0s autopkgtest [19:34:08]: starting date and time: 2025-05-03 19:34:08+0000 0s autopkgtest [19:34:08]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [19:34:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lxfdxd6r/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 autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-10.secgroup --name adt-questing-arm64-python-biopython-20250503-193408-juju-7f2275-prod-proposed-migration-environment-2-f16a332c-bd2a-415f-9978-ca31b7805f95 --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 88s autopkgtest [19:35:36]: testbed dpkg architecture: arm64 89s autopkgtest [19:35:37]: testbed apt version: 3.0.0 89s autopkgtest [19:35:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 89s autopkgtest [19:35:37]: testbed release detected to be: None 90s autopkgtest [19:35:38]: updating testbed package index (apt update) 90s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 90s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 90s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 90s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 90s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.7 kB] 90s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1442 kB] 90s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [149 kB] 91s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [186 kB] 91s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1384 kB] 91s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [27.5 kB] 91s Fetched 3331 kB in 1s (4146 kB/s) 92s Reading package lists... 92s autopkgtest [19:35:40]: upgrading testbed (apt dist-upgrade and autopurge) 92s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 93s Starting 2 pkgProblemResolver with broken count: 0 93s Done 94s Entering ResolveByKeep 94s 94s Calculating upgrade... 95s The following packages will be upgraded: 95s libperl5.40 libsepol2 perl perl-base perl-modules-5.40 95s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 10.4 MB of archives. 95s After this operation, 65.5 kB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libperl5.40 arm64 5.40.1-3 [4780 kB] 95s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl arm64 5.40.1-3 [262 kB] 95s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-base arm64 5.40.1-3 [1786 kB] 95s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-modules-5.40 all 5.40.1-3 [3217 kB] 96s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 libsepol2 arm64 3.8.1-1 [312 kB] 96s Fetched 10.4 MB in 1s (12.0 MB/s) 96s (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 ... 85229 files and directories currently installed.) 96s Preparing to unpack .../libperl5.40_5.40.1-3_arm64.deb ... 96s Unpacking libperl5.40:arm64 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 97s Preparing to unpack .../perl_5.40.1-3_arm64.deb ... 97s Unpacking perl (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 97s Preparing to unpack .../perl-base_5.40.1-3_arm64.deb ... 97s Unpacking perl-base (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 97s Setting up perl-base (5.40.1-3) ... 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 ... 85229 files and directories currently installed.) 97s Preparing to unpack .../perl-modules-5.40_5.40.1-3_all.deb ... 97s Unpacking perl-modules-5.40 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 97s Preparing to unpack .../libsepol2_3.8.1-1_arm64.deb ... 97s Unpacking libsepol2:arm64 (3.8.1-1) over (3.7-1) ... 97s Setting up libsepol2:arm64 (3.8.1-1) ... 97s Setting up perl-modules-5.40 (5.40.1-3) ... 97s Setting up libperl5.40:arm64 (5.40.1-3) ... 97s Setting up perl (5.40.1-3) ... 97s Processing triggers for man-db (2.13.0-1) ... 98s Processing triggers for libc-bin (2.41-6ubuntu1) ... 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 99s Starting pkgProblemResolver with broken count: 0 99s Starting 2 pkgProblemResolver with broken count: 0 99s Done 99s Solving dependencies... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s autopkgtest [19:35:50]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 102s autopkgtest [19:35:50]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 104s Get:1 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (dsc) [3406 B] 104s Get:2 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (tar) [14.6 MB] 104s Get:3 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (diff) [42.8 kB] 104s gpgv: Signature made Tue Mar 4 15:18:59 2025 UTC 104s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 104s gpgv: Can't check signature: No public key 104s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2build1.dsc: no acceptable signature found 105s autopkgtest [19:35:53]: testing package python-biopython version 1.85+dfsg-2build1 106s autopkgtest [19:35:54]: build not needed 112s autopkgtest [19:36:00]: test dependencies: preparing testbed 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 114s The following NEW packages will be installed: 114s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 114s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 114s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 114s libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 114s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 114s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 114s python-biopython-doc python3-all python3-biopython python3-biopython-sql 114s python3-cairo python3-freetype python3-numpy python3-numpy-dev python3-pil 114s python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib x11-common 114s xfonts-encodings xfonts-utils xml-core 114s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 45.6 MB of archives. 