0s autopkgtest [06:23:13]: starting date and time: 2025-05-04 06:23:13+0000 0s autopkgtest [06:23:13]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [06:23:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wwqzydhw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx,src:roman-numerals --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=sphinx/8.2.3-1 roman-numerals/3.1.0-1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-1.secgroup --name adt-questing-amd64-python-biopython-20250504-062313-juju-7f2275-prod-proposed-migration-environment-2-0a6eb235-ebf9-418a-a01b-5a6c8a50344e --image adt/ubuntu-questing-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 68s autopkgtest [06:24:21]: testbed dpkg architecture: amd64 68s autopkgtest [06:24:21]: testbed apt version: 3.0.0 69s autopkgtest [06:24:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 69s autopkgtest [06:24:22]: testbed release detected to be: None 70s autopkgtest [06:24:23]: updating testbed package index (apt update) 70s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 70s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 71s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1298 kB] 71s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [134 kB] 71s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [32.6 kB] 71s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [135 kB] 71s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [188 kB] 71s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [529 kB] 71s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1363 kB] 71s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [50.7 kB] 71s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [26.5 kB] 71s Fetched 3867 kB in 1s (3565 kB/s) 72s Reading package lists... 73s autopkgtest [06:24:26]: upgrading testbed (apt dist-upgrade and autopurge) 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 74s Starting 2 pkgProblemResolver with broken count: 0 74s Done 74s Entering ResolveByKeep 74s 74s Calculating upgrade... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 76s Starting pkgProblemResolver with broken count: 0 76s Starting 2 pkgProblemResolver with broken count: 0 76s Done 76s Solving dependencies... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s autopkgtest [06:24:32]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 15:05:05 UTC 2025 79s autopkgtest [06:24:32]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 82s Get:1 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (dsc) [3406 B] 82s Get:2 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (tar) [14.6 MB] 82s Get:3 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (diff) [42.8 kB] 82s gpgv: Signature made Tue Mar 4 15:18:59 2025 UTC 82s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 82s gpgv: Can't check signature: No public key 82s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2build1.dsc: no acceptable signature found 83s autopkgtest [06:24:36]: testing package python-biopython version 1.85+dfsg-2build1 84s autopkgtest [06:24:37]: build not needed 92s autopkgtest [06:24:45]: test dependencies: preparing testbed 92s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Starting pkgProblemResolver with broken count: 0 93s Starting 2 pkgProblemResolver with broken count: 0 93s Done 94s The following NEW packages will be installed: 94s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 94s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 94s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 94s libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 94s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 94s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 94s python-biopython-doc python3-all python3-biopython python3-biopython-sql 94s python3-cairo python3-freetype python3-numpy python3-numpy-dev python3-pil 94s python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib x11-common 94s xfonts-encodings xfonts-utils xml-core 94s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 49.8 MB of archives. 94s After this operation, 138 MB of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 94s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 94s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran5 amd64 15-20250404-0ubuntu1 [926 kB] 94s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 94s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 95s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 sgml-base all 1.31 [11.4 kB] 95s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 95s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 95s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 95s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 95s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 95s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 95s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 95s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig-config amd64 2.15.0-2.2ubuntu1 [37.8 kB] 95s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libfontconfig1 amd64 2.15.0-2.2ubuntu1 [164 kB] 95s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 95s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 95s Get:18 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 95s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 95s Get:20 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 95s Get:21 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 95s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 95s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 95s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 95s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 95s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 95s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 95s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 95s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 95s Get:30 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 libjs-sphinxdoc all 8.2.3-1 [27.8 kB] 95s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 95s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 95s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 95s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 95s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 95s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 95s Get:37 http://ftpmaster.internal/ubuntu questing/main amd64 libtiff6 amd64 4.7.0-3ubuntu1 [204 kB] 95s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 95s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 95s Get:40 http://ftpmaster.internal/ubuntu questing/universe amd64 python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 96s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 python3-all amd64 3.13.3-1 [882 B] 96s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 96s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 96s Get:44 http://ftpmaster.internal/ubuntu questing/main amd64 python3-cairo amd64 1.27.0-2 [124 kB] 96s Get:45 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 96s Get:46 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 96s Get:47 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-reportlab all 4.3.1-1 [1137 kB] 96s Get:48 http://ftpmaster.internal/ubuntu questing/main amd64 xml-core all 0.19 [20.3 kB] 96s Get:49 http://ftpmaster.internal/ubuntu questing/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 96s Get:50 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-biopython amd64 1.85+dfsg-2build1 [1739 kB] 96s Get:51 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 96s Fetched 49.8 MB in 2s (22.9 MB/s) 96s Selecting previously unselected package python3-numpy-dev:amd64. 97s (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 ... 80517 files and directories currently installed.) 97s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 97s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 97s Selecting previously unselected package libblas3:amd64. 97s Preparing to unpack .../01-libblas3_3.12.1-2_amd64.deb ... 97s Unpacking libblas3:amd64 (3.12.1-2) ... 97s Selecting previously unselected package libgfortran5:amd64. 97s Preparing to unpack .../02-libgfortran5_15-20250404-0ubuntu1_amd64.deb ... 97s Unpacking libgfortran5:amd64 (15-20250404-0ubuntu1) ... 97s Selecting previously unselected package liblapack3:amd64. 97s Preparing to unpack .../03-liblapack3_3.12.1-2_amd64.deb ... 97s Unpacking liblapack3:amd64 (3.12.1-2) ... 97s Selecting previously unselected package python3-numpy. 97s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 97s Unpacking python3-numpy (1:2.2.3+ds-5) ... 97s Selecting previously unselected package sgml-base. 97s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 97s Unpacking sgml-base (1.31) ... 97s Selecting previously unselected package fonts-dejavu-mono. 97s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 97s Unpacking fonts-dejavu-mono (2.37-8) ... 97s Selecting previously unselected package fonts-dejavu-core. 97s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 97s Unpacking fonts-dejavu-core (2.37-8) ... 97s Selecting previously unselected package libfontenc1:amd64. 97s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 97s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 97s Selecting previously unselected package x11-common. 97s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu4_all.deb ... 97s Unpacking x11-common (1:7.7+23ubuntu4) ... 97s Selecting previously unselected package xfonts-encodings. 97s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 97s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 97s Selecting previously unselected package xfonts-utils. 97s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_amd64.deb ... 97s Unpacking xfonts-utils (1:7.7+7) ... 97s Selecting previously unselected package fonts-urw-base35. 97s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 97s Unpacking fonts-urw-base35 (20200910-8) ... 98s Selecting previously unselected package fontconfig-config. 98s Preparing to unpack .../13-fontconfig-config_2.15.0-2.2ubuntu1_amd64.deb ... 98s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 98s Selecting previously unselected package libfontconfig1:amd64. 98s Preparing to unpack .../14-libfontconfig1_2.15.0-2.2ubuntu1_amd64.deb ... 98s Unpacking libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 98s Selecting previously unselected package libpixman-1-0:amd64. 98s Preparing to unpack .../15-libpixman-1-0_0.44.0-3_amd64.deb ... 98s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 98s Selecting previously unselected package libxcb-render0:amd64. 98s Preparing to unpack .../16-libxcb-render0_1.17.0-2_amd64.deb ... 98s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 98s Selecting previously unselected package libxcb-shm0:amd64. 98s Preparing to unpack .../17-libxcb-shm0_1.17.0-2_amd64.deb ... 98s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 98s Selecting previously unselected package libxrender1:amd64. 98s Preparing to unpack .../18-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 98s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 98s Selecting previously unselected package libcairo2:amd64. 98s Preparing to unpack .../19-libcairo2_1.18.4-1_amd64.deb ... 98s Unpacking libcairo2:amd64 (1.18.4-1) ... 98s Selecting previously unselected package libdeflate0:amd64. 98s Preparing to unpack .../20-libdeflate0_1.23-2_amd64.deb ... 98s Unpacking libdeflate0:amd64 (1.23-2) ... 98s Selecting previously unselected package libgomp1:amd64. 98s Preparing to unpack .../21-libgomp1_15-20250404-0ubuntu1_amd64.deb ... 98s Unpacking libgomp1:amd64 (15-20250404-0ubuntu1) ... 98s Selecting previously unselected package libgraphite2-3:amd64. 98s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 98s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 98s Selecting previously unselected package libharfbuzz0b:amd64. 98s Preparing to unpack .../23-libharfbuzz0b_10.2.0-1_amd64.deb ... 98s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 98s Selecting previously unselected package libimagequant0:amd64. 98s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_amd64.deb ... 98s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 98s Selecting previously unselected package libjpeg-turbo8:amd64. 98s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 98s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 98s Selecting previously unselected package libjpeg8:amd64. 98s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_amd64.deb ... 98s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 98s Selecting previously unselected package libjs-jquery. 98s Preparing to unpack .../27-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 98s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 98s Selecting previously unselected package libjs-underscore. 98s Preparing to unpack .../28-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 98s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 98s Selecting previously unselected package libjs-sphinxdoc. 98s Preparing to unpack .../29-libjs-sphinxdoc_8.2.3-1_all.deb ... 98s Unpacking libjs-sphinxdoc (8.2.3-1) ... 98s Selecting previously unselected package liblcms2-2:amd64. 98s Preparing to unpack .../30-liblcms2-2_2.16-2_amd64.deb ... 98s Unpacking liblcms2-2:amd64 (2.16-2) ... 98s Selecting previously unselected package liblerc4:amd64. 98s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 98s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 98s Selecting previously unselected package libraqm0:amd64. 98s Preparing to unpack .../32-libraqm0_0.10.2-1_amd64.deb ... 98s Unpacking libraqm0:amd64 (0.10.2-1) ... 99s Selecting previously unselected package libsharpyuv0:amd64. 99s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1_amd64.deb ... 99s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 99s Selecting previously unselected package libjbig0:amd64. 99s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 99s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 99s Selecting previously unselected package libwebp7:amd64. 99s Preparing to unpack .../35-libwebp7_1.5.0-0.1_amd64.deb ... 99s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 99s Selecting previously unselected package libtiff6:amd64. 99s Preparing to unpack .../36-libtiff6_4.7.0-3ubuntu1_amd64.deb ... 99s Unpacking libtiff6:amd64 (4.7.0-3ubuntu1) ... 99s Selecting previously unselected package libwebpdemux2:amd64. 99s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_amd64.deb ... 99s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 99s Selecting previously unselected package libwebpmux3:amd64. 99s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_amd64.deb ... 99s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 99s Selecting previously unselected package python-biopython-doc. 99s Preparing to unpack .../39-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 99s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 99s Selecting previously unselected package python3-all. 99s Preparing to unpack .../40-python3-all_3.13.3-1_amd64.deb ... 99s Unpacking python3-all (3.13.3-1) ... 99s Selecting previously unselected package libopenjp2-7:amd64. 99s Preparing to unpack .../41-libopenjp2-7_2.5.3-2_amd64.deb ... 99s Unpacking libopenjp2-7:amd64 (2.5.3-2) ... 99s Selecting previously unselected package python3-pil:amd64. 99s Preparing to unpack .../42-python3-pil_11.1.0-5build1_amd64.deb ... 99s Unpacking python3-pil:amd64 (11.1.0-5build1) ... 99s Selecting previously unselected package python3-cairo. 99s Preparing to unpack .../43-python3-cairo_1.27.0-2_amd64.deb ... 99s Unpacking python3-cairo (1.27.0-2) ... 99s Selecting previously unselected package python3-freetype. 99s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 99s Unpacking python3-freetype (2.5.1-1) ... 