0s autopkgtest [12:06:39]: starting date and time: 2025-02-19 12:06:39+0000 0s autopkgtest [12:06:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:06:39]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3v7514r_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-73.secgroup --name adt-plucky-amd64-python-biopython-20250219-120639-juju-7f2275-prod-proposed-migration-environment-2-03bec523-5594-4cf5-a412-f57e47509b8b --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 41s autopkgtest [12:07:20]: testbed dpkg architecture: amd64 41s autopkgtest [12:07:20]: testbed apt version: 2.9.29 41s autopkgtest [12:07:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 42s autopkgtest [12:07:21]: testbed release detected to be: None 42s autopkgtest [12:07:21]: updating testbed package index (apt update) 42s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 42s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 42s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 42s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 42s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 42s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 42s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 42s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 42s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [81.8 kB] 42s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [101 kB] 42s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 42s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 42s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [697 kB] 42s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [265 kB] 42s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3128 B] 42s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [11.5 kB] 42s Fetched 2124 kB in 0s (5482 kB/s) 43s Reading package lists... 44s Reading package lists... 44s Building dependency tree... 44s Reading state information... 44s Calculating upgrade... 44s The following NEW packages will be installed: 44s libapt-pkg7.0 44s The following packages will be upgraded: 44s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 44s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 44s Need to get 5234 kB of archives. 44s After this operation, 4074 kB of additional disk space will be used. 44s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.30 [1131 kB] 45s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.30 [1434 kB] 45s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.30 [222 kB] 45s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 45s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit0 amd64 0.25.5-2ubuntu3 [311 kB] 45s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu1 [555 kB] 45s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 lsof amd64 4.99.4+dfsg-1 [245 kB] 45s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsof0 amd64 4.99.4+dfsg-1 [59.6 kB] 45s Preconfiguring packages ... 45s Fetched 5234 kB in 0s (16.9 MB/s) 45s Selecting previously unselected package libapt-pkg7.0:amd64. 45s (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 ... 108925 files and directories currently installed.) 45s Preparing to unpack .../libapt-pkg7.0_2.9.30_amd64.deb ... 45s Unpacking libapt-pkg7.0:amd64 (2.9.30) ... 45s Setting up libapt-pkg7.0:amd64 (2.9.30) ... 46s (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 ... 108974 files and directories currently installed.) 46s Preparing to unpack .../archives/apt_2.9.30_amd64.deb ... 46s Unpacking apt (2.9.30) over (2.9.29) ... 46s Setting up apt (2.9.30) ... 46s (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 ... 108974 files and directories currently installed.) 46s Preparing to unpack .../0-apt-utils_2.9.30_amd64.deb ... 46s Unpacking apt-utils (2.9.30) over (2.9.29) ... 46s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_amd64.deb ... 47s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 47s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_amd64.deb ... 47s Unpacking libp11-kit0:amd64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 47s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_amd64.deb ... 47s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 47s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_amd64.deb ... 47s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 47s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_amd64.deb ... 47s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 47s Setting up apt-utils (2.9.30) ... 47s Setting up liblsof0 (4.99.4+dfsg-1) ... 47s Setting up iproute2 (6.13.0-1ubuntu1) ... 47s Setting up rsyslog (8.2412.0-2ubuntu1) ... 47s info: The user `syslog' is already a member of `adm'. 48s Setting up libp11-kit0:amd64 (0.25.5-2ubuntu3) ... 48s Setting up lsof (4.99.4+dfsg-1) ... 48s Processing triggers for man-db (2.13.0-1) ... 50s Processing triggers for libc-bin (2.40-4ubuntu1) ... 51s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s autopkgtest [12:07:31]: upgrading testbed (apt dist-upgrade and autopurge) 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 53s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 53s Starting 2 pkgProblemResolver with broken count: 0 53s Done 53s Entering ResolveByKeep 54s 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Starting pkgProblemResolver with broken count: 0 55s Starting 2 pkgProblemResolver with broken count: 0 55s Done 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s autopkgtest [12:07:35]: rebooting testbed after setup commands that affected boot 59s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 71s autopkgtest [12:07:50]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 72s autopkgtest [12:07:51]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 75s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (dsc) [3439 B] 75s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (tar) [14.6 MB] 75s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.85+dfsg-2 (diff) [42.9 kB] 75s gpgv: Signature made Thu Feb 6 14:44:48 2025 UTC 75s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 75s gpgv: issuer "crusoe@debian.org" 75s gpgv: Can't check signature: No public key 75s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2.dsc: no acceptable signature found 76s autopkgtest [12:07:55]: testing package python-biopython version 1.85+dfsg-2 76s autopkgtest [12:07:55]: build not needed 77s autopkgtest [12:07:56]: test dependencies: preparing testbed 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Starting pkgProblemResolver with broken count: 0 78s Starting 2 pkgProblemResolver with broken count: 0 78s Done 79s The following NEW packages will be installed: 79s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 79s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 79s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 79s libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 79s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 79s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 79s python-biopython-doc python3-all python3-biopython python3-biopython-sql 79s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 79s python3-rlpycairo python3.12 python3.12-minimal sgml-base w3c-sgml-lib 79s x11-common xfonts-encodings xfonts-utils xml-core 79s 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 52.2 MB of archives. 79s After this operation, 158 MB of additional disk space will be used. 79s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-minimal amd64 3.12.9-1 [2348 kB] 79s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 79s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12 amd64 3.12.9-1 [671 kB] 79s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 79s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 79s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 79s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 79s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 79s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 79s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 79s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 79s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 79s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 79s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 79s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 79s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 79s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 79s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 79s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 79s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 79s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250213-1ubuntu1 [148 kB] 79s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 79s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 79s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 79s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 79s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 79s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 79s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 79s Get:29 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 79s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 79s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 79s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 79s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 79s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 79s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 79s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 79s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 79s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 79s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 79s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biopython-doc all 1.85+dfsg-2 [18.2 MB] 80s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.1-1~exp2 [894 B] 80s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 80s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 80s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5 [589 kB] 80s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build1 [143 kB] 80s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 80s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 80s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.3.0-1 [1137 kB] 80s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 80s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 80s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.85+dfsg-2 [1745 kB] 80s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython-sql all 1.85+dfsg-2 [26.4 kB] 80s Fetched 52.2 MB in 1s (48.6 MB/s) 80s Selecting previously unselected package python3.12-minimal. 80s (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 ... 108975 files and directories currently installed.) 80s Preparing to unpack .../00-python3.12-minimal_3.12.9-1_amd64.deb ... 80s Unpacking python3.12-minimal (3.12.9-1) ... 80s Selecting previously unselected package sgml-base. 80s Preparing to unpack .../01-sgml-base_1.31_all.deb ... 80s Unpacking sgml-base (1.31) ... 80s Selecting previously unselected package python3.12. 80s Preparing to unpack .../02-python3.12_3.12.9-1_amd64.deb ... 80s Unpacking python3.12 (3.12.9-1) ... 81s Selecting previously unselected package fonts-dejavu-mono. 81s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 81s Unpacking fonts-dejavu-mono (2.37-8) ... 81s Selecting previously unselected package fonts-dejavu-core. 81s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 81s Unpacking fonts-dejavu-core (2.37-8) ... 81s Selecting previously unselected package libfontenc1:amd64. 81s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 81s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 81s Selecting previously unselected package x11-common. 81s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ... 81s Unpacking x11-common (1:7.7+23ubuntu3) ... 81s Selecting previously unselected package xfonts-encodings. 81s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 81s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 81s Selecting previously unselected package xfonts-utils. 81s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_amd64.deb ... 81s Unpacking xfonts-utils (1:7.7+7) ... 81s Selecting previously unselected package fonts-urw-base35. 81s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 81s Unpacking fonts-urw-base35 (20200910-8) ... 81s Selecting previously unselected package fontconfig-config. 81s Preparing to unpack .../10-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 81s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 81s Selecting previously unselected package libblas3:amd64. 81s Preparing to unpack .../11-libblas3_3.12.1-2_amd64.deb ... 81s Unpacking libblas3:amd64 (3.12.1-2) ... 81s Selecting previously unselected package libfontconfig1:amd64. 81s Preparing to unpack .../12-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 81s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 81s Selecting previously unselected package libpixman-1-0:amd64. 81s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_amd64.deb ... 81s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 81s Selecting previously unselected package libxcb-render0:amd64. 81s Preparing to unpack .../14-libxcb-render0_1.17.0-2_amd64.deb ... 81s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 82s Selecting previously unselected package libxcb-shm0:amd64. 82s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_amd64.deb ... 82s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 82s Selecting previously unselected package libxrender1:amd64. 82s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 82s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 82s Selecting previously unselected package libcairo2:amd64. 82s Preparing to unpack .../17-libcairo2_1.18.2-2_amd64.deb ... 82s Unpacking libcairo2:amd64 (1.18.2-2) ... 82s Selecting previously unselected package libdeflate0:amd64. 82s Preparing to unpack .../18-libdeflate0_1.23-1_amd64.deb ... 82s Unpacking libdeflate0:amd64 (1.23-1) ... 82s Selecting previously unselected package libgfortran5:amd64. 82s Preparing to unpack .../19-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 82s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 82s Selecting previously unselected package libgomp1:amd64. 82s Preparing to unpack .../20-libgomp1_15-20250213-1ubuntu1_amd64.deb ... 82s Unpacking libgomp1:amd64 (15-20250213-1ubuntu1) ... 82s Selecting previously unselected package libgraphite2-3:amd64. 82s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 82s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 82s Selecting previously unselected package libharfbuzz0b:amd64. 82s Preparing to unpack .../22-libharfbuzz0b_10.2.0-1_amd64.deb ... 82s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 82s Selecting previously unselected package libimagequant0:amd64. 82s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_amd64.deb ... 82s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 82s Selecting previously unselected package libjpeg-turbo8:amd64. 82s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 82s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 82s Selecting previously unselected package libjpeg8:amd64. 82s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_amd64.deb ... 82s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 82s Selecting previously unselected package libjs-jquery. 82s Preparing to unpack .../26-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 82s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 82s Selecting previously unselected package libjs-underscore. 82s Preparing to unpack .../27-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 82s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 82s Selecting previously unselected package libjs-sphinxdoc. 82s Preparing to unpack .../28-libjs-sphinxdoc_8.1.3-5_all.deb ... 82s Unpacking libjs-sphinxdoc (8.1.3-5) ... 82s Selecting previously unselected package liblapack3:amd64. 82s Preparing to unpack .../29-liblapack3_3.12.1-2_amd64.deb ... 82s Unpacking liblapack3:amd64 (3.12.1-2) ... 82s Selecting previously unselected package liblcms2-2:amd64. 82s Preparing to unpack .../30-liblcms2-2_2.16-2_amd64.deb ... 82s Unpacking liblcms2-2:amd64 (2.16-2) ... 82s Selecting previously unselected package liblerc4:amd64. 82s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 82s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 82s Selecting previously unselected package libraqm0:amd64. 82s Preparing to unpack .../32-libraqm0_0.10.2-1_amd64.deb ... 82s Unpacking libraqm0:amd64 (0.10.2-1) ... 82s Selecting previously unselected package libsharpyuv0:amd64. 82s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1_amd64.deb ... 82s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 82s Selecting previously unselected package libjbig0:amd64. 82s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 82s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 82s Selecting previously unselected package libwebp7:amd64. 82s Preparing to unpack .../35-libwebp7_1.5.0-0.1_amd64.deb ... 82s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 82s Selecting previously unselected package libtiff6:amd64. 82s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 82s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 82s Selecting previously unselected package libwebpdemux2:amd64. 82s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_amd64.deb ... 82s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 82s Selecting previously unselected package libwebpmux3:amd64. 82s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_amd64.deb ... 82s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 82s Selecting previously unselected package python-biopython-doc. 82s Preparing to unpack .../39-python-biopython-doc_1.85+dfsg-2_all.deb ... 82s Unpacking python-biopython-doc (1.85+dfsg-2) ... 83s Selecting previously unselected package python3-all. 83s Preparing to unpack .../40-python3-all_3.13.1-1~exp2_amd64.deb ... 83s Unpacking python3-all (3.13.1-1~exp2) ... 83s Selecting previously unselected package python3-numpy. 83s Preparing to unpack .../41-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 83s Unpacking python3-numpy (1:1.26.4+ds-13) ... 83s Selecting previously unselected package libopenjp2-7:amd64. 83s Preparing to unpack .../42-libopenjp2-7_2.5.0-2ubuntu3_amd64.deb ... 83s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 83s Selecting previously unselected package python3-pil:amd64. 83s Preparing to unpack .../43-python3-pil_11.1.0-5_amd64.deb ... 83s Unpacking python3-pil:amd64 (11.1.0-5) ... 83s Selecting previously unselected package python3-cairo. 83s Preparing to unpack .../44-python3-cairo_1.26.1-2build1_amd64.deb ... 83s Unpacking python3-cairo (1.26.1-2build1) ... 83s Selecting previously unselected package python3-freetype. 83s Preparing to unpack .../45-python3-freetype_2.5.1-1_all.deb ... 83s Unpacking python3-freetype (2.5.1-1) ... 83s Selecting previously unselected package python3-rlpycairo. 83s Preparing to unpack .../46-python3-rlpycairo_0.3.0-3_all.deb ... 83s Unpacking python3-rlpycairo (0.3.0-3) ... 83s Selecting previously unselected package python3-reportlab. 83s Preparing to unpack .../47-python3-reportlab_4.3.0-1_all.deb ... 83s Unpacking python3-reportlab (4.3.0-1) ... 83s Selecting previously unselected package xml-core. 83s Preparing to unpack .../48-xml-core_0.19_all.deb ... 83s Unpacking xml-core (0.19) ... 83s Selecting previously unselected package w3c-sgml-lib. 83s Preparing to unpack .../49-w3c-sgml-lib_1.3-3_all.deb ... 83s Unpacking w3c-sgml-lib (1.3-3) ... 84s Selecting previously unselected package python3-biopython. 84s Preparing to unpack .../50-python3-biopython_1.85+dfsg-2_amd64.deb ... 84s Unpacking python3-biopython (1.85+dfsg-2) ... 84s Selecting previously unselected package python3-biopython-sql. 84s Preparing to unpack .../51-python3-biopython-sql_1.85+dfsg-2_all.deb ... 84s Unpacking python3-biopython-sql (1.85+dfsg-2) ... 84s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 84s Setting up liblcms2-2:amd64 (2.16-2) ... 84s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 84s Setting up python3.12-minimal (3.12.9-1) ... 85s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 85s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 85s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 85s Setting up libxcb-render0:amd64 (1.17.0-2) ... 85s Setting up python3.12 (3.12.9-1) ... 86s Setting up x11-common (1:7.7+23ubuntu3) ... 86s Setting up libdeflate0:amd64 (1.23-1) ... 86s Setting up python3-all (3.13.1-1~exp2) ... 