114s After this operation, 124 MB of additional disk space will be used. 114s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 114s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 114s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15-20250404-0ubuntu1 [444 kB] 114s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 114s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 114s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 sgml-base all 1.31 [11.4 kB] 114s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 114s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 114s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 114s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 114s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 114s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 114s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 114s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 114s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 114s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 114s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 114s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 114s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 114s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 114s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 114s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 114s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 114s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 114s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 114s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 114s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 114s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 114s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 114s Get:30 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libjs-sphinxdoc all 8.2.3-1 [27.8 kB] 114s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 114s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 114s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 114s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 114s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 114s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 114s Get:37 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.7.0-3ubuntu1 [197 kB] 114s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 114s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 114s Get:40 http://ftpmaster.internal/ubuntu questing/universe arm64 python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 114s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 python3-all arm64 3.13.3-1 [880 B] 114s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 114s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 114s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 python3-cairo arm64 1.27.0-2 [122 kB] 114s Get:45 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 114s Get:46 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 115s Get:47 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 115s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 xml-core all 0.19 [20.3 kB] 115s Get:49 http://ftpmaster.internal/ubuntu questing/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 115s Get:50 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython arm64 1.85+dfsg-2build1 [1711 kB] 115s Get:51 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 115s Fetched 45.6 MB in 1s (52.6 MB/s) 115s Selecting previously unselected package python3-numpy-dev:arm64. 115s (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 ... 85229 files and directories currently installed.) 115s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 115s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 115s Selecting previously unselected package libblas3:arm64. 115s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 115s Unpacking libblas3:arm64 (3.12.1-2) ... 115s Selecting previously unselected package libgfortran5:arm64. 115s Preparing to unpack .../02-libgfortran5_15-20250404-0ubuntu1_arm64.deb ... 115s Unpacking libgfortran5:arm64 (15-20250404-0ubuntu1) ... 115s Selecting previously unselected package liblapack3:arm64. 115s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 115s Unpacking liblapack3:arm64 (3.12.1-2) ... 115s Selecting previously unselected package python3-numpy. 115s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 115s Unpacking python3-numpy (1:2.2.3+ds-5) ... 115s Selecting previously unselected package sgml-base. 115s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 115s Unpacking sgml-base (1.31) ... 115s Selecting previously unselected package fonts-dejavu-mono. 115s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 115s Unpacking fonts-dejavu-mono (2.37-8) ... 115s Selecting previously unselected package fonts-dejavu-core. 115s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 115s Unpacking fonts-dejavu-core (2.37-8) ... 115s Selecting previously unselected package libfontenc1:arm64. 115s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 115s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 116s Selecting previously unselected package x11-common. 116s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu4_all.deb ... 116s Unpacking x11-common (1:7.7+23ubuntu4) ... 116s Selecting previously unselected package xfonts-encodings. 116s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 116s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 116s Selecting previously unselected package xfonts-utils. 