99s Selecting previously unselected package python3-rlpycairo. 99s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 99s Unpacking python3-rlpycairo (0.3.0-3) ... 99s Selecting previously unselected package python3-reportlab. 99s Preparing to unpack .../46-python3-reportlab_4.3.1-1_all.deb ... 99s Unpacking python3-reportlab (4.3.1-1) ... 99s Selecting previously unselected package xml-core. 99s Preparing to unpack .../47-xml-core_0.19_all.deb ... 99s Unpacking xml-core (0.19) ... 99s Selecting previously unselected package w3c-sgml-lib. 99s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 99s Unpacking w3c-sgml-lib (1.3-3) ... 99s Selecting previously unselected package python3-biopython. 99s Preparing to unpack .../49-python3-biopython_1.85+dfsg-2build1_amd64.deb ... 99s Unpacking python3-biopython (1.85+dfsg-2build1) ... 100s Selecting previously unselected package python3-biopython-sql. 100s Preparing to unpack .../50-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 100s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 100s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 100s Setting up liblcms2-2:amd64 (2.16-2) ... 100s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 100s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 100s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 100s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 100s Setting up libxcb-render0:amd64 (1.17.0-2) ... 100s Setting up x11-common (1:7.7+23ubuntu4) ... 100s Setting up libdeflate0:amd64 (1.23-2) ... 100s Setting up python3-all (3.13.3-1) ... 100s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 100s Setting up libgomp1:amd64 (15-20250404-0ubuntu1) ... 100s Setting up python3-freetype (2.5.1-1) ... 100s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 100s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 100s Setting up libblas3:amd64 (3.12.1-2) ... 100s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 100s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 100s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 100s Setting up fonts-dejavu-mono (2.37-8) ... 100s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 100s Setting up fonts-dejavu-core (2.37-8) ... 100s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 100s Setting up libgfortran5:amd64 (15-20250404-0ubuntu1) ... 100s Setting up libwebp7:amd64 (1.5.0-0.1) ... 100s Setting up libopenjp2-7:amd64 (2.5.3-2) ... 100s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 100s Setting up sgml-base (1.31) ... 100s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 100s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 100s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 100s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 100s Setting up liblapack3:amd64 (3.12.1-2) ... 100s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 100s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 101s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 101s Setting up xfonts-utils (1:7.7+7) ... 101s Setting up libraqm0:amd64 (0.10.2-1) ... 101s Setting up python3-numpy (1:2.2.3+ds-5) ... 102s Setting up libjs-sphinxdoc (8.2.3-1) ... 102s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 102s Setting up libtiff6:amd64 (4.7.0-3ubuntu1) ... 102s Setting up xml-core (0.19) ... 102s Setting up libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 102s Setting up fonts-urw-base35 (20200910-8) ... 103s Setting up libcairo2:amd64 (1.18.4-1) ... 103s Setting up python3-pil:amd64 (11.1.0-5build1) ... 103s Setting up python3-cairo (1.27.0-2) ... 103s Setting up python3-rlpycairo (0.3.0-3) ... 103s Setting up python3-reportlab (4.3.1-1) ... 104s Processing triggers for libc-bin (2.41-6ubuntu1) ... 104s Processing triggers for man-db (2.13.0-1) ... 105s Processing triggers for sgml-base (1.31) ... 105s Setting up w3c-sgml-lib (1.3-3) ... 133s Setting up python3-biopython (1.85+dfsg-2build1) ... 134s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 136s autopkgtest [06:25:29]: test dependencies: sh debian/tests/run-unit-test 136s autopkgtest [06:25:29]: test dependencies: [----------------------- 136s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 136s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 138s mkdir: created directory 'Bio' 138s mkdir: created directory 'Bio/Align' 138s mkdir: created directory 'Bio/Align/substitution_matrices' 138s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 138s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 139s test_Ace ... ok 139s test_Affy ... ok 141s test_AlignIO ... ok 141s test_AlignIO_ClustalIO ... ok 141s test_AlignIO_EmbossIO ... ok 141s test_AlignIO_FastaIO ... ok 141s test_AlignIO_MauveIO ... ok 141s test_AlignIO_PhylipIO ... ok 141s test_AlignIO_convert ... ok 141s test_AlignInfo ... ok 142s test_Align_Alignment ... ok 142s test_Align_a2m ... ok 142s test_Align_bed ... ok 142s test_Align_bigbed ... ok 142s test_Align_bigmaf ... ok 143s test_Align_bigpsl ... ok 143s test_Align_chain ... ok 143s test_Align_clustal ... ok 146s test_Align_codonalign ... ok 146s test_Align_emboss ... ok 146s test_Align_exonerate ... ok 146s test_Align_fasta ... ok 146s test_Align_hhr ... ok 147s test_Align_maf ... ok 147s test_Align_mauve ... ok 147s test_Align_msf ... ok 147s test_Align_nexus ... ok 147s test_Align_phylip ... ok 147s test_Align_psl ... ok 148s test_Align_sam ... ok 149s test_Align_stockholm ... ok 149s test_Align_tabular ... ok 149s test_Application ... ok 149s test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython 149s test_BioSQL_MySQLdb_online ... skipping. internet not available 149s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 149s test_BioSQL_mysql_connector_online ... skipping. internet not available 149s test_BioSQL_psycopg2_online ... skipping. internet not available 154s test_BioSQL_sqlite3 ... ok 154s test_BioSQL_sqlite3_online ... skipping. internet not available 154s test_Blast_Record ... ok 154s test_Blast_parser ... ok 155s test_CAPS ... ok 155s test_Chi2 ... ok 155s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 155s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 155s test_Cluster ... ok 155s test_CodonTable ... ok 155s test_ColorSpiral ... ok 155s test_Compass ... ok 156s test_Consensus ... ok 156s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 156s test_EMBL_unittest ... ok 156s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 156s test_EmbossPrimer ... ok 160s test_Entrez ... ok 160s test_Entrez_online ... skipping. internet not available 160s test_Entrez_parser ... ok 160s test_Enzyme ... ok 161s test_ExPASy ... skipping. internet not available 161s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 161s test_File ... ok 161s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 161s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 161s ok 163s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 165s ok 165s test_GraphicsChromosome ... ok 165s test_GraphicsDistribution ... ok 166s test_GraphicsGeneral ... ok 166s test_HMMCasino ... ok 166s test_HMMGeneral ... ok 167s test_KEGG ... ok 167s test_KEGG_online ... skipping. internet not available 172s test_KGML_graphics ... ok 172s test_KGML_graphics_online ... skipping. internet not available 173s test_KGML_nographics ... ok 173s test_KeyWList ... ok 173s test_LogisticRegression ... ok 174s test_MafIO_index ... ok 174s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 174s test_MarkovModel ... ok 174s test_Medline ... ok 174s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 174s test_NCBIXML ... Exception ignored in: 174s Traceback (most recent call last): 174s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 174s expat_parser.Parse(NULL, True) 174s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 174s ok 174s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 174s test_NCBI_qblast ... ok 175s test_NMR ... ok 175s test_NaiveBayes ... ok 175s test_Nexus ... ok 175s test_PAML_baseml ... ok 175s test_PAML_codeml ... ok 176s test_PAML_yn00 ... ok 179s test_PDB_CEAligner ... ok 179s test_PDB_DSSP ... ok 179s test_PDB_Dice ... ok 179s test_PDB_Disordered ... ok 180s test_PDB_Exposure ... ok 180s test_PDB_FragmentMapper ... ok 181s test_PDB_KDTree ... ok 181s test_PDB_MMCIF2Dict ... ok 181s test_PDB_MMCIFIO ... ok 182s test_PDB_MMCIFParser ... ok 182s test_PDB_NACCESS ... ok 182s test_PDB_PDBIO ... ok 183s test_PDB_PDBList ... skipping. internet not available 188s test_PDB_PDBMLParser ... ok 188s test_PDB_PDBParser ... ok 188s 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 189s test_PDB_Polypeptide ... ok 189s test_PDB_QCPSuperimposer ... ok 192s test_PDB_SASA ... ok 192s test_PDB_SMCRA ... ok 192s test_PDB_Selection ... ok 192s test_PDB_StructureAlignment ... ok 193s test_PDB_Superimposer ... ok 193s test_PDB_alphafold_db ... skipping. internet not available 193s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 193s 193s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 193s 193s test_PDB_parse_pdb_header ... ok 193s test_PDB_vectors ... ok 193s test_PQR ... ok 193s test_Pathway ... ok 193s test_Phd ... ok 193s test_Phylo ... ok 194s test_PhyloXML ... ok 194s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 194s test_Phylo_NeXML ... ok 194s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 194s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 194s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 194s test_PopGen_GenePop_nodepend ... ok 194s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 194s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 194s test_ProtParam ... ok 194s test_RCSBFormats ... ok 195s test_Restriction ... ok 195s test_SCOP_Astral ... ok 195s test_SCOP_Cla ... ok 195s test_SCOP_Des ... ok 195s test_SCOP_Dom ... ok 195s test_SCOP_Hie ... ok 195s test_SCOP_Raf ... ok 195s test_SCOP_Residues ... ok 195s test_SCOP_Scop ... ok 195s test_SVDSuperimposer ... ok 195s test_SearchIO_blast_tab ... ok 195s test_SearchIO_blast_tab_index ... ok 195s test_SearchIO_blast_xml ... ok 196s test_SearchIO_blast_xml_index ... ok 197s test_SearchIO_blat_psl ... ok 197s test_SearchIO_blat_psl_index ... ok 197s test_SearchIO_exonerate ... ok 197s test_SearchIO_exonerate_text_index ... ok 197s test_SearchIO_exonerate_vulgar_index ... ok 197s test_SearchIO_fasta_m10 ... ok 197s test_SearchIO_fasta_m10_index ... ok 197s test_SearchIO_hhsuite2_text ... ok 197s test_SearchIO_hmmer2_text ... ok 197s test_SearchIO_hmmer2_text_index ... ok 197s test_SearchIO_hmmer3_domtab ... ok 198s test_SearchIO_hmmer3_domtab_index ... ok 198s test_SearchIO_hmmer3_tab ... ok 198s test_SearchIO_hmmer3_tab_index ... ok 198s test_SearchIO_hmmer3_text ... ok 198s test_SearchIO_hmmer3_text_index ... ok 198s test_SearchIO_interproscan_xml ... ok 198s test_SearchIO_model ... ok 198s test_SearchIO_write ... ok 198s test_SeqFeature ... ok 214s test_SeqIO ... ok 214s test_SeqIO_AbiIO ... ok 214s test_SeqIO_FastaIO ... ok 214s test_SeqIO_Gck ... ok 214s test_SeqIO_Gfa ... ok 214s test_SeqIO_Insdc ... ok 214s test_SeqIO_NibIO ... ok 216s test_SeqIO_PdbIO ... ok 216s test_SeqIO_QualityIO ... ok 217s test_SeqIO_SeqXML ... ok 217s test_SeqIO_SffIO ... ok 217s test_SeqIO_SnapGene ... ok 218s test_SeqIO_TwoBitIO ... ok 218s test_SeqIO_UniprotIO ... ok 218s test_SeqIO_Xdna ... ok 218s test_SeqIO_features ... ok 233s test_SeqIO_index ... ok 233s test_SeqIO_online ... skipping. internet not available 233s test_SeqIO_write ... ok 233s test_SeqRecord ... ok 233s test_SeqUtils ... ok 234s test_Seq_objs ... ok 234s test_SwissProt ... ok 234s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 234s test_TogoWS ... skipping. internet not available 235s test_TreeConstruction ... ok 235s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 235s test_UniGene ... ok 235s test_UniProt ... skipping. internet not available 235s test_UniProt_GOA ... ok 235s test_align ... ok 235s test_align_substitution_matrices ... ok 238s test_bgzf ... ok 238s test_cellosaurus ... ok 242s test_codonalign ... ok 242s test_geo ... ok 242s test_kNN ... ok 243s test_motifs ... ok 243s test_motifs_online ... skipping. internet not available 243s 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. 243s warnings.warn( 243s ok 243s test_pairwise2_no_C ... ok 243s test_pairwise_aligner ... ok 243s test_pairwise_alignment_map ... ok 250s test_phenotype ... ok 250s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 250s test_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. 250s test_prodoc ... ok 250s test_prosite ... ok 250s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 250s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 251s test_seq ... ok 251s test_translate ... ok 251s ---------------------------------------------------------------------- 251s Ran 219 tests in 112.038 seconds 251s 251s Skipping any tests requiring internet access 251s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 251s Operating system: posix linux 251s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 251s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 251s autopkgtest [06:27:24]: test dependencies: -----------------------] 252s autopkgtest [06:27:25]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 252s dependencies PASS 252s autopkgtest [06:27:25]: test full_suite: preparing testbed 339s autopkgtest [06:28:52]: testbed dpkg architecture: amd64 339s autopkgtest [06:28:52]: testbed apt version: 3.0.0 340s autopkgtest [06:28:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 340s autopkgtest [06:28:53]: testbed release detected to be: questing 341s autopkgtest [06:28:54]: updating testbed package index (apt update) 341s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 341s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 342s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 342s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 342s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1298 kB] 342s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [32.6 kB] 342s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [134 kB] 342s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [135 kB] 342s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [188 kB] 342s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1363 kB] 342s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [529 kB] 342s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [50.7 kB] 342s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [26.5 kB] 342s Fetched 3867 kB in 1s (3483 kB/s) 343s Reading package lists... 344s autopkgtest [06:28:57]: upgrading testbed (apt dist-upgrade and autopurge) 344s Reading package lists... 344s Building dependency tree... 344s Reading state information... 344s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 344s Starting 2 pkgProblemResolver with broken count: 0 344s Done 345s Entering ResolveByKeep 345s 345s Calculating upgrade... 345s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 346s Reading package lists... 346s Building dependency tree... 346s Reading state information... 346s Starting pkgProblemResolver with broken count: 0 346s Starting 2 pkgProblemResolver with broken count: 0 346s Done 347s Solving dependencies... 347s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 350s Reading package lists... 350s Building dependency tree... 350s Reading state information... 