86s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 86s Setting up libgomp1:amd64 (15-20250213-1ubuntu1) ... 86s Setting up python3-freetype (2.5.1-1) ... 86s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 86s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 86s Setting up libblas3:amd64 (3.12.1-2) ... 86s 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 86s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 86s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 86s Setting up fonts-dejavu-mono (2.37-8) ... 86s Setting up fonts-dejavu-core (2.37-8) ... 86s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 86s Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 86s Setting up libwebp7:amd64 (1.5.0-0.1) ... 86s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 86s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 86s Setting up sgml-base (1.31) ... 86s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 86s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 86s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 86s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 86s Setting up liblapack3:amd64 (3.12.1-2) ... 86s 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 86s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 87s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 87s Setting up xfonts-utils (1:7.7+7) ... 87s Setting up libraqm0:amd64 (0.10.2-1) ... 87s Setting up python3-numpy (1:1.26.4+ds-13) ... 90s Setting up libjs-sphinxdoc (8.1.3-5) ... 90s Setting up python-biopython-doc (1.85+dfsg-2) ... 90s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 90s Setting up xml-core (0.19) ... 90s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 90s Setting up fonts-urw-base35 (20200910-8) ... 90s Setting up libcairo2:amd64 (1.18.2-2) ... 90s Setting up python3-pil:amd64 (11.1.0-5) ... 91s Setting up python3-cairo (1.26.1-2build1) ... 91s Setting up python3-rlpycairo (0.3.0-3) ... 91s Setting up python3-reportlab (4.3.0-1) ... 92s Processing triggers for libc-bin (2.40-4ubuntu1) ... 92s Processing triggers for systemd (257.2-3ubuntu1) ... 92s Processing triggers for man-db (2.13.0-1) ... 94s Processing triggers for sgml-base (1.31) ... 94s Setting up w3c-sgml-lib (1.3-3) ... 121s Setting up python3-biopython (1.85+dfsg-2) ... 124s Setting up python3-biopython-sql (1.85+dfsg-2) ... 125s autopkgtest [12:08:44]: test dependencies: sh debian/tests/run-unit-test 125s autopkgtest [12:08:44]: test dependencies: [----------------------- 125s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 125s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 127s mkdir: created directory 'Bio' 127s mkdir: created directory 'Bio/Align' 127s mkdir: created directory 'Bio/Align/substitution_matrices' 127s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 127s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 127s test_Ace ... ok 127s test_Affy ... ok 130s test_AlignIO ... ok 130s test_AlignIO_ClustalIO ... ok 130s test_AlignIO_EmbossIO ... ok 130s test_AlignIO_FastaIO ... ok 130s test_AlignIO_MauveIO ... ok 130s test_AlignIO_PhylipIO ... ok 130s test_AlignIO_convert ... ok 130s test_AlignInfo ... ok 131s test_Align_Alignment ... ok 131s test_Align_a2m ... ok 131s test_Align_bed ... ok 131s test_Align_bigbed ... ok 131s test_Align_bigmaf ... ok 132s test_Align_bigpsl ... ok 132s test_Align_chain ... ok 132s test_Align_clustal ... ok 135s test_Align_codonalign ... ok 135s test_Align_emboss ... ok 135s test_Align_exonerate ... ok 135s test_Align_fasta ... ok 136s test_Align_hhr ... ok 136s test_Align_maf ... ok 136s test_Align_mauve ... ok 136s test_Align_msf ... ok 137s test_Align_nexus ... ok 137s test_Align_phylip ... ok 137s test_Align_psl ... ok 137s test_Align_sam ... ok 139s test_Align_stockholm ... ok 139s test_Align_tabular ... ok 139s test_Application ... ok 139s test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython 139s test_BioSQL_MySQLdb_online ... skipping. internet not available 139s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 139s test_BioSQL_mysql_connector_online ... skipping. internet not available 139s test_BioSQL_psycopg2_online ... skipping. internet not available 144s test_BioSQL_sqlite3 ... ok 144s test_BioSQL_sqlite3_online ... skipping. internet not available 144s test_Blast_Record ... ok 145s test_Blast_parser ... ok 145s test_CAPS ... ok 145s test_Chi2 ... ok 145s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 145s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 145s test_Cluster ... ok 145s test_CodonTable ... ok 145s test_ColorSpiral ... ok 145s test_Compass ... ok 146s test_Consensus ... ok 146s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 146s test_EMBL_unittest ... ok 146s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 146s test_EmbossPrimer ... ok 150s test_Entrez ... ok 150s test_Entrez_online ... skipping. internet not available 151s test_Entrez_parser ... ok 151s test_Enzyme ... ok 151s test_ExPASy ... skipping. internet not available 151s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 151s test_File ... ok 151s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 151s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 151s ok 153s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 155s ok 156s test_GraphicsChromosome ... ok 156s test_GraphicsDistribution ... ok 157s test_GraphicsGeneral ... ok 157s test_HMMCasino ... ok 157s test_HMMGeneral ... ok 157s test_KEGG ... ok 157s test_KEGG_online ... skipping. internet not available 163s test_KGML_graphics ... ok 163s test_KGML_graphics_online ... skipping. internet not available 164s test_KGML_nographics ... ok 164s test_KeyWList ... ok 164s test_LogisticRegression ... ok 165s test_MafIO_index ... ok 165s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 165s test_MarkovModel ... ok 165s test_Medline ... ok 165s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 166s test_NCBIXML ... Exception ignored in: 166s Traceback (most recent call last): 166s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 166s expat_parser.Parse(NULL, True) 166s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 166s ok 166s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 166s test_NCBI_qblast ... ok 166s test_NMR ... ok 166s test_NaiveBayes ... ok 166s test_Nexus ... ok 166s test_PAML_baseml ... ok 167s test_PAML_codeml ... ok 167s test_PAML_yn00 ... ok 171s test_PDB_CEAligner ... ok 171s test_PDB_DSSP ... ok 172s test_PDB_Dice ... ok 172s test_PDB_Disordered ... ok 172s test_PDB_Exposure ... ok 172s test_PDB_FragmentMapper ... ok 174s test_PDB_KDTree ... ok 174s test_PDB_MMCIF2Dict ... ok 174s test_PDB_MMCIFIO ... ok 175s test_PDB_MMCIFParser ... ok 175s test_PDB_NACCESS ... ok 175s test_PDB_PDBIO ... ok 175s test_PDB_PDBList ... skipping. internet not available 182s test_PDB_PDBMLParser ... ok 183s test_PDB_PDBParser ... ok 183s 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 183s test_PDB_Polypeptide ... ok 183s test_PDB_QCPSuperimposer ... ok 186s test_PDB_SASA ... ok 187s test_PDB_SMCRA ... ok 187s test_PDB_Selection ... ok 187s test_PDB_StructureAlignment ... ok 187s test_PDB_Superimposer ... ok 187s test_PDB_alphafold_db ... skipping. internet not available 187s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 187s 187s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 187s 187s test_PDB_parse_pdb_header ... ok 188s test_PDB_vectors ... ok 188s test_PQR ... ok 188s test_Pathway ... ok 188s test_Phd ... ok 188s test_Phylo ... ok 188s test_PhyloXML ... ok 189s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 189s test_Phylo_NeXML ... ok 189s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 189s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 189s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 189s test_PopGen_GenePop_nodepend ... ok 189s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 189s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 189s test_ProtParam ... ok 190s test_RCSBFormats ... ok 190s test_Restriction ... ok 190s test_SCOP_Astral ... ok 190s test_SCOP_Cla ... ok 190s test_SCOP_Des ... ok 190s test_SCOP_Dom ... ok 190s test_SCOP_Hie ... ok 190s test_SCOP_Raf ... ok 190s test_SCOP_Residues ... ok 190s test_SCOP_Scop ... ok 190s test_SVDSuperimposer ... ok 190s test_SearchIO_blast_tab ... ok 190s test_SearchIO_blast_tab_index ... ok 191s test_SearchIO_blast_xml ... ok 192s test_SearchIO_blast_xml_index ... ok 192s test_SearchIO_blat_psl ... ok 192s test_SearchIO_blat_psl_index ... ok 192s test_SearchIO_exonerate ... ok 192s test_SearchIO_exonerate_text_index ... ok 192s test_SearchIO_exonerate_vulgar_index ... ok 192s test_SearchIO_fasta_m10 ... ok 192s test_SearchIO_fasta_m10_index ... ok 192s test_SearchIO_hhsuite2_text ... ok 193s test_SearchIO_hmmer2_text ... ok 193s test_SearchIO_hmmer2_text_index ... ok 193s test_SearchIO_hmmer3_domtab ... ok 193s test_SearchIO_hmmer3_domtab_index ... ok 193s test_SearchIO_hmmer3_tab ... ok 193s test_SearchIO_hmmer3_tab_index ... ok 193s test_SearchIO_hmmer3_text ... ok 193s test_SearchIO_hmmer3_text_index ... ok 193s test_SearchIO_interproscan_xml ... ok 193s test_SearchIO_model ... ok 194s test_SearchIO_write ... ok 194s test_SeqFeature ... ok 210s test_SeqIO ... ok 210s test_SeqIO_AbiIO ... ok 210s test_SeqIO_FastaIO ... ok 211s test_SeqIO_Gck ... ok 211s test_SeqIO_Gfa ... ok 211s test_SeqIO_Insdc ... ok 211s test_SeqIO_NibIO ... ok 213s test_SeqIO_PdbIO ... ok 213s test_SeqIO_QualityIO ... ok 213s test_SeqIO_SeqXML ... ok 213s test_SeqIO_SffIO ... ok 213s test_SeqIO_SnapGene ... ok 214s test_SeqIO_TwoBitIO ... ok 214s test_SeqIO_UniprotIO ... ok 214s test_SeqIO_Xdna ... ok 215s test_SeqIO_features ... ok 229s test_SeqIO_index ... ok 229s test_SeqIO_online ... skipping. internet not available 229s test_SeqIO_write ... ok 229s test_SeqRecord ... ok 229s test_SeqUtils ... ok 230s test_Seq_objs ... ok 231s test_SwissProt ... ok 231s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 231s test_TogoWS ... skipping. internet not available 231s test_TreeConstruction ... ok 231s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 231s test_UniGene ... ok 231s test_UniProt ... skipping. internet not available 231s test_UniProt_GOA ... ok 232s test_align ... ok 232s test_align_substitution_matrices ... ok 234s test_bgzf ... ok 234s test_cellosaurus ... ok 239s test_codonalign ... ok 239s test_geo ... ok 239s test_kNN ... ok 239s test_motifs ... ok 239s test_motifs_online ... skipping. internet not available 239s 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. 239s warnings.warn( 239s ok 239s test_pairwise2_no_C ... ok 240s test_pairwise_aligner ... ok 240s test_pairwise_alignment_map ... ok 247s test_phenotype ... ok 247s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 247s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 247s test_prodoc ... ok 247s test_prosite ... ok 247s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 247s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 248s test_seq ... ok 248s test_translate ... ok 248s ---------------------------------------------------------------------- 248s Ran 219 tests in 120.381 seconds 248s 248s Skipping any tests requiring internet access 248s Python version: 3.12.9 (main, Feb 5 2025, 01:31:18) [GCC 14.2.0] 248s Operating system: posix linux 248s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 248s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 248s test_Ace ... ok 248s test_Affy ... ok 251s test_AlignIO ... ok 251s test_AlignIO_ClustalIO ... ok 251s test_AlignIO_EmbossIO ... ok 251s test_AlignIO_FastaIO ... ok 251s test_AlignIO_MauveIO ... ok 251s test_AlignIO_PhylipIO ... ok 251s test_AlignIO_convert ... ok 251s test_AlignInfo ... ok 251s test_Align_Alignment ... ok 251s test_Align_a2m ... ok 251s test_Align_bed ... ok 252s test_Align_bigbed ... ok 252s test_Align_bigmaf ... ok 252s test_Align_bigpsl ... ok 253s test_Align_chain ... ok 253s test_Align_clustal ... ok 256s test_Align_codonalign ... ok 256s test_Align_emboss ... ok 256s test_Align_exonerate ... ok 256s test_Align_fasta ... ok 256s test_Align_hhr ... ok 257s test_Align_maf ... ok 257s test_Align_mauve ... ok 257s test_Align_msf ... ok 257s test_Align_nexus ... ok 257s test_Align_phylip ... ok 258s test_Align_psl ... ok 258s test_Align_sam ... ok 260s test_Align_stockholm ... ok 260s test_Align_tabular ... ok 260s test_Application ... ok 260s test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython 260s test_BioSQL_MySQLdb_online ... skipping. internet not available 260s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 260s test_BioSQL_mysql_connector_online ... skipping. internet not available 260s test_BioSQL_psycopg2_online ... skipping. internet not available 265s test_BioSQL_sqlite3 ... ok 265s test_BioSQL_sqlite3_online ... skipping. internet not available 265s test_Blast_Record ... ok 265s test_Blast_parser ... ok 265s test_CAPS ... ok 265s test_Chi2 ... ok 265s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 265s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 266s test_Cluster ... ok 266s test_CodonTable ... ok 266s test_ColorSpiral ... ok 266s test_Compass ... ok 267s test_Consensus ... ok 267s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 267s test_EMBL_unittest ... ok 267s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 267s test_EmbossPrimer ... ok 271s test_Entrez ... ok 271s test_Entrez_online ... skipping. internet not available 272s test_Entrez_parser ... ok 272s test_Enzyme ... ok 272s test_ExPASy ... skipping. internet not available 272s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 272s test_File ... ok 272s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 272s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 272s ok 274s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 276s ok 277s test_GraphicsChromosome ... ok 277s test_GraphicsDistribution ... ok 277s test_GraphicsGeneral ... ok 278s test_HMMCasino ... ok 278s test_HMMGeneral ... ok 278s test_KEGG ... ok 278s test_KEGG_online ... skipping. internet not available 283s test_KGML_graphics ... ok 283s test_KGML_graphics_online ... skipping. internet not available 284s test_KGML_nographics ... ok 284s test_KeyWList ... ok 284s test_LogisticRegression ... ok 285s test_MafIO_index ... ok 285s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 285s test_MarkovModel ... ok 285s test_Medline ... ok 285s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 286s test_NCBIXML ... Exception ignored in: 286s Traceback (most recent call last): 286s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 286s expat_parser.Parse(NULL, True) 286s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 286s ok 286s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 286s test_NCBI_qblast ... ok 286s test_NMR ... ok 286s test_NaiveBayes ... ok 286s test_Nexus ... ok 286s test_PAML_baseml ... ok 287s test_PAML_codeml ... ok 287s test_PAML_yn00 ... ok 291s test_PDB_CEAligner ... ok 291s test_PDB_DSSP ... ok 291s test_PDB_Dice ... ok 291s test_PDB_Disordered ... ok 292s test_PDB_Exposure ... ok 292s test_PDB_FragmentMapper ... ok 293s test_PDB_KDTree ... ok 293s test_PDB_MMCIF2Dict ... ok 294s test_PDB_MMCIFIO ... ok 295s test_PDB_MMCIFParser ... ok 295s test_PDB_NACCESS ... ok 295s test_PDB_PDBIO ... ok 295s test_PDB_PDBList ... skipping. internet not available 301s test_PDB_PDBMLParser ... ok 301s test_PDB_PDBParser ... ok 302s 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 302s test_PDB_Polypeptide ... ok 302s test_PDB_QCPSuperimposer ... ok 305s test_PDB_SASA ... ok 306s test_PDB_SMCRA ... ok 306s test_PDB_Selection ... ok 306s test_PDB_StructureAlignment ... ok 306s test_PDB_Superimposer ... ok 306s test_PDB_alphafold_db ... skipping. internet not available 306s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 306s 306s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 306s 306s test_PDB_parse_pdb_header ... ok 306s test_PDB_vectors ... ok 307s test_PQR ... ok 307s test_Pathway ... ok 307s test_Phd ... ok 307s test_Phylo ... ok 307s test_PhyloXML ... ok 307s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 307s test_Phylo_NeXML ... ok 308s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 308s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 308s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 308s test_PopGen_GenePop_nodepend ... ok 308s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 308s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 308s test_ProtParam ... ok 308s test_RCSBFormats ... ok 308s test_Restriction ... ok 308s test_SCOP_Astral ... ok 308s test_SCOP_Cla ... ok 308s test_SCOP_Des ... ok 309s test_SCOP_Dom ... ok 309s test_SCOP_Hie ... ok 309s test_SCOP_Raf ... ok 309s test_SCOP_Residues ... ok 309s test_SCOP_Scop ... ok 309s test_SVDSuperimposer ... ok 309s test_SearchIO_blast_tab ... ok 309s test_SearchIO_blast_tab_index ... ok 309s test_SearchIO_blast_xml ... ok 310s test_SearchIO_blast_xml_index ... ok 310s test_SearchIO_blat_psl ... ok 310s test_SearchIO_blat_psl_index ... ok 311s test_SearchIO_exonerate ... ok 311s test_SearchIO_exonerate_text_index ... ok 311s test_SearchIO_exonerate_vulgar_index ... ok 311s test_SearchIO_fasta_m10 ... ok 311s test_SearchIO_fasta_m10_index ... ok 311s test_SearchIO_hhsuite2_text ... ok 311s test_SearchIO_hmmer2_text ... ok 311s test_SearchIO_hmmer2_text_index ... ok 311s test_SearchIO_hmmer3_domtab ... ok 311s test_SearchIO_hmmer3_domtab_index ... ok 312s test_SearchIO_hmmer3_tab ... ok 312s test_SearchIO_hmmer3_tab_index ... ok 312s test_SearchIO_hmmer3_text ... ok 312s test_SearchIO_hmmer3_text_index ... ok 312s test_SearchIO_interproscan_xml ... ok 312s test_SearchIO_model ... ok 312s test_SearchIO_write ... ok 312s test_SeqFeature ... ok 329s test_SeqIO ... ok 329s test_SeqIO_AbiIO ... ok 329s test_SeqIO_FastaIO ... ok 329s test_SeqIO_Gck ... ok 329s test_SeqIO_Gfa ... ok 329s test_SeqIO_Insdc ... ok 329s test_SeqIO_NibIO ... ok 331s test_SeqIO_PdbIO ... ok 332s test_SeqIO_QualityIO ... ok 332s test_SeqIO_SeqXML ... ok 332s test_SeqIO_SffIO ... ok 332s test_SeqIO_SnapGene ... ok 333s test_SeqIO_TwoBitIO ... ok 333s test_SeqIO_UniprotIO ... ok 333s test_SeqIO_Xdna ... ok 333s test_SeqIO_features ... ok 348s test_SeqIO_index ... ok 348s test_SeqIO_online ... skipping. internet not available 348s test_SeqIO_write ... ok 348s test_SeqRecord ... ok 348s test_SeqUtils ... ok 349s test_Seq_objs ... ok 349s test_SwissProt ... ok 349s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 350s test_TogoWS ... skipping. internet not available 350s test_TreeConstruction ... ok 350s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 350s test_UniGene ... ok 350s test_UniProt ... skipping. internet not available 350s test_UniProt_GOA ... ok 350s test_align ... ok 351s test_align_substitution_matrices ... ok 353s test_bgzf ... ok 353s test_cellosaurus ... ok 358s test_codonalign ... ok 358s test_geo ... ok 358s test_kNN ... ok 358s test_motifs ... ok 358s test_motifs_online ... skipping. internet not available 358s 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. 358s warnings.warn( 358s ok 358s test_pairwise2_no_C ... ok 359s test_pairwise_aligner ... ok 359s test_pairwise_alignment_map ... ok 366s test_phenotype ... ok 366s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 366s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 366s test_prodoc ... ok 366s test_prosite ... ok 366s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 366s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 366s test_seq ... ok 366s test_translate ... ok 366s ---------------------------------------------------------------------- 366s Ran 219 tests in 118.234 seconds 366s 366s Skipping any tests requiring internet access 366s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 366s Operating system: posix linux 367s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 367s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 367s autopkgtest [12:12:46]: test dependencies: -----------------------] 367s autopkgtest [12:12:46]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 367s dependencies PASS 367s autopkgtest [12:12:46]: test full_suite: preparing testbed 432s autopkgtest [12:13:51]: testbed dpkg architecture: amd64 432s autopkgtest [12:13:51]: testbed apt version: 2.9.29 432s autopkgtest [12:13:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 432s autopkgtest [12:13:51]: testbed release detected to be: plucky 432s autopkgtest [12:13:51]: updating testbed package index (apt update) 432s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 432s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 432s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 432s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 432s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 432s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 432s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 432s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 432s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [101 kB] 432s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [81.8 kB] 432s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 432s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 432s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [265 kB] 433s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [697 kB] 433s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3128 B] 433s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [11.5 kB] 433s Fetched 2124 kB in 0s (5435 kB/s) 434s Reading package lists... 