116s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_arm64.deb ... 116s Unpacking xfonts-utils (1:7.7+7) ... 116s Selecting previously unselected package fonts-urw-base35. 116s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 116s Unpacking fonts-urw-base35 (20200910-8) ... 116s Selecting previously unselected package fontconfig-config. 116s Preparing to unpack .../13-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 116s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 116s Selecting previously unselected package libfontconfig1:arm64. 116s Preparing to unpack .../14-libfontconfig1_2.15.0-2.2ubuntu1_arm64.deb ... 116s Unpacking libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 116s Selecting previously unselected package libpixman-1-0:arm64. 116s Preparing to unpack .../15-libpixman-1-0_0.44.0-3_arm64.deb ... 116s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 116s Selecting previously unselected package libxcb-render0:arm64. 116s Preparing to unpack .../16-libxcb-render0_1.17.0-2_arm64.deb ... 116s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 116s Selecting previously unselected package libxcb-shm0:arm64. 116s Preparing to unpack .../17-libxcb-shm0_1.17.0-2_arm64.deb ... 116s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 116s Selecting previously unselected package libxrender1:arm64. 116s Preparing to unpack .../18-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 116s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 116s Selecting previously unselected package libcairo2:arm64. 116s Preparing to unpack .../19-libcairo2_1.18.4-1_arm64.deb ... 116s Unpacking libcairo2:arm64 (1.18.4-1) ... 116s Selecting previously unselected package libdeflate0:arm64. 116s Preparing to unpack .../20-libdeflate0_1.23-2_arm64.deb ... 116s Unpacking libdeflate0:arm64 (1.23-2) ... 116s Selecting previously unselected package libgomp1:arm64. 116s Preparing to unpack .../21-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 116s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 116s Selecting previously unselected package libgraphite2-3:arm64. 116s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 116s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 116s Selecting previously unselected package libharfbuzz0b:arm64. 116s Preparing to unpack .../23-libharfbuzz0b_10.2.0-1_arm64.deb ... 116s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 116s Selecting previously unselected package libimagequant0:arm64. 116s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_arm64.deb ... 116s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 116s Selecting previously unselected package libjpeg-turbo8:arm64. 116s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 116s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 116s Selecting previously unselected package libjpeg8:arm64. 116s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_arm64.deb ... 116s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 116s Selecting previously unselected package libjs-jquery. 116s Preparing to unpack .../27-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 116s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 117s Selecting previously unselected package libjs-underscore. 117s Preparing to unpack .../28-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 117s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 117s Selecting previously unselected package libjs-sphinxdoc. 117s Preparing to unpack .../29-libjs-sphinxdoc_8.2.3-1_all.deb ... 117s Unpacking libjs-sphinxdoc (8.2.3-1) ... 117s Selecting previously unselected package liblcms2-2:arm64. 117s Preparing to unpack .../30-liblcms2-2_2.16-2_arm64.deb ... 117s Unpacking liblcms2-2:arm64 (2.16-2) ... 117s Selecting previously unselected package liblerc4:arm64. 117s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 117s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 117s Selecting previously unselected package libraqm0:arm64. 117s Preparing to unpack .../32-libraqm0_0.10.2-1_arm64.deb ... 117s Unpacking libraqm0:arm64 (0.10.2-1) ... 117s Selecting previously unselected package libsharpyuv0:arm64. 117s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1_arm64.deb ... 117s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 117s Selecting previously unselected package libjbig0:arm64. 117s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 117s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 117s Selecting previously unselected package libwebp7:arm64. 117s Preparing to unpack .../35-libwebp7_1.5.0-0.1_arm64.deb ... 117s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 117s Selecting previously unselected package libtiff6:arm64. 117s Preparing to unpack .../36-libtiff6_4.7.0-3ubuntu1_arm64.deb ... 117s Unpacking libtiff6:arm64 (4.7.0-3ubuntu1) ... 117s Selecting previously unselected package libwebpdemux2:arm64. 117s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_arm64.deb ... 117s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 117s Selecting previously unselected package libwebpmux3:arm64. 117s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_arm64.deb ... 117s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 117s Selecting previously unselected package python-biopython-doc. 117s Preparing to unpack .../39-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 117s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 117s Selecting previously unselected package python3-all. 117s Preparing to unpack .../40-python3-all_3.13.3-1_arm64.deb ... 117s Unpacking python3-all (3.13.3-1) ... 117s Selecting previously unselected package libopenjp2-7:arm64. 