pom-java_33-2build1_all.deb ... 398s Unpacking libapache-pom-java (33-2build1) ... 398s Selecting previously unselected package libarpack2t64:amd64. 398s Preparing to unpack .../164-libarpack2t64_3.9.1-6_amd64.deb ... 398s Unpacking libarpack2t64:amd64 (3.9.1-6) ... 398s Selecting previously unselected package libcolamd3:amd64. 398s Preparing to unpack .../165-libcolamd3_1%3a7.12.1+dfsg-1_amd64.deb ... 398s Unpacking libcolamd3:amd64 (1:7.12.1+dfsg-1) ... 398s Selecting previously unselected package libcommons-parent-java. 398s Preparing to unpack .../166-libcommons-parent-java_56-1build1_all.deb ... 398s Unpacking libcommons-parent-java (56-1build1) ... 398s Selecting previously unselected package libcommons-logging-java. 398s Preparing to unpack .../167-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 398s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 398s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 398s Preparing to unpack .../168-libevent-pthreads-2.1-7t64_2.1.12-stable-10build1_amd64.deb ... 398s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 398s Selecting previously unselected package libexpat1-dev:amd64. 398s Preparing to unpack .../169-libexpat1-dev_2.7.3-1_amd64.deb ... 398s Unpacking libexpat1-dev:amd64 (2.7.3-1) ... 398s Selecting previously unselected package libpsm2-2. 398s Preparing to unpack .../170-libpsm2-2_11.2.185-2.1_amd64.deb ... 398s Unpacking libpsm2-2 (11.2.185-2.1) ... 398s Selecting previously unselected package librdmacm1t64:amd64. 398s Preparing to unpack .../171-librdmacm1t64_61.0-2ubuntu1_amd64.deb ... 398s Unpacking librdmacm1t64:amd64 (61.0-2ubuntu1) ... 398s Selecting previously unselected package libfabric1:amd64. 398s Preparing to unpack .../172-libfabric1_2.1.0-1.1_amd64.deb ... 398s Unpacking libfabric1:amd64 (2.1.0-1.1) ... 398s Selecting previously unselected package libglpk40:amd64. 398s Preparing to unpack .../173-libglpk40_5.0-2_amd64.deb ... 398s Unpacking libglpk40:amd64 (5.0-2) ... 398s Selecting previously unselected package libhtscodecs2:amd64. 398s Preparing to unpack .../174-libhtscodecs2_1.6.1-2build1_amd64.deb ... 398s Unpacking libhtscodecs2:amd64 (1.6.1-2build1) ... 398s Selecting previously unselected package libhts3t64:amd64. 398s Preparing to unpack .../175-libhts3t64_1.22.1+ds2-1_amd64.deb ... 398s Unpacking libhts3t64:amd64 (1.22.1+ds2-1) ... 398s Selecting previously unselected package libhwloc15:amd64. 398s Preparing to unpack .../176-libhwloc15_2.12.2-1_amd64.deb ... 398s Unpacking libhwloc15:amd64 (2.12.2-1) ... 398s Selecting previously unselected package libplfit0:amd64. 398s Preparing to unpack .../177-libplfit0_0.9.6+ds-2ubuntu1_amd64.deb ... 398s Unpacking libplfit0:amd64 (0.9.6+ds-2ubuntu1) ... 398s Selecting previously unselected package libigraph4:amd64. 398s Preparing to unpack .../178-libigraph4_1.0.1+ds-3_amd64.deb ... 398s Unpacking libigraph4:amd64 (1.0.1+ds-3) ... 398s Selecting previously unselected package libjs-jquery. 398s Preparing to unpack .../179-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 398s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 398s Selecting previously unselected package libjson-perl. 398s Preparing to unpack .../180-libjson-perl_4.10000-1_all.deb ... 398s Unpacking libjson-perl (4.10000-1) ... 398s Selecting previously unselected package libmbedcrypto16:amd64. 398s Preparing to unpack .../181-libmbedcrypto16_3.6.5-0.1ubuntu2_amd64.deb ... 398s Unpacking libmbedcrypto16:amd64 (3.6.5-0.1ubuntu2) ... 398s Selecting previously unselected package libmbedx509-7:amd64. 398s Preparing to unpack .../182-libmbedx509-7_3.6.5-0.1ubuntu2_amd64.deb ... 398s Unpacking libmbedx509-7:amd64 (3.6.5-0.1ubuntu2) ... 398s Selecting previously unselected package libmbedtls21:amd64. 398s Preparing to unpack .../183-libmbedtls21_3.6.5-0.1ubuntu2_amd64.deb ... 398s Unpacking libmbedtls21:amd64 (3.6.5-0.1ubuntu2) ... 398s Selecting previously unselected package ncbi-vdb-data. 398s Preparing to unpack .../184-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ... 398s Unpacking ncbi-vdb-data (3.2.1+dfsg-2) ... 398s Selecting previously unselected package libncbi-vdb3:amd64. 399s Preparing to unpack .../185-libncbi-vdb3_3.2.1+dfsg-2_amd64.deb ... 399s Unpacking libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... 399s Selecting previously unselected package libibumad3:amd64. 399s Preparing to unpack .../186-libibumad3_61.0-2ubuntu1_amd64.deb ... 399s Unpacking libibumad3:amd64 (61.0-2ubuntu1) ... 399s Selecting previously unselected package libibmad5:amd64. 399s Preparing to unpack .../187-libibmad5_61.0-2ubuntu1_amd64.deb ... 399s Unpacking libibmad5:amd64 (61.0-2ubuntu1) ... 399s Selecting previously unselected package libucx0:amd64. 399s Preparing to unpack .../188-libucx0_1.20.0+ds-4_amd64.deb ... 399s Unpacking libucx0:amd64 (1.20.0+ds-4) ... 399s Selecting previously unselected package libpciaccess0:amd64. 399s Preparing to unpack .../189-libpciaccess0_0.18.1-1ubuntu2_amd64.deb ... 399s Unpacking libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 399s Selecting previously unselected package libxnvctrl0:amd64. 399s Preparing to unpack .../190-libxnvctrl0_510.47.03-0ubuntu6_amd64.deb ... 399s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu6) ... 399s Selecting previously unselected package libze1:amd64. 399s Preparing to unpack .../191-libze1_1.27.0-1_amd64.deb ... 399s Unpacking libze1:amd64 (1.27.0-1) ... 399s Selecting previously unselected package ocl-icd-libopencl1:amd64. 399s Preparing to unpack .../192-ocl-icd-libopencl1_2.3.4-1_amd64.deb ... 399s Unpacking ocl-icd-libopencl1:amd64 (2.3.4-1) ... 399s Selecting previously unselected package libhwloc-plugins:amd64. 399s Preparing to unpack .../193-libhwloc-plugins_2.12.2-1_amd64.deb ... 399s Unpacking libhwloc-plugins:amd64 (2.12.2-1) ... 399s Selecting previously unselected package libopenmpi40:amd64. 399s Preparing to unpack .../194-libopenmpi40_5.0.8-8ubuntu1_amd64.deb ... 399s Unpacking libopenmpi40:amd64 (5.0.8-8ubuntu1) ... 399s Selecting previously unselected package libpython3.14:amd64. 399s Preparing to unpack .../195-libpython3.14_3.14.2-1_amd64.deb ... 399s Unpacking libpython3.14:amd64 (3.14.2-1) ... 399s Selecting previously unselected package zlib1g-dev:amd64. 399s Preparing to unpack .../196-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_amd64.deb ... 399s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 399s Selecting previously unselected package libpython3.14-dev:amd64. 399s Preparing to unpack .../197-libpython3.14-dev_3.14.2-1_amd64.deb ... 399s Unpacking libpython3.14-dev:amd64 (3.14.2-1) ... 399s Selecting previously unselected package libpython3-dev:amd64. 399s Preparing to unpack .../198-libpython3-dev_3.14.2-1_amd64.deb ... 399s Unpacking libpython3-dev:amd64 (3.14.2-1) ... 399s Selecting previously unselected package libpython3.13-dev:amd64. 399s Preparing to unpack .../199-libpython3.13-dev_3.13.11-1_amd64.deb ... 399s Unpacking libpython3.13-dev:amd64 (3.13.11-1) ... 399s Selecting previously unselected package libpython3-all-dev:amd64. 399s Preparing to unpack .../200-libpython3-all-dev_3.14.2-1_amd64.deb ... 399s Unpacking libpython3-all-dev:amd64 (3.14.2-1) ... 399s Selecting previously unselected package libqhull-r8.0:amd64. 399s Preparing to unpack .../201-libqhull-r8.0_2020.2-8_amd64.deb ... 399s Unpacking libqhull-r8.0:amd64 (2020.2-8) ... 399s Selecting previously unselected package libraqm0:amd64. 399s Preparing to unpack .../202-libraqm0_0.10.3-1_amd64.deb ... 399s Unpacking libraqm0:amd64 (0.10.3-1) ... 399s Selecting previously unselected package libtcl8.6:amd64. 399s Preparing to unpack .../203-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 399s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 400s Selecting previously unselected package libxft2:amd64. 400s Preparing to unpack .../204-libxft2_2.3.6-1build2_amd64.deb ... 400s Unpacking libxft2:amd64 (2.3.6-1build2) ... 