434s Reading package lists... 434s Building dependency tree... 434s Reading state information... 435s Calculating upgrade... 435s The following NEW packages will be installed: 435s libapt-pkg7.0 435s The following packages will be upgraded: 435s apt apt-utils iproute2 liblsof0 libp11-kit0 lsof rsyslog 435s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 435s Need to get 5234 kB of archives. 435s After this operation, 4074 kB of additional disk space will be used. 435s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.30 [1131 kB] 435s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.30 [1434 kB] 435s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.30 [222 kB] 435s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 435s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit0 amd64 0.25.5-2ubuntu3 [311 kB] 435s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu1 [555 kB] 435s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 lsof amd64 4.99.4+dfsg-1 [245 kB] 435s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsof0 amd64 4.99.4+dfsg-1 [59.6 kB] 435s Preconfiguring packages ... 435s Fetched 5234 kB in 0s (38.0 MB/s) 435s Selecting previously unselected package libapt-pkg7.0:amd64. 436s (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 ... 108925 files and directories currently installed.) 436s Preparing to unpack .../libapt-pkg7.0_2.9.30_amd64.deb ... 436s Unpacking libapt-pkg7.0:amd64 (2.9.30) ... 436s Setting up libapt-pkg7.0:amd64 (2.9.30) ... 436s (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 ... 108974 files and directories currently installed.) 436s Preparing to unpack .../archives/apt_2.9.30_amd64.deb ... 436s Unpacking apt (2.9.30) over (2.9.29) ... 436s Setting up apt (2.9.30) ... 437s (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 ... 108974 files and directories currently installed.) 437s Preparing to unpack .../0-apt-utils_2.9.30_amd64.deb ... 437s Unpacking apt-utils (2.9.30) over (2.9.29) ... 437s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_amd64.deb ... 437s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 437s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_amd64.deb ... 437s Unpacking libp11-kit0:amd64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 437s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_amd64.deb ... 437s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 437s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_amd64.deb ... 437s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 437s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_amd64.deb ... 437s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 437s Setting up apt-utils (2.9.30) ... 437s Setting up liblsof0 (4.99.4+dfsg-1) ... 437s Setting up iproute2 (6.13.0-1ubuntu1) ... 437s Setting up rsyslog (8.2412.0-2ubuntu1) ... 438s info: The user `syslog' is already a member of `adm'. 439s Setting up libp11-kit0:amd64 (0.25.5-2ubuntu3) ... 439s Setting up lsof (4.99.4+dfsg-1) ... 439s Processing triggers for man-db (2.13.0-1) ... 440s Processing triggers for libc-bin (2.40-4ubuntu1) ... 442s Reading package lists... 442s Building dependency tree... 442s Reading state information... 442s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 442s autopkgtest [12:14:01]: upgrading testbed (apt dist-upgrade and autopurge) 442s Reading package lists... 443s Building dependency tree... 443s Reading state information... 443s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 443s Starting 2 pkgProblemResolver with broken count: 0 443s Done 444s Entering ResolveByKeep 444s 444s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 444s Reading package lists... 445s Building dependency tree... 445s Reading state information... 445s Starting pkgProblemResolver with broken count: 0 445s Starting 2 pkgProblemResolver with broken count: 0 445s Done 445s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 446s autopkgtest [12:14:05]: rebooting testbed after setup commands that affected boot 449s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 462s Reading package lists... 463s Building dependency tree... 463s Reading state information... 463s Starting pkgProblemResolver with broken count: 0 463s Starting 2 pkgProblemResolver with broken count: 0 463s Done 464s The following NEW packages will be installed: 464s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 464s clustalw cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper 464s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 464s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 464s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 464s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 464s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 464s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext ghostscript hevea 464s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 464s intltool-debian libamd-comgr2 libamd3 libamdhip64-5 libaom3 464s libapache-pom-java libarchive-zip-perl libargtable2-0 libarpack2t64 libasan8 464s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libcairo2 464s libcc1-0 libcifpp-data libcifpp7 libcolamd3 libcommons-logging-java 464s libcommons-parent-java libcups2t64 libde265-0 libdebhelper-perl libdeflate0 464s libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfftw3-double3 464s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 464s libgcc-14-dev libgd3 libgfortran5 libglpk40 libgomp1 libgraphite2-3 464s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 464s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhsakmt1 464s libhts3t64 libhtscodecs2 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 464s libibumad3 libice6 libidn12 libigraph3t64 libijs-0.35 libimagequant0 464s libisl23 libitm1 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery 464s libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 464s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblqr-1-0 liblsan0 464s libltdl7 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 464s libmbedtls21 libmbedx509-7 libmpc3 libmpfi0 libmunge2 libmysqlclient21 464s libnetpbm11t64 libopenjp2-7 libopenmpi40 libpaper-utils libpaper2 464s libpciaccess0 libpdfbox-java libpixman-1-0 libplfit0 libpmix2t64 libpotrace0 464s libpq5 libpsm-infinipath1 libpsm2-2 libptexenc1 libpython3-all-dev 464s libpython3-dev libpython3.12-dev libpython3.13-dev libqhull-r8.0 464s libquadmath0 libraqm0 libraw23t64 librdmacm1t64 libsharpyuv0 libsm6 464s libstdc++-14-dev libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 464s libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 libucx0 libwebp7 464s libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 464s libxmu6 libxnvctrl0 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 464s libzzip-0-13t64 m4 mafft mpi-default-bin muscle3 mysql-common ncbi-blast+ 464s ncbi-data netpbm ocl-icd-libopencl1 openmpi-bin openmpi-common phylip phyml 464s po-debconf poppler-data prank preview-latex-style probcons 464s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 464s python3-all-dev python3-biopython python3-biopython-sql python3-brotli 464s python3-cairo python3-contourpy python3-cycler python3-dateutil 464s python3-decorator python3-defusedxml python3-dev python3-docutils 464s python3-fonttools python3-freetype python3-fs python3-igraph 464s python3-imagesize python3-kiwisolver python3-lxml python3-lz4 464s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 464s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 464s python3-packaging python3-pil python3-pil.imagetk python3-platformdirs 464s python3-psycopg2 python3-pytz python3-rdflib python3-reportlab 464s python3-rlpycairo python3-roman python3-scipy python3-snowballstemmer 464s python3-sphinx python3-sphinx-rtd-theme python3-sphinxcontrib.jquery 464s python3-sympy python3-tabulate python3-texttable python3-tk python3-tz 464s python3-ufolib2 python3.12 python3.12-dev python3.12-minimal python3.12-tk 464s python3.13-dev python3.13-tk raxml samtools sgml-base sphinx-common 464s sphinx-rtd-theme-common t-coffee t1utils tex-common texlive-base 464s texlive-binaries texlive-fonts-recommended texlive-latex-base 464s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 464s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 464s xfonts-encodings xfonts-utils xml-core zlib1g-dev 464s 0 upgraded, 297 newly installed, 0 to remove and 0 not upgraded. 464s Need to get 486 MB of archives. 464s After this operation, 2135 MB of additional disk space will be used. 464s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-minimal amd64 3.12.9-1 [2348 kB] 464s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-5 [263 kB] 464s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 flex amd64 2.6.4-8.2build1 [301 kB] 464s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 464s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250213-1ubuntu1 [148 kB] 464s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-2fakesync1build1 [839 kB] 464s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 464s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 464s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 464s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 464s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 464s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 464s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 464s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 464s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 464s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 464s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libaom3 amd64 3.12.0-1 [2742 kB] 464s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-aomdec amd64 1.19.5-1build1 [11.6 kB] 464s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libde265-0 amd64 1.0.15-1build4 [168 kB] 464s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-libde265 amd64 1.19.5-1build1 [9074 B] 464s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif1 amd64 1.19.5-1build1 [422 kB] 464s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 464s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 464s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 464s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 464s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblqr-1-0 amd64 0.4.2-2.1build2 [28.5 kB] 464s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.5.4-3build1 [46.2 kB] 464s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 464s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libraw23t64 amd64 0.21.3-1 [433 kB] 464s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 464s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 464s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 464s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 464s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 464s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 464s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 464s Get:37 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmagickcore-7.q16-10 amd64 8:7.1.1.43+dfsg1-1 [2306 kB] 464s Get:38 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmagickwand-7.q16-10 amd64 8:7.1.1.43+dfsg1-1 [347 kB] 464s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-data all 0.4.12-1 [2060 kB] 464s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 464s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12 amd64 3.12.9-1 [671 kB] 464s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 464s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 464s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.17-3 [572 kB] 464s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.23.1-1 [619 kB] 464s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 464s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 464s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 464s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 464s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 464s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 464s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 464s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 464s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 464s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [11.9 MB] 464s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu1 [1032 B] 464s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 464s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 464s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250213-1ubuntu1 [47.0 kB] 464s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250213-1ubuntu1 [28.5 kB] 464s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250213-1ubuntu1 [3059 kB] 464s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250213-1ubuntu1 [1356 kB] 464s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250213-1ubuntu1 [2757 kB] 464s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250213-1ubuntu1 [1206 kB] 464s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250213-1ubuntu1 [1678 kB] 464s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250213-1ubuntu1 [152 kB] 464s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu1 [2814 kB] 464s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [23.3 MB] 465s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu1 [536 kB] 465s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 465s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 465s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu1 [2507 kB] 465s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [13.4 MB] 465s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu1 [21.8 kB] 465s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 465s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 465s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 465s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 bwa amd64 0.7.18-1 [204 kB] 465s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 libargtable2-0 amd64 13-3 [16.3 kB] 465s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 clustalo amd64 1.2.4-8build1 [202 kB] 465s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 clustalw amd64 2.1+lgpl-7 [275 kB] 465s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 465s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.5.4-3build1 [168 kB] 465s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 465s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 465s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 465s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 465s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-2 [47.0 kB] 465s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 465s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.23.1-1 [1086 kB] 465s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 465s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 465s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.24.1ubuntu2 [895 kB] 465s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20250108 [117 kB] 465s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 dialign amd64 2.2.1-13 [154 kB] 465s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 465s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 465s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcifpp-data all 7.0.9-1 [481 kB] 465s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcifpp7 amd64 7.0.9-1 [1144 kB] 465s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 dssp amd64 4.4.10-1 [786 kB] 465s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 465s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 465s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 465s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 465s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB] 465s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libgd3 amd64 2.3.3-12ubuntu3 [127 kB] 465s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1build3 [432 kB] 465s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 mysql-common all 5.8+1.1.1 [6800 B] 465s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libmysqlclient21 amd64 8.0.40-1 [1250 kB] 465s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libpq5 amd64 17.3-3 [154 kB] 465s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss-lib amd64 6.6.0+dfsg-12ubuntu2 [2976 kB] 465s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss-data all 6.6.0+dfsg-12ubuntu2 [61.0 MB] 466s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss amd64 6.6.0+dfsg-12ubuntu2 [980 kB] 466s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 466s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lmodern all 2.005-1 [4799 kB] 467s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 467s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs-common all 10.04.0~dfsg1-2ubuntu1 [176 kB] 467s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs10-common all 10.04.0~dfsg1-2ubuntu1 [488 kB] 467s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-14ubuntu1 [30.5 kB] 467s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-14ubuntu1 [23.3 kB] 467s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-14ubuntu1 [27.5 kB] 467s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.11-0ubuntu2 [292 kB] 467s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libidn12 amd64 1.42-3 [58.5 kB] 467s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libijs-0.35 amd64 0.35-15.1build1 [15.3 kB] 467s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig2dec0 amd64 0.20-1build3 [65.0 kB] 467s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 467s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 467s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 467s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 467s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs10 amd64 10.04.0~dfsg1-2ubuntu1 [4607 kB] 467s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 ghostscript amd64 10.04.0~dfsg1-2ubuntu1 [43.7 kB] 467s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetpbm11t64 amd64 2:11.09.02-2 [125 kB] 467s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 netpbm amd64 2:11.09.02-2 [2286 kB] 467s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 tex-common all 6.18 [32.8 kB] 467s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 467s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5build2 [67.0 kB] 467s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5build2 [43.7 kB] 467s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5build2 [62.5 kB] 467s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5build2 [145 kB] 467s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 t1utils amd64 1.41-4build3 [61.3 kB] 467s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 467s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 467s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 467s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 467s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] 467s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpotrace0 amd64 1.16-2build1 [17.7 kB] 467s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 libteckit0 amd64 2.5.12+ds1-1 [411 kB] 467s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB] 467s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libxaw7 amd64 2:1.0.16-1 [207 kB] 467s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 467s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2build1 [28.1 kB] 467s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-binaries amd64 2024.20240313.70630+ds-5build2 [9799 kB] 467s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 467s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-base all 2024.20241115-1 [22.5 MB] 467s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 467s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick-7.q16 amd64 8:7.1.1.43+dfsg1-1 [704 kB] 