351s Starting pkgProblemResolver with broken count: 0 351s Starting 2 pkgProblemResolver with broken count: 0 351s Done 351s The following NEW packages will be installed: 351s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 351s clustalw cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper 351s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 351s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 351s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 351s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 351s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 351s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext ghostscript hevea 351s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 351s intltool-debian libamd-comgr2 libamd3 libamdhip64-5 libaom3 351s libapache-pom-java libarchive-zip-perl libargtable2-0 libarpack2t64 libasan8 351s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libcairo2 351s libcc1-0 libcifpp-data libcifpp7 libcolamd3 libcommons-logging-java 351s libcommons-parent-java libcups2t64 libde265-0 libdebhelper-perl libdeflate0 351s libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfftw3-double3 351s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 351s libgcc-14-dev libgd3 libgfortran5 libglpk40 libgomp1 libgraphite2-3 351s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 351s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhsakmt1 351s libhts3t64 libhtscodecs2 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 351s libibumad3 libice6 libidn12 libigraph3t64 libijs-0.35 libimagequant0 351s libisl23 libitm1 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery 351s libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 351s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblqr-1-0 liblsan0 351s libltdl7 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 351s libmbedtls21 libmbedx509-7 libmpc3 libmpfi0 libmunge2 libmysqlclient24 351s libnetpbm11t64 libopenjp2-7 libopenmpi40 libpaper-utils libpaper2 351s libpciaccess0 libpdfbox-java libpixman-1-0 libplfit0 libpmix2t64 libpotrace0 351s libpq5 libpsm-infinipath1 libpsm2-2 libptexenc1 libpython3-all-dev 351s libpython3-dev libpython3.13-dev libqhull-r8.0 libquadmath0 libraqm0 351s libraw23t64 librdmacm1t64 libsharpyuv0 libsm6 libstdc++-14-dev 351s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 351s libtiff6 libtk8.6 libtool libtsan2 libubsan1 libucx0 libwebp7 libwebpdemux2 351s libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 351s libxnvctrl0 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 351s m4 mafft mpi-default-bin muscle3 mysql-common ncbi-blast+ ncbi-data netpbm 351s ocl-icd-libopencl1 openmpi-bin openmpi-common phylip phyml po-debconf 351s poppler-data prank preview-latex-style probcons python-biopython-doc 351s python-matplotlib-data python3-alabaster python3-all python3-all-dev 351s python3-biopython python3-biopython-sql python3-brotli python3-cairo 351s python3-contourpy python3-cycler python3-decorator python3-defusedxml 351s python3-dev python3-docutils python3-fonttools python3-freetype python3-fs 351s python3-igraph python3-imagesize python3-kiwisolver python3-lxml python3-lz4 351s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 351s python3-mysqldb python3-networkx python3-numpy python3-numpy-dev 351s python3-numpydoc python3-pil python3-pil.imagetk python3-platformdirs 351s python3-psycopg2 python3-rdflib python3-reportlab python3-rlpycairo 351s python3-roman python3-roman-numerals python3-scipy python3-snowballstemmer 351s python3-sphinx python3-sphinx-rtd-theme python3-sphinxcontrib.jquery 351s python3-sympy python3-tabulate python3-texttable python3-tk python3-ufolib2 351s python3.13-dev python3.13-tk raxml samtools sgml-base sphinx-common 351s sphinx-rtd-theme-common t-coffee t1utils tex-common texlive-base 351s texlive-binaries texlive-fonts-recommended texlive-latex-base 351s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 351s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 351s xfonts-encodings xfonts-utils xml-core zlib1g-dev 351s 0 upgraded, 290 newly installed, 0 to remove and 0 not upgraded. 351s Need to get 486 MB of archives. 351s After this operation, 2072 MB of additional disk space will be used. 351s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 m4 amd64 1.4.19-7 [263 kB] 352s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 flex amd64 2.6.4-8.2build1 [301 kB] 352s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-lato all 2.015-1 [2781 kB] 352s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 352s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 libfftw3-double3 amd64 3.3.10-2fakesync1build1 [839 kB] 352s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 352s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 352s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 352s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 352s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 352s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 352s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 352s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig-config amd64 2.15.0-2.2ubuntu1 [37.8 kB] 352s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libfontconfig1 amd64 2.15.0-2.2ubuntu1 [164 kB] 352s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 352s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 libaom3 amd64 3.12.1-1 [1944 kB] 352s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 libheif-plugin-aomdec amd64 1.19.7-1 [11.6 kB] 352s Get:18 http://ftpmaster.internal/ubuntu questing/main amd64 libde265-0 amd64 1.0.15-1build5 [285 kB] 352s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 libheif-plugin-libde265 amd64 1.19.7-1 [9060 B] 352s Get:20 http://ftpmaster.internal/ubuntu questing/main amd64 libheif1 amd64 1.19.7-1 [428 kB] 352s Get:21 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 352s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 352s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 352s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 352s Get:25 http://ftpmaster.internal/ubuntu questing/universe amd64 liblqr-1-0 amd64 0.4.2-2.1build2 [28.5 kB] 352s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 libltdl7 amd64 2.5.4-4 [46.5 kB] 352s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 352s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 libraw23t64 amd64 0.21.4-2 [376 kB] 352s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 352s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 353s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 353s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 libtiff6 amd64 4.7.0-3ubuntu1 [204 kB] 353s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 353s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 353s Get:35 http://ftpmaster.internal/ubuntu questing/universe amd64 imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 353s Get:36 http://ftpmaster.internal/ubuntu questing/universe amd64 libmagickcore-7.q16-10 amd64 8:7.1.1.43+dfsg1-1 [2306 kB] 353s Get:37 http://ftpmaster.internal/ubuntu questing/universe amd64 libmagickwand-7.q16-10 amd64 8:7.1.1.43+dfsg1-1 [347 kB] 353s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 poppler-data all 0.4.12-1 [2060 kB] 353s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 353s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 353s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran5 amd64 15-20250404-0ubuntu1 [926 kB] 353s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 353s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 353s Get:44 http://ftpmaster.internal/ubuntu questing/main amd64 sgml-base all 1.31 [11.4 kB] 353s Get:45 http://ftpmaster.internal/ubuntu questing/main amd64 autoconf all 2.72-3ubuntu1 [383 kB] 353s Get:46 http://ftpmaster.internal/ubuntu questing/main amd64 autotools-dev all 20240727.1 [43.4 kB] 353s Get:47 http://ftpmaster.internal/ubuntu questing/main amd64 automake all 1:1.17-3ubuntu1 [572 kB] 353s Get:48 http://ftpmaster.internal/ubuntu questing/main amd64 autopoint all 0.23.1-1 [619 kB] 353s Get:49 http://ftpmaster.internal/ubuntu questing/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 353s Get:50 http://ftpmaster.internal/ubuntu questing/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 353s Get:51 http://ftpmaster.internal/ubuntu questing/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 353s Get:52 http://ftpmaster.internal/ubuntu questing/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 353s Get:53 http://ftpmaster.internal/ubuntu questing/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 353s Get:54 http://ftpmaster.internal/ubuntu questing/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 353s Get:55 http://ftpmaster.internal/ubuntu questing/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 353s Get:56 http://ftpmaster.internal/ubuntu questing/main amd64 libisl23 amd64 0.27-1 [685 kB] 353s Get:57 http://ftpmaster.internal/ubuntu questing/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 353s Get:58 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [11.9 MB] 353s Get:59 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-14 amd64 14.2.0-19ubuntu2 [1030 B] 353s Get:60 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 353s Get:61 http://ftpmaster.internal/ubuntu questing/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 353s Get:62 http://ftpmaster.internal/ubuntu questing/main amd64 libcc1-0 amd64 15-20250404-0ubuntu1 [47.1 kB] 353s Get:63 http://ftpmaster.internal/ubuntu questing/main amd64 libitm1 amd64 15-20250404-0ubuntu1 [29.5 kB] 353s Get:64 http://ftpmaster.internal/ubuntu questing/main amd64 libasan8 amd64 15-20250404-0ubuntu1 [3076 kB] 353s Get:65 http://ftpmaster.internal/ubuntu questing/main amd64 liblsan0 amd64 15-20250404-0ubuntu1 [1362 kB] 353s Get:66 http://ftpmaster.internal/ubuntu questing/main amd64 libtsan2 amd64 15-20250404-0ubuntu1 [2760 kB] 354s Get:67 http://ftpmaster.internal/ubuntu questing/main amd64 libubsan1 amd64 15-20250404-0ubuntu1 [1211 kB] 354s Get:68 http://ftpmaster.internal/ubuntu questing/main amd64 libhwasan0 amd64 15-20250404-0ubuntu1 [1687 kB] 354s Get:69 http://ftpmaster.internal/ubuntu questing/main amd64 libquadmath0 amd64 15-20250404-0ubuntu1 [153 kB] 354s Get:70 http://ftpmaster.internal/ubuntu questing/main amd64 libgcc-14-dev amd64 14.2.0-19ubuntu2 [2815 kB] 354s Get:71 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [23.3 MB] 354s Get:72 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-14 amd64 14.2.0-19ubuntu2 [540 kB] 354s Get:73 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 354s Get:74 http://ftpmaster.internal/ubuntu questing/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 354s Get:75 http://ftpmaster.internal/ubuntu questing/main amd64 libstdc++-14-dev amd64 14.2.0-19ubuntu2 [2510 kB] 354s Get:76 http://ftpmaster.internal/ubuntu questing/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [13.4 MB] 355s Get:77 http://ftpmaster.internal/ubuntu questing/main amd64 g++-14 amd64 14.2.0-19ubuntu2 [23.0 kB] 355s Get:78 http://ftpmaster.internal/ubuntu questing/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 355s Get:79 http://ftpmaster.internal/ubuntu questing/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 355s Get:80 http://ftpmaster.internal/ubuntu questing/main amd64 build-essential amd64 12.12ubuntu1 [5080 B] 355s Get:81 http://ftpmaster.internal/ubuntu questing/universe amd64 bwa amd64 0.7.18-1 [204 kB] 355s Get:82 http://ftpmaster.internal/ubuntu questing/universe amd64 libargtable2-0 amd64 13-3 [16.3 kB] 355s Get:83 http://ftpmaster.internal/ubuntu questing/universe amd64 clustalo amd64 1.2.4-8build1 [202 kB] 355s Get:84 http://ftpmaster.internal/ubuntu questing/universe amd64 clustalw amd64 2.1+lgpl-7 [275 kB] 355s Get:85 http://ftpmaster.internal/ubuntu questing/main amd64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 355s Get:86 http://ftpmaster.internal/ubuntu questing/main amd64 libtool all 2.5.4-4 [168 kB] 355s Get:87 http://ftpmaster.internal/ubuntu questing/main amd64 dh-autoreconf all 20 [16.1 kB] 355s Get:88 http://ftpmaster.internal/ubuntu questing/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 355s Get:89 http://ftpmaster.internal/ubuntu questing/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 355s Get:90 http://ftpmaster.internal/ubuntu questing/main amd64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 355s Get:91 http://ftpmaster.internal/ubuntu questing/main amd64 debugedit amd64 1:5.1-2 [47.0 kB] 355s Get:92 http://ftpmaster.internal/ubuntu questing/main amd64 dwz amd64 0.15-1build6 [115 kB] 355s Get:93 http://ftpmaster.internal/ubuntu questing/main amd64 gettext amd64 0.23.1-1 [1086 kB] 355s Get:94 http://ftpmaster.internal/ubuntu questing/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 355s Get:95 http://ftpmaster.internal/ubuntu questing/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 355s Get:96 http://ftpmaster.internal/ubuntu questing/main amd64 debhelper all 13.24.1ubuntu2 [895 kB] 355s Get:97 http://ftpmaster.internal/ubuntu questing/universe amd64 dh-python all 6.20250308 [118 kB] 355s Get:98 http://ftpmaster.internal/ubuntu questing/universe amd64 dialign amd64 2.2.1-13 [154 kB] 355s Get:99 http://ftpmaster.internal/ubuntu questing/main amd64 xml-core all 0.19 [20.3 kB] 355s Get:100 http://ftpmaster.internal/ubuntu questing/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 355s Get:101 http://ftpmaster.internal/ubuntu questing/universe amd64 libcifpp-data all 7.0.9-1 [481 kB] 355s Get:102 http://ftpmaster.internal/ubuntu questing/universe amd64 libcifpp7 amd64 7.0.9-1 [1144 kB] 355s Get:103 http://ftpmaster.internal/ubuntu questing/universe amd64 dssp amd64 4.4.10-1 [786 kB] 355s Get:104 http://ftpmaster.internal/ubuntu questing/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 355s Get:105 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 355s Get:106 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 355s Get:107 http://ftpmaster.internal/ubuntu questing/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 355s Get:108 http://ftpmaster.internal/ubuntu questing/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB] 355s Get:109 http://ftpmaster.internal/ubuntu questing/main amd64 libgd3 amd64 2.3.3-12ubuntu3 [127 kB] 355s Get:110 http://ftpmaster.internal/ubuntu questing/universe amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1build3 [432 kB] 355s Get:111 http://ftpmaster.internal/ubuntu questing/main amd64 mysql-common all 5.8+1.1.1ubuntu1 [6922 B] 355s Get:112 http://ftpmaster.internal/ubuntu questing/main amd64 libmysqlclient24 amd64 8.4.4-0ubuntu2 [1257 kB] 356s Get:113 http://ftpmaster.internal/ubuntu questing/main amd64 libpq5 amd64 17.4-1 [155 kB] 356s Get:114 http://ftpmaster.internal/ubuntu questing/universe amd64 emboss-lib amd64 6.6.0+dfsg-15ubuntu2 [3277 kB] 356s Get:115 http://ftpmaster.internal/ubuntu questing/universe amd64 emboss-data all 6.6.0+dfsg-15ubuntu2 [61.0 MB] 358s Get:116 http://ftpmaster.internal/ubuntu questing/universe amd64 emboss amd64 6.6.0+dfsg-15ubuntu2 [1014 kB] 358s Get:117 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 358s Get:118 http://ftpmaster.internal/ubuntu questing/universe amd64 fonts-lmodern all 2.005-1 [4799 kB] 358s Get:119 http://ftpmaster.internal/ubuntu questing/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 358s Get:120 http://ftpmaster.internal/ubuntu questing/main amd64 libgs-common all 10.05.0dfsg1-0ubuntu1 [176 kB] 358s Get:121 http://ftpmaster.internal/ubuntu questing/main amd64 libgs10-common all 10.05.0dfsg1-0ubuntu1 [490 kB] 358s Get:122 http://ftpmaster.internal/ubuntu questing/main amd64 libavahi-common-data amd64 0.8-16ubuntu2 [31.0 kB] 358s Get:123 http://ftpmaster.internal/ubuntu questing/main amd64 libavahi-common3 amd64 0.8-16ubuntu2 [23.6 kB] 358s Get:124 http://ftpmaster.internal/ubuntu questing/main amd64 libavahi-client3 amd64 0.8-16ubuntu2 [27.5 kB] 358s Get:125 http://ftpmaster.internal/ubuntu questing/main amd64 libcups2t64 amd64 2.4.12-0ubuntu1 [292 kB] 358s Get:126 http://ftpmaster.internal/ubuntu questing/main amd64 libidn12 amd64 1.43-1 [60.4 kB] 358s