400s Selecting previously unselected package libxss1:amd64. 400s Preparing to unpack .../205-libxss1_1%3a1.2.3-1build4_amd64.deb ... 400s Unpacking libxss1:amd64 (1:1.2.3-1build4) ... 400s Selecting previously unselected package libtk8.6:amd64. 400s Preparing to unpack .../206-libtk8.6_8.6.17-1_amd64.deb ... 400s Unpacking libtk8.6:amd64 (8.6.17-1) ... 400s Selecting previously unselected package libxslt1.1:amd64. 400s Preparing to unpack .../207-libxslt1.1_1.1.43-0.3_amd64.deb ... 400s Unpacking libxslt1.1:amd64 (1.1.43-0.3) ... 400s Selecting previously unselected package libzopfli1. 400s Preparing to unpack .../208-libzopfli1_1.0.3-3_amd64.deb ... 400s Unpacking libzopfli1 (1.0.3-3) ... 400s Selecting previously unselected package lmodern. 400s Preparing to unpack .../209-lmodern_2.005-1build1_all.deb ... 400s Unpacking lmodern (2.005-1build1) ... 400s Selecting previously unselected package mafft. 400s Preparing to unpack .../210-mafft_7.525-1_amd64.deb ... 400s Unpacking mafft (7.525-1) ... 400s Selecting previously unselected package muscle3. 400s Preparing to unpack .../211-muscle3_3.8.1551-3build1_amd64.deb ... 400s Unpacking muscle3 (3.8.1551-3build1) ... 400s Selecting previously unselected package ncbi-data. 400s Preparing to unpack .../212-ncbi-data_6.1.20170106+dfsg2-7_all.deb ... 400s Unpacking ncbi-data (6.1.20170106+dfsg2-7) ... 400s Selecting previously unselected package ncbi-blast+. 400s Preparing to unpack .../213-ncbi-blast+_2.16.0+ds-7_amd64.deb ... 400s Unpacking ncbi-blast+ (2.16.0+ds-7) ... 400s Selecting previously unselected package openmpi-common. 400s Preparing to unpack .../214-openmpi-common_5.0.8-8ubuntu1_all.deb ... 400s Unpacking openmpi-common (5.0.8-8ubuntu1) ... 400s Selecting previously unselected package openmpi-bin. 400s Preparing to unpack .../215-openmpi-bin_5.0.8-8ubuntu1_amd64.deb ... 400s Unpacking openmpi-bin (5.0.8-8ubuntu1) ... 401s Selecting previously unselected package phylip. 401s Preparing to unpack .../216-phylip_1%3a3.697+dfsg-4build2_amd64.deb ... 401s Unpacking phylip (1:3.697+dfsg-4build2) ... 401s Selecting previously unselected package mpi-default-bin. 401s Preparing to unpack .../217-mpi-default-bin_1.20_amd64.deb ... 401s Unpacking mpi-default-bin (1.20) ... 401s Selecting previously unselected package phyml. 401s Preparing to unpack .../218-phyml_3%3a3.3.20220408-4build1_amd64.deb ... 401s Unpacking phyml (3:3.3.20220408-4build1) ... 401s Selecting previously unselected package prank. 401s Preparing to unpack .../219-prank_250331-1_amd64.deb ... 401s Unpacking prank (250331-1) ... 401s Selecting previously unselected package preview-latex-style. 401s Preparing to unpack .../220-preview-latex-style_13.2-1.1_all.deb ... 401s Unpacking preview-latex-style (13.2-1.1) ... 401s Selecting previously unselected package probcons. 401s Preparing to unpack .../221-probcons_1.12-15_amd64.deb ... 401s Unpacking probcons (1.12-15) ... 401s Selecting previously unselected package python-biopython-doc. 401s Preparing to unpack .../222-python-biopython-doc_1.86+dfsg-1_all.deb ... 401s Unpacking python-biopython-doc (1.86+dfsg-1) ... 401s Selecting previously unselected package python-matplotlib-data. 401s Preparing to unpack .../223-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 401s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 401s Selecting previously unselected package python3-all. 401s Preparing to unpack .../224-python3-all_3.14.2-1_amd64.deb ... 401s Unpacking python3-all (3.14.2-1) ... 401s Selecting previously unselected package python3.14-dev. 401s Preparing to unpack .../225-python3.14-dev_3.14.2-1_amd64.deb ... 401s Unpacking python3.14-dev (3.14.2-1) ... 401s Selecting previously unselected package python3-dev. 401s Preparing to unpack .../226-python3-dev_3.14.2-1_amd64.deb ... 401s Unpacking python3-dev (3.14.2-1) ... 401s Selecting previously unselected package python3.13-dev. 401s Preparing to unpack .../227-python3.13-dev_3.13.11-1_amd64.deb ... 401s Unpacking python3.13-dev (3.13.11-1) ... 401s Selecting previously unselected package python3-all-dev. 401s Preparing to unpack .../228-python3-all-dev_3.14.2-1_amd64.deb ... 401s Unpacking python3-all-dev (3.14.2-1) ... 401s Selecting previously unselected package python3-charset-normalizer. 401s Preparing to unpack .../229-python3-charset-normalizer_3.4.4-2_amd64.deb ... 401s Unpacking python3-charset-normalizer (3.4.4-2) ... 401s Selecting previously unselected package python3.13-tk. 401s Preparing to unpack .../230-python3.13-tk_3.13.11-1_amd64.deb ... 401s Unpacking python3.13-tk (3.13.11-1) ... 401s Selecting previously unselected package python3.14-tk. 401s Preparing to unpack .../231-python3.14-tk_3.14.2-1_amd64.deb ... 401s Unpacking python3.14-tk (3.14.2-1) ... 401s Selecting previously unselected package python3-tk. 401s Preparing to unpack .../232-python3-tk_3.14.2-1_amd64.deb ... 401s Unpacking python3-tk (3.14.2-1) ... 401s Selecting previously unselected package python3-pil.imagetk:amd64. 401s Preparing to unpack .../233-python3-pil.imagetk_12.0.0-1ubuntu1_amd64.deb ... 401s Unpacking python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 401s Selecting previously unselected package python3-pil:amd64. 401s Preparing to unpack .../234-python3-pil_12.0.0-1ubuntu1_amd64.deb ... 401s Unpacking python3-pil:amd64 (12.0.0-1ubuntu1) ... 401s Selecting previously unselected package python3-cairo. 401s Preparing to unpack .../235-python3-cairo_1.27.0-2build1_amd64.deb ... 401s Unpacking python3-cairo (1.27.0-2build1) ... 401s Selecting previously unselected package python3-freetype. 401s Preparing to unpack .../236-python3-freetype_2.5.1-2_all.deb ... 401s Unpacking python3-freetype (2.5.1-2) ... 401s Selecting previously unselected package python3-rlpycairo. 401s Preparing to unpack .../237-python3-rlpycairo_0.3.0-4_all.deb ... 401s Unpacking python3-rlpycairo (0.3.0-4) ... 401s Selecting previously unselected package python3-reportlab. 401s Preparing to unpack .../238-python3-reportlab_4.4.9-1_all.deb ... 401s Unpacking python3-reportlab (4.4.9-1) ... 401s Selecting previously unselected package w3c-sgml-lib. 402s Preparing to unpack .../239-w3c-sgml-lib_1.3-3build1_all.deb ... 402s Unpacking w3c-sgml-lib (1.3-3build1) ... 402s Selecting previously unselected package python3-biopython. 402s Preparing to unpack .../240-python3-biopython_1.86+dfsg-1_amd64.deb ... 402s Unpacking python3-biopython (1.86+dfsg-1) ... 402s Selecting previously unselected package python3-biopython-sql. 402s Preparing to unpack .../241-python3-biopython-sql_1.86+dfsg-1_all.deb ... 402s Unpacking python3-biopython-sql (1.86+dfsg-1) ... 402s Selecting previously unselected package python3-brotli. 402s Preparing to unpack .../242-python3-brotli_1.1.0-2build6_amd64.deb ... 402s Unpacking python3-brotli (1.1.0-2build6) ... 402s Selecting previously unselected package python3-contourpy. 402s Preparing to unpack .../243-python3-contourpy_1.3.3-1_amd64.deb ... 402s Unpacking python3-contourpy (1.3.3-1) ... 402s Selecting previously unselected package python3-cycler. 402s Preparing to unpack .../244-python3-cycler_0.12.1-2_all.deb ... 402s Unpacking python3-cycler (0.12.1-2) ... 402s Selecting previously unselected package python3-decorator. 402s Preparing to unpack .../245-python3-decorator_5.2.1-2_all.deb ... 402s Unpacking python3-decorator (5.2.1-2) ... 402s Selecting previously unselected package python3-defusedxml. 402s Preparing to unpack .../246-python3-defusedxml_0.7.1-3build1_all.deb ... 402s Unpacking python3-defusedxml (0.7.1-3build1) ... 402s Selecting previously unselected package python3-roman-numerals. 402s Preparing to unpack .../247-python3-roman-numerals_4.1.0-1_all.deb ... 402s Unpacking python3-roman-numerals (4.1.0-1) ... 402s Selecting previously unselected package python3-docutils. 402s Preparing to unpack .../248-python3-docutils_0.22.4+dfsg-1_all.deb ... 402s Unpacking python3-docutils (0.22.4+dfsg-1) ... 402s Selecting previously unselected package python3-lxml:amd64. 