467s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick amd64 8:7.1.1.43+dfsg1-1 [14.1 kB] 467s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 hevea amd64 2.36-2 [2023 kB] 467s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-20 [26.0 MB] 467s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 468s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-3 [13.5 kB] 468s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd3 amd64 1:7.8.3+dfsg-3 [31.0 kB] 468s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 468s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 468s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 468s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 468s Get:167 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 468s Get:168 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 468s Get:169 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 468s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 libarpack2t64 amd64 3.9.1-4 [120 kB] 468s Get:171 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-3 [19.5 kB] 468s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 468s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 468s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 468s Get:175 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB] 468s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 468s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 468s Get:178 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 55.0-1ubuntu1 [71.5 kB] 468s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3ubuntu1 [658 kB] 468s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglpk40 amd64 5.0-1build2 [369 kB] 468s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 468s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 468s Get:183 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB] 468s Get:184 http://ftpmaster.internal/ubuntu plucky/universe amd64 libplfit0 amd64 0.9.4+ds-1ubuntu5 [31.8 kB] 468s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 libigraph3t64 amd64 0.10.15+ds-2 [1027 kB] 468s Get:186 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 468s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 468s Get:188 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 468s Get:189 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 468s Get:190 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 468s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 468s Get:192 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB] 468s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB] 468s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB] 468s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 468s Get:196 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 468s Get:197 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 468s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 468s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.12.0-1 [16.0 kB] 468s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.6-3 [714 kB] 468s Get:201 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 55.0-1ubuntu1 [29.7 kB] 468s Get:202 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 55.0-1ubuntu1 [42.7 kB] 468s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.17.0+ds-3build1 [1162 kB] 468s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi40 amd64 5.0.6-4 [2523 kB] 468s Get:205 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 468s Get:206 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-dev amd64 3.13.2-1 [5501 kB] 468s Get:207 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.13.1-1~exp2 [10.5 kB] 468s Get:208 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.9-1 [5702 kB] 468s Get:209 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-all-dev amd64 3.13.1-1~exp2 [922 B] 468s Get:210 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 468s Get:211 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 468s Get:212 http://ftpmaster.internal/ubuntu plucky/universe amd64 mafft amd64 7.505-1 [795 kB] 468s Get:213 http://ftpmaster.internal/ubuntu plucky/universe amd64 muscle3 amd64 3.8.1551-3 [198 kB] 468s Get:214 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 468s Get:215 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6build1 [15.8 MB] 468s Get:216 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-common all 5.0.6-4 [97.7 kB] 468s Get:217 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-bin amd64 5.0.6-4 [191 kB] 468s Get:218 http://ftpmaster.internal/ubuntu plucky/universe amd64 phylip amd64 1:3.697+dfsg-4build1 [874 kB] 468s Get:219 http://ftpmaster.internal/ubuntu plucky/universe amd64 mpi-default-bin amd64 1.18 [2510 B] 468s Get:220 http://ftpmaster.internal/ubuntu plucky/universe amd64 phyml amd64 3:3.3.20220408-4build1 [1081 kB] 468s Get:221 http://ftpmaster.internal/ubuntu plucky/universe amd64 prank amd64 0.0.170427+dfsg-3 [396 kB] 468s Get:222 http://ftpmaster.internal/ubuntu plucky/universe amd64 preview-latex-style all 13.2-1 [347 kB] 468s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 probcons amd64 1.12-14 [125 kB] 468s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biopython-doc all 1.85+dfsg-2 [18.2 MB] 469s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 469s Get:226 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.1-1~exp2 [894 B] 469s Get:227 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-dev amd64 3.13.2-1 [508 kB] 469s Get:228 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.13.1-1~exp2 [26.7 kB] 469s Get:229 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.9-1 [505 kB] 469s Get:230 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all-dev amd64 3.13.1-1~exp2 [918 B] 469s Get:231 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 469s Get:232 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 469s Get:233 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-1 [107 kB] 469s Get:234 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 469s Get:235 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5 [9936 B] 469s Get:236 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5 [589 kB] 469s Get:237 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build1 [143 kB] 469s Get:238 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 469s Get:239 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 469s Get:240 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.3.0-1 [1137 kB] 469s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 469s Get:242 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.85+dfsg-2 [1745 kB] 469s Get:243 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython-sql all 1.85+dfsg-2 [26.4 kB] 469s Get:244 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build3 [368 kB] 469s Get:245 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1 [271 kB] 469s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 469s Get:247 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 469s Get:248 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 469s Get:249 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-defusedxml all 0.7.1-3 [42.2 kB] 469s Get:250 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-roman all 5.0-1 [10.3 kB] 469s Get:251 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 469s Get:252 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 469s Get:253 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 469s Get:254 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 469s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-6 [90.7 kB] 469s Get:256 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1 [1831 kB] 469s Get:257 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1 [27.4 kB] 469s Get:258 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 469s Get:259 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 469s Get:260 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 469s Get:261 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 469s Get:262 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 469s Get:263 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2 [1755 kB] 469s Get:264 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-imagesize all 1.4.1-1 [6844 B] 469s Get:265 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3 [70.4 kB] 469s Get:266 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 469s Get:267 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu2 [4697 kB] 469s Get:268 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-msgpack amd64 1.0.3-3build3 [113 kB] 469s Get:269 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mmtf all 1.1.3-1 [16.2 kB] 469s Get:270 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-mysqldb amd64 1.4.6-2build4 [49.3 kB] 469s Get:271 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 469s Get:272 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 sphinx-common all 8.1.3-5 [663 kB] 469s Get:273 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 469s Get:274 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 469s Get:275 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-sphinx all 8.1.3-5 [474 kB] 469s Get:276 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tabulate all 0.9.0-1 [45.3 kB] 469s Get:277 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numpydoc all 1.8.0-1 [52.4 kB] 469s Get:278 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psycopg2 amd64 2.9.10-1 [146 kB] 469s Get:279 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rdflib all 7.1.1-2 [426 kB] 469s Get:280 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 469s Get:281 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 469s Get:282 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 469s Get:283 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-texttable all 1.7.0-1 [11.2 kB] 469s Get:284 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB] 469s Get:285 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.21-1 [655 kB] 469s Get:286 http://ftpmaster.internal/ubuntu plucky/universe amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [929 kB] 469s Get:287 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-fonts-recommended all 2024.20241115-1 [4973 kB] 469s Get:288 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-base all 2024.20241115-1 [1260 kB] 469s Get:289 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfontbox-java all 1:1.8.16-5 [208 kB] 469s Get:290 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 470s Get:291 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-recommended all 2024.20241115-1 [8739 kB] 470s Get:292 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-pictures all 2024.20241115-1 [17.0 MB] 470s Get:293 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-extra all 2024.20250114-1 [24.3 MB] 470s Get:294 http://ftpmaster.internal/ubuntu plucky/universe amd64 wise-data all 2.4.1-25 [83.0 kB] 470s Get:295 http://ftpmaster.internal/ubuntu plucky/universe amd64 wise amd64 2.4.1-25 [843 kB] 470s Get:296 http://ftpmaster.internal/ubuntu plucky/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 470s Get:297 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-igraph amd64 0.11.8+ds-1build1 [343 kB] 471s Preconfiguring packages ... 471s Fetched 486 MB in 6s (78.4 MB/s) 471s Selecting previously unselected package python3.12-minimal. 471s (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 ... 108975 files and directories currently installed.) 471s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_amd64.deb ... 471s Unpacking python3.12-minimal (3.12.9-1) ... 471s Selecting previously unselected package m4. 471s Preparing to unpack .../001-m4_1.4.19-5_amd64.deb ... 471s Unpacking m4 (1.4.19-5) ... 471s Selecting previously unselected package flex. 471s Preparing to unpack .../002-flex_2.6.4-8.2build1_amd64.deb ... 471s Unpacking flex (2.6.4-8.2build1) ... 471s Selecting previously unselected package fonts-lato. 471s Preparing to unpack .../003-fonts-lato_2.015-1_all.deb ... 471s Unpacking fonts-lato (2.015-1) ... 471s Selecting previously unselected package libgomp1:amd64. 471s Preparing to unpack .../004-libgomp1_15-20250213-1ubuntu1_amd64.deb ... 471s Unpacking libgomp1:amd64 (15-20250213-1ubuntu1) ... 471s Selecting previously unselected package libfftw3-double3:amd64. 471s Preparing to unpack .../005-libfftw3-double3_3.3.10-2fakesync1build1_amd64.deb ... 471s Unpacking libfftw3-double3:amd64 (3.3.10-2fakesync1build1) ... 471s Selecting previously unselected package fonts-dejavu-mono. 471s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 471s Unpacking fonts-dejavu-mono (2.37-8) ... 471s Selecting previously unselected package fonts-dejavu-core. 472s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 472s Unpacking fonts-dejavu-core (2.37-8) ... 472s Selecting previously unselected package libfontenc1:amd64. 472s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 472s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 472s Selecting previously unselected package x11-common. 472s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu3_all.deb ... 472s Unpacking x11-common (1:7.7+23ubuntu3) ... 472s Selecting previously unselected package xfonts-encodings. 472s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 472s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 472s Selecting previously unselected package xfonts-utils. 472s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_amd64.deb ... 472s Unpacking xfonts-utils (1:7.7+7) ... 472s Selecting previously unselected package fonts-urw-base35. 472s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 472s Unpacking fonts-urw-base35 (20200910-8) ... 472s Selecting previously unselected package fontconfig-config. 472s Preparing to unpack .../013-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 472s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 472s Selecting previously unselected package libfontconfig1:amd64. 472s Preparing to unpack .../014-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 472s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 472s Selecting previously unselected package libsharpyuv0:amd64. 472s Preparing to unpack .../015-libsharpyuv0_1.5.0-0.1_amd64.deb ... 472s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 472s Selecting previously unselected package libaom3:amd64. 472s Preparing to unpack .../016-libaom3_3.12.0-1_amd64.deb ... 472s Unpacking libaom3:amd64 (3.12.0-1) ... 472s Selecting previously unselected package libheif-plugin-aomdec:amd64. 472s Preparing to unpack .../017-libheif-plugin-aomdec_1.19.5-1build1_amd64.deb ... 472s Unpacking libheif-plugin-aomdec:amd64 (1.19.5-1build1) ... 472s Selecting previously unselected package libde265-0:amd64. 472s Preparing to unpack .../018-libde265-0_1.0.15-1build4_amd64.deb ... 472s Unpacking libde265-0:amd64 (1.0.15-1build4) ... 472s Selecting previously unselected package libheif-plugin-libde265:amd64. 472s Preparing to unpack .../019-libheif-plugin-libde265_1.19.5-1build1_amd64.deb ... 472s Unpacking libheif-plugin-libde265:amd64 (1.19.5-1build1) ... 472s Selecting previously unselected package libheif1:amd64. 472s Preparing to unpack .../020-libheif1_1.19.5-1build1_amd64.deb ... 472s Unpacking libheif1:amd64 (1.19.5-1build1) ... 472s Selecting previously unselected package libjbig0:amd64. 472s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 472s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 472s Selecting previously unselected package libjpeg-turbo8:amd64. 473s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 473s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 473s Selecting previously unselected package libjpeg8:amd64. 473s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_amd64.deb ... 473s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 473s Selecting previously unselected package liblcms2-2:amd64. 473s Preparing to unpack .../024-liblcms2-2_2.16-2_amd64.deb ... 473s Unpacking liblcms2-2:amd64 (2.16-2) ... 473s Selecting previously unselected package liblqr-1-0:amd64. 473s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_amd64.deb ... 473s Unpacking liblqr-1-0:amd64 (0.4.2-2.1build2) ... 473s Selecting previously unselected package libltdl7:amd64. 473s Preparing to unpack .../026-libltdl7_2.5.4-3build1_amd64.deb ... 473s Unpacking libltdl7:amd64 (2.5.4-3build1) ... 473s Selecting previously unselected package libopenjp2-7:amd64. 473s Preparing to unpack .../027-libopenjp2-7_2.5.0-2ubuntu3_amd64.deb ... 473s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 473s Selecting previously unselected package libraw23t64:amd64. 473s Preparing to unpack .../028-libraw23t64_0.21.3-1_amd64.deb ... 473s Unpacking libraw23t64:amd64 (0.21.3-1) ... 473s Selecting previously unselected package libdeflate0:amd64. 473s Preparing to unpack .../029-libdeflate0_1.23-1_amd64.deb ... 473s Unpacking libdeflate0:amd64 (1.23-1) ... 473s Selecting previously unselected package liblerc4:amd64. 473s Preparing to unpack .../030-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 473s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 473s Selecting previously unselected package libwebp7:amd64. 473s Preparing to unpack .../031-libwebp7_1.5.0-0.1_amd64.deb ... 473s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 473s Selecting previously unselected package libtiff6:amd64. 473s Preparing to unpack .../032-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 473s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 473s Selecting previously unselected package libwebpdemux2:amd64. 473s Preparing to unpack .../033-libwebpdemux2_1.5.0-0.1_amd64.deb ... 473s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 473s Selecting previously unselected package libwebpmux3:amd64. 473s Preparing to unpack .../034-libwebpmux3_1.5.0-0.1_amd64.deb ... 473s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 473s Selecting previously unselected package imagemagick-7-common. 473s Preparing to unpack .../035-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 473s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 473s Selecting previously unselected package libmagickcore-7.q16-10:amd64. 473s Preparing to unpack .../036-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_amd64.deb ... 473s Unpacking libmagickcore-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... 473s Selecting previously unselected package libmagickwand-7.q16-10:amd64. 473s Preparing to unpack .../037-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_amd64.deb ... 473s Unpacking libmagickwand-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... 473s Selecting previously unselected package poppler-data. 473s Preparing to unpack .../038-poppler-data_0.4.12-1_all.deb ... 473s Unpacking poppler-data (0.4.12-1) ... 473s Selecting previously unselected package sgml-base. 473s Preparing to unpack .../039-sgml-base_1.31_all.deb ... 473s Unpacking sgml-base (1.31) ... 473s Selecting previously unselected package python3.12. 473s Preparing to unpack .../040-python3.12_3.12.9-1_amd64.deb ... 473s Unpacking python3.12 (3.12.9-1) ... 473s Selecting previously unselected package autoconf. 473s Preparing to unpack .../041-autoconf_2.72-3_all.deb ... 473s Unpacking autoconf (2.72-3) ... 473s Selecting previously unselected package autotools-dev. 473s Preparing to unpack .../042-autotools-dev_20220109.1_all.deb ... 473s Unpacking autotools-dev (20220109.1) ... 473s Selecting previously unselected package automake. 473s Preparing to unpack .../043-automake_1%3a1.17-3_all.deb ... 473s Unpacking automake (1:1.17-3) ... 473s Selecting previously unselected package autopoint. 473s Preparing to unpack .../044-autopoint_0.23.1-1_all.deb ... 473s Unpacking autopoint (0.23.1-1) ... 473s Selecting previously unselected package libtcl8.6:amd64. 473s Preparing to unpack .../045-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 473s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 474s Selecting previously unselected package libxrender1:amd64. 474s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 474s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 474s Selecting previously unselected package libxft2:amd64. 474s Preparing to unpack .../047-libxft2_2.3.6-1build1_amd64.deb ... 474s Unpacking libxft2:amd64 (2.3.6-1build1) ... 474s Selecting previously unselected package libxss1:amd64. 474s Preparing to unpack .../048-libxss1_1%3a1.2.3-1build3_amd64.deb ... 474s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 474s Selecting previously unselected package libtk8.6:amd64. 474s Preparing to unpack .../049-libtk8.6_8.6.16-1_amd64.deb ... 474s Unpacking libtk8.6:amd64 (8.6.16-1) ... 474s Selecting previously unselected package tk8.6-blt2.5. 