Get:127 http://ftpmaster.internal/ubuntu questing/main amd64 libijs-0.35 amd64 0.35-15.2 [15.4 kB] 358s Get:128 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig2dec0 amd64 0.20-1build3 [65.0 kB] 358s Get:129 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 358s Get:130 http://ftpmaster.internal/ubuntu questing/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 358s Get:131 http://ftpmaster.internal/ubuntu questing/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 358s Get:132 http://ftpmaster.internal/ubuntu questing/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 358s Get:133 http://ftpmaster.internal/ubuntu questing/main amd64 libgs10 amd64 10.05.0dfsg1-0ubuntu1 [4615 kB] 359s Get:134 http://ftpmaster.internal/ubuntu questing/main amd64 ghostscript amd64 10.05.0dfsg1-0ubuntu1 [42.8 kB] 359s Get:135 http://ftpmaster.internal/ubuntu questing/universe amd64 libnetpbm11t64 amd64 2:11.09.02-2 [125 kB] 359s Get:136 http://ftpmaster.internal/ubuntu questing/universe amd64 netpbm amd64 2:11.09.02-2 [2286 kB] 359s Get:137 http://ftpmaster.internal/ubuntu questing/universe amd64 tex-common all 6.19 [29.8 kB] 359s Get:138 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 359s Get:139 http://ftpmaster.internal/ubuntu questing/universe amd64 libkpathsea6 amd64 2024.20240313.70630+ds-6 [67.3 kB] 359s Get:140 http://ftpmaster.internal/ubuntu questing/universe amd64 libptexenc1 amd64 2024.20240313.70630+ds-6 [43.7 kB] 359s Get:141 http://ftpmaster.internal/ubuntu questing/universe amd64 libsynctex2 amd64 2024.20240313.70630+ds-6 [62.5 kB] 359s Get:142 http://ftpmaster.internal/ubuntu questing/universe amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-6 [145 kB] 359s Get:143 http://ftpmaster.internal/ubuntu questing/main amd64 t1utils amd64 1.41-4build3 [61.3 kB] 359s Get:144 http://ftpmaster.internal/ubuntu questing/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 359s Get:145 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 359s Get:146 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 359s Get:147 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 359s Get:148 http://ftpmaster.internal/ubuntu questing/universe amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] 359s Get:149 http://ftpmaster.internal/ubuntu questing/universe amd64 libpotrace0 amd64 1.16-2build1 [17.7 kB] 359s Get:150 http://ftpmaster.internal/ubuntu questing/universe amd64 libteckit0 amd64 2.5.12+ds1-1 [411 kB] 359s Get:151 http://ftpmaster.internal/ubuntu questing/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB] 359s Get:152 http://ftpmaster.internal/ubuntu questing/main amd64 libxaw7 amd64 2:1.0.16-1 [207 kB] 359s Get:153 http://ftpmaster.internal/ubuntu questing/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 359s Get:154 http://ftpmaster.internal/ubuntu questing/universe amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.1 [30.0 kB] 359s Get:155 http://ftpmaster.internal/ubuntu questing/universe amd64 texlive-binaries amd64 2024.20240313.70630+ds-6 [9789 kB] 359s Get:156 http://ftpmaster.internal/ubuntu questing/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 359s Get:157 http://ftpmaster.internal/ubuntu questing/universe amd64 texlive-base all 2024.20250309-1 [22.7 MB] 360s Get:158 http://ftpmaster.internal/ubuntu questing/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 360s Get:159 http://ftpmaster.internal/ubuntu questing/universe amd64 imagemagick-7.q16 amd64 8:7.1.1.43+dfsg1-1 [704 kB] 360s Get:160 http://ftpmaster.internal/ubuntu questing/universe amd64 imagemagick amd64 8:7.1.1.43+dfsg1-1 [14.1 kB] 360s Get:161 http://ftpmaster.internal/ubuntu questing/universe amd64 hevea amd64 2.36-2 [2023 kB] 360s Get:162 http://ftpmaster.internal/ubuntu questing/universe amd64 libllvm17t64 amd64 1:17.0.6-21 [26.0 MB] 361s Get:163 http://ftpmaster.internal/ubuntu questing/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 361s Get:164 http://ftpmaster.internal/ubuntu questing/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-3 [13.5 kB] 361s Get:165 http://ftpmaster.internal/ubuntu questing/universe amd64 libamd3 amd64 1:7.8.3+dfsg-3 [31.0 kB] 361s Get:166 http://ftpmaster.internal/ubuntu questing/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 361s Get:167 http://ftpmaster.internal/ubuntu questing/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 361s Get:168 http://ftpmaster.internal/ubuntu questing/universe amd64 libamdhip64-5 amd64 5.7.1-5.1 [9695 kB] 362s Get:169 http://ftpmaster.internal/ubuntu questing/universe amd64 libapache-pom-java all 33-2 [5874 B] 362s Get:170 http://ftpmaster.internal/ubuntu questing/universe amd64 libarpack2t64 amd64 3.9.1-6 [108 kB] 362s Get:171 http://ftpmaster.internal/ubuntu questing/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-3 [19.5 kB] 362s Get:172 http://ftpmaster.internal/ubuntu questing/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 362s Get:173 http://ftpmaster.internal/ubuntu questing/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 362s Get:174 http://ftpmaster.internal/ubuntu questing/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 362s Get:175 http://ftpmaster.internal/ubuntu questing/main amd64 libexpat1-dev amd64 2.7.1-1 [148 kB] 362s Get:176 http://ftpmaster.internal/ubuntu questing/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.4 [179 kB] 362s Get:177 http://ftpmaster.internal/ubuntu questing/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 362s Get:178 http://ftpmaster.internal/ubuntu questing/main amd64 librdmacm1t64 amd64 56.0-4ubuntu1 [71.5 kB] 362s Get:179 http://ftpmaster.internal/ubuntu questing/universe amd64 libfabric1 amd64 1.17.0-3.1 [789 kB] 362s Get:180 http://ftpmaster.internal/ubuntu questing/universe amd64 libglpk40 amd64 5.0-1build2 [369 kB] 362s Get:181 http://ftpmaster.internal/ubuntu questing/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 362s Get:182 http://ftpmaster.internal/ubuntu questing/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 362s Get:183 http://ftpmaster.internal/ubuntu questing/universe amd64 libhwloc15 amd64 2.12.0-1 [194 kB] 362s Get:184 http://ftpmaster.internal/ubuntu questing/universe amd64 libplfit0 amd64 0.9.6+ds-2ubuntu1 [31.9 kB] 362s Get:185 http://ftpmaster.internal/ubuntu questing/universe amd64 libigraph3t64 amd64 0.10.15+ds-3 [1027 kB] 362s Get:186 http://ftpmaster.internal/ubuntu questing/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 362s Get:187 http://ftpmaster.internal/ubuntu questing/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 362s Get:188 http://ftpmaster.internal/ubuntu questing/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 362s Get:189 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 libjs-sphinxdoc all 8.2.3-1 [27.8 kB] 362s Get:190 http://ftpmaster.internal/ubuntu questing/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 362s Get:191 http://ftpmaster.internal/ubuntu questing/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 362s Get:192 http://ftpmaster.internal/ubuntu questing/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB] 362s Get:193 http://ftpmaster.internal/ubuntu questing/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB] 362s Get:194 http://ftpmaster.internal/ubuntu questing/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB] 362s Get:195 http://ftpmaster.internal/ubuntu questing/universe amd64 libmunge2 amd64 0.5.16-1 [16.5 kB] 362s Get:196 http://ftpmaster.internal/ubuntu questing/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 362s Get:197 http://ftpmaster.internal/ubuntu questing/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 362s Get:198 http://ftpmaster.internal/ubuntu questing/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 362s Get:199 http://ftpmaster.internal/ubuntu questing/universe amd64 libhwloc-plugins amd64 2.12.0-1 [16.0 kB] 362s Get:200 http://ftpmaster.internal/ubuntu questing/universe amd64 libpmix2t64 amd64 5.0.6-5 [714 kB] 362s Get:201 http://ftpmaster.internal/ubuntu questing/main amd64 libibumad3 amd64 56.0-4ubuntu1 [31.2 kB] 362s Get:202 http://ftpmaster.internal/ubuntu questing/main amd64 libibmad5 amd64 56.0-4ubuntu1 [43.9 kB] 362s Get:203 http://ftpmaster.internal/ubuntu questing/universe amd64 libucx0 amd64 1.18.1+ds-2 [1293 kB] 363s Get:204 http://ftpmaster.internal/ubuntu questing/universe amd64 libopenmpi40 amd64 5.0.7-1 [2526 kB] 363s Get:205 http://ftpmaster.internal/ubuntu questing/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 363s Get:206 http://ftpmaster.internal/ubuntu questing/main amd64 libpython3.13-dev amd64 3.13.3-1 [5507 kB] 364s Get:207 http://ftpmaster.internal/ubuntu questing/main amd64 libpython3-dev amd64 3.13.3-1 [10.8 kB] 365s Get:208 http://ftpmaster.internal/ubuntu questing/main amd64 libpython3-all-dev amd64 3.13.3-1 [906 B] 365s Get:209 http://ftpmaster.internal/ubuntu questing/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 365s Get:210 http://ftpmaster.internal/ubuntu questing/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu4 [176 kB] 365s Get:211 http://ftpmaster.internal/ubuntu questing/universe amd64 mafft amd64 7.505-1 [795 kB] 365s Get:212 http://ftpmaster.internal/ubuntu questing/universe amd64 muscle3 amd64 3.8.1551-3 [198 kB] 365s Get:213 http://ftpmaster.internal/ubuntu questing/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 365s Get:214 http://ftpmaster.internal/ubuntu questing/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6build1 [15.8 MB] 365s Get:215 http://ftpmaster.internal/ubuntu questing/universe amd64 openmpi-common all 5.0.7-1 [97.9 kB] 365s Get:216 http://ftpmaster.internal/ubuntu questing/universe amd64 openmpi-bin amd64 5.0.7-1 [192 kB] 365s Get:217 http://ftpmaster.internal/ubuntu questing/universe amd64 phylip amd64 1:3.697+dfsg-4build1 [874 kB] 365s Get:218 http://ftpmaster.internal/ubuntu questing/universe amd64 mpi-default-bin amd64 1.18 [2510 B] 365s Get:219 http://ftpmaster.internal/ubuntu questing/universe amd64 phyml amd64 3:3.3.20220408-4build1 [1081 kB] 365s Get:220 http://ftpmaster.internal/ubuntu questing/universe amd64 prank amd64 0.0.170427+dfsg-3 [396 kB] 365s Get:221 http://ftpmaster.internal/ubuntu questing/universe amd64 preview-latex-style all 13.2-1 [347 kB] 365s Get:222 http://ftpmaster.internal/ubuntu questing/universe amd64 probcons amd64 1.12-14 [125 kB] 365s Get:223 http://ftpmaster.internal/ubuntu questing/universe amd64 python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 366s Get:224 http://ftpmaster.internal/ubuntu questing/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 366s Get:225 http://ftpmaster.internal/ubuntu questing/main amd64 python3-all amd64 3.13.3-1 [882 B] 366s Get:226 http://ftpmaster.internal/ubuntu questing/main amd64 python3.13-dev amd64 3.13.3-1 [508 kB] 366s Get:227 http://ftpmaster.internal/ubuntu questing/main amd64 python3-dev amd64 3.13.3-1 [26.7 kB] 366s Get:228 http://ftpmaster.internal/ubuntu questing/main amd64 python3-all-dev amd64 3.13.3-1 [904 B] 366s Get:229 http://ftpmaster.internal/ubuntu questing/main amd64 python3.13-tk amd64 3.13.3-1 [107 kB] 366s Get:230 http://ftpmaster.internal/ubuntu questing/main amd64 python3-tk amd64 3.13.3-1 [9856 B] 366s Get:231 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 366s Get:232 http://ftpmaster.internal/ubuntu questing/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 366s Get:233 http://ftpmaster.internal/ubuntu questing/main amd64 python3-cairo amd64 1.27.0-2 [124 kB] 366s Get:234 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 366s Get:235 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 366s Get:236 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-reportlab all 4.3.1-1 [1137 kB] 366s Get:237 http://ftpmaster.internal/ubuntu questing/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 366s Get:238 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-biopython amd64 1.85+dfsg-2build1 [1739 kB] 366s Get:239 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 366s Get:240 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 366s Get:241 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 366s Get:242 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 366s Get:243 http://ftpmaster.internal/ubuntu questing/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 366s Get:244 http://ftpmaster.internal/ubuntu questing/main amd64 python3-defusedxml all 0.7.1-3 [42.2 kB] 366s Get:245 http://ftpmaster.internal/ubuntu questing/main amd64 python3-roman all 5.0-1 [10.3 kB] 366s Get:246 http://ftpmaster.internal/ubuntu questing/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 366s Get:247 http://ftpmaster.internal/ubuntu questing/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 366s Get:248 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 366s Get:249 http://ftpmaster.internal/ubuntu questing/main amd64 python3-lxml amd64 5.3.2-1 [1407 kB] 367s Get:250 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 367s Get:251 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 367s Get:252 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 367s Get:253 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 367s Get:254 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 367s Get:255 http://ftpmaster.internal/ubuntu questing/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 368s Get:256 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 368s Get:257 http://ftpmaster.internal/ubuntu questing/main amd64 python3-imagesize all 1.4.1-1 [6844 B] 368s Get:258 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 368s Get:259 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 368s Get:260 http://ftpmaster.internal/ubuntu questing/main amd64 python3-msgpack amd64 1.0.3-3build4 [87.7 kB] 368s Get:261 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-mmtf all 1.1.3-1 [16.2 kB] 368s Get:262 http://ftpmaster.internal/ubuntu questing/main amd64 python3-mysqldb amd64 1.4.6-2build6 [48.8 kB] 368s Get:263 http://ftpmaster.internal/ubuntu questing/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 369s Get:264 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 sphinx-common all 8.2.3-1 [656 kB] 369s Get:265 http://ftpmaster.internal/ubuntu questing/main amd64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 369s Get:266 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-roman-numerals all 3.1.0-1ubuntu1 [8432 B] 369s Get:267 http://ftpmaster.internal/ubuntu questing/main amd64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 369s Get:268 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 python3-sphinx all 8.2.3-1 [482 kB] 369s Get:269 http://ftpmaster.internal/ubuntu questing/main amd64 python3-tabulate all 0.9.0-1 [45.3 kB] 369s Get:270 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-numpydoc all 1.8.0-1 [52.4 kB] 369s Get:271 http://ftpmaster.internal/ubuntu questing/main amd64 python3-psycopg2 amd64 2.9.10-1build1 [142 kB] 369s Get:272 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-rdflib all 7.1.1-2 [426 kB] 369s Get:273 http://ftpmaster.internal/ubuntu questing/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 369s Get:274 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 369s Get:275 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 369s Get:276 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-texttable all 1.7.0-1 [11.2 kB] 369s Get:277 http://ftpmaster.internal/ubuntu questing/universe amd64 raxml amd64 8.2.13+dfsg-2 [1670 kB] 369s Get:278 http://ftpmaster.internal/ubuntu questing/universe amd64 samtools amd64 1.21-1 [655 kB] 369s Get:279 http://ftpmaster.internal/ubuntu questing/universe amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [929 kB] 369s Get:280 http://ftpmaster.internal/ubuntu questing/universe amd64 texlive-fonts-recommended all 2024.20250309-1 [4974 kB] 369s Get:281 http://ftpmaster.internal/ubuntu questing/universe amd64 texlive-latex-base all 2024.20250309-1 [1276 kB] 369s Get:282 http://ftpmaster.internal/ubuntu questing/universe amd64 libfontbox-java all 1:1.8.16-5 [208 kB] 369s Get:283 http://ftpmaster.internal/ubuntu questing/universe amd64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 369s Get:284 http://ftpmaster.internal/ubuntu questing/universe amd64 texlive-latex-recommended all 2024.20250309-1 [8727 kB] 370s Get:285 http://ftpmaster.internal/ubuntu questing/universe amd64 texlive-pictures all 2024.20250309-1 [17.0 MB] 370s Get:286 http://ftpmaster.internal/ubuntu questing/universe amd64 texlive-latex-extra all 2024.20250309-2 [24.8 MB] 371s Get:287 http://ftpmaster.internal/ubuntu questing/universe amd64 wise-data all 2.4.1-25 [83.0 kB] 371s Get:288 http://ftpmaster.internal/ubuntu questing/universe amd64 wise amd64 2.4.1-25 [843 kB] 371s Get:289 http://ftpmaster.internal/ubuntu questing/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 371s Get:290 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-igraph amd64 0.11.8+ds-1build1 [343 kB] 372s Preconfiguring packages ... 