402s Preparing to unpack .../249-python3-lxml_6.0.2-1_amd64.deb ... 402s Unpacking python3-lxml:amd64 (6.0.2-1) ... 402s Selecting previously unselected package python3-lz4. 402s Preparing to unpack .../250-python3-lz4_4.4.5+dfsg-1_amd64.deb ... 402s Unpacking python3-lz4 (4.4.5+dfsg-1) ... 402s Selecting previously unselected package python3-scipy. 402s Preparing to unpack .../251-python3-scipy_1.16.3-3_amd64.deb ... 402s Unpacking python3-scipy (1.16.3-3) ... 403s Selecting previously unselected package python3-mpmath. 403s Preparing to unpack .../252-python3-mpmath_1.3.0-2_all.deb ... 403s Unpacking python3-mpmath (1.3.0-2) ... 403s Selecting previously unselected package python3-sympy. 403s Preparing to unpack .../253-python3-sympy_1.14.0-2_all.deb ... 403s Unpacking python3-sympy (1.14.0-2) ... 403s Selecting previously unselected package python3-ufolib2. 403s Preparing to unpack .../254-python3-ufolib2_0.18.1+dfsg1-1_all.deb ... 403s Unpacking python3-ufolib2 (0.18.1+dfsg1-1) ... 403s Selecting previously unselected package python3-zopfli. 403s Preparing to unpack .../255-python3-zopfli_0.4.0-1_amd64.deb ... 403s Unpacking python3-zopfli (0.4.0-1) ... 403s Selecting previously unselected package unicode-data. 403s Preparing to unpack .../256-unicode-data_16.0.0-1build1_all.deb ... 403s Unpacking unicode-data (16.0.0-1build1) ... 403s Selecting previously unselected package python3-fonttools. 403s Preparing to unpack .../257-python3-fonttools_4.61.1-3_amd64.deb ... 403s Unpacking python3-fonttools (4.61.1-3) ... 403s Selecting previously unselected package python3-imagesize. 403s Preparing to unpack .../258-python3-imagesize_1.4.1-1build1_all.deb ... 403s Unpacking python3-imagesize (1.4.1-1build1) ... 403s Selecting previously unselected package python3-kiwisolver. 403s Preparing to unpack .../259-python3-kiwisolver_1.4.10~rc0-1_amd64.deb ... 403s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 403s Selecting previously unselected package python3-matplotlib. 403s Preparing to unpack .../260-python3-matplotlib_3.10.7+dfsg1-1_amd64.deb ... 403s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 404s Selecting previously unselected package python3-msgpack. 404s Preparing to unpack .../261-python3-msgpack_1.1.2-1_amd64.deb ... 404s Unpacking python3-msgpack (1.1.2-1) ... 404s Selecting previously unselected package python3-mmtf. 404s Preparing to unpack .../262-python3-mmtf_1.1.3-1build1_all.deb ... 404s Unpacking python3-mmtf (1.1.3-1build1) ... 404s Selecting previously unselected package python3-mysqldb. 404s Preparing to unpack .../263-python3-mysqldb_1.4.6-2build7_amd64.deb ... 404s Unpacking python3-mysqldb (1.4.6-2build7) ... 404s Selecting previously unselected package python3-networkx. 404s Preparing to unpack .../264-python3-networkx_3.2.1-4ubuntu2_all.deb ... 404s Unpacking python3-networkx (3.2.1-4ubuntu2) ... 404s Selecting previously unselected package sphinx-common. 404s Preparing to unpack .../265-sphinx-common_8.2.3-12_all.deb ... 404s Unpacking sphinx-common (8.2.3-12) ... 404s Selecting previously unselected package python3-alabaster. 404s Preparing to unpack .../266-python3-alabaster_0.7.16-0.1build1_all.deb ... 404s Unpacking python3-alabaster (0.7.16-0.1build1) ... 404s Selecting previously unselected package python3-snowballstemmer. 404s Preparing to unpack .../267-python3-snowballstemmer_3.0.1-1_all.deb ... 404s Unpacking python3-snowballstemmer (3.0.1-1) ... 404s Selecting previously unselected package python3-sphinx. 404s Preparing to unpack .../268-python3-sphinx_8.2.3-12_all.deb ... 404s Unpacking python3-sphinx (8.2.3-12) ... 404s Selecting previously unselected package python3-numpydoc. 404s Preparing to unpack .../269-python3-numpydoc_1.9.0-1_all.deb ... 404s Unpacking python3-numpydoc (1.9.0-1) ... 404s Selecting previously unselected package python3-psycopg2. 404s Preparing to unpack .../270-python3-psycopg2_2.9.11-1_amd64.deb ... 404s Unpacking python3-psycopg2 (2.9.11-1) ... 404s Selecting previously unselected package python3-rdflib. 404s Preparing to unpack .../271-python3-rdflib_7.1.1-3_all.deb ... 404s Unpacking python3-rdflib (7.1.1-3) ... 404s Selecting previously unselected package sphinx-rtd-theme-common. 405s Preparing to unpack .../272-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 405s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 405s Selecting previously unselected package python3-sphinxcontrib.jquery. 405s Preparing to unpack .../273-python3-sphinxcontrib.jquery_4.1-6_all.deb ... 405s Unpacking python3-sphinxcontrib.jquery (4.1-6) ... 405s Selecting previously unselected package python3-sphinx-rtd-theme. 405s Preparing to unpack .../274-python3-sphinx-rtd-theme_3.0.2+dfsg-3_all.deb ... 405s Unpacking python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 405s Selecting previously unselected package python3-texttable. 405s Preparing to unpack .../275-python3-texttable_1.7.0-1_all.deb ... 405s Unpacking python3-texttable (1.7.0-1) ... 405s Selecting previously unselected package raxml. 405s Preparing to unpack .../276-raxml_8.2.13+dfsg-3_amd64.deb ... 405s Unpacking raxml (8.2.13+dfsg-3) ... 405s Selecting previously unselected package samtools. 405s Preparing to unpack .../277-samtools_1.22.1-1_amd64.deb ... 405s Unpacking samtools (1.22.1-1) ... 405s Selecting previously unselected package t-coffee. 405s Preparing to unpack .../278-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1build1_amd64.deb ... 405s Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1build1) ... 405s Selecting previously unselected package texlive-fonts-recommended. 405s Preparing to unpack .../279-texlive-fonts-recommended_2025.20251127-1_all.deb ... 405s Unpacking texlive-fonts-recommended (2025.20251127-1) ... 405s Selecting previously unselected package texlive-luatex. 405s Preparing to unpack .../280-texlive-luatex_2025.20251127-1_all.deb ... 405s Unpacking texlive-luatex (2025.20251127-1) ... 406s Selecting previously unselected package texlive-latex-base. 406s Preparing to unpack .../281-texlive-latex-base_2025.20251127-1_all.deb ... 406s Unpacking texlive-latex-base (2025.20251127-1) ... 406s Selecting previously unselected package libfontbox-java. 406s Preparing to unpack .../282-libfontbox-java_1%3a1.8.16-5_all.deb ... 406s Unpacking libfontbox-java (1:1.8.16-5) ... 406s Selecting previously unselected package libpdfbox-java. 406s Preparing to unpack .../283-libpdfbox-java_1%3a1.8.16-5_all.deb ... 406s Unpacking libpdfbox-java (1:1.8.16-5) ... 406s Selecting previously unselected package texlive-latex-recommended. 406s Preparing to unpack .../284-texlive-latex-recommended_2025.20251127-1_all.deb ... 406s Unpacking texlive-latex-recommended (2025.20251127-1) ... 407s Selecting previously unselected package texlive-pictures. 407s Preparing to unpack .../285-texlive-pictures_2025.20251127-1_all.deb ... 407s Unpacking texlive-pictures (2025.20251127-1) ... 408s Selecting previously unselected package texlive-latex-extra. 408s Preparing to unpack .../286-texlive-latex-extra_2025.20251127-2_all.deb ... 408s Unpacking texlive-latex-extra (2025.20251127-2) ... 410s Selecting previously unselected package wise-data. 410s Preparing to unpack .../287-wise-data_2.4.1-27_all.deb ... 410s Unpacking wise-data (2.4.1-27) ... 410s Selecting previously unselected package wise. 410s Preparing to unpack .../288-wise_2.4.1-27_amd64.deb ... 410s Unpacking wise (2.4.1-27) ... 410s Selecting previously unselected package fasttree. 410s Preparing to unpack .../289-fasttree_2.1.11-2build1_amd64.deb ... 410s Unpacking fasttree (2.1.11-2build1) ... 410s Selecting previously unselected package python3-igraph. 410s Preparing to unpack .../290-python3-igraph_1.0.0+ds-1_amd64.deb ... 410s Unpacking python3-igraph (1.0.0+ds-1) ... 410s Setting up libhtscodecs2:amd64 (1.6.1-2build1) ... 410s Setting up dh-python (7.20251231) ... 410s Setting up libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 410s Setting up liblcms2-2:amd64 (2.17-1) ... 