474s Preparing to unpack .../050-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 474s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 474s Selecting previously unselected package blt. 474s Preparing to unpack .../051-blt_2.5.3+dfsg-7build1_amd64.deb ... 474s Unpacking blt (2.5.3+dfsg-7build1) ... 474s Selecting previously unselected package libisl23:amd64. 474s Preparing to unpack .../052-libisl23_0.27-1_amd64.deb ... 474s Unpacking libisl23:amd64 (0.27-1) ... 474s Selecting previously unselected package libmpc3:amd64. 474s Preparing to unpack .../053-libmpc3_1.3.1-1build2_amd64.deb ... 474s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 474s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 474s Preparing to unpack .../054-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu1_amd64.deb ... 474s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 474s Selecting previously unselected package cpp-14. 474s Preparing to unpack .../055-cpp-14_14.2.0-17ubuntu1_amd64.deb ... 474s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 474s Selecting previously unselected package cpp-x86-64-linux-gnu. 474s Preparing to unpack .../056-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 474s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 474s Selecting previously unselected package cpp. 474s Preparing to unpack .../057-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 474s Unpacking cpp (4:14.2.0-1ubuntu1) ... 474s Selecting previously unselected package libcc1-0:amd64. 474s Preparing to unpack .../058-libcc1-0_15-20250213-1ubuntu1_amd64.deb ... 474s Unpacking libcc1-0:amd64 (15-20250213-1ubuntu1) ... 474s Selecting previously unselected package libitm1:amd64. 474s Preparing to unpack .../059-libitm1_15-20250213-1ubuntu1_amd64.deb ... 474s Unpacking libitm1:amd64 (15-20250213-1ubuntu1) ... 474s Selecting previously unselected package libasan8:amd64. 474s Preparing to unpack .../060-libasan8_15-20250213-1ubuntu1_amd64.deb ... 474s Unpacking libasan8:amd64 (15-20250213-1ubuntu1) ... 474s Selecting previously unselected package liblsan0:amd64. 474s Preparing to unpack .../061-liblsan0_15-20250213-1ubuntu1_amd64.deb ... 474s Unpacking liblsan0:amd64 (15-20250213-1ubuntu1) ... 474s Selecting previously unselected package libtsan2:amd64. 474s Preparing to unpack .../062-libtsan2_15-20250213-1ubuntu1_amd64.deb ... 474s Unpacking libtsan2:amd64 (15-20250213-1ubuntu1) ... 474s Selecting previously unselected package libubsan1:amd64. 474s Preparing to unpack .../063-libubsan1_15-20250213-1ubuntu1_amd64.deb ... 474s Unpacking libubsan1:amd64 (15-20250213-1ubuntu1) ... 475s Selecting previously unselected package libhwasan0:amd64. 475s Preparing to unpack .../064-libhwasan0_15-20250213-1ubuntu1_amd64.deb ... 475s Unpacking libhwasan0:amd64 (15-20250213-1ubuntu1) ... 475s Selecting previously unselected package libquadmath0:amd64. 475s Preparing to unpack .../065-libquadmath0_15-20250213-1ubuntu1_amd64.deb ... 475s Unpacking libquadmath0:amd64 (15-20250213-1ubuntu1) ... 475s Selecting previously unselected package libgcc-14-dev:amd64. 475s Preparing to unpack .../066-libgcc-14-dev_14.2.0-17ubuntu1_amd64.deb ... 475s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu1) ... 475s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 475s Preparing to unpack .../067-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu1_amd64.deb ... 475s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 475s Selecting previously unselected package gcc-14. 475s Preparing to unpack .../068-gcc-14_14.2.0-17ubuntu1_amd64.deb ... 475s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 475s Selecting previously unselected package gcc-x86-64-linux-gnu. 475s Preparing to unpack .../069-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 475s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 475s Selecting previously unselected package gcc. 475s Preparing to unpack .../070-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 475s Unpacking gcc (4:14.2.0-1ubuntu1) ... 475s Selecting previously unselected package libstdc++-14-dev:amd64. 475s Preparing to unpack .../071-libstdc++-14-dev_14.2.0-17ubuntu1_amd64.deb ... 475s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu1) ... 475s Selecting previously unselected package g++-14-x86-64-linux-gnu. 475s Preparing to unpack .../072-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu1_amd64.deb ... 475s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 476s Selecting previously unselected package g++-14. 476s Preparing to unpack .../073-g++-14_14.2.0-17ubuntu1_amd64.deb ... 476s Unpacking g++-14 (14.2.0-17ubuntu1) ... 476s Selecting previously unselected package g++-x86-64-linux-gnu. 476s Preparing to unpack .../074-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 476s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 476s Selecting previously unselected package g++. 476s Preparing to unpack .../075-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 476s Unpacking g++ (4:14.2.0-1ubuntu1) ... 476s Selecting previously unselected package build-essential. 476s Preparing to unpack .../076-build-essential_12.10ubuntu1_amd64.deb ... 476s Unpacking build-essential (12.10ubuntu1) ... 476s Selecting previously unselected package bwa. 476s Preparing to unpack .../077-bwa_0.7.18-1_amd64.deb ... 476s Unpacking bwa (0.7.18-1) ... 476s Selecting previously unselected package libargtable2-0. 476s Preparing to unpack .../078-libargtable2-0_13-3_amd64.deb ... 476s Unpacking libargtable2-0 (13-3) ... 476s Selecting previously unselected package clustalo. 476s Preparing to unpack .../079-clustalo_1.2.4-8build1_amd64.deb ... 476s Unpacking clustalo (1.2.4-8build1) ... 476s Selecting previously unselected package clustalw. 476s Preparing to unpack .../080-clustalw_2.1+lgpl-7_amd64.deb ... 476s Unpacking clustalw (2.1+lgpl-7) ... 476s Selecting previously unselected package libdebhelper-perl. 476s Preparing to unpack .../081-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 476s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 476s Selecting previously unselected package libtool. 476s Preparing to unpack .../082-libtool_2.5.4-3build1_all.deb ... 476s Unpacking libtool (2.5.4-3build1) ... 476s Selecting previously unselected package dh-autoreconf. 476s Preparing to unpack .../083-dh-autoreconf_20_all.deb ... 476s Unpacking dh-autoreconf (20) ... 476s Selecting previously unselected package libarchive-zip-perl. 476s Preparing to unpack .../084-libarchive-zip-perl_1.68-1_all.deb ... 476s Unpacking libarchive-zip-perl (1.68-1) ... 476s Selecting previously unselected package libfile-stripnondeterminism-perl. 476s Preparing to unpack .../085-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 476s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 476s Selecting previously unselected package dh-strip-nondeterminism. 476s Preparing to unpack .../086-dh-strip-nondeterminism_1.14.1-2_all.deb ... 476s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 476s Selecting previously unselected package debugedit. 476s Preparing to unpack .../087-debugedit_1%3a5.1-2_amd64.deb ... 476s Unpacking debugedit (1:5.1-2) ... 476s Selecting previously unselected package dwz. 476s Preparing to unpack .../088-dwz_0.15-1build6_amd64.deb ... 476s Unpacking dwz (0.15-1build6) ... 476s Selecting previously unselected package gettext. 476s Preparing to unpack .../089-gettext_0.23.1-1_amd64.deb ... 476s Unpacking gettext (0.23.1-1) ... 476s Selecting previously unselected package intltool-debian. 476s Preparing to unpack .../090-intltool-debian_0.35.0+20060710.6_all.deb ... 476s Unpacking intltool-debian (0.35.0+20060710.6) ... 476s Selecting previously unselected package po-debconf. 476s Preparing to unpack .../091-po-debconf_1.0.21+nmu1_all.deb ... 476s Unpacking po-debconf (1.0.21+nmu1) ... 476s Selecting previously unselected package debhelper. 476s Preparing to unpack .../092-debhelper_13.24.1ubuntu2_all.deb ... 476s Unpacking debhelper (13.24.1ubuntu2) ... 477s Selecting previously unselected package dh-python. 477s Preparing to unpack .../093-dh-python_6.20250108_all.deb ... 477s Unpacking dh-python (6.20250108) ... 477s Selecting previously unselected package dialign. 477s Preparing to unpack .../094-dialign_2.2.1-13_amd64.deb ... 477s Unpacking dialign (2.2.1-13) ... 477s Selecting previously unselected package xml-core. 477s Preparing to unpack .../095-xml-core_0.19_all.deb ... 477s Unpacking xml-core (0.19) ... 477s Selecting previously unselected package docutils-common. 477s Preparing to unpack .../096-docutils-common_0.21.2+dfsg-2_all.deb ... 477s Unpacking docutils-common (0.21.2+dfsg-2) ... 477s Selecting previously unselected package libcifpp-data. 477s Preparing to unpack .../097-libcifpp-data_7.0.9-1_all.deb ... 477s Unpacking libcifpp-data (7.0.9-1) ... 477s Selecting previously unselected package libcifpp7:amd64. 477s Preparing to unpack .../098-libcifpp7_7.0.9-1_amd64.deb ... 477s Unpacking libcifpp7:amd64 (7.0.9-1) ... 477s Selecting previously unselected package dssp. 477s Preparing to unpack .../099-dssp_4.4.10-1_amd64.deb ... 477s Unpacking dssp (4.4.10-1) ... 477s Selecting previously unselected package libimagequant0:amd64. 477s Preparing to unpack .../100-libimagequant0_2.18.0-1build1_amd64.deb ... 477s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 477s Selecting previously unselected package libgraphite2-3:amd64. 477s Preparing to unpack .../101-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 477s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 477s Selecting previously unselected package libharfbuzz0b:amd64. 477s Preparing to unpack .../102-libharfbuzz0b_10.2.0-1_amd64.deb ... 477s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 477s Selecting previously unselected package libraqm0:amd64. 477s Preparing to unpack .../103-libraqm0_0.10.2-1_amd64.deb ... 477s Unpacking libraqm0:amd64 (0.10.2-1) ... 477s Selecting previously unselected package libxpm4:amd64. 477s Preparing to unpack .../104-libxpm4_1%3a3.5.17-1build2_amd64.deb ... 477s Unpacking libxpm4:amd64 (1:3.5.17-1build2) ... 477s Selecting previously unselected package libgd3:amd64. 477s Preparing to unpack .../105-libgd3_2.3.3-12ubuntu3_amd64.deb ... 477s Unpacking libgd3:amd64 (2.3.3-12ubuntu3) ... 477s Selecting previously unselected package libhpdf-2.3.0:amd64. 477s Preparing to unpack .../106-libhpdf-2.3.0_2.3.0+dfsg-1build3_amd64.deb ... 477s Unpacking libhpdf-2.3.0:amd64 (2.3.0+dfsg-1build3) ... 477s Selecting previously unselected package mysql-common. 477s Preparing to unpack .../107-mysql-common_5.8+1.1.1_all.deb ... 477s Unpacking mysql-common (5.8+1.1.1) ... 477s Selecting previously unselected package libmysqlclient21:amd64. 477s Preparing to unpack .../108-libmysqlclient21_8.0.40-1_amd64.deb ... 477s Unpacking libmysqlclient21:amd64 (8.0.40-1) ... 477s Selecting previously unselected package libpq5:amd64. 477s Preparing to unpack .../109-libpq5_17.3-3_amd64.deb ... 477s Unpacking libpq5:amd64 (17.3-3) ... 477s Selecting previously unselected package emboss-lib. 477s Preparing to unpack .../110-emboss-lib_6.6.0+dfsg-12ubuntu2_amd64.deb ... 477s Unpacking emboss-lib (6.6.0+dfsg-12ubuntu2) ... 478s Selecting previously unselected package emboss-data. 478s Preparing to unpack .../111-emboss-data_6.6.0+dfsg-12ubuntu2_all.deb ... 478s Unpacking emboss-data (6.6.0+dfsg-12ubuntu2) ... 481s Selecting previously unselected package emboss. 481s Preparing to unpack .../112-emboss_6.6.0+dfsg-12ubuntu2_amd64.deb ... 481s Unpacking emboss (6.6.0+dfsg-12ubuntu2) ... 481s Selecting previously unselected package fonts-font-awesome. 481s Preparing to unpack .../113-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 481s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 481s Selecting previously unselected package fonts-lmodern. 481s Preparing to unpack .../114-fonts-lmodern_2.005-1_all.deb ... 481s Unpacking fonts-lmodern (2.005-1) ... 481s Selecting previously unselected package fonts-lyx. 481s Preparing to unpack .../115-fonts-lyx_2.4.3-1_all.deb ... 481s Unpacking fonts-lyx (2.4.3-1) ... 481s Selecting previously unselected package libgs-common. 481s Preparing to unpack .../116-libgs-common_10.04.0~dfsg1-2ubuntu1_all.deb ... 481s Unpacking libgs-common (10.04.0~dfsg1-2ubuntu1) ... 481s Selecting previously unselected package libgs10-common. 481s Preparing to unpack .../117-libgs10-common_10.04.0~dfsg1-2ubuntu1_all.deb ... 481s Unpacking libgs10-common (10.04.0~dfsg1-2ubuntu1) ... 481s Selecting previously unselected package libavahi-common-data:amd64. 481s Preparing to unpack .../118-libavahi-common-data_0.8-14ubuntu1_amd64.deb ... 481s Unpacking libavahi-common-data:amd64 (0.8-14ubuntu1) ... 481s Selecting previously unselected package libavahi-common3:amd64. 481s Preparing to unpack .../119-libavahi-common3_0.8-14ubuntu1_amd64.deb ... 481s Unpacking libavahi-common3:amd64 (0.8-14ubuntu1) ... 481s Selecting previously unselected package libavahi-client3:amd64. 481s Preparing to unpack .../120-libavahi-client3_0.8-14ubuntu1_amd64.deb ... 481s Unpacking libavahi-client3:amd64 (0.8-14ubuntu1) ... 481s Selecting previously unselected package libcups2t64:amd64. 481s Preparing to unpack .../121-libcups2t64_2.4.11-0ubuntu2_amd64.deb ... 481s Unpacking libcups2t64:amd64 (2.4.11-0ubuntu2) ... 481s Selecting previously unselected package libidn12:amd64. 481s Preparing to unpack .../122-libidn12_1.42-3_amd64.deb ... 481s Unpacking libidn12:amd64 (1.42-3) ... 481s Selecting previously unselected package libijs-0.35:amd64. 481s Preparing to unpack .../123-libijs-0.35_0.35-15.1build1_amd64.deb ... 481s Unpacking libijs-0.35:amd64 (0.35-15.1build1) ... 481s Selecting previously unselected package libjbig2dec0:amd64. 481s Preparing to unpack .../124-libjbig2dec0_0.20-1build3_amd64.deb ... 481s Unpacking libjbig2dec0:amd64 (0.20-1build3) ... 481s Selecting previously unselected package libpaper2:amd64. 481s Preparing to unpack .../125-libpaper2_2.2.5-0.3_amd64.deb ... 481s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 481s Selecting previously unselected package libice6:amd64. 481s Preparing to unpack .../126-libice6_2%3a1.1.1-1_amd64.deb ... 481s Unpacking libice6:amd64 (2:1.1.1-1) ... 481s Selecting previously unselected package libsm6:amd64. 481s Preparing to unpack .../127-libsm6_2%3a1.2.4-1_amd64.deb ... 481s Unpacking libsm6:amd64 (2:1.2.4-1) ... 481s Selecting previously unselected package libxt6t64:amd64. 481s Preparing to unpack .../128-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 481s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 481s Selecting previously unselected package libgs10:amd64. 481s Preparing to unpack .../129-libgs10_10.04.0~dfsg1-2ubuntu1_amd64.deb ... 481s Unpacking libgs10:amd64 (10.04.0~dfsg1-2ubuntu1) ... 482s Selecting previously unselected package ghostscript. 482s Preparing to unpack .../130-ghostscript_10.04.0~dfsg1-2ubuntu1_amd64.deb ... 482s Unpacking ghostscript (10.04.0~dfsg1-2ubuntu1) ... 482s Selecting previously unselected package libnetpbm11t64:amd64. 482s Preparing to unpack .../131-libnetpbm11t64_2%3a11.09.02-2_amd64.deb ... 482s Unpacking libnetpbm11t64:amd64 (2:11.09.02-2) ... 482s Selecting previously unselected package netpbm. 482s Preparing to unpack .../132-netpbm_2%3a11.09.02-2_amd64.deb ... 482s Unpacking netpbm (2:11.09.02-2) ... 482s Selecting previously unselected package tex-common. 482s Preparing to unpack .../133-tex-common_6.18_all.deb ... 482s Unpacking tex-common (6.18) ... 482s Selecting previously unselected package libpaper-utils. 482s Preparing to unpack .../134-libpaper-utils_2.2.5-0.3_amd64.deb ... 482s Unpacking libpaper-utils (2.2.5-0.3) ... 482s Selecting previously unselected package libkpathsea6:amd64. 482s Preparing to unpack .../135-libkpathsea6_2024.20240313.70630+ds-5build2_amd64.deb ... 482s Unpacking libkpathsea6:amd64 (2024.20240313.70630+ds-5build2) ... 482s Selecting previously unselected package libptexenc1:amd64. 482s Preparing to unpack .../136-libptexenc1_2024.20240313.70630+ds-5build2_amd64.deb ... 482s Unpacking libptexenc1:amd64 (2024.20240313.70630+ds-5build2) ... 482s Selecting previously unselected package libsynctex2:amd64. 482s Preparing to unpack .../137-libsynctex2_2024.20240313.70630+ds-5build2_amd64.deb ... 482s Unpacking libsynctex2:amd64 (2024.20240313.70630+ds-5build2) ... 482s Selecting previously unselected package libtexlua53-5:amd64. 482s Preparing to unpack .../138-libtexlua53-5_2024.20240313.70630+ds-5build2_amd64.deb ... 482s Unpacking libtexlua53-5:amd64 (2024.20240313.70630+ds-5build2) ... 482s Selecting previously unselected package t1utils. 482s Preparing to unpack .../139-t1utils_1.41-4build3_amd64.deb ... 482s Unpacking t1utils (1.41-4build3) ... 482s Selecting previously unselected package libpixman-1-0:amd64. 482s Preparing to unpack .../140-libpixman-1-0_0.44.0-3_amd64.deb ... 482s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 482s Selecting previously unselected package libxcb-render0:amd64. 482s Preparing to unpack .../141-libxcb-render0_1.17.0-2_amd64.deb ... 482s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 482s Selecting previously unselected package libxcb-shm0:amd64. 482s Preparing to unpack .../142-libxcb-shm0_1.17.0-2_amd64.deb ... 482s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 482s Selecting previously unselected package libcairo2:amd64. 482s Preparing to unpack .../143-libcairo2_1.18.2-2_amd64.deb ... 482s Unpacking libcairo2:amd64 (1.18.2-2) ... 482s Selecting previously unselected package libmpfi0:amd64. 482s Preparing to unpack .../144-libmpfi0_1.5.4+ds-4_amd64.deb ... 482s Unpacking libmpfi0:amd64 (1.5.4+ds-4) ... 482s Selecting previously unselected package libpotrace0:amd64. 482s Preparing to unpack .../145-libpotrace0_1.16-2build1_amd64.deb ... 482s Unpacking libpotrace0:amd64 (1.16-2build1) ... 482s Selecting previously unselected package libteckit0:amd64. 482s Preparing to unpack .../146-libteckit0_2.5.12+ds1-1_amd64.deb ... 482s Unpacking libteckit0:amd64 (2.5.12+ds1-1) ... 482s Selecting previously unselected package libxmu6:amd64. 482s Preparing to unpack .../147-libxmu6_2%3a1.1.3-3build2_amd64.deb ... 482s Unpacking libxmu6:amd64 (2:1.1.3-3build2) ... 482s Selecting previously unselected package libxaw7:amd64. 482s Preparing to unpack .../148-libxaw7_2%3a1.0.16-1_amd64.deb ... 482s Unpacking libxaw7:amd64 (2:1.0.16-1) ... 482s Selecting previously unselected package libxi6:amd64. 483s Preparing to unpack .../149-libxi6_2%3a1.8.2-1_amd64.deb ... 483s Unpacking libxi6:amd64 (2:1.8.2-1) ... 483s Selecting previously unselected package libzzip-0-13t64:amd64. 483s Preparing to unpack .../150-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_amd64.deb ... 483s Unpacking libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2build1) ... 483s Selecting previously unselected package texlive-binaries. 483s Preparing to unpack .../151-texlive-binaries_2024.20240313.70630+ds-5build2_amd64.deb ... 483s Unpacking texlive-binaries (2024.20240313.70630+ds-5build2) ... 483s Selecting previously unselected package xdg-utils. 483s Preparing to unpack .../152-xdg-utils_1.2.1-2ubuntu1_all.deb ... 483s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 483s Selecting previously unselected package texlive-base. 483s Preparing to unpack .../153-texlive-base_2024.20241115-1_all.deb ... 483s Unpacking texlive-base (2024.20241115-1) ... 484s Selecting previously unselected package hicolor-icon-theme. 484s Preparing to unpack .../154-hicolor-icon-theme_0.18-2_all.deb ... 484s Unpacking hicolor-icon-theme (0.18-2) ... 484s Selecting previously unselected package imagemagick-7.q16. 484s Preparing to unpack .../155-imagemagick-7.q16_8%3a7.1.1.43+dfsg1-1_amd64.deb ... 484s Unpacking imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 484s Selecting previously unselected package imagemagick. 484s Preparing to unpack .../156-imagemagick_8%3a7.1.1.43+dfsg1-1_amd64.deb ... 484s Unpacking imagemagick (8:7.1.1.43+dfsg1-1) ... 484s Selecting previously unselected package hevea. 484s Preparing to unpack .../157-hevea_2.36-2_amd64.deb ... 484s Unpacking hevea (2.36-2) ... 484s Selecting previously unselected package libllvm17t64:amd64. 484s Preparing to unpack .../158-libllvm17t64_1%3a17.0.6-20_amd64.deb ... 484s Unpacking libllvm17t64:amd64 (1:17.0.6-20) ... 485s Selecting previously unselected package libamd-comgr2:amd64. 485s Preparing to unpack .../159-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 485s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 485s Selecting previously unselected package libsuitesparseconfig7:amd64. 485s Preparing to unpack .../160-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_amd64.deb ... 485s Unpacking libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-3) ... 