372s Fetched 486 MB in 20s (24.4 MB/s) 372s Selecting previously unselected package m4. 372s (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 ... 80517 files and directories currently installed.) 372s Preparing to unpack .../000-m4_1.4.19-7_amd64.deb ... 372s Unpacking m4 (1.4.19-7) ... 372s Selecting previously unselected package flex. 372s Preparing to unpack .../001-flex_2.6.4-8.2build1_amd64.deb ... 372s Unpacking flex (2.6.4-8.2build1) ... 372s Selecting previously unselected package fonts-lato. 372s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 372s Unpacking fonts-lato (2.015-1) ... 373s Selecting previously unselected package libgomp1:amd64. 373s Preparing to unpack .../003-libgomp1_15-20250404-0ubuntu1_amd64.deb ... 373s Unpacking libgomp1:amd64 (15-20250404-0ubuntu1) ... 373s Selecting previously unselected package libfftw3-double3:amd64. 373s Preparing to unpack .../004-libfftw3-double3_3.3.10-2fakesync1build1_amd64.deb ... 373s Unpacking libfftw3-double3:amd64 (3.3.10-2fakesync1build1) ... 373s Selecting previously unselected package fonts-dejavu-mono. 373s Preparing to unpack .../005-fonts-dejavu-mono_2.37-8_all.deb ... 373s Unpacking fonts-dejavu-mono (2.37-8) ... 373s Selecting previously unselected package fonts-dejavu-core. 373s Preparing to unpack .../006-fonts-dejavu-core_2.37-8_all.deb ... 373s Unpacking fonts-dejavu-core (2.37-8) ... 373s Selecting previously unselected package libfontenc1:amd64. 373s Preparing to unpack .../007-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 373s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 373s Selecting previously unselected package x11-common. 373s Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu4_all.deb ... 373s Unpacking x11-common (1:7.7+23ubuntu4) ... 373s Selecting previously unselected package xfonts-encodings. 373s Preparing to unpack .../009-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 373s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 373s Selecting previously unselected package xfonts-utils. 373s Preparing to unpack .../010-xfonts-utils_1%3a7.7+7_amd64.deb ... 373s Unpacking xfonts-utils (1:7.7+7) ... 373s Selecting previously unselected package fonts-urw-base35. 373s Preparing to unpack .../011-fonts-urw-base35_20200910-8_all.deb ... 373s Unpacking fonts-urw-base35 (20200910-8) ... 373s Selecting previously unselected package fontconfig-config. 373s Preparing to unpack .../012-fontconfig-config_2.15.0-2.2ubuntu1_amd64.deb ... 373s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 373s Selecting previously unselected package libfontconfig1:amd64. 373s Preparing to unpack .../013-libfontconfig1_2.15.0-2.2ubuntu1_amd64.deb ... 373s Unpacking libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 373s Selecting previously unselected package libsharpyuv0:amd64. 373s Preparing to unpack .../014-libsharpyuv0_1.5.0-0.1_amd64.deb ... 373s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 373s Selecting previously unselected package libaom3:amd64. 373s Preparing to unpack .../015-libaom3_3.12.1-1_amd64.deb ... 373s Unpacking libaom3:amd64 (3.12.1-1) ... 373s Selecting previously unselected package libheif-plugin-aomdec:amd64. 373s Preparing to unpack .../016-libheif-plugin-aomdec_1.19.7-1_amd64.deb ... 373s Unpacking libheif-plugin-aomdec:amd64 (1.19.7-1) ... 373s Selecting previously unselected package libde265-0:amd64. 373s Preparing to unpack .../017-libde265-0_1.0.15-1build5_amd64.deb ... 373s Unpacking libde265-0:amd64 (1.0.15-1build5) ... 373s Selecting previously unselected package libheif-plugin-libde265:amd64. 373s Preparing to unpack .../018-libheif-plugin-libde265_1.19.7-1_amd64.deb ... 373s Unpacking libheif-plugin-libde265:amd64 (1.19.7-1) ... 374s Selecting previously unselected package libheif1:amd64. 374s Preparing to unpack .../019-libheif1_1.19.7-1_amd64.deb ... 374s Unpacking libheif1:amd64 (1.19.7-1) ... 374s Selecting previously unselected package libjbig0:amd64. 374s Preparing to unpack .../020-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 374s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 374s Selecting previously unselected package libjpeg-turbo8:amd64. 374s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 374s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 374s Selecting previously unselected package libjpeg8:amd64. 374s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_amd64.deb ... 374s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 374s Selecting previously unselected package liblcms2-2:amd64. 374s Preparing to unpack .../023-liblcms2-2_2.16-2_amd64.deb ... 374s Unpacking liblcms2-2:amd64 (2.16-2) ... 374s Selecting previously unselected package liblqr-1-0:amd64. 374s Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1build2_amd64.deb ... 374s Unpacking liblqr-1-0:amd64 (0.4.2-2.1build2) ... 374s Selecting previously unselected package libltdl7:amd64. 374s Preparing to unpack .../025-libltdl7_2.5.4-4_amd64.deb ... 374s Unpacking libltdl7:amd64 (2.5.4-4) ... 374s Selecting previously unselected package libopenjp2-7:amd64. 374s Preparing to unpack .../026-libopenjp2-7_2.5.3-2_amd64.deb ... 374s Unpacking libopenjp2-7:amd64 (2.5.3-2) ... 374s Selecting previously unselected package libraw23t64:amd64. 374s Preparing to unpack .../027-libraw23t64_0.21.4-2_amd64.deb ... 374s Unpacking libraw23t64:amd64 (0.21.4-2) ... 374s Selecting previously unselected package libdeflate0:amd64. 374s Preparing to unpack .../028-libdeflate0_1.23-2_amd64.deb ... 374s Unpacking libdeflate0:amd64 (1.23-2) ... 374s Selecting previously unselected package liblerc4:amd64. 374s Preparing to unpack .../029-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 374s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 374s Selecting previously unselected package libwebp7:amd64. 374s Preparing to unpack .../030-libwebp7_1.5.0-0.1_amd64.deb ... 374s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 374s Selecting previously unselected package libtiff6:amd64. 374s Preparing to unpack .../031-libtiff6_4.7.0-3ubuntu1_amd64.deb ... 374s Unpacking libtiff6:amd64 (4.7.0-3ubuntu1) ... 374s Selecting previously unselected package libwebpdemux2:amd64. 374s Preparing to unpack .../032-libwebpdemux2_1.5.0-0.1_amd64.deb ... 374s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 374s Selecting previously unselected package libwebpmux3:amd64. 374s Preparing to unpack .../033-libwebpmux3_1.5.0-0.1_amd64.deb ... 374s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 374s Selecting previously unselected package imagemagick-7-common. 374s Preparing to unpack .../034-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 374s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 374s Selecting previously unselected package libmagickcore-7.q16-10:amd64. 374s Preparing to unpack .../035-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_amd64.deb ... 374s Unpacking libmagickcore-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... 374s Selecting previously unselected package libmagickwand-7.q16-10:amd64. 374s Preparing to unpack .../036-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_amd64.deb ... 374s Unpacking libmagickwand-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... 374s Selecting previously unselected package poppler-data. 374s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 374s Unpacking poppler-data (0.4.12-1) ... 374s Selecting previously unselected package python3-numpy-dev:amd64. 374s Preparing to unpack .../038-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 374s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 374s Selecting previously unselected package libblas3:amd64. 374s Preparing to unpack .../039-libblas3_3.12.1-2_amd64.deb ... 374s Unpacking libblas3:amd64 (3.12.1-2) ... 374s Selecting previously unselected package libgfortran5:amd64. 374s Preparing to unpack .../040-libgfortran5_15-20250404-0ubuntu1_amd64.deb ... 374s Unpacking libgfortran5:amd64 (15-20250404-0ubuntu1) ... 374s Selecting previously unselected package liblapack3:amd64. 374s Preparing to unpack .../041-liblapack3_3.12.1-2_amd64.deb ... 374s Unpacking liblapack3:amd64 (3.12.1-2) ... 374s Selecting previously unselected package python3-numpy. 374s Preparing to unpack .../042-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 375s Unpacking python3-numpy (1:2.2.3+ds-5) ... 375s Selecting previously unselected package sgml-base. 375s Preparing to unpack .../043-sgml-base_1.31_all.deb ... 375s Unpacking sgml-base (1.31) ... 375s Selecting previously unselected package autoconf. 375s Preparing to unpack .../044-autoconf_2.72-3ubuntu1_all.deb ... 375s Unpacking autoconf (2.72-3ubuntu1) ... 375s Selecting previously unselected package autotools-dev. 375s Preparing to unpack .../045-autotools-dev_20240727.1_all.deb ... 375s Unpacking autotools-dev (20240727.1) ... 375s Selecting previously unselected package automake. 375s Preparing to unpack .../046-automake_1%3a1.17-3ubuntu1_all.deb ... 375s Unpacking automake (1:1.17-3ubuntu1) ... 375s Selecting previously unselected package autopoint. 375s Preparing to unpack .../047-autopoint_0.23.1-1_all.deb ... 375s Unpacking autopoint (0.23.1-1) ... 375s Selecting previously unselected package libtcl8.6:amd64. 375s Preparing to unpack .../048-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 375s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 375s Selecting previously unselected package libxrender1:amd64. 375s Preparing to unpack .../049-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 375s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 375s Selecting previously unselected package libxft2:amd64. 375s Preparing to unpack .../050-libxft2_2.3.6-1build1_amd64.deb ... 375s Unpacking libxft2:amd64 (2.3.6-1build1) ... 375s Selecting previously unselected package libxss1:amd64. 375s Preparing to unpack .../051-libxss1_1%3a1.2.3-1build3_amd64.deb ... 375s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 375s Selecting previously unselected package libtk8.6:amd64. 375s Preparing to unpack .../052-libtk8.6_8.6.16-1_amd64.deb ... 375s Unpacking libtk8.6:amd64 (8.6.16-1) ... 375s Selecting previously unselected package tk8.6-blt2.5. 375s Preparing to unpack .../053-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 375s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 375s Selecting previously unselected package blt. 375s Preparing to unpack .../054-blt_2.5.3+dfsg-8_amd64.deb ... 375s Unpacking blt (2.5.3+dfsg-8) ... 375s Selecting previously unselected package libisl23:amd64. 375s Preparing to unpack .../055-libisl23_0.27-1_amd64.deb ... 375s Unpacking libisl23:amd64 (0.27-1) ... 375s Selecting previously unselected package libmpc3:amd64. 375s Preparing to unpack .../056-libmpc3_1.3.1-1build2_amd64.deb ... 375s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 375s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 375s Preparing to unpack .../057-cpp-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 375s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 375s Selecting previously unselected package cpp-14. 375s Preparing to unpack .../058-cpp-14_14.2.0-19ubuntu2_amd64.deb ... 375s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 375s Selecting previously unselected package cpp-x86-64-linux-gnu. 376s Preparing to unpack .../059-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 376s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 376s Selecting previously unselected package cpp. 376s Preparing to unpack .../060-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 376s Unpacking cpp (4:14.2.0-1ubuntu1) ... 376s Selecting previously unselected package libcc1-0:amd64. 376s Preparing to unpack .../061-libcc1-0_15-20250404-0ubuntu1_amd64.deb ... 376s Unpacking libcc1-0:amd64 (15-20250404-0ubuntu1) ... 376s Selecting previously unselected package libitm1:amd64. 376s Preparing to unpack .../062-libitm1_15-20250404-0ubuntu1_amd64.deb ... 376s Unpacking libitm1:amd64 (15-20250404-0ubuntu1) ... 376s Selecting previously unselected package libasan8:amd64. 376s Preparing to unpack .../063-libasan8_15-20250404-0ubuntu1_amd64.deb ... 376s Unpacking libasan8:amd64 (15-20250404-0ubuntu1) ... 376s Selecting previously unselected package liblsan0:amd64. 376s Preparing to unpack .../064-liblsan0_15-20250404-0ubuntu1_amd64.deb ... 376s Unpacking liblsan0:amd64 (15-20250404-0ubuntu1) ... 376s Selecting previously unselected package libtsan2:amd64. 376s Preparing to unpack .../065-libtsan2_15-20250404-0ubuntu1_amd64.deb ... 376s Unpacking libtsan2:amd64 (15-20250404-0ubuntu1) ... 376s Selecting previously unselected package libubsan1:amd64. 376s Preparing to unpack .../066-libubsan1_15-20250404-0ubuntu1_amd64.deb ... 376s Unpacking libubsan1:amd64 (15-20250404-0ubuntu1) ... 376s Selecting previously unselected package libhwasan0:amd64. 376s Preparing to unpack .../067-libhwasan0_15-20250404-0ubuntu1_amd64.deb ... 376s Unpacking libhwasan0:amd64 (15-20250404-0ubuntu1) ... 376s Selecting previously unselected package libquadmath0:amd64. 376s Preparing to unpack .../068-libquadmath0_15-20250404-0ubuntu1_amd64.deb ... 376s Unpacking libquadmath0:amd64 (15-20250404-0ubuntu1) ... 376s Selecting previously unselected package libgcc-14-dev:amd64. 376s Preparing to unpack .../069-libgcc-14-dev_14.2.0-19ubuntu2_amd64.deb ... 376s Unpacking libgcc-14-dev:amd64 (14.2.0-19ubuntu2) ... 376s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 376s Preparing to unpack .../070-gcc-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 376s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 376s Selecting previously unselected package gcc-14. 376s Preparing to unpack .../071-gcc-14_14.2.0-19ubuntu2_amd64.deb ... 376s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 376s Selecting previously unselected package gcc-x86-64-linux-gnu. 376s Preparing to unpack .../072-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 376s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 376s Selecting previously unselected package gcc. 376s Preparing to unpack .../073-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 376s Unpacking gcc (4:14.2.0-1ubuntu1) ... 377s Selecting previously unselected package libstdc++-14-dev:amd64. 377s Preparing to unpack .../074-libstdc++-14-dev_14.2.0-19ubuntu2_amd64.deb ... 377s Unpacking libstdc++-14-dev:amd64 (14.2.0-19ubuntu2) ... 377s Selecting previously unselected package g++-14-x86-64-linux-gnu. 377s Preparing to unpack .../075-g++-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 377s Unpacking g++-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 377s Selecting previously unselected package g++-14. 