410s Setting up ncbi-data (6.1.20170106+dfsg2-7) ... 410s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 410s Setting up libsharpyuv0:amd64 (1.5.0-0.1build1) ... 410s Setting up python3-texttable (1.7.0-1) ... 410s Setting up libaom3:amd64 (3.13.1-2) ... 410s Setting up libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 410s Setting up mysql-common (5.8+1.1.1ubuntu2) ... 410s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 410s Setting up libhpdf-2.3.0:amd64 (2.3.0+dfsg-1build4) ... 410s Setting up fonts-lato (2.015-1build1) ... 410s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu2) ... 410s Setting up libxpm4:amd64 (1:3.5.17-1build3) ... 410s Setting up hicolor-icon-theme (0.18-2build1) ... 410s Setting up libxi6:amd64 (2:1.8.2-2) ... 410s Setting up probcons (1.12-15) ... 410s Setting up libxrender1:amd64 (1:0.9.12-1) ... 410s Setting up python3-lz4 (4.4.5+dfsg-1) ... 410s Setting up libxcb-render0:amd64 (1.17.0-2build1) ... 410s Setting up python3-defusedxml (0.7.1-3build1) ... 411s Setting up mafft (7.525-1) ... 411s Setting up libarchive-zip-perl (1.68-1) ... 411s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10build1) ... 411s Setting up imagemagick-7-common (8:7.1.2.12+dfsg1-1) ... 411s Setting up python3-charset-normalizer (3.4.4-2) ... 411s Setting up bwa (0.7.19-1) ... 411s Setting up python3-alabaster (0.7.16-0.1build1) ... 411s Setting up fonts-lyx (2.5.0~RC2-3) ... 411s Setting up libijs-0.35:amd64 (0.35-16) ... 411s Setting up libdebhelper-perl (13.28ubuntu1) ... 411s Setting up libgs-common (10.05.0dfsg1-0ubuntu4) ... 411s Setting up libfontbox-java (1:1.8.16-5) ... 411s Setting up phylip (1:3.697+dfsg-4build2) ... 411s Setting up x11-common (1:7.7+24ubuntu1) ... 412s Setting up libpq5:amd64 (18.1-2) ... 412s Setting up libibumad3:amd64 (61.0-2ubuntu1) ... 412s Setting up libdeflate0:amd64 (1.23-2) ... 412s Setting up m4 (1.4.20-2) ... 412s Setting up libqhull-r8.0:amd64 (2020.2-8) ... 412s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 412s Setting up libibmad5:amd64 (61.0-2ubuntu1) ... 412s Setting up libgomp1:amd64 (15.2.0-11ubuntu1) ... 412s Setting up python3-freetype (2.5.1-2) ... 412s Setting up emboss-data (6.6.0+dfsg-15ubuntu3) ... 412s Setting up python3-networkx (3.2.1-4ubuntu2) ... 415s Setting up libmysqlclient24:amd64 (8.4.7-0ubuntu3) ... 415s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ... 415s Setting up libnetpbm11t64:amd64 (2:11.10.02-1build1) ... 415s Setting up libze1:amd64 (1.27.0-1) ... 415s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1build1) ... 415s Setting up poppler-data (0.4.12-1build1) ... 415s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu6) ... 415s Setting up unicode-data (16.0.0-1build1) ... 415s Setting up python3-mysqldb (1.4.6-2build7) ... 415s Setting up tex-common (6.20) ... 415s update-language: texlive-base not installed and configured, doing nothing! 415s Setting up python3-decorator (5.2.1-2) ... 415s Setting up libfontenc1:amd64 (1:1.1.8-1build2) ... 415s Setting up autotools-dev (20240727.1) ... 415s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 415s 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 415s Setting up libexpat1-dev:amd64 (2.7.3-1) ... 415s Setting up libzzip-0-13t64:amd64 (0.13.78+dfsg.1-0.2) ... 415s Setting up libzopfli1 (1.0.3-3) ... 415s Setting up libjbig2dec0:amd64 (0.20-1build4) ... 415s Setting up python3-snowballstemmer (3.0.1-1) ... 416s Setting up libteckit0:amd64 (2.5.13+ds-1) ... 416s Setting up python3-brotli (1.1.0-2build6) ... 416s Setting up libapache-pom-java (33-2build1) ... 416s Setting up libavahi-common-data:amd64 (0.8-17ubuntu2) ... 416s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 416s Setting up muscle3 (3.8.1551-3build1) ... 416s Setting up t1utils (1.41-4build4) ... 416s Setting up libquadmath0:amd64 (15.2.0-11ubuntu1) ... 416s Setting up python3-cycler (0.12.1-2) ... 416s Setting up libtexlua53-5:amd64 (2025.20250727.75242+ds-5build1) ... 416s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 416s Setting up fonts-dejavu-mono (2.37-8build1) ... 416s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 417s Setting up libhwloc15:amd64 (2.12.2-1) ... 417s Setting up libmpc3:amd64 (1.3.1-2) ... 417s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 417s Setting up libidn12:amd64 (1.43-2) ... 417s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 417s Setting up autopoint (0.23.2-1) ... 417s Setting up libmpfi0:amd64 (1.5.4+ds-4) ... 417s Setting up python3-psycopg2 (2.9.11-1) ... 417s Setting up fonts-dejavu-core (2.37-8build1) ... 417s Setting up wise-data (2.4.1-27) ... 417s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 417s Setting up libltdl7:amd64 (2.5.4-9) ... 417s Setting up libfftw3-double3:amd64 (3.3.10-2fakesync1build2) ... 417s Setting up libcifpp-data (9.0.5-2) ... 417s Setting up libkpathsea6:amd64 (2025.20250727.75242+ds-5build1) ... 417s Setting up libgfortran5:amd64 (15.2.0-11ubuntu1) ... 417s Setting up autoconf (2.72-3.1ubuntu1) ... 417s Setting up libwebp7:amd64 (1.5.0-0.1build1) ... 417s Setting up libubsan1:amd64 (15.2.0-11ubuntu1) ... 417s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 417s Setting up fonts-dejavu-extra (2.37-8build1) ... 417s Setting up dwz (0.16-2) ... 417s Setting up liblqr-1-0:amd64 (0.4.2-2.2) ... 417s Setting up ocl-icd-libopencl1:amd64 (2.3.4-1) ... 417s Setting up libhwasan0:amd64 (15.2.0-11ubuntu1) ... 417s Setting up python3-rdflib (7.1.1-3) ... 418s Setting up libamd-comgr3:amd64 (7.1.0+dfsg-0ubuntu2) ... 418s Setting up libasan8:amd64 (15.2.0-11ubuntu1) ... 418s Setting up libjson-perl (4.10000-1) ... 418s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 418s Setting up libpsm2-2 (11.2.185-2.1) ... 418s Setting up openmpi-common (5.0.8-8ubuntu1) ... 418s Setting up clustalw (2.1+lgpl-7build1) ... 418s Setting up libpython3.14:amd64 (3.14.2-1) ... 418s Setting up debugedit (1:5.2-3) ... 418s Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... 418s Setting up fonts-lmodern (2.005-1build1) ... 418s Setting up libsuitesparseconfig7:amd64 (1:7.12.1+dfsg-1) ... 418s Setting up librdmacm1t64:amd64 (61.0-2ubuntu1) ... 418s Setting up python3-roman-numerals (4.1.0-1) ... 418s Setting up libopenjp2-7:amd64 (2.5.4-1) ... 418s Setting up python3.13-minimal (3.13.11-1) ... 419s Setting up libharfbuzz0b:amd64 (12.3.0-4) ... 419s Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... 419s Setting up fasttree (2.1.11-2build1) ... 419s Setting up libpython3.14-dev:amd64 (3.14.2-1) ... 419s Setting up sgml-base (1.31+nmu1) ... 419s Setting up python3-msgpack (1.1.2-1) ... 420s Setting up libplfit0:amd64 (0.9.6+ds-2ubuntu1) ... 420s Setting up libxss1:amd64 (1:1.2.3-1build4) ... 420s Setting up libmbedcrypto16:amd64 (3.6.5-0.1ubuntu2) ... 420s Setting up libpaper2:amd64 (2.2.5-0.3build1) ... 420s Setting up libtsan2:amd64 (15.2.0-11ubuntu1) ... 420s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 420s Setting up python3-mpmath (1.3.0-2) ... 421s Setting up libisl23:amd64 (0.27-1build1) ... 421s Setting up libde265-0:amd64 (1.0.16-1build1) ... 421s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 421s Setting up libwebpmux3:amd64 (1.5.0-0.1build1) ... 421s Setting up dialign (2.2.1-13build1) ... 421s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 421s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 421s Setting up xdg-utils (1.2.1-2ubuntu2) ... 421s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 421s Setting up libcc1-0:amd64 (15.2.0-11ubuntu1) ... 421s Setting up liblsan0:amd64 (15.2.0-11ubuntu1) ... 421s Setting up libhsakmt1:amd64 (6.4.3+dfsg-3) ... 421s Setting up libitm1:amd64 (15.2.0-11ubuntu1) ... 421s Setting up libsynctex2:amd64 (2025.20250727.75242+ds-5build1) ... 421s Setting up prank (250331-1) ... 421s Setting up libargtable2-0:amd64 (13-4) ... 421s Setting up raxml (8.2.13+dfsg-3) ... 421s Setting up python3-imagesize (1.4.1-1build1) ... 