485s Selecting previously unselected package libamd3:amd64. 485s Preparing to unpack .../161-libamd3_1%3a7.8.3+dfsg-3_amd64.deb ... 485s Unpacking libamd3:amd64 (1:7.8.3+dfsg-3) ... 485s Selecting previously unselected package libhsakmt1:amd64. 485s Preparing to unpack .../162-libhsakmt1_5.7.0-1build1_amd64.deb ... 485s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 485s Selecting previously unselected package libhsa-runtime64-1. 485s Preparing to unpack .../163-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 485s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 485s Selecting previously unselected package libamdhip64-5. 485s Preparing to unpack .../164-libamdhip64-5_5.7.1-5_amd64.deb ... 485s Unpacking libamdhip64-5 (5.7.1-5) ... 485s Selecting previously unselected package libapache-pom-java. 485s Preparing to unpack .../165-libapache-pom-java_33-2_all.deb ... 485s Unpacking libapache-pom-java (33-2) ... 485s Selecting previously unselected package libblas3:amd64. 485s Preparing to unpack .../166-libblas3_3.12.1-2_amd64.deb ... 485s Unpacking libblas3:amd64 (3.12.1-2) ... 485s Selecting previously unselected package libgfortran5:amd64. 485s Preparing to unpack .../167-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 485s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 485s Selecting previously unselected package liblapack3:amd64. 485s Preparing to unpack .../168-liblapack3_3.12.1-2_amd64.deb ... 485s Unpacking liblapack3:amd64 (3.12.1-2) ... 485s Selecting previously unselected package libarpack2t64:amd64. 485s Preparing to unpack .../169-libarpack2t64_3.9.1-4_amd64.deb ... 485s Unpacking libarpack2t64:amd64 (3.9.1-4) ... 485s Selecting previously unselected package libcolamd3:amd64. 485s Preparing to unpack .../170-libcolamd3_1%3a7.8.3+dfsg-3_amd64.deb ... 485s Unpacking libcolamd3:amd64 (1:7.8.3+dfsg-3) ... 486s Selecting previously unselected package libcommons-parent-java. 486s Preparing to unpack .../171-libcommons-parent-java_56-1_all.deb ... 486s Unpacking libcommons-parent-java (56-1) ... 486s Selecting previously unselected package libcommons-logging-java. 486s Preparing to unpack .../172-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 486s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 486s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 486s Preparing to unpack .../173-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 486s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 486s Selecting previously unselected package libexpat1-dev:amd64. 486s Preparing to unpack .../174-libexpat1-dev_2.6.4-1_amd64.deb ... 486s Unpacking libexpat1-dev:amd64 (2.6.4-1) ... 486s Selecting previously unselected package libpsm-infinipath1. 486s Preparing to unpack .../175-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 486s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 486s Selecting previously unselected package libpsm2-2. 486s Preparing to unpack .../176-libpsm2-2_11.2.185-2.1_amd64.deb ... 486s Unpacking libpsm2-2 (11.2.185-2.1) ... 486s Selecting previously unselected package librdmacm1t64:amd64. 486s Preparing to unpack .../177-librdmacm1t64_55.0-1ubuntu1_amd64.deb ... 486s Unpacking librdmacm1t64:amd64 (55.0-1ubuntu1) ... 486s Selecting previously unselected package libfabric1:amd64. 486s Preparing to unpack .../178-libfabric1_1.17.0-3ubuntu1_amd64.deb ... 486s Unpacking libfabric1:amd64 (1.17.0-3ubuntu1) ... 486s Selecting previously unselected package libglpk40:amd64. 486s Preparing to unpack .../179-libglpk40_5.0-1build2_amd64.deb ... 486s Unpacking libglpk40:amd64 (5.0-1build2) ... 486s Selecting previously unselected package libhtscodecs2:amd64. 486s Preparing to unpack .../180-libhtscodecs2_1.6.1-2_amd64.deb ... 486s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 486s Selecting previously unselected package libhts3t64:amd64. 486s Preparing to unpack .../181-libhts3t64_1.21+ds-1_amd64.deb ... 486s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 486s Selecting previously unselected package libhwloc15:amd64. 486s Preparing to unpack .../182-libhwloc15_2.12.0-1_amd64.deb ... 486s Unpacking libhwloc15:amd64 (2.12.0-1) ... 486s Selecting previously unselected package libplfit0:amd64. 486s Preparing to unpack .../183-libplfit0_0.9.4+ds-1ubuntu5_amd64.deb ... 486s Unpacking libplfit0:amd64 (0.9.4+ds-1ubuntu5) ... 486s Selecting previously unselected package libigraph3t64:amd64. 486s Preparing to unpack .../184-libigraph3t64_0.10.15+ds-2_amd64.deb ... 486s Unpacking libigraph3t64:amd64 (0.10.15+ds-2) ... 486s Selecting previously unselected package libjs-jquery. 486s Preparing to unpack .../185-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 486s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 486s Selecting previously unselected package libjs-jquery-ui. 486s Preparing to unpack .../186-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 486s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 486s Selecting previously unselected package libjs-underscore. 486s Preparing to unpack .../187-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 486s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 486s Selecting previously unselected package libjs-sphinxdoc. 486s Preparing to unpack .../188-libjs-sphinxdoc_8.1.3-5_all.deb ... 486s Unpacking libjs-sphinxdoc (8.1.3-5) ... 486s Selecting previously unselected package libjson-perl. 486s Preparing to unpack .../189-libjson-perl_4.10000-1_all.deb ... 486s Unpacking libjson-perl (4.10000-1) ... 486s Selecting previously unselected package liblbfgsb0:amd64. 486s Preparing to unpack .../190-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 486s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 486s Selecting previously unselected package libmbedcrypto16:amd64. 486s Preparing to unpack .../191-libmbedcrypto16_3.6.2-3ubuntu1_amd64.deb ... 486s Unpacking libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 486s Selecting previously unselected package libmbedx509-7:amd64. 486s Preparing to unpack .../192-libmbedx509-7_3.6.2-3ubuntu1_amd64.deb ... 486s Unpacking libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 486s Selecting previously unselected package libmbedtls21:amd64. 486s Preparing to unpack .../193-libmbedtls21_3.6.2-3ubuntu1_amd64.deb ... 486s Unpacking libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 486s Selecting previously unselected package libmunge2:amd64. 486s Preparing to unpack .../194-libmunge2_0.5.16-1_amd64.deb ... 486s Unpacking libmunge2:amd64 (0.5.16-1) ... 486s Selecting previously unselected package libpciaccess0:amd64. 486s Preparing to unpack .../195-libpciaccess0_0.17-3build1_amd64.deb ... 486s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 486s Selecting previously unselected package libxnvctrl0:amd64. 486s Preparing to unpack .../196-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 486s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 486s Selecting previously unselected package ocl-icd-libopencl1:amd64. 486s Preparing to unpack .../197-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 486s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 486s Selecting previously unselected package libhwloc-plugins:amd64. 486s Preparing to unpack .../198-libhwloc-plugins_2.12.0-1_amd64.deb ... 486s Unpacking libhwloc-plugins:amd64 (2.12.0-1) ... 486s Selecting previously unselected package libpmix2t64:amd64. 486s Preparing to unpack .../199-libpmix2t64_5.0.6-3_amd64.deb ... 486s Unpacking libpmix2t64:amd64 (5.0.6-3) ... 487s Selecting previously unselected package libibumad3:amd64. 487s Preparing to unpack .../200-libibumad3_55.0-1ubuntu1_amd64.deb ... 487s Unpacking libibumad3:amd64 (55.0-1ubuntu1) ... 487s Selecting previously unselected package libibmad5:amd64. 487s Preparing to unpack .../201-libibmad5_55.0-1ubuntu1_amd64.deb ... 487s Unpacking libibmad5:amd64 (55.0-1ubuntu1) ... 487s Selecting previously unselected package libucx0:amd64. 487s Preparing to unpack .../202-libucx0_1.17.0+ds-3build1_amd64.deb ... 487s Unpacking libucx0:amd64 (1.17.0+ds-3build1) ... 487s Selecting previously unselected package libopenmpi40:amd64. 487s Preparing to unpack .../203-libopenmpi40_5.0.6-4_amd64.deb ... 487s Unpacking libopenmpi40:amd64 (5.0.6-4) ... 487s Selecting previously unselected package zlib1g-dev:amd64. 487s Preparing to unpack .../204-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 487s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 487s Selecting previously unselected package libpython3.13-dev:amd64. 487s Preparing to unpack .../205-libpython3.13-dev_3.13.2-1_amd64.deb ... 487s Unpacking libpython3.13-dev:amd64 (3.13.2-1) ... 487s Selecting previously unselected package libpython3-dev:amd64. 487s Preparing to unpack .../206-libpython3-dev_3.13.1-1~exp2_amd64.deb ... 487s Unpacking libpython3-dev:amd64 (3.13.1-1~exp2) ... 487s Selecting previously unselected package libpython3.12-dev:amd64. 487s Preparing to unpack .../207-libpython3.12-dev_3.12.9-1_amd64.deb ... 487s Unpacking libpython3.12-dev:amd64 (3.12.9-1) ... 487s Selecting previously unselected package libpython3-all-dev:amd64. 487s Preparing to unpack .../208-libpython3-all-dev_3.13.1-1~exp2_amd64.deb ... 487s Unpacking libpython3-all-dev:amd64 (3.13.1-1~exp2) ... 487s Selecting previously unselected package libqhull-r8.0:amd64. 487s Preparing to unpack .../209-libqhull-r8.0_2020.2-6build1_amd64.deb ... 487s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 487s Selecting previously unselected package libxslt1.1:amd64. 487s Preparing to unpack .../210-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 487s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 487s Selecting previously unselected package mafft. 487s Preparing to unpack .../211-mafft_7.505-1_amd64.deb ... 487s Unpacking mafft (7.505-1) ... 487s Selecting previously unselected package muscle3. 487s Preparing to unpack .../212-muscle3_3.8.1551-3_amd64.deb ... 487s Unpacking muscle3 (3.8.1551-3) ... 487s Selecting previously unselected package ncbi-data. 487s Preparing to unpack .../213-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 487s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 488s Selecting previously unselected package ncbi-blast+. 488s Preparing to unpack .../214-ncbi-blast+_2.16.0+ds-6build1_amd64.deb ... 488s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 488s Selecting previously unselected package openmpi-common. 488s Preparing to unpack .../215-openmpi-common_5.0.6-4_all.deb ... 488s Unpacking openmpi-common (5.0.6-4) ... 488s Selecting previously unselected package openmpi-bin. 488s Preparing to unpack .../216-openmpi-bin_5.0.6-4_amd64.deb ... 488s Unpacking openmpi-bin (5.0.6-4) ... 488s Selecting previously unselected package phylip. 488s Preparing to unpack .../217-phylip_1%3a3.697+dfsg-4build1_amd64.deb ... 488s Unpacking phylip (1:3.697+dfsg-4build1) ... 488s Selecting previously unselected package mpi-default-bin. 488s Preparing to unpack .../218-mpi-default-bin_1.18_amd64.deb ... 488s Unpacking mpi-default-bin (1.18) ... 488s Selecting previously unselected package phyml. 488s Preparing to unpack .../219-phyml_3%3a3.3.20220408-4build1_amd64.deb ... 488s Unpacking phyml (3:3.3.20220408-4build1) ... 488s Selecting previously unselected package prank. 488s Preparing to unpack .../220-prank_0.0.170427+dfsg-3_amd64.deb ... 488s Unpacking prank (0.0.170427+dfsg-3) ... 488s Selecting previously unselected package preview-latex-style. 488s Preparing to unpack .../221-preview-latex-style_13.2-1_all.deb ... 488s Unpacking preview-latex-style (13.2-1) ... 488s Selecting previously unselected package probcons. 488s Preparing to unpack .../222-probcons_1.12-14_amd64.deb ... 488s Unpacking probcons (1.12-14) ... 488s Selecting previously unselected package python-biopython-doc. 488s Preparing to unpack .../223-python-biopython-doc_1.85+dfsg-2_all.deb ... 488s Unpacking python-biopython-doc (1.85+dfsg-2) ... 489s Selecting previously unselected package python-matplotlib-data. 489s Preparing to unpack .../224-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 489s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 489s Selecting previously unselected package python3-all. 489s Preparing to unpack .../225-python3-all_3.13.1-1~exp2_amd64.deb ... 489s Unpacking python3-all (3.13.1-1~exp2) ... 489s Selecting previously unselected package python3.13-dev. 489s Preparing to unpack .../226-python3.13-dev_3.13.2-1_amd64.deb ... 489s Unpacking python3.13-dev (3.13.2-1) ... 489s Selecting previously unselected package python3-dev. 489s Preparing to unpack .../227-python3-dev_3.13.1-1~exp2_amd64.deb ... 489s Unpacking python3-dev (3.13.1-1~exp2) ... 489s Selecting previously unselected package python3.12-dev. 489s Preparing to unpack .../228-python3.12-dev_3.12.9-1_amd64.deb ... 489s Unpacking python3.12-dev (3.12.9-1) ... 489s Selecting previously unselected package python3-all-dev. 489s Preparing to unpack .../229-python3-all-dev_3.13.1-1~exp2_amd64.deb ... 489s Unpacking python3-all-dev (3.13.1-1~exp2) ... 489s Selecting previously unselected package python3-numpy. 489s Preparing to unpack .../230-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 489s Unpacking python3-numpy (1:1.26.4+ds-13) ... 489s Selecting previously unselected package python3.12-tk. 489s Preparing to unpack .../231-python3.12-tk_3.12.9-1_amd64.deb ... 489s Unpacking python3.12-tk (3.12.9-1) ... 489s Selecting previously unselected package python3.13-tk. 489s Preparing to unpack .../232-python3.13-tk_3.13.2-1_amd64.deb ... 489s Unpacking python3.13-tk (3.13.2-1) ... 489s Selecting previously unselected package python3-tk:amd64. 489s Preparing to unpack .../233-python3-tk_3.13.1-1_amd64.deb ... 489s Unpacking python3-tk:amd64 (3.13.1-1) ... 489s Selecting previously unselected package python3-pil.imagetk:amd64. 489s Preparing to unpack .../234-python3-pil.imagetk_11.1.0-5_amd64.deb ... 489s Unpacking python3-pil.imagetk:amd64 (11.1.0-5) ... 489s Selecting previously unselected package python3-pil:amd64. 489s Preparing to unpack .../235-python3-pil_11.1.0-5_amd64.deb ... 489s Unpacking python3-pil:amd64 (11.1.0-5) ... 489s Selecting previously unselected package python3-cairo. 489s Preparing to unpack .../236-python3-cairo_1.26.1-2build1_amd64.deb ... 489s Unpacking python3-cairo (1.26.1-2build1) ... 489s Selecting previously unselected package python3-freetype. 489s Preparing to unpack .../237-python3-freetype_2.5.1-1_all.deb ... 489s Unpacking python3-freetype (2.5.1-1) ... 489s Selecting previously unselected package python3-rlpycairo. 489s Preparing to unpack .../238-python3-rlpycairo_0.3.0-3_all.deb ... 489s Unpacking python3-rlpycairo (0.3.0-3) ... 489s Selecting previously unselected package python3-reportlab. 489s Preparing to unpack .../239-python3-reportlab_4.3.0-1_all.deb ... 489s Unpacking python3-reportlab (4.3.0-1) ... 490s Selecting previously unselected package w3c-sgml-lib. 490s Preparing to unpack .../240-w3c-sgml-lib_1.3-3_all.deb ... 490s Unpacking w3c-sgml-lib (1.3-3) ... 490s Selecting previously unselected package python3-biopython. 490s Preparing to unpack .../241-python3-biopython_1.85+dfsg-2_amd64.deb ... 490s Unpacking python3-biopython (1.85+dfsg-2) ... 490s Selecting previously unselected package python3-biopython-sql. 490s Preparing to unpack .../242-python3-biopython-sql_1.85+dfsg-2_all.deb ... 490s Unpacking python3-biopython-sql (1.85+dfsg-2) ... 490s Selecting previously unselected package python3-brotli. 490s Preparing to unpack .../243-python3-brotli_1.1.0-2build3_amd64.deb ... 490s Unpacking python3-brotli (1.1.0-2build3) ... 490s Selecting previously unselected package python3-contourpy. 490s Preparing to unpack .../244-python3-contourpy_1.3.1-1_amd64.deb ... 490s Unpacking python3-contourpy (1.3.1-1) ... 490s Selecting previously unselected package python3-cycler. 490s Preparing to unpack .../245-python3-cycler_0.12.1-1_all.deb ... 490s Unpacking python3-cycler (0.12.1-1) ... 490s Selecting previously unselected package python3-dateutil. 490s Preparing to unpack .../246-python3-dateutil_2.9.0-3_all.deb ... 490s Unpacking python3-dateutil (2.9.0-3) ... 490s Selecting previously unselected package python3-decorator. 490s Preparing to unpack .../247-python3-decorator_5.1.1-5_all.deb ... 490s Unpacking python3-decorator (5.1.1-5) ... 490s Selecting previously unselected package python3-defusedxml. 490s Preparing to unpack .../248-python3-defusedxml_0.7.1-3_all.deb ... 490s Unpacking python3-defusedxml (0.7.1-3) ... 490s Selecting previously unselected package python3-roman. 490s Preparing to unpack .../249-python3-roman_5.0-1_all.deb ... 490s Unpacking python3-roman (5.0-1) ... 490s Selecting previously unselected package python3-docutils. 490s Preparing to unpack .../250-python3-docutils_0.21.2+dfsg-2_all.deb ... 490s Unpacking python3-docutils (0.21.2+dfsg-2) ... 490s Selecting previously unselected package python3-pytz. 490s Preparing to unpack .../251-python3-pytz_2025.1-3_all.deb ... 490s Unpacking python3-pytz (2025.1-3) ... 490s Selecting previously unselected package python3-tz. 490s Preparing to unpack .../252-python3-tz_2025.1-3_all.deb ... 490s Unpacking python3-tz (2025.1-3) ... 490s Selecting previously unselected package python3-platformdirs. 490s Preparing to unpack .../253-python3-platformdirs_4.3.6-1_all.deb ... 490s Unpacking python3-platformdirs (4.3.6-1) ... 490s Selecting previously unselected package python3-fs. 490s Preparing to unpack .../254-python3-fs_2.4.16-6_all.deb ... 490s Unpacking python3-fs (2.4.16-6) ... 490s Selecting previously unselected package python3-lxml:amd64. 490s Preparing to unpack .../255-python3-lxml_5.3.1-1_amd64.deb ... 490s Unpacking python3-lxml:amd64 (5.3.1-1) ... 491s Selecting previously unselected package python3-lz4. 491s Preparing to unpack .../256-python3-lz4_4.4.0+dfsg-1_amd64.deb ... 491s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 491s Selecting previously unselected package python3-scipy. 491s Preparing to unpack .../257-python3-scipy_1.14.1-4ubuntu1_amd64.deb ... 491s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 491s Selecting previously unselected package python3-mpmath. 491s Preparing to unpack .../258-python3-mpmath_1.3.0-1_all.deb ... 491s Unpacking python3-mpmath (1.3.0-1) ... 491s Selecting previously unselected package python3-sympy. 491s Preparing to unpack .../259-python3-sympy_1.13.3-1_all.deb ... 491s Unpacking python3-sympy (1.13.3-1) ... 492s Selecting previously unselected package python3-ufolib2. 492s Preparing to unpack .../260-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 492s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 492s Selecting previously unselected package unicode-data. 492s Preparing to unpack .../261-unicode-data_15.1.0-1_all.deb ... 492s Unpacking unicode-data (15.1.0-1) ... 492s Selecting previously unselected package python3-fonttools. 492s Preparing to unpack .../262-python3-fonttools_4.55.3-2_amd64.deb ... 492s Unpacking python3-fonttools (4.55.3-2) ... 492s Selecting previously unselected package python3-imagesize. 492s Preparing to unpack .../263-python3-imagesize_1.4.1-1_all.deb ... 492s Unpacking python3-imagesize (1.4.1-1) ... 492s Selecting previously unselected package python3-kiwisolver. 492s Preparing to unpack .../264-python3-kiwisolver_1.4.7-3_amd64.deb ... 492s Unpacking python3-kiwisolver (1.4.7-3) ... 492s Selecting previously unselected package python3-packaging. 492s Preparing to unpack .../265-python3-packaging_24.2-1_all.deb ... 492s Unpacking python3-packaging (24.2-1) ... 492s Selecting previously unselected package python3-matplotlib. 492s Preparing to unpack .../266-python3-matplotlib_3.8.3-3ubuntu2_amd64.deb ... 492s Unpacking python3-matplotlib (3.8.3-3ubuntu2) ... 492s Selecting previously unselected package python3-msgpack. 492s Preparing to unpack .../267-python3-msgpack_1.0.3-3build3_amd64.deb ... 492s Unpacking python3-msgpack (1.0.3-3build3) ... 492s Selecting previously unselected package python3-mmtf. 492s Preparing to unpack .../268-python3-mmtf_1.1.3-1_all.deb ... 492s Unpacking python3-mmtf (1.1.3-1) ... 492s Selecting previously unselected package python3-mysqldb. 492s Preparing to unpack .../269-python3-mysqldb_1.4.6-2build4_amd64.deb ... 492s Unpacking python3-mysqldb (1.4.6-2build4) ... 492s Selecting previously unselected package python3-networkx. 492s Preparing to unpack .../270-python3-networkx_3.2.1-4ubuntu1_all.deb ... 492s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 493s Selecting previously unselected package sphinx-common. 493s Preparing to unpack .../271-sphinx-common_8.1.3-5_all.deb ... 493s Unpacking sphinx-common (8.1.3-5) ... 493s Selecting previously unselected package python3-alabaster. 