377s Preparing to unpack .../076-g++-14_14.2.0-19ubuntu2_amd64.deb ... 377s Unpacking g++-14 (14.2.0-19ubuntu2) ... 377s Selecting previously unselected package g++-x86-64-linux-gnu. 377s Preparing to unpack .../077-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 377s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 377s Selecting previously unselected package g++. 377s Preparing to unpack .../078-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 377s Unpacking g++ (4:14.2.0-1ubuntu1) ... 377s Selecting previously unselected package build-essential. 377s Preparing to unpack .../079-build-essential_12.12ubuntu1_amd64.deb ... 377s Unpacking build-essential (12.12ubuntu1) ... 377s Selecting previously unselected package bwa. 377s Preparing to unpack .../080-bwa_0.7.18-1_amd64.deb ... 377s Unpacking bwa (0.7.18-1) ... 377s Selecting previously unselected package libargtable2-0. 377s Preparing to unpack .../081-libargtable2-0_13-3_amd64.deb ... 377s Unpacking libargtable2-0 (13-3) ... 377s Selecting previously unselected package clustalo. 377s Preparing to unpack .../082-clustalo_1.2.4-8build1_amd64.deb ... 377s Unpacking clustalo (1.2.4-8build1) ... 377s Selecting previously unselected package clustalw. 377s Preparing to unpack .../083-clustalw_2.1+lgpl-7_amd64.deb ... 377s Unpacking clustalw (2.1+lgpl-7) ... 377s Selecting previously unselected package libdebhelper-perl. 377s Preparing to unpack .../084-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 377s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 377s Selecting previously unselected package libtool. 377s Preparing to unpack .../085-libtool_2.5.4-4_all.deb ... 377s Unpacking libtool (2.5.4-4) ... 377s Selecting previously unselected package dh-autoreconf. 377s Preparing to unpack .../086-dh-autoreconf_20_all.deb ... 377s Unpacking dh-autoreconf (20) ... 377s Selecting previously unselected package libarchive-zip-perl. 377s Preparing to unpack .../087-libarchive-zip-perl_1.68-1_all.deb ... 377s Unpacking libarchive-zip-perl (1.68-1) ... 377s Selecting previously unselected package libfile-stripnondeterminism-perl. 377s Preparing to unpack .../088-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 377s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 377s Selecting previously unselected package dh-strip-nondeterminism. 377s Preparing to unpack .../089-dh-strip-nondeterminism_1.14.1-2_all.deb ... 377s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 377s Selecting previously unselected package debugedit. 377s Preparing to unpack .../090-debugedit_1%3a5.1-2_amd64.deb ... 377s Unpacking debugedit (1:5.1-2) ... 377s Selecting previously unselected package dwz. 377s Preparing to unpack .../091-dwz_0.15-1build6_amd64.deb ... 377s Unpacking dwz (0.15-1build6) ... 377s Selecting previously unselected package gettext. 377s Preparing to unpack .../092-gettext_0.23.1-1_amd64.deb ... 377s Unpacking gettext (0.23.1-1) ... 378s Selecting previously unselected package intltool-debian. 378s Preparing to unpack .../093-intltool-debian_0.35.0+20060710.6_all.deb ... 378s Unpacking intltool-debian (0.35.0+20060710.6) ... 378s Selecting previously unselected package po-debconf. 378s Preparing to unpack .../094-po-debconf_1.0.21+nmu1_all.deb ... 378s Unpacking po-debconf (1.0.21+nmu1) ... 378s Selecting previously unselected package debhelper. 378s Preparing to unpack .../095-debhelper_13.24.1ubuntu2_all.deb ... 378s Unpacking debhelper (13.24.1ubuntu2) ... 378s Selecting previously unselected package dh-python. 378s Preparing to unpack .../096-dh-python_6.20250308_all.deb ... 378s Unpacking dh-python (6.20250308) ... 378s Selecting previously unselected package dialign. 378s Preparing to unpack .../097-dialign_2.2.1-13_amd64.deb ... 378s Unpacking dialign (2.2.1-13) ... 378s Selecting previously unselected package xml-core. 378s Preparing to unpack .../098-xml-core_0.19_all.deb ... 378s Unpacking xml-core (0.19) ... 378s Selecting previously unselected package docutils-common. 378s Preparing to unpack .../099-docutils-common_0.21.2+dfsg-2_all.deb ... 378s Unpacking docutils-common (0.21.2+dfsg-2) ... 378s Selecting previously unselected package libcifpp-data. 378s Preparing to unpack .../100-libcifpp-data_7.0.9-1_all.deb ... 378s Unpacking libcifpp-data (7.0.9-1) ... 378s Selecting previously unselected package libcifpp7:amd64. 378s Preparing to unpack .../101-libcifpp7_7.0.9-1_amd64.deb ... 378s Unpacking libcifpp7:amd64 (7.0.9-1) ... 378s Selecting previously unselected package dssp. 378s Preparing to unpack .../102-dssp_4.4.10-1_amd64.deb ... 378s Unpacking dssp (4.4.10-1) ... 378s Selecting previously unselected package libimagequant0:amd64. 378s Preparing to unpack .../103-libimagequant0_2.18.0-1build1_amd64.deb ... 378s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 378s Selecting previously unselected package libgraphite2-3:amd64. 378s Preparing to unpack .../104-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 378s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 378s Selecting previously unselected package libharfbuzz0b:amd64. 378s Preparing to unpack .../105-libharfbuzz0b_10.2.0-1_amd64.deb ... 378s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 378s Selecting previously unselected package libraqm0:amd64. 378s Preparing to unpack .../106-libraqm0_0.10.2-1_amd64.deb ... 378s Unpacking libraqm0:amd64 (0.10.2-1) ... 378s Selecting previously unselected package libxpm4:amd64. 378s Preparing to unpack .../107-libxpm4_1%3a3.5.17-1build2_amd64.deb ... 378s Unpacking libxpm4:amd64 (1:3.5.17-1build2) ... 378s Selecting previously unselected package libgd3:amd64. 378s Preparing to unpack .../108-libgd3_2.3.3-12ubuntu3_amd64.deb ... 378s Unpacking libgd3:amd64 (2.3.3-12ubuntu3) ... 378s Selecting previously unselected package libhpdf-2.3.0:amd64. 378s Preparing to unpack .../109-libhpdf-2.3.0_2.3.0+dfsg-1build3_amd64.deb ... 378s Unpacking libhpdf-2.3.0:amd64 (2.3.0+dfsg-1build3) ... 378s Selecting previously unselected package mysql-common. 378s Preparing to unpack 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previously unselected package libavahi-common-data:amd64. 382s Preparing to unpack .../121-libavahi-common-data_0.8-16ubuntu2_amd64.deb ... 382s Unpacking libavahi-common-data:amd64 (0.8-16ubuntu2) ... 382s Selecting previously unselected package libavahi-common3:amd64. 382s Preparing to unpack .../122-libavahi-common3_0.8-16ubuntu2_amd64.deb ... 382s Unpacking libavahi-common3:amd64 (0.8-16ubuntu2) ... 382s Selecting previously unselected package libavahi-client3:amd64. 382s Preparing to unpack .../123-libavahi-client3_0.8-16ubuntu2_amd64.deb ... 382s Unpacking libavahi-client3:amd64 (0.8-16ubuntu2) ... 382s Selecting previously unselected package libcups2t64:amd64. 382s Preparing to unpack .../124-libcups2t64_2.4.12-0ubuntu1_amd64.deb ... 382s Unpacking libcups2t64:amd64 (2.4.12-0ubuntu1) ... 382s Selecting previously unselected package libidn12:amd64. 382s Preparing to unpack .../125-libidn12_1.43-1_amd64.deb ... 382s Unpacking libidn12:amd64 (1.43-1) ... 382s Selecting previously unselected package libijs-0.35:amd64. 382s Preparing to unpack .../126-libijs-0.35_0.35-15.2_amd64.deb ... 382s Unpacking libijs-0.35:amd64 (0.35-15.2) ... 382s Selecting previously unselected package libjbig2dec0:amd64. 382s Preparing to unpack .../127-libjbig2dec0_0.20-1build3_amd64.deb ... 382s Unpacking libjbig2dec0:amd64 (0.20-1build3) ... 382s Selecting previously unselected package libpaper2:amd64. 382s Preparing to unpack .../128-libpaper2_2.2.5-0.3_amd64.deb ... 382s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 382s Selecting previously unselected package libice6:amd64. 382s Preparing to unpack .../129-libice6_2%3a1.1.1-1_amd64.deb ... 382s Unpacking libice6:amd64 (2:1.1.1-1) ... 382s Selecting previously unselected package libsm6:amd64. 382s Preparing to unpack .../130-libsm6_2%3a1.2.4-1_amd64.deb ... 382s Unpacking libsm6:amd64 (2:1.2.4-1) ... 382s Selecting previously unselected package libxt6t64:amd64. 382s Preparing to unpack .../131-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb 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package libpaper-utils. 382s Preparing to unpack .../137-libpaper-utils_2.2.5-0.3_amd64.deb ... 382s Unpacking libpaper-utils (2.2.5-0.3) ... 382s Selecting previously unselected package libkpathsea6:amd64. 382s Preparing to unpack .../138-libkpathsea6_2024.20240313.70630+ds-6_amd64.deb ... 382s Unpacking libkpathsea6:amd64 (2024.20240313.70630+ds-6) ... 382s Selecting previously unselected package libptexenc1:amd64. 382s Preparing to unpack .../139-libptexenc1_2024.20240313.70630+ds-6_amd64.deb ... 382s Unpacking libptexenc1:amd64 (2024.20240313.70630+ds-6) ... 383s Selecting previously unselected package libsynctex2:amd64. 383s Preparing to unpack .../140-libsynctex2_2024.20240313.70630+ds-6_amd64.deb ... 383s Unpacking libsynctex2:amd64 (2024.20240313.70630+ds-6) ... 383s Selecting previously unselected package libtexlua53-5:amd64. 383s Preparing to unpack .../141-libtexlua53-5_2024.20240313.70630+ds-6_amd64.deb ... 383s Unpacking libtexlua53-5:amd64 (2024.20240313.70630+ds-6) ... 383s Selecting previously unselected package t1utils. 383s Preparing to unpack .../142-t1utils_1.41-4build3_amd64.deb ... 383s Unpacking t1utils (1.41-4build3) ... 383s Selecting previously unselected package libpixman-1-0:amd64. 383s Preparing to unpack .../143-libpixman-1-0_0.44.0-3_amd64.deb ... 383s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 383s Selecting previously unselected package libxcb-render0:amd64. 383s Preparing to unpack .../144-libxcb-render0_1.17.0-2_amd64.deb ... 383s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 383s Selecting previously unselected package libxcb-shm0:amd64. 383s Preparing to unpack .../145-libxcb-shm0_1.17.0-2_amd64.deb ... 383s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 383s Selecting previously unselected package libcairo2:amd64. 383s Preparing to unpack .../146-libcairo2_1.18.4-1_amd64.deb ... 383s Unpacking libcairo2:amd64 (1.18.4-1) ... 383s Selecting previously unselected package libmpfi0:amd64. 383s Preparing to unpack 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package imagemagick-7.q16. 384s Preparing to unpack .../158-imagemagick-7.q16_8%3a7.1.1.43+dfsg1-1_amd64.deb ... 384s Unpacking imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 384s Selecting previously unselected package imagemagick. 384s Preparing to unpack .../159-imagemagick_8%3a7.1.1.43+dfsg1-1_amd64.deb ... 384s Unpacking imagemagick (8:7.1.1.43+dfsg1-1) ... 384s Selecting previously unselected package hevea. 384s Preparing to unpack .../160-hevea_2.36-2_amd64.deb ... 384s Unpacking hevea (2.36-2) ... 384s Selecting previously unselected package libllvm17t64:amd64. 384s Preparing to unpack .../161-libllvm17t64_1%3a17.0.6-21_amd64.deb ... 384s Unpacking libllvm17t64:amd64 (1:17.0.6-21) ... 385s Selecting previously unselected package libamd-comgr2:amd64. 385s Preparing to unpack .../162-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 385s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 385s Selecting previously unselected package libsuitesparseconfig7:amd64. 385s Preparing to unpack .../163-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_amd64.deb ... 385s Unpacking libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-3) ... 385s Selecting previously unselected package libamd3:amd64. 385s Preparing to unpack .../164-libamd3_1%3a7.8.3+dfsg-3_amd64.deb ... 385s Unpacking libamd3:amd64 (1:7.8.3+dfsg-3) ... 385s Selecting previously unselected package libhsakmt1:amd64. 385s Preparing to unpack .../165-libhsakmt1_5.7.0-1build1_amd64.deb ... 385s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 385s Selecting previously unselected package libhsa-runtime64-1. 385s Preparing to unpack .../166-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 385s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 385s Selecting previously unselected package libamdhip64-5. 385s Preparing to unpack .../167-libamdhip64-5_5.7.1-5.1_amd64.deb ... 385s Unpacking libamdhip64-5 (5.7.1-5.1) ... 385s Selecting previously unselected package libapache-pom-java. 385s 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... 386s Selecting previously unselected package libigraph3t64:amd64. 386s Preparing to unpack .../184-libigraph3t64_0.10.15+ds-3_amd64.deb ... 386s Unpacking libigraph3t64:amd64 (0.10.15+ds-3) ... 386s Selecting previously unselected package libjs-jquery. 386s Preparing to unpack .../185-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 386s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 386s Selecting previously unselected package libjs-jquery-ui. 386s Preparing to unpack .../186-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 386s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 386s Selecting previously unselected package libjs-underscore. 386s Preparing to unpack .../187-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 386s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 386s Selecting previously unselected package libjs-sphinxdoc. 386s Preparing to unpack .../188-libjs-sphinxdoc_8.2.3-1_all.deb ... 386s Unpacking libjs-sphinxdoc (8.2.3-1) ... 386s Selecting previously unselected package libjson-perl. 386s Preparing to unpack .../189-libjson-perl_4.10000-1_all.deb ... 386s Unpacking libjson-perl (4.10000-1) ... 386s Selecting previously unselected package liblbfgsb0:amd64. 386s Preparing to unpack .../190-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 386s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 386s Selecting previously unselected package libmbedcrypto16:amd64. 386s Preparing to unpack .../191-libmbedcrypto16_3.6.2-3ubuntu1_amd64.deb ... 386s Unpacking libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 386s Selecting previously unselected package libmbedx509-7:amd64. 386s Preparing to unpack .../192-libmbedx509-7_3.6.2-3ubuntu1_amd64.deb ... 386s Unpacking libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 386s Selecting previously unselected package libmbedtls21:amd64. 386s Preparing to unpack .../193-libmbedtls21_3.6.2-3ubuntu1_amd64.deb ... 386s Unpacking libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 386s Selecting previously unselected package libmunge2:amd64. 386s 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.../199-libpmix2t64_5.0.6-5_amd64.deb ... 386s Unpacking libpmix2t64:amd64 (5.0.6-5) ... 386s Selecting previously unselected package libibumad3:amd64. 386s Preparing to unpack .../200-libibumad3_56.0-4ubuntu1_amd64.deb ... 386s Unpacking libibumad3:amd64 (56.0-4ubuntu1) ... 386s Selecting previously unselected package libibmad5:amd64. 386s Preparing to unpack .../201-libibmad5_56.0-4ubuntu1_amd64.deb ... 386s Unpacking libibmad5:amd64 (56.0-4ubuntu1) ... 386s Selecting previously unselected package libucx0:amd64. 386s Preparing to unpack .../202-libucx0_1.18.1+ds-2_amd64.deb ... 386s Unpacking libucx0:amd64 (1.18.1+ds-2) ... 387s Selecting previously unselected package libopenmpi40:amd64. 387s Preparing to unpack .../203-libopenmpi40_5.0.7-1_amd64.deb ... 387s Unpacking libopenmpi40:amd64 (5.0.7-1) ... 387s Selecting previously unselected package zlib1g-dev:amd64. 387s Preparing to unpack .../204-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 387s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 387s Selecting previously unselected package libpython3.13-dev:amd64. 387s Preparing to unpack .../205-libpython3.13-dev_3.13.3-1_amd64.deb ... 387s Unpacking libpython3.13-dev:amd64 (3.13.3-1) ... 387s Selecting previously unselected package libpython3-dev:amd64. 387s Preparing to unpack .../206-libpython3-dev_3.13.3-1_amd64.deb ... 387s Unpacking libpython3-dev:amd64 (3.13.3-1) ... 387s Selecting previously unselected package libpython3-all-dev:amd64. 