421s Setting up libpotrace0:amd64 (1.16-2build2) ... 421s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 421s Setting up automake (1:1.18.1-3build1) ... 421s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 421s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 421s Setting up libfabric1:amd64 (2.1.0-1.1) ... 421s Setting up python3-sympy (1.14.0-2) ... 434s /usr/lib/python3/dist-packages/sympy/testing/runtests.py:283: SyntaxWarning: 'return' in a 'finally' block 434s return p.returncode 435s Setting up libice6:amd64 (2:1.1.1-1build1) ... 435s Setting up flex (2.6.4-8.2build2) ... 435s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 435s 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 435s Setting up gettext (0.23.2-1) ... 435s Setting up libarpack2t64:amd64 (3.9.1-6) ... 435s Setting up libgcc-15-dev:amd64 (15.2.0-11ubuntu1) ... 435s Setting up libpython3-dev:amd64 (3.14.2-1) ... 435s Setting up libamd3:amd64 (1:7.12.1+dfsg-1) ... 435s Setting up libpdfbox-java (1:1.8.16-5) ... 435s Setting up python3.14-dev (3.14.2-1) ... 435s Setting up libcolamd3:amd64 (1:7.12.1+dfsg-1) ... 435s Setting up python3.13 (3.13.11-1) ... 436s Setting up libcifpp9:amd64 (9.0.5-2) ... 436s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 436s Setting up wise (2.4.1-27) ... 436s Setting up preview-latex-style (13.2-1.1) ... 436s Setting up libwebpdemux2:amd64 (1.5.0-0.1build1) ... 436s Setting up libcommons-parent-java (56-1build1) ... 436s Setting up libavahi-common3:amd64 (0.8-17ubuntu2) ... 436s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 436s Setting up python3-all (3.14.2-1) ... 436s Setting up libpaper-utils (2.2.5-0.3build1) ... 436s Setting up clustalo (1.2.4-8build2) ... 436s Setting up cpp-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 436s Setting up dssp (4.5.7-1) ... 436s Setting up xfonts-utils (1:7.7+7build1) ... 436s Setting up libhwloc-plugins:amd64 (2.12.2-1) ... 436s Setting up python3-zopfli (0.4.0-1) ... 436s Setting up samtools (1.22.1-1) ... 436s Setting up intltool-debian (0.35.0+20060710.6build1) ... 436s Setting up gcc-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 436s Setting up libmbedx509-7:amd64 (3.6.5-0.1ubuntu2) ... 436s Setting up libstdc++-15-dev:amd64 (15.2.0-11ubuntu1) ... 436s Setting up libptexenc1:amd64 (2025.20250727.75242+ds-5build1) ... 436s Setting up libglpk40:amd64 (5.0-2) ... 436s Setting up libraqm0:amd64 (0.10.3-1) ... 436s Setting up libpython3.13-dev:amd64 (3.13.11-1) ... 436s Setting up sphinx-common (8.2.3-12) ... 436s Setting up python3-dev (3.14.2-1) ... 436s Setting up python3-numpy (1:2.3.5+ds-3) ... 440s Setting up libraw23t64:amd64 (0.21.4-2) ... 440s Setting up libmbedtls21:amd64 (3.6.5-0.1ubuntu2) ... 440s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 440s Setting up cpp-15 (15.2.0-11ubuntu1) ... 440s Setting up python3-lxml:amd64 (6.0.2-1) ... 440s Setting up python-biopython-doc (1.86+dfsg-1) ... 440s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 440s Setting up libhsa-runtime64-1:amd64 (6.4.3+dfsg-3) ... 441s Setting up lmodern (2.005-1build1) ... 441s Setting up xml-core (0.19build1) ... 441s Setting up python3-contourpy (1.3.3-1) ... 441s Setting up libfontconfig1:amd64 (2.15.0-2.4ubuntu1) ... 441s Setting up libsm6:amd64 (2:1.2.6-1) ... 441s Setting up libavahi-client3:amd64 (0.8-17ubuntu2) ... 441s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 441s Setting up g++-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 441s Setting up libxft2:amd64 (2.3.6-1build2) ... 441s Setting up python3-scipy (1.16.3-3) ... 449s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 449s Setting up python3.13-dev (3.13.11-1) ... 449s Setting up libigraph4:amd64 (1.0.1+ds-3) ... 449s Setting up po-debconf (1.0.22) ... 449s Setting up libtk8.6:amd64 (8.6.17-1) ... 449s Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... 449s Setting up python3-mmtf (1.1.3-1build1) ... 450s Setting up fonts-urw-base35 (20200910-8build1) ... 450s Setting up libcairo2:amd64 (1.18.4-3) ... 450s Setting up python3.13-tk (3.13.11-1) ... 450s Setting up ncbi-blast+ (2.16.0+ds-7) ... 450s Setting up python3-pil:amd64 (12.0.0-1ubuntu1) ... 451s Setting up gcc-15 (15.2.0-11ubuntu1) ... 451s Setting up libpython3-all-dev:amd64 (3.14.2-1) ... 451s Setting up libamdhip64-6:amd64 (6.4.3-4) ... 451s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ... 451s Setting up netpbm (2:11.10.02-1build1) ... 451s Setting up python3-igraph (1.0.0+ds-1) ... 451s Setting up cpp (4:15.2.0-4ubuntu1) ... 451s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 451s Setting up g++-15 (15.2.0-11ubuntu1) ... 451s Setting up libcups2t64:amd64 (2.4.16-1ubuntu1) ... 451s Setting up python3-all-dev (3.14.2-1) ... 451s Setting up libgs10-common (10.05.0dfsg1-0ubuntu4) ... 451s Setting up libucx0:amd64 (1.20.0+ds-4) ... 451s Setting up libxmu6:amd64 (2:1.1.3-4) ... 451s Setting up python3.14-tk (3.14.2-1) ... 452s Setting up python3-cairo (1.27.0-2build1) ... 452s Setting up libtool (2.5.4-9) ... 452s Setting up python3-tk (3.14.2-1) ... 452s Setting up libxaw7:amd64 (2:1.0.16-1build1) ... 452s Setting up gcc (4:15.2.0-4ubuntu1) ... 452s Setting up dh-autoreconf (21) ... 452s Setting up python3-pil.imagetk:amd64 (12.0.0-1ubuntu1) ... 452s Setting up python3-rlpycairo (0.3.0-4) ... 452s Setting up python3-reportlab (4.4.9-1) ... 454s Setting up g++ (4:15.2.0-4ubuntu1) ... 454s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 454s Setting up texlive-binaries (2025.20250727.75242+ds-5build1) ... 454s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 454s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 454s Setting up build-essential (12.12ubuntu2) ... 454s Setting up texlive-base (2025.20251127-1) ... 455s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 455s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 455s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 455s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 456s Setting up libgs10:amd64 (10.05.0dfsg1-0ubuntu4) ... 456s Setting up libopenmpi40:amd64 (5.0.8-8ubuntu1) ... 456s Setting up texlive-luatex (2025.20251127-1) ... 456s Setting up debhelper (13.28ubuntu1) ... 456s Setting up ghostscript (10.05.0dfsg1-0ubuntu4) ... 456s Setting up texlive-latex-base (2025.20251127-1) ... 456s Setting up texlive-latex-recommended (2025.20251127-1) ... 456s Setting up texlive-pictures (2025.20251127-1) ... 456s Setting up texlive-fonts-recommended (2025.20251127-1) ... 456s Setting up openmpi-bin (5.0.8-8ubuntu1) ... 456s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 456s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 456s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 456s Setting up mpi-default-bin (1.20) ... 456s Setting up texlive-latex-extra (2025.20251127-2) ... 456s Setting up phyml (3:3.3.20220408-4build1) ... 456s Setting up python3-fonttools (4.61.1-3) ... 458s Setting up python3-ufolib2 (0.18.1+dfsg1-1) ... 458s Setting up libheif-plugin-aomdec:amd64 (1.21.2-1) ... 458s Setting up libheif-plugin-libde265:amd64 (1.21.2-1) ... 458s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 462s Setting up libheif1:amd64 (1.21.2-1) ... 462s Setting up libgd3:amd64 (2.3.3-13ubuntu1) ... 462s Setting up libmagickcore-7.q16-10:amd64 (8:7.1.2.12+dfsg1-1) ... 462s Setting up emboss-lib (6.6.0+dfsg-15ubuntu3) ... 462s Setting up libmagickwand-7.q16-10:amd64 (8:7.1.2.12+dfsg1-1) ... 462s Setting up emboss (6.6.0+dfsg-15ubuntu3) ... 462s Setting up imagemagick-7.q16 (8:7.1.2.12+dfsg1-1) ... 