493s Preparing to unpack .../272-python3-alabaster_0.7.16-0.1_all.deb ... 493s Unpacking python3-alabaster (0.7.16-0.1) ... 493s Selecting previously unselected package python3-snowballstemmer. 493s Preparing to unpack .../273-python3-snowballstemmer_2.2.0-4build1_all.deb ... 493s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 493s Selecting previously unselected package python3-sphinx. 493s Preparing to unpack .../274-python3-sphinx_8.1.3-5_all.deb ... 493s Unpacking python3-sphinx (8.1.3-5) ... 493s Selecting previously unselected package python3-tabulate. 493s Preparing to unpack .../275-python3-tabulate_0.9.0-1_all.deb ... 493s Unpacking python3-tabulate (0.9.0-1) ... 493s Selecting previously unselected package python3-numpydoc. 493s Preparing to unpack .../276-python3-numpydoc_1.8.0-1_all.deb ... 493s Unpacking python3-numpydoc (1.8.0-1) ... 493s Selecting previously unselected package python3-psycopg2. 493s Preparing to unpack .../277-python3-psycopg2_2.9.10-1_amd64.deb ... 493s Unpacking python3-psycopg2 (2.9.10-1) ... 493s Selecting previously unselected package python3-rdflib. 493s Preparing to unpack .../278-python3-rdflib_7.1.1-2_all.deb ... 493s Unpacking python3-rdflib (7.1.1-2) ... 493s Selecting previously unselected package sphinx-rtd-theme-common. 493s Preparing to unpack .../279-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 493s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 493s Selecting previously unselected package python3-sphinxcontrib.jquery. 494s Preparing to unpack .../280-python3-sphinxcontrib.jquery_4.1-5_all.deb ... 494s Unpacking python3-sphinxcontrib.jquery (4.1-5) ... 494s Selecting previously unselected package python3-sphinx-rtd-theme. 494s Preparing to unpack .../281-python3-sphinx-rtd-theme_3.0.2+dfsg-2_all.deb ... 494s Unpacking python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 494s Selecting previously unselected package python3-texttable. 494s Preparing to unpack .../282-python3-texttable_1.7.0-1_all.deb ... 494s Unpacking python3-texttable (1.7.0-1) ... 494s Selecting previously unselected package raxml. 494s Preparing to unpack .../283-raxml_8.2.13+dfsg-1_amd64.deb ... 494s Unpacking raxml (8.2.13+dfsg-1) ... 494s Selecting previously unselected package samtools. 494s Preparing to unpack .../284-samtools_1.21-1_amd64.deb ... 494s Unpacking samtools (1.21-1) ... 494s Selecting previously unselected package t-coffee. 494s Preparing to unpack .../285-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_amd64.deb ... 494s Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 494s Selecting previously unselected package texlive-fonts-recommended. 494s Preparing to unpack .../286-texlive-fonts-recommended_2024.20241115-1_all.deb ... 494s Unpacking texlive-fonts-recommended (2024.20241115-1) ... 494s Selecting previously unselected package texlive-latex-base. 494s Preparing to unpack .../287-texlive-latex-base_2024.20241115-1_all.deb ... 494s Unpacking texlive-latex-base (2024.20241115-1) ... 495s Selecting previously unselected package libfontbox-java. 495s Preparing to unpack .../288-libfontbox-java_1%3a1.8.16-5_all.deb ... 495s Unpacking libfontbox-java (1:1.8.16-5) ... 495s Selecting previously unselected package libpdfbox-java. 495s Preparing to unpack .../289-libpdfbox-java_1%3a1.8.16-5_all.deb ... 495s Unpacking libpdfbox-java (1:1.8.16-5) ... 495s Selecting previously unselected package texlive-latex-recommended. 495s Preparing to unpack .../290-texlive-latex-recommended_2024.20241115-1_all.deb ... 495s Unpacking texlive-latex-recommended (2024.20241115-1) ... 495s Selecting previously unselected package texlive-pictures. 495s Preparing to unpack .../291-texlive-pictures_2024.20241115-1_all.deb ... 495s Unpacking texlive-pictures (2024.20241115-1) ... 496s Selecting previously unselected package texlive-latex-extra. 496s Preparing to unpack .../292-texlive-latex-extra_2024.20250114-1_all.deb ... 496s Unpacking texlive-latex-extra (2024.20250114-1) ... 498s Selecting previously unselected package wise-data. 498s Preparing to unpack .../293-wise-data_2.4.1-25_all.deb ... 498s Unpacking wise-data (2.4.1-25) ... 498s Selecting previously unselected package wise. 498s Preparing to unpack .../294-wise_2.4.1-25_amd64.deb ... 498s Unpacking wise (2.4.1-25) ... 498s Selecting previously unselected package fasttree. 498s Preparing to unpack .../295-fasttree_2.1.11-2_amd64.deb ... 498s Unpacking fasttree (2.1.11-2) ... 498s Selecting previously unselected package python3-igraph. 498s Preparing to unpack .../296-python3-igraph_0.11.8+ds-1build1_amd64.deb ... 498s Unpacking python3-igraph (0.11.8+ds-1build1) ... 498s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 498s Setting up dh-python (6.20250108) ... 498s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 498s Setting up liblcms2-2:amd64 (2.16-2) ... 498s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 498s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 498s Setting up python3.12-minimal (3.12.9-1) ... 499s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 499s Setting up python3-texttable (1.7.0-1) ... 499s Setting up libaom3:amd64 (3.12.0-1) ... 499s Setting up libpciaccess0:amd64 (0.17-3build1) ... 499s Setting up mysql-common (5.8+1.1.1) ... 499s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 499s Setting up libmysqlclient21:amd64 (8.0.40-1) ... 499s Setting up libhpdf-2.3.0:amd64 (2.3.0+dfsg-1build3) ... 499s Setting up fonts-lato (2.015-1) ... 499s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 499s Setting up libxpm4:amd64 (1:3.5.17-1build2) ... 499s Setting up hicolor-icon-theme (0.18-2) ... 499s Setting up libxi6:amd64 (2:1.8.2-1) ... 499s Setting up probcons (1.12-14) ... 499s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 499s Setting up python3-lz4 (4.4.0+dfsg-1) ... 499s Setting up libxcb-render0:amd64 (1.17.0-2) ... 499s Setting up python3-defusedxml (0.7.1-3) ... 500s Setting up mafft (7.505-1) ... 500s Setting up libarchive-zip-perl (1.68-1) ... 500s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 500s Setting up imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 500s Setting up bwa (0.7.18-1) ... 500s Setting up python3-alabaster (0.7.16-0.1) ... 500s Setting up fonts-lyx (2.4.3-1) ... 500s Setting up libijs-0.35:amd64 (0.35-15.1build1) ... 500s Setting up libdebhelper-perl (13.24.1ubuntu2) ... 500s Setting up libgs-common (10.04.0~dfsg1-2ubuntu1) ... 500s Setting up python3.12 (3.12.9-1) ... 501s Setting up libfontbox-java (1:1.8.16-5) ... 501s Setting up phylip (1:3.697+dfsg-4build1) ... 501s Setting up x11-common (1:7.7+23ubuntu3) ... 501s Setting up libpq5:amd64 (17.3-3) ... 501s Setting up libibumad3:amd64 (55.0-1ubuntu1) ... 501s Setting up libdeflate0:amd64 (1.23-1) ... 501s Setting up python3-tabulate (0.9.0-1) ... 501s Setting up m4 (1.4.19-5) ... 501s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 501s Setting up python3-all (3.13.1-1~exp2) ... 501s Setting up python3-pytz (2025.1-3) ... 502s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 502s Setting up libibmad5:amd64 (55.0-1ubuntu1) ... 502s Setting up libgomp1:amd64 (15-20250213-1ubuntu1) ... 502s Setting up python3-freetype (2.5.1-1) ... 502s Setting up emboss-data (6.6.0+dfsg-12ubuntu2) ... 502s Setting up python3-networkx (3.2.1-4ubuntu1) ... 504s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 504s Setting up libnetpbm11t64:amd64 (2:11.09.02-2) ... 504s Setting up python3-platformdirs (4.3.6-1) ... 504s Setting up python3-tz (2025.1-3) ... 504s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 504s Setting up poppler-data (0.4.12-1) ... 504s Setting up python3-fs (2.4.16-6) ... 504s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 504s Setting up unicode-data (15.1.0-1) ... 504s Setting up python3-mysqldb (1.4.6-2build4) ... 505s Setting up tex-common (6.18) ... 505s update-language: texlive-base not installed and configured, doing nothing! 505s Setting up python3-roman (5.0-1) ... 505s Setting up python3-decorator (5.1.1-5) ... 505s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 505s Setting up autotools-dev (20220109.1) ... 505s Setting up libblas3:amd64 (3.12.1-2) ... 505s 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 505s Setting up python3-packaging (24.2-1) ... 505s Setting up libmunge2:amd64 (0.5.16-1) ... 505s Setting up libllvm17t64:amd64 (1:17.0.6-20) ... 505s Setting up libexpat1-dev:amd64 (2.6.4-1) ... 505s Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2build1) ... 505s Setting up libjbig2dec0:amd64 (0.20-1build3) ... 505s Setting up python3-snowballstemmer (2.2.0-4build1) ... 506s Setting up libteckit0:amd64 (2.5.12+ds1-1) ... 506s Setting up python3-brotli (1.1.0-2build3) ... 506s Setting up libapache-pom-java (33-2) ... 506s Setting up libavahi-common-data:amd64 (0.8-14ubuntu1) ... 506s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 506s Setting up muscle3 (3.8.1551-3) ... 506s Setting up t1utils (1.41-4build3) ... 506s Setting up libquadmath0:amd64 (15-20250213-1ubuntu1) ... 506s Setting up python3-cycler (0.12.1-1) ... 506s Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-5build2) ... 506s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 506s Setting up fonts-dejavu-mono (2.37-8) ... 506s Setting up python3-kiwisolver (1.4.7-3) ... 506s Setting up libhwloc15:amd64 (2.12.0-1) ... 506s Setting up libmpc3:amd64 (1.3.1-1build2) ... 506s Setting up libidn12:amd64 (1.42-3) ... 506s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 506s Setting up autopoint (0.23.1-1) ... 506s Setting up libmpfi0:amd64 (1.5.4+ds-4) ... 506s Setting up python3-psycopg2 (2.9.10-1) ... 506s Setting up fonts-dejavu-core (2.37-8) ... 507s Setting up wise-data (2.4.1-25) ... 507s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 507s Setting up libltdl7:amd64 (2.5.4-3build1) ... 507s Setting up libfftw3-double3:amd64 (3.3.10-2fakesync1build1) ... 507s Setting up libcifpp-data (7.0.9-1) ... 507s Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-5build2) ... 507s Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 507s Setting up autoconf (2.72-3) ... 507s Setting up libwebp7:amd64 (1.5.0-0.1) ... 507s Setting up libubsan1:amd64 (15-20250213-1ubuntu1) ... 507s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 507s Setting up dwz (0.15-1build6) ... 507s Setting up liblqr-1-0:amd64 (0.4.2-2.1build2) ... 507s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 507s Setting up libhwasan0:amd64 (15-20250213-1ubuntu1) ... 507s Setting up python3-rdflib (7.1.1-2) ... 507s Setting up libasan8:amd64 (15-20250213-1ubuntu1) ... 507s Setting up libjson-perl (4.10000-1) ... 507s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 507s Setting up libpsm2-2 (11.2.185-2.1) ... 507s Setting up openmpi-common (5.0.6-4) ... 507s Setting up clustalw (2.1+lgpl-7) ... 507s Setting up debugedit (1:5.1-2) ... 507s Setting up libhts3t64:amd64 (1.21+ds-1) ... 507s Setting up fonts-lmodern (2.005-1) ... 507s Setting up libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-3) ... 507s Setting up librdmacm1t64:amd64 (55.0-1ubuntu1) ... 507s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 507s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 507s Setting up python3-dateutil (2.9.0-3) ... 508s Setting up fasttree (2.1.11-2) ... 508s Setting up sgml-base (1.31) ... 508s Setting up python3-msgpack (1.0.3-3build3) ... 508s Setting up libplfit0:amd64 (0.9.4+ds-1ubuntu5) ... 508s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 508s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 508s Setting up libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 508s Setting up libpaper2:amd64 (2.2.5-0.3) ... 508s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 508s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 508s Setting up libtsan2:amd64 (15-20250213-1ubuntu1) ... 508s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 508s Setting up python3-mpmath (1.3.0-1) ... 509s Setting up libisl23:amd64 (0.27-1) ... 509s Setting up libde265-0:amd64 (1.0.15-1build4) ... 509s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 509s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 509s Setting up dialign (2.2.1-13) ... 509s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 509s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 509s Setting up xdg-utils (1.2.1-2ubuntu1) ... 509s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 509s Setting up libcc1-0:amd64 (15-20250213-1ubuntu1) ... 509s Setting up liblsan0:amd64 (15-20250213-1ubuntu1) ... 509s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 509s Setting up libitm1:amd64 (15-20250213-1ubuntu1) ... 509s Setting up libsynctex2:amd64 (2024.20240313.70630+ds-5build2) ... 509s Setting up prank (0.0.170427+dfsg-3) ... 509s Setting up libargtable2-0 (13-3) ... 509s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 509s Setting up raxml (8.2.13+dfsg-1) ... 509s Setting up python3-imagesize (1.4.1-1) ... 509s Setting up libpotrace0:amd64 (1.16-2build1) ... 509s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 509s Setting up automake (1:1.17-3) ... 509s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 509s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 509s Setting up libfabric1:amd64 (1.17.0-3ubuntu1) ... 509s Setting up python3-sympy (1.13.3-1) ... 519s Setting up libice6:amd64 (2:1.1.1-1) ... 519s Setting up flex (2.6.4-8.2build1) ... 519s Setting up liblapack3:amd64 (3.12.1-2) ... 519s 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 519s Setting up gettext (0.23.1-1) ... 519s Setting up libarpack2t64:amd64 (3.9.1-4) ... 519s Setting up libamd3:amd64 (1:7.8.3+dfsg-3) ... 519s Setting up libpdfbox-java (1:1.8.16-5) ... 519s Setting up libcolamd3:amd64 (1:7.8.3+dfsg-3) ... 519s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 519s Setting up wise (2.4.1-25) ... 519s Setting up preview-latex-style (13.2-1) ... 519s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 519s Setting up libcommons-parent-java (56-1) ... 519s Setting up libavahi-common3:amd64 (0.8-14ubuntu1) ... 519s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 519s Setting up libcifpp7:amd64 (7.0.9-1) ... 519s Setting up libpython3.12-dev:amd64 (3.12.9-1) ... 519s Setting up libpaper-utils (2.2.5-0.3) ... 519s Setting up clustalo (1.2.4-8build1) ... 519s Setting up dssp (4.4.10-1) ... 519s Setting up xfonts-utils (1:7.7+7) ... 519s Setting up libhwloc-plugins:amd64 (2.12.0-1) ... 519s Setting up samtools (1.21-1) ... 519s Setting up intltool-debian (0.35.0+20060710.6) ... 519s Setting up libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 519s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 519s Setting up libptexenc1:amd64 (2024.20240313.70630+ds-5build2) ... 519s Setting up libglpk40:amd64 (5.0-1build2) ... 519s Setting up libraqm0:amd64 (0.10.2-1) ... 519s Setting up libpython3.13-dev:amd64 (3.13.2-1) ... 519s Setting up python3.12-dev (3.12.9-1) ... 519s Setting up cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 519s Setting up libpmix2t64:amd64 (5.0.6-3) ... 519s Setting up python3-numpy (1:1.26.4+ds-13) ... 522s Setting up libjs-sphinxdoc (8.1.3-5) ... 522s Setting up libraw23t64:amd64 (0.21.3-1) ... 522s Setting up cpp-14 (14.2.0-17ubuntu1) ... 522s Setting up libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 522s Setting up dh-strip-nondeterminism (1.14.1-2) ... 522s Setting up python3-lxml:amd64 (5.3.1-1) ... 523s Setting up python-biopython-doc (1.85+dfsg-2) ... 523s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 523s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 523s Setting up xml-core (0.19) ... 523s Setting up python3-contourpy (1.3.1-1) ... 523s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 523s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu1) ... 523s Setting up libigraph3t64:amd64 (0.10.15+ds-2) ... 523s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu1) ... 523s Setting up libsm6:amd64 (2:1.2.4-1) ... 523s Setting up libavahi-client3:amd64 (0.8-14ubuntu1) ... 523s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 523s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 523s Setting up libxft2:amd64 (2.3.6-1build1) ... 523s Setting up python3-scipy (1.14.1-4ubuntu1) ... 529s Setting up libpython3-dev:amd64 (3.13.1-1~exp2) ... 529s Setting up python3.13-dev (3.13.2-1) ... 529s Setting up po-debconf (1.0.21+nmu1) ... 529s Setting up libtk8.6:amd64 (8.6.16-1) ... 529s Setting up python3.12-tk (3.12.9-1) ... 529s Setting up python3-mmtf (1.1.3-1) ... 529s Setting up fonts-urw-base35 (20200910-8) ... 529s Setting up libcairo2:amd64 (1.18.2-2) ... 529s Setting up python3.13-tk (3.13.2-1) ... 529s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 529s Setting up python3-pil:amd64 (11.1.0-5) ... 530s Setting up libamdhip64-5 (5.7.1-5) ... 530s Setting up libpython3-all-dev:amd64 (3.13.1-1~exp2) ... 530s Setting up sphinx-common (8.1.3-5) ... 530s Setting up python3-dev (3.13.1-1~exp2) ... 530s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 530s Setting up netpbm (2:11.09.02-2) ... 530s Setting up python3-igraph (0.11.8+ds-1build1) ... 530s Setting up cpp (4:14.2.0-1ubuntu1) ... 530s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 530s Setting up libcups2t64:amd64 (2.4.11-0ubuntu2) ... 530s Setting up python3-all-dev (3.13.1-1~exp2) ... 530s Setting up libgs10-common (10.04.0~dfsg1-2ubuntu1) ... 530s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 530s Setting up libucx0:amd64 (1.17.0+ds-3build1) ... 530s Setting up libxmu6:amd64 (2:1.1.3-3build2) ... 530s Setting up python3-cairo (1.26.1-2build1) ... 530s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 530s Setting up blt (2.5.3+dfsg-7build1) ... 530s Setting up python3-tk:amd64 (3.13.1-1) ... 531s Setting up libxaw7:amd64 (2:1.0.16-1) ... 531s Setting up gcc-14 (14.2.0-17ubuntu1) ... 531s Setting up python3-pil.imagetk:amd64 (11.1.0-5) ... 531s Setting up python3-rlpycairo (0.3.0-3) ... 531s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 531s Setting up python3-reportlab (4.3.0-1) ... 532s Setting up texlive-binaries (2024.20240313.70630+ds-5build2) ... 532s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 532s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 532s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 532s Setting up g++-14 (14.2.0-17ubuntu1) ... 532s Setting up texlive-base (2024.20241115-1) ... 533s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 533s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 533s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 534s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 534s Setting up libgs10:amd64 (10.04.0~dfsg1-2ubuntu1) ... 534s Setting up libopenmpi40:amd64 (5.0.6-4) ... 534s Setting up libtool (2.5.4-3build1) ... 534s Setting up ghostscript (10.04.0~dfsg1-2ubuntu1) ... 534s Setting up gcc (4:14.2.0-1ubuntu1) ... 534s Setting up dh-autoreconf (20) ... 534s Setting up texlive-latex-base (2024.20241115-1) ... 534s Setting up texlive-latex-recommended (2024.20241115-1) ... 534s Setting up texlive-pictures (2024.20241115-1) ... 534s Setting up g++ (4:14.2.0-1ubuntu1) ... 534s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 534s Setting up texlive-fonts-recommended (2024.20241115-1) ... 534s Setting up build-essential (12.10ubuntu1) ... 534s Setting up openmpi-bin (5.0.6-4) ... 534s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 534s 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 534s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 534s Setting up mpi-default-bin (1.18) ... 534s Setting up debhelper (13.24.1ubuntu2) ... 534s Setting up texlive-latex-extra (2024.20250114-1) ... 534s Setting up phyml (3:3.3.20220408-4build1) ... 534s Setting up python3-fonttools (4.55.3-2) ... 536s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 536s Setting up libheif-plugin-aomdec:amd64 (1.19.5-1build1) ... 536s Setting up libheif-plugin-libde265:amd64 (1.19.5-1build1) ... 536s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 538s Setting up libheif1:amd64 (1.19.5-1build1) ... 538s Setting up libgd3:amd64 (2.3.3-12ubuntu3) ... 538s Setting up libmagickcore-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... 538s Setting up emboss-lib (6.6.0+dfsg-12ubuntu2) ... 538s Setting up libmagickwand-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... 538s Setting up emboss (6.6.0+dfsg-12ubuntu2) ... 