387s Preparing to unpack .../207-libpython3-all-dev_3.13.3-1_amd64.deb ... 387s Unpacking libpython3-all-dev:amd64 (3.13.3-1) ... 387s Selecting previously unselected package libqhull-r8.0:amd64. 387s Preparing to unpack .../208-libqhull-r8.0_2020.2-6build1_amd64.deb ... 387s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 387s Selecting previously unselected package libxslt1.1:amd64. 387s Preparing to unpack .../209-libxslt1.1_1.1.39-0exp1ubuntu4_amd64.deb ... 387s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu4) ... 387s Selecting previously unselected package mafft. 387s Preparing to unpack .../210-mafft_7.505-1_amd64.deb ... 387s Unpacking mafft (7.505-1) ... 387s Selecting previously unselected package muscle3. 387s Preparing to unpack .../211-muscle3_3.8.1551-3_amd64.deb ... 387s Unpacking muscle3 (3.8.1551-3) ... 387s Selecting previously unselected package ncbi-data. 387s Preparing to unpack .../212-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 387s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 387s Selecting previously unselected package ncbi-blast+. 387s Preparing to unpack .../213-ncbi-blast+_2.16.0+ds-6build1_amd64.deb ... 387s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 388s Selecting previously unselected package openmpi-common. 388s Preparing to unpack .../214-openmpi-common_5.0.7-1_all.deb ... 388s Unpacking openmpi-common (5.0.7-1) ... 388s Selecting previously unselected package openmpi-bin. 388s Preparing to unpack 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unselected package probcons. 388s Preparing to unpack .../221-probcons_1.12-14_amd64.deb ... 388s Unpacking probcons (1.12-14) ... 388s Selecting previously unselected package python-biopython-doc. 388s Preparing to unpack .../222-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 388s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 388s Selecting previously unselected package python-matplotlib-data. 388s Preparing to unpack .../223-python-matplotlib-data_3.8.3-7build1_all.deb ... 388s Unpacking python-matplotlib-data (3.8.3-7build1) ... 388s Selecting previously unselected package python3-all. 388s Preparing to unpack .../224-python3-all_3.13.3-1_amd64.deb ... 388s Unpacking python3-all (3.13.3-1) ... 388s Selecting previously unselected package python3.13-dev. 388s Preparing to unpack .../225-python3.13-dev_3.13.3-1_amd64.deb ... 388s Unpacking python3.13-dev (3.13.3-1) ... 389s Selecting previously unselected package python3-dev. 389s Preparing to unpack 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python3-pil:amd64 (11.1.0-5build1) ... 389s Selecting previously unselected package python3-cairo. 389s Preparing to unpack .../232-python3-cairo_1.27.0-2_amd64.deb ... 389s Unpacking python3-cairo (1.27.0-2) ... 389s Selecting previously unselected package python3-freetype. 389s Preparing to unpack .../233-python3-freetype_2.5.1-1_all.deb ... 389s Unpacking python3-freetype (2.5.1-1) ... 389s Selecting previously unselected package python3-rlpycairo. 389s Preparing to unpack .../234-python3-rlpycairo_0.3.0-3_all.deb ... 389s Unpacking python3-rlpycairo (0.3.0-3) ... 389s Selecting previously unselected package python3-reportlab. 389s Preparing to unpack .../235-python3-reportlab_4.3.1-1_all.deb ... 389s Unpacking python3-reportlab (4.3.1-1) ... 389s Selecting previously unselected package w3c-sgml-lib. 389s Preparing to unpack .../236-w3c-sgml-lib_1.3-3_all.deb ... 389s Unpacking w3c-sgml-lib (1.3-3) ... 389s Selecting previously unselected package python3-biopython. 389s Preparing to unpack .../237-python3-biopython_1.85+dfsg-2build1_amd64.deb ... 389s Unpacking python3-biopython (1.85+dfsg-2build1) ... 389s Selecting previously unselected package python3-biopython-sql. 389s Preparing to unpack .../238-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 389s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 389s Selecting previously unselected package python3-brotli. 389s Preparing to unpack .../239-python3-brotli_1.1.0-2build4_amd64.deb ... 389s Unpacking python3-brotli (1.1.0-2build4) ... 389s Selecting previously unselected package python3-contourpy. 389s Preparing to unpack .../240-python3-contourpy_1.3.1-1build1_amd64.deb ... 389s Unpacking python3-contourpy (1.3.1-1build1) ... 389s Selecting previously unselected package python3-cycler. 389s Preparing to unpack .../241-python3-cycler_0.12.1-1_all.deb ... 389s Unpacking python3-cycler (0.12.1-1) ... 389s Selecting previously unselected package python3-decorator. 389s Preparing to unpack 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up python3-lz4 (4.4.0+dfsg-1build1) ... 397s Setting up libxcb-render0:amd64 (1.17.0-2) ... 397s Setting up python3-defusedxml (0.7.1-3) ... 397s Setting up mafft (7.505-1) ... 397s Setting up libarchive-zip-perl (1.68-1) ... 397s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 397s Setting up imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 397s Setting up bwa (0.7.18-1) ... 397s Setting up python3-alabaster (0.7.16-0.1) ... 397s Setting up fonts-lyx (2.4.3-1) ... 397s Setting up libijs-0.35:amd64 (0.35-15.2) ... 397s Setting up libdebhelper-perl (13.24.1ubuntu2) ... 397s Setting up libgs-common (10.05.0dfsg1-0ubuntu1) ... 397s Setting up libfontbox-java (1:1.8.16-5) ... 397s Setting up phylip (1:3.697+dfsg-4build1) ... 397s Setting up x11-common (1:7.7+23ubuntu4) ... 398s Setting up libpq5:amd64 (17.4-1) ... 398s Setting up libibumad3:amd64 (56.0-4ubuntu1) ... 398s Setting up libdeflate0:amd64 (1.23-2) ... 398s Setting up python3-tabulate (0.9.0-1) ... 398s Setting up m4 (1.4.19-7) ... 398s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 398s Setting up python3-all (3.13.3-1) ... 398s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 398s Setting up libibmad5:amd64 (56.0-4ubuntu1) ... 398s Setting up libgomp1:amd64 (15-20250404-0ubuntu1) ... 398s Setting up python3-freetype (2.5.1-1) ... 398s Setting up emboss-data (6.6.0+dfsg-15ubuntu2) ... 398s Setting up python3-networkx (3.2.1-4ubuntu1) ... 400s Setting up libmysqlclient24:amd64 (8.4.4-0ubuntu2) ... 400s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 400s Setting up libnetpbm11t64:amd64 (2:11.09.02-2) ... 400s Setting up python3-platformdirs (4.3.6-1) ... 400s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 400s Setting up poppler-data (0.4.12-1) ... 400s Setting up python3-fs (2.4.16-7) ... 400s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 400s Setting up unicode-data (15.1.0-1) ... 400s Setting up python3-mysqldb (1.4.6-2build6) ... 400s Setting up tex-common (6.19) ... 400s update-language: texlive-base not installed and configured, doing nothing! 400s Setting up python3-roman (5.0-1) ... 401s Setting up python3-decorator (5.1.1-5) ... 401s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 401s Setting up autotools-dev (20240727.1) ... 401s Setting up libblas3:amd64 (3.12.1-2) ... 401s 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 401s Setting up libmunge2:amd64 (0.5.16-1) ... 401s Setting up libllvm17t64:amd64 (1:17.0.6-21) ... 401s Setting up libexpat1-dev:amd64 (2.7.1-1) ... 401s Setting up libzzip-0-13t64:amd64 (0.13.78+dfsg.1-0.1) ... 401s Setting up libjbig2dec0:amd64 (0.20-1build3) ... 401s Setting up python3-snowballstemmer (2.2.0-4build1) ... 401s Setting up libteckit0:amd64 (2.5.12+ds1-1) ... 401s Setting up python3-brotli (1.1.0-2build4) ... 401s Setting up libapache-pom-java (33-2) ... 401s Setting up libavahi-common-data:amd64 (0.8-16ubuntu2) ... 401s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 401s Setting up muscle3 (3.8.1551-3) ... 401s Setting up t1utils (1.41-4build3) ... 401s Setting up libquadmath0:amd64 (15-20250404-0ubuntu1) ... 401s Setting up python3-cycler (0.12.1-1) ... 401s Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-6) ... 401s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 401s Setting up fonts-dejavu-mono (2.37-8) ... 401s Setting up python3-kiwisolver (1.4.7-3build1) ... 401s Setting up libhwloc15:amd64 (2.12.0-1) ... 401s Setting up libmpc3:amd64 (1.3.1-1build2) ... 401s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 401s Setting up libidn12:amd64 (1.43-1) ... 401s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 401s Setting up autopoint (0.23.1-1) ... 401s Setting up libmpfi0:amd64 (1.5.4+ds-4) ... 401s Setting up python3-psycopg2 (2.9.10-1build1) ... 401s Setting up fonts-dejavu-core (2.37-8) ... 401s Setting up wise-data (2.4.1-25) ... 401s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 401s Setting up libltdl7:amd64 (2.5.4-4) ... 401s Setting up libfftw3-double3:amd64 (3.3.10-2fakesync1build1) ... 401s Setting up libcifpp-data (7.0.9-1) ... 401s Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-6) ... 401s Setting up libgfortran5:amd64 (15-20250404-0ubuntu1) ... 401s Setting up autoconf (2.72-3ubuntu1) ... 401s Setting up libwebp7:amd64 (1.5.0-0.1) ... 401s Setting up libubsan1:amd64 (15-20250404-0ubuntu1) ... 401s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 401s Setting up dwz (0.15-1build6) ... 401s Setting up liblqr-1-0:amd64 (0.4.2-2.1build2) ... 401s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 401s Setting up libhwasan0:amd64 (15-20250404-0ubuntu1) ... 402s Setting up python3-rdflib (7.1.1-2) ... 402s Setting up libasan8:amd64 (15-20250404-0ubuntu1) ... 402s Setting up libjson-perl (4.10000-1) ... 402s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu4) ... 402s Setting up libpsm2-2 (11.2.185-2.1) ... 402s Setting up openmpi-common (5.0.7-1) ... 402s Setting up clustalw (2.1+lgpl-7) ... 402s Setting up debugedit (1:5.1-2) ... 402s Setting up libhts3t64:amd64 (1.21+ds-1) ... 402s Setting up fonts-lmodern (2.005-1) ... 402s Setting up libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-3) ... 402s Setting up librdmacm1t64:amd64 (56.0-4ubuntu1) ... 402s Setting up python3-roman-numerals (3.1.0-1ubuntu1) ... 402s Setting up libopenjp2-7:amd64 (2.5.3-2) ... 402s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 402s Setting up fasttree (2.1.11-2) ... 402s Setting up sgml-base (1.31) ... 402s Setting up python3-msgpack (1.0.3-3build4) ... 402s Setting up libplfit0:amd64 (0.9.6+ds-2ubuntu1) ... 402s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 402s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 402s Setting up libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 402s Setting up libpaper2:amd64 (2.2.5-0.3) ... 402s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.4) ... 402s 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 402s Setting up libtsan2:amd64 (15-20250404-0ubuntu1) ... 402s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 402s Setting up python3-mpmath (1.3.0-1) ... 403s Setting up libisl23:amd64 (0.27-1) ... 403s Setting up libde265-0:amd64 (1.0.15-1build5) ... 403s Setting up python-matplotlib-data (3.8.3-7build1) ... 403s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 403s Setting up dialign (2.2.1-13) ... 403s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 403s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 403s Setting up xdg-utils (1.2.1-2ubuntu1) ... 403s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 403s Setting up libcc1-0:amd64 (15-20250404-0ubuntu1) ... 403s Setting up liblsan0:amd64 (15-20250404-0ubuntu1) ... 403s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 403s Setting up libitm1:amd64 (15-20250404-0ubuntu1) ... 403s Setting up libsynctex2:amd64 (2024.20240313.70630+ds-6) ... 403s Setting up prank (0.0.170427+dfsg-3) ... 403s Setting up libargtable2-0 (13-3) ... 403s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 403s Setting up raxml (8.2.13+dfsg-2) ... 403s Setting up python3-imagesize (1.4.1-1) ... 403s Setting up libpotrace0:amd64 (1.16-2build1) ... 403s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 403s Setting up automake (1:1.17-3ubuntu1) ... 403s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 403s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 403s Setting up libfabric1:amd64 (1.17.0-3.1) ... 403s Setting up python3-sympy (1.13.3-5) ... 408s Setting up libice6:amd64 (2:1.1.1-1) ... 408s Setting up flex (2.6.4-8.2build1) ... 408s Setting up liblapack3:amd64 (3.12.1-2) ... 408s 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 408s Setting up gettext (0.23.1-1) ... 408s Setting up libarpack2t64:amd64 (3.9.1-6) ... 408s Setting up libamd3:amd64 (1:7.8.3+dfsg-3) ... 408s Setting up libpdfbox-java (1:1.8.16-5) ... 408s Setting up libcolamd3:amd64 (1:7.8.3+dfsg-3) ... 408s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 408s Setting up wise (2.4.1-25) ... 408s Setting up preview-latex-style (13.2-1) ... 408s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 408s Setting up libcommons-parent-java (56-1) ... 408s Setting up libavahi-common3:amd64 (0.8-16ubuntu2) ... 408s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 408s Setting up libcifpp7:amd64 (7.0.9-1) ... 408s Setting up libpaper-utils (2.2.5-0.3) ... 408s Setting up clustalo (1.2.4-8build1) ... 408s Setting up dssp (4.4.10-1) ... 408s Setting up xfonts-utils (1:7.7+7) ... 408s Setting up libhwloc-plugins:amd64 (2.12.0-1) ... 408s Setting up samtools (1.21-1) ... 408s Setting up intltool-debian (0.35.0+20060710.6) ... 408s Setting up libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 408s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 408s Setting up libptexenc1:amd64 (2024.20240313.70630+ds-6) ... 408s Setting up libglpk40:amd64 (5.0-1build2) ... 408s Setting up libraqm0:amd64 (0.10.2-1) ... 408s Setting up libpython3.13-dev:amd64 (3.13.3-1) ... 408s Setting up cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 408s Setting up libpmix2t64:amd64 (5.0.6-5) ... 408s Setting up python3-numpy (1:2.2.3+ds-5) ... 410s Setting up libjs-sphinxdoc (8.2.3-1) ... 410s Setting up libraw23t64:amd64 (0.21.4-2) ... 410s Setting up cpp-14 (14.2.0-19ubuntu2) ... 410s Setting up libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 410s Setting up dh-strip-nondeterminism (1.14.1-2) ... 410s Setting up python3-lxml:amd64 (5.3.2-1) ... 410s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 410s Setting up libtiff6:amd64 (4.7.0-3ubuntu1) ... 410s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 410s Setting up xml-core (0.19) ... 410s Setting up python3-contourpy (1.3.1-1build1) ... 410s Setting up libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 410s Setting up libgcc-14-dev:amd64 (14.2.0-19ubuntu2) ... 410s Setting up libigraph3t64:amd64 (0.10.15+ds-3) ... 410s Setting up libstdc++-14-dev:amd64 (14.2.0-19ubuntu2) ... 410s Setting up libsm6:amd64 (2:1.2.4-1) ... 410s Setting up libavahi-client3:amd64 (0.8-16ubuntu2) ... 410s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 410s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 410s Setting up libxft2:amd64 (2.3.6-1build1) ... 410s Setting up python3-scipy (1.14.1-4ubuntu2) ... 413s Setting up libpython3-dev:amd64 (3.13.3-1) ... 413s Setting up python3.13-dev (3.13.3-1) ... 413s Setting up po-debconf (1.0.21+nmu1) ... 413s Setting up libtk8.6:amd64 (8.6.16-1) ... 413s Setting up python3-mmtf (1.1.3-1) ... 413s Setting up fonts-urw-base35 (20200910-8) ... 413s Setting up libcairo2:amd64 (1.18.4-1) ... 413s Setting up python3.13-tk (3.13.3-1) ... 414s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 414s Setting up python3-pil:amd64 (11.1.0-5build1) ... 414s Setting up libamdhip64-5 (5.7.1-5.1) ... 414s Setting up libpython3-all-dev:amd64 (3.13.3-1) ... 414s Setting up sphinx-common (8.2.3-1) ... 414s Setting up python3-dev (3.13.3-1) ... 414s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 414s Setting up netpbm (2:11.09.02-2) ... 414s Setting up python3-igraph (0.11.8+ds-1build1) ... 414s Setting up cpp (4:14.2.0-1ubuntu1) ... 