462s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 462s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 462s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 462s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 462s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 462s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 462s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 462s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 462s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 462s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 462s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 462s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 462s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 462s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 462s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 462s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 462s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 462s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 462s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 462s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 462s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 462s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 462s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 462s update-alternatives: warning: skip creation of /usr/share/man/man1/magick.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick) doesn't exist 462s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 462s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-im7.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick-im7) doesn't exist 462s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 462s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script) doesn't exist 462s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 462s update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script-im7.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script-im7) doesn't exist 462s Setting up hevea (2.36-2build3) ... 462s Setting up imagemagick (8:7.1.2.12+dfsg1-1) ... 462s Processing triggers for install-info (7.2-5) ... 462s Processing triggers for libc-bin (2.42-2ubuntu4) ... 462s Processing triggers for systemd (259-1ubuntu2) ... 462s Processing triggers for man-db (2.13.1-1) ... 464s Processing triggers for shared-mime-info (2.4-5build2) ... 465s Processing triggers for sgml-base (1.31+nmu1) ... 465s Setting up w3c-sgml-lib (1.3-3build1) ... 494s Setting up docutils-common (0.22.4+dfsg-1) ... 494s Setting up python3-biopython (1.86+dfsg-1) ... 497s Setting up python3-biopython-sql (1.86+dfsg-1) ... 497s Processing triggers for sgml-base (1.31+nmu1) ... 497s Setting up python3-docutils (0.22.4+dfsg-1) ... 498s Setting up python3-sphinx (8.2.3-12) ... 499s Setting up python3-sphinxcontrib.jquery (4.1-6) ... 500s Setting up python3-numpydoc (1.9.0-1) ... 500s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 500s Processing triggers for tex-common (6.20) ... 501s Running updmap-sys. This may take some time... done. 501s Running mktexlsr /var/lib/texmf ... done. 501s Building format(s) --all. 551s This may take some time... done. 556s autopkgtest [13:52:22]: test full_suite: sh debian/tests/run-unit-test 556s autopkgtest [13:52:22]: test full_suite: [----------------------- 558s mkdir: created directory 'Bio' 558s mkdir: created directory 'Bio/Align' 558s mkdir: created directory 'Bio/Align/substitution_matrices' 558s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 558s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 559s test_Ace ... ok 559s test_Affy ... ok 559s test_AlignIO ... ok 559s test_AlignIO_ClustalIO ... ok 559s test_AlignIO_EmbossIO ... ok 559s test_AlignIO_FastaIO ... ok 559s test_AlignIO_MauveIO ... ok 559s test_AlignIO_PhylipIO ... ok 559s test_AlignIO_convert ... ok 559s test_Align_Alignment ... ok 559s test_Align_a2m ... ok 559s test_Align_bed ... ok 560s test_Align_bigbed ... ok 560s test_Align_bigmaf ... ok 561s test_Align_bigpsl ... ok 561s test_Align_chain ... ok 561s test_Align_clustal ... ok 567s test_Align_codonalign ... ok 567s test_Align_emboss ... ok 567s test_Align_exonerate ... ok 567s test_Align_fasta ... ok 567s test_Align_format_matrix ... ok 568s test_Align_hhr ... ok 569s test_Align_maf ... ok 569s test_Align_mauve ... ok 569s test_Align_msf ... ok 569s test_Align_nexus ... ok 569s test_Align_phylip ... ok 569s test_Align_psl ... ok 570s test_Align_sam ... ok 571s test_Align_stockholm ... ok 572s test_Align_tabular ... ok 572s test_BioSQL_MySQLdb_online ... skipping. internet not available 572s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 572s test_BioSQL_mysql_connector_online ... skipping. internet not available 572s test_BioSQL_psycopg2_online ... skipping. internet not available 576s test_BioSQL_sqlite3 ... ok 576s test_BioSQL_sqlite3_online ... skipping. internet not available 576s test_Blast_Record ... ok 577s test_Blast_parser ... ok 577s test_CAPS ... ok 577s test_Chi2 ... ok 577s test_Cluster ... ok 577s test_CodonTable ... ok 577s test_ColorSpiral ... ok 577s test_Compass ... ok 578s test_Consensus ... ok 578s test_EMBL_unittest ... ok 578s test_EmbossPrimer ... ok 582s test_Entrez ... ok 582s test_Entrez_online ... skipping. internet not available 583s test_Entrez_parser ... ok 583s test_Enzyme ... ok 583s test_ExPASy ... skipping. internet not available 583s test_File ... ok 583s test_GenBank ... ok 585s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 587s ok 588s test_GraphicsChromosome ... ok 588s test_GraphicsDistribution ... ok 589s test_GraphicsGeneral ... ok 589s test_KEGG ... ok 589s test_KEGG_online ... skipping. internet not available 594s test_KGML_graphics ... ok 594s test_KGML_graphics_online ... skipping. internet not available 594s test_KGML_nographics ... ok 594s test_KeyWList ... ok 595s test_MafIO_index ... ok 595s test_Medline ... ok 596s test_NCBIXML ... Exception ignored in: 596s Traceback (most recent call last): 596s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 596s expat_parser.Parse(NULL, True) 596s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 596s ok 596s test_NCBI_qblast ... ok 596s test_NMR ... ok 596s test_Nexus ... ok 596s test_PAML_baseml ... ok 597s test_PAML_codeml ... ok 597s test_PAML_yn00 ... ok 601s test_PDB_CEAligner ... ok 602s test_PDB_DSSP ... ok 603s test_PDB_Dice ... ok 603s test_PDB_Disordered ... ok 603s test_PDB_Exposure ... ok 603s test_PDB_FragmentMapper ... ok 605s test_PDB_KDTree ... ok 605s test_PDB_MMCIF2Dict ... ok 605s test_PDB_MMCIFIO ... ok 606s test_PDB_MMCIFParser ... ok 606s test_PDB_NACCESS ... ok 607s test_PDB_PDBIO ... ok 607s test_PDB_PDBList ... skipping. internet not available 613s test_PDB_PDBMLParser ... ok 613s test_PDB_PDBParser ... ok 613s 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 613s test_PDB_Polypeptide ... ok 613s test_PDB_QCPSuperimposer ... ok 617s test_PDB_SASA ... ok 617s test_PDB_SMCRA ... ok 618s test_PDB_Selection ... ok 618s test_PDB_StructureAlignment ... ok 618s test_PDB_Superimposer ... ok 618s test_PDB_alphafold_db ... skipping. internet not available 622s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 622s warnings.warn( 622s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 622s warnings.warn( 622s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 622s warnings.warn( 622s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 622s warnings.warn( 622s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 622s warnings.warn( 622s ok 629s test_PDB_internal_coords ... ok 629s test_PDB_parse_pdb_header ... ok 629s test_PDB_vectors ... ok 630s test_PQR ... ok 630s test_Pathway ... ok 630s test_Phd ... ok 631s test_Phylo ... ok 631s test_PhyloXML ... ok 632s test_Phylo_CDAO ... ok 632s test_Phylo_NeXML ... ok 634s test_Phylo_igraph ... ok 636s test_Phylo_matplotlib ... ok 637s test_Phylo_networkx ... ok 638s test_PopGen_GenePop_nodepend ... ok 638s test_ProtParam ... ok 639s test_RCSBFormats ... ok 640s test_Restriction ... ok 641s test_SCOP_Astral ... ok 641s test_SCOP_Cla ... ok 642s test_SCOP_Des ... ok 642s test_SCOP_Dom ... ok 643s test_SCOP_Hie ... ok 643s test_SCOP_Raf ... ok 644s test_SCOP_Residues ... ok 645s test_SCOP_Scop ... ok 645s test_SVDSuperimposer ... ok 646s test_SearchIO_blast_tab ... ok 647s test_SearchIO_blast_tab_index ... ok 647s