538s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 538s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 538s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 538s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 538s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 538s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 538s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 538s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 538s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 538s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 538s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 538s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 538s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 538s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 538s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 538s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 538s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 538s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 538s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 538s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 538s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 538s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 538s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 538s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 538s 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 538s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 538s 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 538s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 538s 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 538s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 538s 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 538s Setting up hevea (2.36-2) ... 538s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 538s Processing triggers for install-info (7.1.1-1) ... 539s Processing triggers for libc-bin (2.40-4ubuntu1) ... 539s Processing triggers for systemd (257.2-3ubuntu1) ... 539s Processing triggers for man-db (2.13.0-1) ... 541s Processing triggers for shared-mime-info (2.4-5) ... 541s Warning: program compiled against libxml 212 using older 209 541s Processing triggers for sgml-base (1.31) ... 541s Setting up w3c-sgml-lib (1.3-3) ... 567s Setting up docutils-common (0.21.2+dfsg-2) ... 567s Setting up python3-biopython (1.85+dfsg-2) ... 569s Setting up python3-biopython-sql (1.85+dfsg-2) ... 569s Processing triggers for sgml-base (1.31) ... 569s Setting up python3-docutils (0.21.2+dfsg-2) ... 570s Setting up python3-sphinx (8.1.3-5) ... 571s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 571s Setting up python3-numpydoc (1.8.0-1) ... 571s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 572s Processing triggers for tex-common (6.18) ... 572s Running updmap-sys. This may take some time... done. 572s Running mktexlsr /var/lib/texmf ... done. 572s Building format(s) --all. 622s This may take some time... done. 637s autopkgtest [12:17:16]: test full_suite: sh debian/tests/run-unit-test 637s autopkgtest [12:17:16]: test full_suite: [----------------------- 639s mkdir: created directory 'Bio' 639s mkdir: created directory 'Bio/Align' 639s mkdir: created directory 'Bio/Align/substitution_matrices' 639s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 639s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 640s test_Ace ... ok 640s test_Affy ... ok 642s test_AlignIO ... ok 642s test_AlignIO_ClustalIO ... ok 642s test_AlignIO_EmbossIO ... ok 642s test_AlignIO_FastaIO ... ok 643s test_AlignIO_MauveIO ... ok 643s test_AlignIO_PhylipIO ... ok 643s test_AlignIO_convert ... ok 643s test_AlignInfo ... ok 643s test_Align_Alignment ... ok 643s test_Align_a2m ... ok 643s test_Align_bed ... ok 643s test_Align_bigbed ... ok 644s test_Align_bigmaf ... ok 644s test_Align_bigpsl ... ok 644s test_Align_chain ... ok 644s test_Align_clustal ... ok 649s test_Align_codonalign ... ok 649s test_Align_emboss ... ok 649s test_Align_exonerate ... ok 649s test_Align_fasta ... ok 649s test_Align_hhr ... ok 650s test_Align_maf ... ok 650s test_Align_mauve ... ok 650s test_Align_msf ... ok 650s test_Align_nexus ... ok 650s test_Align_phylip ... ok 651s test_Align_psl ... ok 651s test_Align_sam ... ok 653s test_Align_stockholm ... ok 653s test_Align_tabular ... ok 653s test_Application ... ok 654s test_BWA_tool ... ok 654s test_BioSQL_MySQLdb_online ... skipping. internet not available 654s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 654s test_BioSQL_mysql_connector_online ... skipping. internet not available 654s test_BioSQL_psycopg2_online ... skipping. internet not available 658s test_BioSQL_sqlite3 ... ok 658s test_BioSQL_sqlite3_online ... skipping. internet not available 658s test_Blast_Record ... ok 659s test_Blast_parser ... ok 659s test_CAPS ... ok 659s test_Chi2 ... ok 659s test_ClustalOmega_tool ... ok 660s test_Clustalw_tool ... ok 660s test_Cluster ... ok 660s test_CodonTable ... ok 661s test_ColorSpiral ... ok 661s test_Compass ... ok 662s test_Consensus ... ok 663s test_Dialign_tool ... ok 663s test_EMBL_unittest ... ok 668s test_Emboss ... ok 668s test_EmbossPrimer ... ok 673s test_Entrez ... ok 673s test_Entrez_online ... skipping. internet not available 673s test_Entrez_parser ... ok 673s test_Enzyme ... ok 673s test_ExPASy ... skipping. internet not available 673s test_Fasttree_tool ... ok 673s test_File ... ok 673s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 673s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 673s ok 675s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 677s ok 678s test_GraphicsChromosome ... ok 678s test_GraphicsDistribution ... ok 679s test_GraphicsGeneral ... ok 679s test_HMMCasino ... ok 679s test_HMMGeneral ... ok 679s test_KEGG ... ok 679s test_KEGG_online ... skipping. internet not available 685s test_KGML_graphics ... ok 685s test_KGML_graphics_online ... skipping. internet not available 686s test_KGML_nographics ... ok 686s test_KeyWList ... ok 686s test_LogisticRegression ... ok 687s test_MafIO_index ... ok 688s test_Mafft_tool ... ok 688s test_MarkovModel ... ok 688s test_Medline ... ok 689s test_Muscle_tool ... ok 689s test_NCBIXML ... Exception ignored in: 689s Traceback (most recent call last): 689s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 689s expat_parser.Parse(NULL, True) 689s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 689s ok 691s test_NCBI_BLAST_tools ... ok 691s test_NCBI_qblast ... ok 691s test_NMR ... ok 691s test_NaiveBayes ... ok 691s test_Nexus ... ok 691s test_PAML_baseml ... ok 692s test_PAML_codeml ... ok 692s test_PAML_yn00 ... ok 696s test_PDB_CEAligner ... ok 698s test_PDB_DSSP ... ok 698s test_PDB_Dice ... ok 698s test_PDB_Disordered ... ok 698s test_PDB_Exposure ... ok 698s test_PDB_FragmentMapper ... ok 700s test_PDB_KDTree ... ok 700s test_PDB_MMCIF2Dict ... ok 700s test_PDB_MMCIFIO ... ok 701s test_PDB_MMCIFParser ... ok 701s test_PDB_NACCESS ... ok 701s test_PDB_PDBIO ... ok 702s test_PDB_PDBList ... skipping. internet not available 708s test_PDB_PDBMLParser ... ok 709s test_PDB_PDBParser ... ok 709s 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 709s test_PDB_Polypeptide ... ok 709s test_PDB_QCPSuperimposer ... ok 712s test_PDB_SASA ... ok 713s test_PDB_SMCRA ... ok 713s test_PDB_Selection ... ok 713s test_PDB_StructureAlignment ... ok 713s test_PDB_Superimposer ... ok 713s test_PDB_alphafold_db ... skipping. internet not available 716s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 716s warnings.warn( 716s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 716s warnings.warn( 716s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 716s warnings.warn( 716s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 716s warnings.warn( 716s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 716s warnings.warn( 716s ok 725s test_PDB_internal_coords ... ok 725s test_PDB_parse_pdb_header ... ok 725s test_PDB_vectors ... ok 725s test_PQR ... ok 725s test_Pathway ... ok 726s test_Phd ... ok 726s test_Phylo ... ok 726s test_PhyloXML ... ok 727s test_Phylo_CDAO ... ok 727s test_Phylo_NeXML ... ok 728s test_Phylo_igraph ... ok 731s test_Phylo_matplotlib ... ok 731s test_Phylo_networkx ... ok 731s test_PopGen_GenePop_nodepend ... ok 733s test_Prank_tool ... ok 734s test_Probcons_tool ... ok 734s test_ProtParam ... ok 735s test_RCSBFormats ... ok 735s test_Restriction ... ok 736s test_SCOP_Astral ... ok 736s test_SCOP_Cla ... ok 736s test_SCOP_Des ... ok 737s test_SCOP_Dom ... ok 737s test_SCOP_Hie ... ok 738s test_SCOP_Raf ... ok 738s test_SCOP_Residues ... ok 738s test_SCOP_Scop ... ok 739s test_SVDSuperimposer ... ok 739s test_SearchIO_blast_tab ... ok 739s test_SearchIO_blast_tab_index ... ok 740s test_SearchIO_blast_xml ... ok 741s test_SearchIO_blast_xml_index ... ok 742s test_SearchIO_blat_psl ... ok 742s test_SearchIO_blat_psl_index ... ok 743s test_SearchIO_exonerate ... ok 743s test_SearchIO_exonerate_text_index ... ok 743s test_SearchIO_exonerate_vulgar_index ... ok 744s test_SearchIO_fasta_m10 ... ok 744s test_SearchIO_fasta_m10_index ... ok 745s test_SearchIO_hhsuite2_text ... ok 745s test_SearchIO_hmmer2_text ... ok 746s test_SearchIO_hmmer2_text_index ... ok 746s test_SearchIO_hmmer3_domtab ... ok 747s test_SearchIO_hmmer3_domtab_index ... ok 747s test_SearchIO_hmmer3_tab ... ok 747s test_SearchIO_hmmer3_tab_index ... ok 748s test_SearchIO_hmmer3_text ... ok 748s test_SearchIO_hmmer3_text_index ... ok 749s test_SearchIO_interproscan_xml ... ok 749s test_SearchIO_model ... ok 750s test_SearchIO_write ... ok 750s test_SeqFeature ... ok 766s test_SeqIO ... ok 767s test_SeqIO_AbiIO ... ok 767s test_SeqIO_FastaIO ... ok 767s test_SeqIO_Gck ... ok 768s test_SeqIO_Gfa ... ok 768s test_SeqIO_Insdc ... ok 769s test_SeqIO_NibIO ... ok 771s test_SeqIO_PdbIO ... ok 772s test_SeqIO_QualityIO ... ok 772s test_SeqIO_SeqXML ... ok 772s test_SeqIO_SffIO ... ok 773s test_SeqIO_SnapGene ... ok 774s test_SeqIO_TwoBitIO ... ok 774s test_SeqIO_UniprotIO ... ok 775s test_SeqIO_Xdna ... ok 776s test_SeqIO_features ... ok 789s test_SeqIO_index ... ok 790s test_SeqIO_online ... skipping. internet not available 790s test_SeqIO_write ... ok 790s test_SeqRecord ... ok 791s test_SeqUtils ... ok 792s test_Seq_objs ... ok 793s test_SwissProt ... ok 796s test_TCoffee_tool ... ok 797s test_TogoWS ... skipping. internet not available 797s test_TreeConstruction ... ok 798s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 798s test_UniGene ... ok 799s test_UniProt ... skipping. internet not available 799s test_UniProt_GOA ... ok 799s test_align ... ok 800s test_align_substitution_matrices ... ok 802s test_bgzf ... ok 803s test_cellosaurus ... ok 808s test_codonalign ... ok 809s test_geo ... ok 809s test_kNN ... ok 810s test_motifs ... ok 810s test_motifs_online ... skipping. internet not available 811s 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. 811s warnings.warn( 811s ok 811s test_pairwise2_no_C ... ok 812s test_pairwise_aligner ... ok 812s test_pairwise_alignment_map ... ok 819s test_phenotype ... ok 820s test_phenotype_fit ... ok 820s test_phyml_tool ... ok 821s test_prodoc ... ok 821s test_prosite ... ok 821s test_raxml_tool ... ok 822s test_samtools_tool ... ok 822s test_seq ... ok 823s test_translate ... ok 823s Skipping any tests requiring internet access 823s Python version: 3.12.9 (main, Feb 5 2025, 01:31:18) [GCC 14.2.0] 823s Operating system: posix linux 823s ---------------------------------------------------------------------- 823s Ran 219 tests in 183.138 seconds 823s 824s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 824s sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 825s test_Ace ... ok 825s test_Affy ... ok 827s test_AlignIO ... ok 827s test_AlignIO_ClustalIO ... ok 827s test_AlignIO_EmbossIO ... ok 827s test_AlignIO_FastaIO ... ok 827s test_AlignIO_MauveIO ... ok 827s test_AlignIO_PhylipIO ... ok 827s test_AlignIO_convert ... ok 827s test_AlignInfo ... ok 827s test_Align_Alignment ... ok 827s test_Align_a2m ... ok 827s test_Align_bed ... ok 828s test_Align_bigbed ... ok 828s test_Align_bigmaf ... ok 828s test_Align_bigpsl ... ok 828s test_Align_chain ... ok 829s test_Align_clustal ... ok 834s test_Align_codonalign ... ok 834s test_Align_emboss ... ok 834s test_Align_exonerate ... ok 834s test_Align_fasta ... ok 834s test_Align_hhr ... ok 835s test_Align_maf ... ok 835s test_Align_mauve ... ok 835s test_Align_msf ... ok 835s test_Align_nexus ... ok 835s test_Align_phylip ... ok 835s test_Align_psl ... ok 836s test_Align_sam ... ok 837s test_Align_stockholm ... ok 837s test_Align_tabular ... ok 837s test_Application ... ok 838s test_BWA_tool ... ok 838s test_BioSQL_MySQLdb_online ... skipping. internet not available 838s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 838s test_BioSQL_mysql_connector_online ... skipping. internet not available 838s test_BioSQL_psycopg2_online ... skipping. internet not available 842s test_BioSQL_sqlite3 ... ok 842s test_BioSQL_sqlite3_online ... skipping. internet not available 842s test_Blast_Record ... ok 843s test_Blast_parser ... ok 843s test_CAPS ... ok 843s test_Chi2 ... ok 844s test_ClustalOmega_tool ... ok 845s test_Clustalw_tool ... ok 845s test_Cluster ... ok 845s test_CodonTable ... ok 845s test_ColorSpiral ... ok 845s test_Compass ... ok 846s test_Consensus ... ok 847s test_Dialign_tool ... ok 847s test_EMBL_unittest ... ok 852s test_Emboss ... ok 852s test_EmbossPrimer ... ok 856s test_Entrez ... ok 856s test_Entrez_online ... skipping. internet not available 857s test_Entrez_parser ... ok 857s test_Enzyme ... ok 857s test_ExPASy ... skipping. internet not available 857s test_Fasttree_tool ... ok 857s test_File ... ok 857s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 857s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 857s ok 859s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 861s ok 861s test_GraphicsChromosome ... ok 862s test_GraphicsDistribution ... ok 862s test_GraphicsGeneral ... ok 863s test_HMMCasino ... ok 863s test_HMMGeneral ... ok 863s test_KEGG ... ok 863s test_KEGG_online ... skipping. internet not available 868s test_KGML_graphics ... ok 868s test_KGML_graphics_online ... skipping. internet not available 868s test_KGML_nographics ... ok 869s test_KeyWList ... ok 869s test_LogisticRegression ... ok 869s test_MafIO_index ... ok 871s test_Mafft_tool ... ok 871s test_MarkovModel ... ok 871s test_Medline ... ok 871s test_Muscle_tool ... ok 872s test_NCBIXML ... Exception ignored in: 872s Traceback (most recent call last): 872s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 872s expat_parser.Parse(NULL, True) 872s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 872s ok 874s test_NCBI_BLAST_tools ... ok 874s test_NCBI_qblast ... ok 874s test_NMR ... ok 874s test_NaiveBayes ... ok 874s test_Nexus ... ok 874s test_PAML_baseml ... ok 875s test_PAML_codeml ... ok 875s test_PAML_yn00 ... ok 878s test_PDB_CEAligner ... ok 880s test_PDB_DSSP ... ok 880s test_PDB_Dice ... ok 880s test_PDB_Disordered ... ok 880s test_PDB_Exposure ... ok 880s test_PDB_FragmentMapper ... ok 882s test_PDB_KDTree ... ok 882s test_PDB_MMCIF2Dict ... ok 882s test_PDB_MMCIFIO ... ok 883s test_PDB_MMCIFParser ... ok 883s test_PDB_NACCESS ... ok 884s test_PDB_PDBIO ... ok 884s test_PDB_PDBList ... skipping. internet not available 890s test_PDB_PDBMLParser ... ok 890s test_PDB_PDBParser ... ok 890s 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 890s test_PDB_Polypeptide ... ok 890s test_PDB_QCPSuperimposer ... ok 893s test_PDB_SASA ... ok 894s test_PDB_SMCRA ... ok 894s test_PDB_Selection ... ok 894s test_PDB_StructureAlignment ... ok 894s test_PDB_Superimposer ... ok 894s test_PDB_alphafold_db ... skipping. internet not available 898s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 898s warnings.warn( 898s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 898s warnings.warn( 898s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 898s warnings.warn( 898s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 898s warnings.warn( 898s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 898s warnings.warn( 898s ok 905s test_PDB_internal_coords ... ok 905s test_PDB_parse_pdb_header ... ok 905s test_PDB_vectors ... ok 905s test_PQR ... ok 906s test_Pathway ... ok 906s test_Phd ... ok 906s test_Phylo ... ok 907s test_PhyloXML ... ok 907s test_Phylo_CDAO ... ok 907s test_Phylo_NeXML ... ok 908s test_Phylo_igraph ... ok 910s test_Phylo_matplotlib ... ok 910s test_Phylo_networkx ... ok 911s test_PopGen_GenePop_nodepend ... ok 912s test_Prank_tool ... ok 913s test_Probcons_tool ... ok 913s test_ProtParam ... ok 914s test_RCSBFormats ... ok 915s test_Restriction ... ok 915s test_SCOP_Astral ... ok 915s test_SCOP_Cla ... ok 916s test_SCOP_Des ... ok 916s test_SCOP_Dom ... ok 917s test_SCOP_Hie ... ok 917s test_SCOP_Raf ... ok 917s test_SCOP_Residues ... ok 918s test_SCOP_Scop ... ok 918s test_SVDSuperimposer ... ok 919s test_SearchIO_blast_tab ... ok 919s test_SearchIO_blast_tab_index ... ok 920s test_SearchIO_blast_xml ... ok 921s test_SearchIO_blast_xml_index ... ok 922s test_SearchIO_blat_psl ... ok 922s test_SearchIO_blat_psl_index ... ok 922s test_SearchIO_exonerate ... ok 923s test_SearchIO_exonerate_text_index ... ok 923s test_SearchIO_exonerate_vulgar_index ... ok 924s test_SearchIO_fasta_m10 ... ok 924s test_SearchIO_fasta_m10_index ... ok 925s test_SearchIO_hhsuite2_text ... ok 925s test_SearchIO_hmmer2_text ... ok 926s test_SearchIO_hmmer2_text_index ... ok 926s test_SearchIO_hmmer3_domtab ... ok 927s test_SearchIO_hmmer3_domtab_index ... ok 927s test_SearchIO_hmmer3_tab ... ok 927s test_SearchIO_hmmer3_tab_index ... ok 928s test_SearchIO_hmmer3_text ... ok 928s test_SearchIO_hmmer3_text_index ... ok 929s test_SearchIO_interproscan_xml ... ok 929s test_SearchIO_model ... ok 930s test_SearchIO_write ... ok 930s test_SeqFeature ... ok 946s test_SeqIO ... ok 946s test_SeqIO_AbiIO ... ok 947s test_SeqIO_FastaIO ... ok 947s test_SeqIO_Gck ... ok 948s test_SeqIO_Gfa ... ok 948s test_SeqIO_Insdc ... ok 949s test_SeqIO_NibIO ... ok 951s test_SeqIO_PdbIO ... ok 951s test_SeqIO_QualityIO ... ok 952s test_SeqIO_SeqXML ... ok 952s test_SeqIO_SffIO ... ok 953s test_SeqIO_SnapGene ... ok 954s test_SeqIO_TwoBitIO ... ok 954s test_SeqIO_UniprotIO ... ok 955s test_SeqIO_Xdna ... ok 956s test_SeqIO_features ... ok 969s test_SeqIO_index ... ok 969s test_SeqIO_online ... skipping. internet not available 970s test_SeqIO_write ... ok 970s test_SeqRecord ... ok 970s test_SeqUtils ... ok 972s test_Seq_objs ... ok 972s test_SwissProt ... ok 976s test_TCoffee_tool ... ok 976s test_TogoWS ... skipping. internet not available 977s test_TreeConstruction ... ok 977s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 978s test_UniGene ... ok 978s test_UniProt ... skipping. internet not available 978s test_UniProt_GOA ... ok 979s test_align ... ok 980s test_align_substitution_matrices ... ok 982s test_bgzf ... ok 983s test_cellosaurus ... ok 989s test_codonalign ... ok 989s test_geo ... ok 989s test_kNN ... ok 990s test_motifs ... ok 990s test_motifs_online ... skipping. internet not available 991s 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. 991s warnings.warn( 991s ok 991s test_pairwise2_no_C ... ok 992s test_pairwise_aligner ... ok 993s test_pairwise_alignment_map ... ok 1000s test_phenotype ... ok 1000s test_phenotype_fit ... ok 1000s test_phyml_tool ... ok 1001s test_prodoc ... ok 1001s test_prosite ... ok 1002s test_raxml_tool ... ok 1002s test_samtools_tool ... ok 1003s test_seq ... ok 1003s test_translate ... ok 1003s Skipping any tests requiring internet access 1003s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 1003s Operating system: posix linux 1003s ---------------------------------------------------------------------- 1003s Ran 219 tests in 178.901 seconds 1003s 1004s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1004s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1005s autopkgtest [12:23:24]: test full_suite: -----------------------] 1005s full_suite PASS 1005s autopkgtest [12:23:24]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1006s autopkgtest [12:23:25]: @@@@@@@@@@@@@@@@@@@@ summary 1006s dependencies PASS 1006s full_suite PASS 1017s nova [W] Skipping flock for amd64 1017s Creating nova instance adt-plucky-amd64-python-biopython-20250219-120639-juju-7f2275-prod-proposed-migration-environment-2-03bec523-5594-4cf5-a412-f57e47509b8b from image adt/ubuntu-plucky-amd64-server-20250218.img (UUID 0c5f6311-785d-4524-a0d8-db541aaf5c09)... 1017s nova [W] Timed out waiting for 604e6e08-4195-4f90-b1cc-b1de403db504 to get deleted. 1017s nova [W] Skipping flock for amd64 1017s Creating nova instance adt-plucky-amd64-python-biopython-20250219-120639-juju-7f2275-prod-proposed-migration-environment-2-03bec523-5594-4cf5-a412-f57e47509b8b from image adt/ubuntu-plucky-amd64-server-20250218.img (UUID 0c5f6311-785d-4524-a0d8-db541aaf5c09)... 1017s nova [W] Timed out waiting for 3e12a576-a476-4c1b-8bb7-fdc6619f8830 to get deleted.