414s Setting up gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 414s Setting up libcups2t64:amd64 (2.4.12-0ubuntu1) ... 414s Setting up python3-all-dev (3.13.3-1) ... 414s Setting up libgs10-common (10.05.0dfsg1-0ubuntu1) ... 414s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 414s Setting up libucx0:amd64 (1.18.1+ds-2) ... 414s Setting up libxmu6:amd64 (2:1.1.3-3build2) ... 414s Setting up python3-cairo (1.27.0-2) ... 414s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 414s Setting up blt (2.5.3+dfsg-8) ... 414s Setting up python3-tk:amd64 (3.13.3-1) ... 414s Setting up libxaw7:amd64 (2:1.0.16-1) ... 414s Setting up gcc-14 (14.2.0-19ubuntu2) ... 414s Setting up python3-pil.imagetk:amd64 (11.1.0-5build1) ... 414s Setting up python3-rlpycairo (0.3.0-3) ... 415s Setting up g++-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 415s Setting up python3-reportlab (4.3.1-1) ... 415s Setting up texlive-binaries (2024.20240313.70630+ds-6) ... 415s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 415s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 415s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 415s Setting up g++-14 (14.2.0-19ubuntu2) ... 415s Setting up texlive-base (2024.20250309-1) ... 416s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 416s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 416s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 417s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 417s Setting up libgs10:amd64 (10.05.0dfsg1-0ubuntu1) ... 417s Setting up libopenmpi40:amd64 (5.0.7-1) ... 417s Setting up libtool (2.5.4-4) ... 417s Setting up ghostscript (10.05.0dfsg1-0ubuntu1) ... 417s Setting up gcc (4:14.2.0-1ubuntu1) ... 417s Setting up dh-autoreconf (20) ... 417s Setting up texlive-latex-base (2024.20250309-1) ... 417s Setting up texlive-latex-recommended (2024.20250309-1) ... 417s Setting up texlive-pictures (2024.20250309-1) ... 417s Setting up g++ (4:14.2.0-1ubuntu1) ... 417s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 417s Setting up texlive-fonts-recommended (2024.20250309-1) ... 417s Setting up build-essential (12.12ubuntu1) ... 417s Setting up openmpi-bin (5.0.7-1) ... 417s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 417s 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 417s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 417s Setting up mpi-default-bin (1.18) ... 417s Setting up debhelper (13.24.1ubuntu2) ... 417s Setting up texlive-latex-extra (2024.20250309-2) ... 417s Setting up phyml (3:3.3.20220408-4build1) ... 417s Setting up python3-fonttools (4.55.3-2build1) ... 418s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 418s Setting up libheif-plugin-aomdec:amd64 (1.19.7-1) ... 418s Setting up libheif-plugin-libde265:amd64 (1.19.7-1) ... 418s Setting up python3-matplotlib (3.8.3-7build1) ... 420s Setting up libheif1:amd64 (1.19.7-1) ... 420s Setting up libgd3:amd64 (2.3.3-12ubuntu3) ... 420s Setting up libmagickcore-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... 420s Setting up emboss-lib (6.6.0+dfsg-15ubuntu2) ... 420s Setting up libmagickwand-7.q16-10:amd64 (8:7.1.1.43+dfsg1-1) ... 420s Setting up emboss (6.6.0+dfsg-15ubuntu2) ... 420s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 420s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 420s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 420s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 420s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 420s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 420s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 420s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 420s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 420s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 420s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 420s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 420s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 420s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 420s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 420s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 420s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 420s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 420s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 420s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 420s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 420s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 420s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 420s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 420s 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 420s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 420s 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 420s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 420s 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 420s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 420s 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 420s Setting up hevea (2.36-2) ... 420s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 420s Processing triggers for install-info (7.1.1-1) ... 420s Processing triggers for libc-bin (2.41-6ubuntu1) ... 420s Processing triggers for man-db (2.13.0-1) ... 422s Processing triggers for shared-mime-info (2.4-5build1) ... 423s Processing triggers for sgml-base (1.31) ... 423s Setting up w3c-sgml-lib (1.3-3) ... 450s Setting up docutils-common (0.21.2+dfsg-2) ... 450s Setting up python3-biopython (1.85+dfsg-2build1) ... 451s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 451s Processing triggers for sgml-base (1.31) ... 451s Setting up python3-docutils (0.21.2+dfsg-2) ... 452s Setting up python3-sphinx (8.2.3-1) ... 453s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 453s Setting up python3-numpydoc (1.8.0-1) ... 453s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 453s Processing triggers for tex-common (6.19) ... 453s Running updmap-sys. This may take some time... done. 453s Running mktexlsr /var/lib/texmf ... done. 454s Building format(s) --all. 510s This may take some time... done. 520s autopkgtest [06:31:53]: test full_suite: sh debian/tests/run-unit-test 520s autopkgtest [06:31:53]: test full_suite: [----------------------- 523s mkdir: created directory 'Bio' 523s mkdir: created directory 'Bio/Align' 523s mkdir: created directory 'Bio/Align/substitution_matrices' 523s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 523s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 523s test_Ace ... ok 523s test_Affy ... ok 526s test_AlignIO ... ok 526s test_AlignIO_ClustalIO ... ok 526s test_AlignIO_EmbossIO ... ok 526s test_AlignIO_FastaIO ... ok 526s test_AlignIO_MauveIO ... ok 526s test_AlignIO_PhylipIO ... ok 526s test_AlignIO_convert ... ok 526s test_AlignInfo ... ok 526s test_Align_Alignment ... ok 526s test_Align_a2m ... ok 526s test_Align_bed ... ok 526s test_Align_bigbed ... ok 527s test_Align_bigmaf ... ok 527s test_Align_bigpsl ... ok 527s test_Align_chain ... ok 527s test_Align_clustal ... ok 532s test_Align_codonalign ... ok 532s test_Align_emboss ... ok 532s test_Align_exonerate ... ok 532s test_Align_fasta ... ok 533s test_Align_hhr ... ok 533s test_Align_maf ... ok 533s test_Align_mauve ... ok 534s test_Align_msf ... ok 534s test_Align_nexus ... ok 534s test_Align_phylip ... ok 534s test_Align_psl ... ok 534s test_Align_sam ... ok 535s test_Align_stockholm ... ok 536s test_Align_tabular ... ok 536s test_Application ... ok 536s test_BWA_tool ... ok 536s test_BioSQL_MySQLdb_online ... skipping. internet not available 536s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 536s test_BioSQL_mysql_connector_online ... skipping. internet not available 536s test_BioSQL_psycopg2_online ... skipping. internet not available 541s test_BioSQL_sqlite3 ... ok 541s test_BioSQL_sqlite3_online ... skipping. internet not available 541s test_Blast_Record ... ok 542s test_Blast_parser ... ok 542s test_CAPS ... ok 542s test_Chi2 ... ok 542s test_ClustalOmega_tool ... ok 543s test_Clustalw_tool ... ok 543s test_Cluster ... ok 544s test_CodonTable ... ok 544s test_ColorSpiral ... ok 544s test_Compass ... ok 545s test_Consensus ... ok 546s test_Dialign_tool ... ok 546s test_EMBL_unittest ... ok 551s test_Emboss ... ok 551s test_EmbossPrimer ... ok 556s test_Entrez ... ok 556s test_Entrez_online ... skipping. internet not available 556s test_Entrez_parser ... ok 556s test_Enzyme ... ok 556s test_ExPASy ... skipping. internet not available 556s test_Fasttree_tool ... ok 556s test_File ... ok 556s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 556s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 556s ok 558s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 560s ok 561s test_GraphicsChromosome ... ok 561s test_GraphicsDistribution ... ok 562s test_GraphicsGeneral ... ok 562s test_HMMCasino ... ok 562s test_HMMGeneral ... ok 562s test_KEGG ... ok 562s test_KEGG_online ... skipping. internet not available 568s test_KGML_graphics ... ok 568s test_KGML_graphics_online ... skipping. internet not available 568s test_KGML_nographics ... ok 568s test_KeyWList ... ok 569s test_LogisticRegression ... ok 569s test_MafIO_index ... ok 571s test_Mafft_tool ... ok 571s test_MarkovModel ... ok 571s test_Medline ... ok 572s test_Muscle_tool ... ok 572s test_NCBIXML ... Exception ignored in: 572s Traceback (most recent call last): 572s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 572s expat_parser.Parse(NULL, True) 572s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 572s ok 574s test_NCBI_BLAST_tools ... ok 574s test_NCBI_qblast ... ok 574s test_NMR ... ok 574s test_NaiveBayes ... ok 574s test_Nexus ... ok 574s test_PAML_baseml ... ok 575s test_PAML_codeml ... ok 575s test_PAML_yn00 ... ok 579s test_PDB_CEAligner ... ok 580s test_PDB_DSSP ... ok 580s test_PDB_Dice ... ok 580s test_PDB_Disordered ... ok 581s test_PDB_Exposure ... ok 581s test_PDB_FragmentMapper ... ok 582s test_PDB_KDTree ... ok 582s test_PDB_MMCIF2Dict ... ok 582s test_PDB_MMCIFIO ... ok 583s test_PDB_MMCIFParser ... ok 583s test_PDB_NACCESS ... ok 584s test_PDB_PDBIO ... ok 584s test_PDB_PDBList ... skipping. internet not available 590s test_PDB_PDBMLParser ... ok 590s test_PDB_PDBParser ... ok 590s 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 590s test_PDB_Polypeptide ... ok 590s test_PDB_QCPSuperimposer ... ok 593s test_PDB_SASA ... ok 594s test_PDB_SMCRA ... ok 594s test_PDB_Selection ... ok 594s test_PDB_StructureAlignment ... ok 594s test_PDB_Superimposer ... ok 594s test_PDB_alphafold_db ... skipping. internet not available 597s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 597s warnings.warn( 597s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 597s warnings.warn( 597s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 597s warnings.warn( 597s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 597s warnings.warn( 597s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 597s warnings.warn( 597s ok 604s test_PDB_internal_coords ... ok 604s test_PDB_parse_pdb_header ... ok 605s test_PDB_vectors ... ok 605s test_PQR ... ok 605s test_Pathway ... ok 605s test_Phd ... ok 606s test_Phylo ... ok 606s test_PhyloXML ... ok 607s test_Phylo_CDAO ... ok 607s test_Phylo_NeXML ... ok 608s test_Phylo_igraph ... ok 611s test_Phylo_matplotlib ... ok 611s test_Phylo_networkx ... ok 612s test_PopGen_GenePop_nodepend ... ok 613s test_Prank_tool ... ok 614s test_Probcons_tool ... ok 615s test_ProtParam ... ok 615s test_RCSBFormats ... ok 616s test_Restriction ... ok 616s test_SCOP_Astral ... ok 617s test_SCOP_Cla ... ok 617s test_SCOP_Des ... ok 618s test_SCOP_Dom ... ok 618s test_SCOP_Hie ... ok 619s test_SCOP_Raf ... ok 619s test_SCOP_Residues ... ok 620s test_SCOP_Scop ... ok 620s test_SVDSuperimposer ... ok 620s test_SearchIO_blast_tab ... ok 621s test_SearchIO_blast_tab_index ... ok 622s test_SearchIO_blast_xml ... ok 623s test_SearchIO_blast_xml_index ... ok 624s test_SearchIO_blat_psl ... ok 624s test_SearchIO_blat_psl_index ... ok 625s test_SearchIO_exonerate ... ok 625s test_SearchIO_exonerate_text_index ... ok 625s test_SearchIO_exonerate_vulgar_index ... ok 626s test_SearchIO_fasta_m10 ... ok 626s test_SearchIO_fasta_m10_index ... ok 627s test_SearchIO_hhsuite2_text ... ok 627s test_SearchIO_hmmer2_text ... ok 628s test_SearchIO_hmmer2_text_index ... ok 628s test_SearchIO_hmmer3_domtab ... ok 629s test_SearchIO_hmmer3_domtab_index ... ok 629s test_SearchIO_hmmer3_tab ... ok 630s test_SearchIO_hmmer3_tab_index ... ok 630s test_SearchIO_hmmer3_text ... ok 631s test_SearchIO_hmmer3_text_index ... ok 631s test_SearchIO_interproscan_xml ... ok 632s test_SearchIO_model ... ok 633s test_SearchIO_write ... ok 633s test_SeqFeature ... ok 650s test_SeqIO ... ok 650s test_SeqIO_AbiIO ... ok 651s test_SeqIO_FastaIO ... ok 651s test_SeqIO_Gck ... ok 652s test_SeqIO_Gfa ... ok 652s test_SeqIO_Insdc ... ok 653s test_SeqIO_NibIO ... ok 655s test_SeqIO_PdbIO ... ok 656s test_SeqIO_QualityIO ... ok 656s test_SeqIO_SeqXML ... ok 657s test_SeqIO_SffIO ... ok 657s test_SeqIO_SnapGene ... ok 658s test_SeqIO_TwoBitIO ... ok 659s test_SeqIO_UniprotIO ... ok 659s test_SeqIO_Xdna ... ok 660s test_SeqIO_features ... ok 675s test_SeqIO_index ... ok 676s test_SeqIO_online ... skipping. internet not available 676s test_SeqIO_write ... ok 677s test_SeqRecord ... ok 677s test_SeqUtils ... ok 679s test_Seq_objs ... ok 679s test_SwissProt ... ok 683s test_TCoffee_tool ... ok 683s test_TogoWS ... skipping. internet not available 684s test_TreeConstruction ... ok 684s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 685s test_UniGene ... ok 685s test_UniProt ... skipping. internet not available 686s test_UniProt_GOA ... ok 686s test_align ... ok 687s test_align_substitution_matrices ... ok 690s test_bgzf ... ok 690s test_cellosaurus ... ok 697s test_codonalign ... ok 697s test_geo ... ok 698s test_kNN ... ok 699s test_motifs ... ok 699s test_motifs_online ... skipping. internet not available 700s 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. 700s warnings.warn( 700s ok 700s test_pairwise2_no_C ... ok 701s test_pairwise_aligner ... ok 701s test_pairwise_alignment_map ... ok 709s test_phenotype ... ok 710s test_phenotype_fit ... ok 710s test_phyml_tool ... ok 711s test_prodoc ... ok 711s test_prosite ... ok 712s test_raxml_tool ... ok 712s test_samtools_tool ... ok 713s test_seq ... ok 713s test_translate ... ok 714s ---------------------------------------------------------------------- 714s Ran 219 tests in 190.739 seconds 714s 714s Skipping any tests requiring internet access 714s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 714s Operating system: posix linux 715s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 715s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 716s autopkgtest [06:35:09]: test full_suite: -----------------------] 716s full_suite PASS 716s autopkgtest [06:35:09]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 716s autopkgtest [06:35:09]: @@@@@@@@@@@@@@@@@@@@ summary 716s dependencies PASS 716s full_suite PASS 785s nova [W] Skipping flock for amd64 785s Creating nova instance adt-questing-amd64-python-biopython-20250504-062313-juju-7f2275-prod-proposed-migration-environment-2-0a6eb235-ebf9-418a-a01b-5a6c8a50344e from image adt/ubuntu-questing-amd64-server-20250504.img (UUID 4cf89fcc-bb54-4e0d-9acf-e03be076f6e4)... 785s nova [W] Timed out waiting for ae8bb030-8d38-4aee-8445-9ce8091e2f91 to get deleted. 785s nova [W] Skipping flock for amd64 785s Creating nova instance adt-questing-amd64-python-biopython-20250504-062313-juju-7f2275-prod-proposed-migration-environment-2-0a6eb235-ebf9-418a-a01b-5a6c8a50344e from image adt/ubuntu-questing-amd64-server-20250504.img (UUID 4cf89fcc-bb54-4e0d-9acf-e03be076f6e4)... 785s nova [W] Timed out waiting for ccdda9c0-d33b-482a-bb87-0e6a0f8275f6 to get deleted.