117s Preparing to unpack .../41-libopenjp2-7_2.5.3-2_arm64.deb ... 117s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 117s Selecting previously unselected package python3-pil:arm64. 117s Preparing to unpack .../42-python3-pil_11.1.0-5build1_arm64.deb ... 117s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 117s Selecting previously unselected package python3-cairo. 117s Preparing to unpack .../43-python3-cairo_1.27.0-2_arm64.deb ... 117s Unpacking python3-cairo (1.27.0-2) ... 117s Selecting previously unselected package python3-freetype. 117s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 117s Unpacking python3-freetype (2.5.1-1) ... 117s Selecting previously unselected package python3-rlpycairo. 117s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 117s Unpacking python3-rlpycairo (0.3.0-3) ... 117s Selecting previously unselected package python3-reportlab. 117s Preparing to unpack .../46-python3-reportlab_4.3.1-1_all.deb ... 117s Unpacking python3-reportlab (4.3.1-1) ... 117s Selecting previously unselected package xml-core. 117s Preparing to unpack .../47-xml-core_0.19_all.deb ... 117s Unpacking xml-core (0.19) ... 117s Selecting previously unselected package w3c-sgml-lib. 117s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 117s Unpacking w3c-sgml-lib (1.3-3) ... 118s Selecting previously unselected package python3-biopython. 118s Preparing to unpack .../49-python3-biopython_1.85+dfsg-2build1_arm64.deb ... 118s Unpacking python3-biopython (1.85+dfsg-2build1) ... 118s Selecting previously unselected package python3-biopython-sql. 118s Preparing to unpack .../50-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 118s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 118s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 118s Setting up liblcms2-2:arm64 (2.16-2) ... 118s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 118s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 118s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 118s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 118s Setting up libxcb-render0:arm64 (1.17.0-2) ... 118s Setting up x11-common (1:7.7+23ubuntu4) ... 118s Setting up libdeflate0:arm64 (1.23-2) ... 118s Setting up python3-all (3.13.3-1) ... 118s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 118s Setting up libgomp1:arm64 (15-20250404-0ubuntu1) ... 118s Setting up python3-freetype (2.5.1-1) ... 118s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 118s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 118s Setting up libblas3:arm64 (3.12.1-2) ... 118s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 118s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 118s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 118s Setting up fonts-dejavu-mono (2.37-8) ... 118s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 118s Setting up fonts-dejavu-core (2.37-8) ... 118s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 118s Setting up libgfortran5:arm64 (15-20250404-0ubuntu1) ... 118s Setting up libwebp7:arm64 (1.5.0-0.1) ... 118s Setting up libopenjp2-7:arm64 (2.5.3-2) ... 118s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 118s Setting up sgml-base (1.31) ... 118s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 118s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 118s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 118s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 118s Setting up liblapack3:arm64 (3.12.1-2) ... 118s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 118s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 118s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 118s Setting up xfonts-utils (1:7.7+7) ... 118s Setting up libraqm0:arm64 (0.10.2-1) ... 118s Setting up python3-numpy (1:2.2.3+ds-5) ... 120s Setting up libjs-sphinxdoc (8.2.3-1) ... 120s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 120s Setting up libtiff6:arm64 (4.7.0-3ubuntu1) ... 120s Setting up xml-core (0.19) ... 120s Setting up libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 120s Setting up fonts-urw-base35 (20200910-8) ... 121s Setting up libcairo2:arm64 (1.18.4-1) ... 121s Setting up python3-pil:arm64 (11.1.0-5build1) ... 121s Setting up python3-cairo (1.27.0-2) ... 121s Setting up python3-rlpycairo (0.3.0-3) ... 121s Setting up python3-reportlab (4.3.1-1) ... 122s Processing triggers for libc-bin (2.41-6ubuntu1) ... 122s Processing triggers for man-db (2.13.0-1) ... 123s Processing triggers for sgml-base (1.31) ... 123s Setting up w3c-sgml-lib (1.3-3) ... 148s Setting up python3-biopython (1.85+dfsg-2build1) ... 149s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 150s autopkgtest [19:36:38]: test dependencies: sh debian/tests/run-unit-test 150s autopkgtest [19:36:38]: test dependencies: [----------------------- 151s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 151s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 153s mkdir: created directory 'Bio' 153s mkdir: created directory 'Bio/Align' 153s mkdir: created directory 'Bio/Align/substitution_matrices' 153s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 153s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 153s test_Ace ... ok 153s test_Affy ... ok 155s test_AlignIO ... ok 155s test_AlignIO_ClustalIO ... ok 155s test_AlignIO_EmbossIO ... ok 155s test_AlignIO_FastaIO ... ok 155s test_AlignIO_MauveIO ... ok 155s test_AlignIO_PhylipIO ... ok 156s test_AlignIO_convert ... ok 156s test_AlignInfo ... ok 156s test_Align_Alignment ... ok 156s test_Align_a2m ... ok 156s test_Align_bed ... ok 156s test_Align_bigbed ... ok 157s