test_SearchIO_blast_xml ... ok 649s test_SearchIO_blast_xml_index ... ok 650s test_SearchIO_blat_psl ... ok 651s test_SearchIO_blat_psl_index ... ok 651s test_SearchIO_exonerate ... ok 652s test_SearchIO_exonerate_text_index ... ok 652s test_SearchIO_exonerate_vulgar_index ... ok 653s test_SearchIO_fasta_m10 ... ok 654s test_SearchIO_fasta_m10_index ... ok 654s test_SearchIO_hhsuite2_text ... ok 655s test_SearchIO_hmmer2_text ... ok 656s test_SearchIO_hmmer2_text_index ... ok 656s test_SearchIO_hmmer3_domtab ... ok 657s test_SearchIO_hmmer3_domtab_index ... ok 657s test_SearchIO_hmmer3_tab ... ok 658s test_SearchIO_hmmer3_tab_index ... ok 659s test_SearchIO_hmmer3_text ... ok 659s test_SearchIO_hmmer3_text_index ... ok 660s test_SearchIO_infernal_tab ... ok 660s test_SearchIO_infernal_tab_index ... ok 661s test_SearchIO_infernal_text ... ok 662s test_SearchIO_infernal_text_index ... ok 662s test_SearchIO_interproscan_xml ... ok 663s test_SearchIO_model ... ok 664s test_SearchIO_write ... ok 664s test_SeqFeature ... ok 682s test_SeqIO ... ok 683s test_SeqIO_AbiIO ... ok 684s test_SeqIO_FastaIO ... ok 684s test_SeqIO_Gck ... ok 685s test_SeqIO_Gfa ... ok 686s test_SeqIO_Insdc ... ok 686s test_SeqIO_NibIO ... ok 688s test_SeqIO_PdbIO ... ok 689s test_SeqIO_QualityIO ... ok 690s test_SeqIO_SeqXML ... ok 691s test_SeqIO_SffIO ... ok 691s test_SeqIO_SnapGene ... ok 692s test_SeqIO_TwoBitIO ... ok 693s test_SeqIO_UniprotIO ... ok 694s test_SeqIO_Xdna ... ok 695s test_SeqIO_features ... ok 709s test_SeqIO_index ... ok 709s test_SeqIO_online ... skipping. internet not available 710s test_SeqIO_write ... ok 711s test_SeqRecord ... ok 711s test_SeqUtils ... ok 713s test_Seq_objs ... ok 714s test_SwissProt ... ok 714s test_TogoWS ... skipping. internet not available 715s test_TreeConstruction ... ok 716s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 716s test_UniGene ... ok 717s test_UniProt ... skipping. internet not available 718s test_UniProt_GOA ... ok 718s test_align ... ok 719s test_align_substitution_matrices ... ok 722s test_bgzf ... ok 723s test_cellosaurus ... ok 729s test_codonalign ... ok 730s test_geo ... ok 730s test_motifs ... ok 731s test_motifs_online ... skipping. internet not available 732s 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. 732s warnings.warn( 732s ok 732s test_pairwise2_no_C ... ok 733s test_pairwise_aligner ... ok 734s test_pairwise_alignment_map ... ok 741s test_phenotype ... ok 742s test_phenotype_fit ... ok 743s test_prodoc ... ok 743s test_prosite ... ok 744s test_seq ... ok 745s test_translate ... ok 745s Skipping any tests requiring internet access 745s Python version: 3.13.11 (main, Dec 6 2025, 13:15:20) [GCC 15.2.0] 745s Operating system: posix linux 745s ---------------------------------------------------------------------- 745s Ran 201 tests in 186.625 seconds 745s 746s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 746s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 747s test_Ace ... ok 747s test_Affy ... ok 748s test_AlignIO ... ok 748s test_AlignIO_ClustalIO ... ok 748s test_AlignIO_EmbossIO ... ok 748s test_AlignIO_FastaIO ... ok 748s test_AlignIO_MauveIO ... ok 748s test_AlignIO_PhylipIO ... ok 748s test_AlignIO_convert ... ok 748s test_Align_Alignment ... ok 748s test_Align_a2m ... ok 748s test_Align_bed ... ok 749s test_Align_bigbed ... ok 749s test_Align_bigmaf ... ok 750s test_Align_bigpsl ... ok 750s test_Align_chain ... ok 750s test_Align_clustal ... ok 755s test_Align_codonalign ... FAIL 755s test_Align_emboss ... ok 756s test_Align_exonerate ... ok 756s test_Align_fasta ... ok 756s test_Align_format_matrix ... ok 756s test_Align_hhr ... ok 757s test_Align_maf ... ok 757s test_Align_mauve ... ok 757s test_Align_msf ... ok 758s test_Align_nexus ... ok 758s test_Align_phylip ... ok 758s test_Align_psl ... ok 758s test_Align_sam ... ok 760s test_Align_stockholm ... ok 761s test_Align_tabular ... ok 761s test_BioSQL_MySQLdb_online ... skipping. internet not available 761s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 761s test_BioSQL_mysql_connector_online ... skipping. internet not available 761s test_BioSQL_psycopg2_online ... skipping. internet not available 765s test_BioSQL_sqlite3 ... ok 765s test_BioSQL_sqlite3_online ... skipping. internet not available 765s test_Blast_Record ... ok 765s test_Blast_parser ... ok 766s test_CAPS ... ok 766s test_Chi2 ... ERROR 766s test_Cluster ... ok 766s test_CodonTable ... ok 766s test_ColorSpiral ... ok 766s test_Compass ... ok 766s test_Consensus ... ERROR 766s test_EMBL_unittest ... ok 766s test_EmbossPrimer ... ok 770s test_Entrez ... ok 770s test_Entrez_online ... skipping. internet not available 771s test_Entrez_parser ... ok 771s test_Enzyme ... ok 771s test_ExPASy ... skipping. internet not available 771s test_File ... ok 771s test_GenBank ... ok 773s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 775s ok 776s test_GraphicsChromosome ... ok 776s test_GraphicsDistribution ... ok 776s test_GraphicsGeneral ... ok 777s test_KEGG ... ok 777s test_KEGG_online ... skipping. internet not available 781s test_KGML_graphics ... ok 781s test_KGML_graphics_online ... skipping. internet not available 782s test_KGML_nographics ... ok 782s test_KeyWList ... ok 783s test_MafIO_index ... ok 783s test_Medline ... ok 783s test_NCBIXML ... Exception ignored while closing generator : 783s Traceback (most recent call last): 783s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 783s expat_parser.Parse(NULL, True) 783s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 783s ok 783s test_NCBI_qblast ... ok 783s test_NMR ... ok 784s test_Nexus ... ok 784s test_PAML_baseml ... ERROR 784s test_PAML_codeml ... ERROR 784s test_PAML_yn00 ... ERROR 787s test_PDB_CEAligner ... ok 789s test_PDB_DSSP ... ok 789s test_PDB_Dice ... ok 789s test_PDB_Disordered ... ok 789s test_PDB_Exposure ... ok 789s test_PDB_FragmentMapper ... ok 791s test_PDB_KDTree ... ok 792s test_PDB_MMCIF2Dict ... ok 792s test_PDB_MMCIFIO ... ok 793s test_PDB_MMCIFParser ... ok 793s test_PDB_NACCESS ... ok 793s test_PDB_PDBIO ... ok 793s test_PDB_PDBList ... skipping. internet not available 798s test_PDB_PDBMLParser ... ok 798s test_PDB_PDBParser ... ok 798s 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 798s test_PDB_Polypeptide ... ok 798s test_PDB_QCPSuperimposer ... ok 802s test_PDB_SASA ... ok 802s test_PDB_SMCRA ... ok 803s test_PDB_Selection ... ok 803s test_PDB_StructureAlignment ... ok 803s test_PDB_Superimposer ... ok 803s test_PDB_alphafold_db ... skipping. internet not available 806s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 806s warnings.warn( 806s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 806s warnings.warn( 806s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 806s warnings.warn( 806s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 806s warnings.warn( 806s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 806s warnings.warn( 806s ok 813s test_PDB_internal_coords ... ok 813s test_PDB_parse_pdb_header ... ok 813s test_PDB_vectors ... ok 814s test_PQR ... ok 814s test_Pathway ... ok 814s test_Phd ... ok 815s test_Phylo ... ERROR 815s test_PhyloXML ... ERROR 815s test_Phylo_CDAO ... ERROR 815s test_Phylo_NeXML ... ERROR 816s test_Phylo_igraph ... ERROR 816s test_Phylo_matplotlib ... ERROR 816s test_Phylo_networkx ... ERROR 816s test_PopGen_GenePop_nodepend ... ok 817s test_ProtParam ... ok 817s test_RCSBFormats ... ok 818s test_Restriction ... ok 818s test_SCOP_Astral ... ok 818s test_SCOP_Cla ... ok 818s test_SCOP_Des ... ok 818s test_SCOP_Dom ... ok 819s test_SCOP_Hie ... ok 819s test_SCOP_Raf ... ok 819s test_SCOP_Residues ... ok 820s test_SCOP_Scop ... ok 820s test_SVDSuperimposer ... ok 820s test_SearchIO_blast_tab ... ok 820s test_SearchIO_blast_tab_index ... ok 821s test_SearchIO_blast_xml ... ok 822s test_SearchIO_blast_xml_index ... ok 823s test_SearchIO_blat_psl ... ok 823s test_SearchIO_blat_psl_index ... ok 823s test_SearchIO_exonerate ... ok 824s test_SearchIO_exonerate_text_index ... ok 824s test_SearchIO_exonerate_vulgar_index ... ok 824s test_SearchIO_fasta_m10 ... ok 824s test_SearchIO_fasta_m10_index ... ok 825s test_SearchIO_hhsuite2_text ... ok 825s test_SearchIO_hmmer2_text ... ok 825s test_SearchIO_hmmer2_text_index ... ok 826s test_SearchIO_hmmer3_domtab ... ok 826s test_SearchIO_hmmer3_domtab_index ... ok 826s test_SearchIO_hmmer3_tab ... ok 826s test_SearchIO_hmmer3_tab_index ... ok 827s test_SearchIO_hmmer3_text ... ok 827s test_SearchIO_hmmer3_text_index ... ok 827s test_SearchIO_infernal_tab ... ok 828s test_SearchIO_infernal_tab_index ... ok 828s test_SearchIO_infernal_text ... ok 828s test_SearchIO_infernal_text_index ... ok 828s test_SearchIO_interproscan_xml ... ok 829s test_SearchIO_model ... ok 829s test_SearchIO_write ... ok 829s test_SeqFeature ... ok 843s test_SeqIO ... ok 844s test_SeqIO_AbiIO ... ok 844s test_SeqIO_FastaIO ... ok 845s test_SeqIO_Gck ... ok 845s test_SeqIO_Gfa ... ok 845s test_SeqIO_Insdc ... ok 845s test_SeqIO_NibIO ... ok 847s test_SeqIO_PdbIO ... ok 847s test_SeqIO_QualityIO ... ok 848s test_SeqIO_SeqXML ... ok 848s test_SeqIO_SffIO ... ok 848s test_SeqIO_SnapGene ... ok 849s test_SeqIO_TwoBitIO ... ok 850s test_SeqIO_UniprotIO ... ok 850s test_SeqIO_Xdna ... ok 851s test_SeqIO_features ... ok 865s test_SeqIO_index ... ok 865s test_SeqIO_online ... skipping. internet not available 865s test_SeqIO_write ... ok 866s test_SeqRecord ... ok 866s test_SeqUtils ... ok 867s test_Seq_objs ... ok 868s test_SwissProt ... ok 868s test_TogoWS ... skipping. internet not available 868s test_TreeConstruction ... ERROR 869s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 869s test_UniGene ... ok 869s test_UniProt ... skipping. internet not available 870s test_UniProt_GOA ... ok 870s test_align ... ok 871s test_align_substitution_matrices ... ok 873s test_bgzf ... ok 873s test_cellosaurus ... ok 877s test_codonalign ... FAIL 878s test_geo ... ok 878s test_motifs ... ok 878s test_motifs_online ... skipping. internet not available 879s 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. 879s warnings.warn( 879s ok 879s test_pairwise2_no_C ... ok 880s test_pairwise_aligner ... ok 880s test_pairwise_alignment_map ... ok 888s test_phenotype ... ok 888s test_phenotype_fit ... ok 888s test_prodoc ... ok 889s test_prosite ... ok 889s test_seq ... ok 889s test_translate ... ok 890s ====================================================================== 890s ERROR: test_dn_ds (test_Align_codonalign.Test_dn_ds.test_dn_ds) 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 8313, in test_dn_ds 890s dn, ds = calculate_dn_ds_matrix(alignment) 890s ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/Bio/Align/analysis.py", line 1012, in calculate_dn_ds_matrix 890s from Bio.Phylo.TreeConstruction import DistanceMatrix 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s 890s ====================================================================== 890s ERROR: test_Chi2 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_Chi2.py", line 10, in 890s from Bio.Phylo.PAML import chi2 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_Consensus 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_Consensus.py", line 15, in 890s from Bio import Phylo 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_PAML_baseml 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_PAML_baseml.py", line 12, in 890s from Bio.Phylo.PAML import baseml 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_PAML_codeml 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_PAML_codeml.py", line 13, in 890s from Bio.Phylo.PAML import codeml 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_PAML_yn00 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_PAML_yn00.py", line 13, in 890s from Bio.Phylo.PAML import yn00 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_Phylo 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_Phylo.py", line 13, in 890s from Bio import Phylo 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_PhyloXML 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_PhyloXML.py", line 17, in 890s from Bio.Phylo import PhyloXML as PX 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_Phylo_CDAO 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_Phylo_CDAO.py", line 13, in 890s import Bio.Phylo as bp 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_Phylo_NeXML 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_Phylo_NeXML.py", line 14, in 890s from Bio import Phylo 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_Phylo_igraph 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_Phylo_igraph.py", line 13, in 890s from Bio import Phylo 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_Phylo_matplotlib 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_Phylo_matplotlib.py", line 13, in 890s from Bio import Phylo 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_Phylo_networkx 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_Phylo_networkx.py", line 12, in 890s from Bio import Phylo 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_TreeConstruction 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 890s suite = loader.loadTestsFromName(name) 890s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 890s module = __import__(module_name) 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_TreeConstruction.py", line 16, in 890s from Bio import Phylo 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s ====================================================================== 890s ERROR: test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) 890s ---------------------------------------------------------------------- 890s Traceback (most recent call last): 890s File "/tmp/autopkgtest.SSXo8g/autopkgtest_tmp/Tests/test_codonalign.py", line 381, in test_dn_ds_matrix 890s dn, ds = self.aln.get_dn_ds_matrix() 890s ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 890s File "/usr/lib/python3/dist-packages/Bio/codonalign/codonalignment.py", line 159, in get_dn_ds_matrix 890s from Bio.Phylo.TreeConstruction import DistanceMatrix as DM 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 890s from Bio.Phylo._io import convert 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 890s from Bio.Phylo import CDAOIO 890s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 890s import rdflib 890s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 890s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 890s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 890s from rdflib.resource import Resource 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 890s class Resource: 890s ...<164 lines>... 890s return "Resource(%s,%s)" % (self._graph, self._identifier) 890s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 890s def value(self, p=RDF.value, o=None, default=None, any=True): 890s ^^^^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 890s return cls.__getitem__(name) 890s ~~~~~~~~~~~~~~~^^^^^^ 890s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 890s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 890s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 890s 890s ---------------------------------------------------------------------- 890s Ran 201 tests in 142.068 seconds 890s 890s FAILED (failures = 15) 890s Skipping any tests requiring internet access 890s Python version: 3.14.2 (main, Dec 6 2025, 13:20:08) [GCC 15.2.0] 890s Operating system: posix linux 890s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 890s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 891s autopkgtest [13:57:57]: test full_suite: -----------------------] 891s autopkgtest [13:57:57]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 891s full_suite FAIL non-zero exit status 1 892s autopkgtest [13:57:58]: @@@@@@@@@@@@@@@@@@@@ summary 892s dependencies PASS 892s full_suite FAIL non-zero exit status 1