test_Align_bigmaf ... ok 157s test_Align_bigpsl ... ok 157s test_Align_chain ... ok 157s test_Align_clustal ... ok 160s test_Align_codonalign ... ok 160s test_Align_emboss ... ok 160s test_Align_exonerate ... ok 160s test_Align_fasta ... ok 161s test_Align_hhr ... ok 161s test_Align_maf ... ok 161s test_Align_mauve ... ok 161s test_Align_msf ... ok 161s test_Align_nexus ... ok 161s test_Align_phylip ... ok 162s test_Align_psl ... ok 162s test_Align_sam ... ok 164s test_Align_stockholm ... ok 164s test_Align_tabular ... ok 164s test_Application ... ok 164s test_BioSQL_MySQLdb_online ... skipping. internet not available 164s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 164s test_BioSQL_mysql_connector_online ... skipping. internet not available 164s test_BioSQL_psycopg2_online ... skipping. internet not available 168s test_BioSQL_sqlite3 ... ok 168s test_BioSQL_sqlite3_online ... skipping. internet not available 168s test_Blast_Record ... ok 169s test_Blast_parser ... ok 169s test_CAPS ... ok 169s test_Chi2 ... ok 169s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 169s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 169s test_Cluster ... ok 169s test_CodonTable ... ok 169s test_ColorSpiral ... ok 169s test_Compass ... ok 170s test_Consensus ... ok 170s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 170s test_EMBL_unittest ... ok 170s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 170s test_EmbossPrimer ... ok 175s test_Entrez ... ok 175s test_Entrez_online ... skipping. internet not available 175s test_Entrez_parser ... ok 175s test_Enzyme ... ok 175s test_ExPASy ... skipping. internet not available 175s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 175s test_File ... ok 175s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 175s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 176s ok 177s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 179s ok 180s test_GraphicsChromosome ... ok 180s test_GraphicsDistribution ... ok 180s test_GraphicsGeneral ... ok 181s test_HMMCasino ... ok 181s test_HMMGeneral ... ok 181s test_KEGG ... ok 181s test_KEGG_online ... skipping. internet not available 185s test_KGML_graphics ... ok 185s test_KGML_graphics_online ... skipping. internet not available 186s test_KGML_nographics ... ok 186s test_KeyWList ... ok 186s test_LogisticRegression ... ok 187s test_MafIO_index ... ok 187s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 187s test_MarkovModel ... ok 187s test_Medline ... ok 187s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 188s test_NCBIXML ... Exception ignored in: 188s Traceback (most recent call last): 188s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 188s expat_parser.Parse(NULL, True) 188s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 188s ok 188s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 188s test_NCBI_qblast ... ok 188s test_NMR ... ok 188s test_NaiveBayes ... ok 188s test_Nexus ... ok 188s test_PAML_baseml ... ok 189s test_PAML_codeml ... ok 189s test_PAML_yn00 ... ok 193s test_PDB_CEAligner ... ok 193s test_PDB_DSSP ... ok 193s test_PDB_Dice ... ok 193s test_PDB_Disordered ... ok 193s test_PDB_Exposure ... ok 194s test_PDB_FragmentMapper ... ok 195s test_PDB_KDTree ... ok 195s test_PDB_MMCIF2Dict ... ok 196s test_PDB_MMCIFIO ... ok 196s test_PDB_MMCIFParser ... ok 197s test_PDB_NACCESS ... ok 197s test_PDB_PDBIO ... ok 197s test_PDB_PDBList ... skipping. internet not available 203s test_PDB_PDBMLParser ... ok 203s test_PDB_PDBParser ... ok 203s 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 203s test_PDB_Polypeptide ... ok 203s test_PDB_QCPSuperimposer ... ok 206s test_PDB_SASA ... ok 207s test_PDB_SMCRA ... ok 207s test_PDB_Selection ... ok 207s test_PDB_StructureAlignment ... ok 207s test_PDB_Superimposer ... ok 207s test_PDB_alphafold_db ... skipping. internet not available 207s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 207s 207s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 207s 207s test_PDB_parse_pdb_header ... ok 207s test_PDB_vectors ... ok 207s test_PQR ... ok 207s test_Pathway ... ok 207s test_Phd ... ok 208s test_Phylo ... ok 208s test_PhyloXML ... ok 208s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 208s test_Phylo_NeXML ... ok 208s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 208s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 208s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 208s test_PopGen_GenePop_nodepend ... ok 209s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 209s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 209s test_ProtParam ... ok 209s test_RCSBFormats ... ok 209s test_Restriction ... ok 209s test_SCOP_Astral ... ok 209s test_SCOP_Cla ... ok 209s test_SCOP_Des ... ok 209s test_SCOP_Dom ... ok 209s test_SCOP_Hie ... ok 210s test_SCOP_Raf ... ok 210s test_SCOP_Residues ... ok 210s test_SCOP_Scop ... ok 210s test_SVDSuperimposer ... ok 210s test_SearchIO_blast_tab ... ok 210s test_SearchIO_blast_tab_index ... ok 210s test_SearchIO_blast_xml ... ok 211s test_SearchIO_blast_xml_index ... ok 211s test_SearchIO_blat_psl ... ok 211s test_SearchIO_blat_psl_index ... ok 212s test_SearchIO_exonerate ... ok 212s test_SearchIO_exonerate_text_index ... ok 212s test_SearchIO_exonerate_vulgar_index ... ok 212s test_SearchIO_fasta_m10 ... ok 212s test_SearchIO_fasta_m10_index ... ok 212s test_SearchIO_hhsuite2_text ... ok 212s test_SearchIO_hmmer2_text ... ok 212s test_SearchIO_hmmer2_text_index ... ok 212s test_SearchIO_hmmer3_domtab ... ok 212s test_SearchIO_hmmer3_domtab_index ... ok 213s test_SearchIO_hmmer3_tab ... ok 213s test_SearchIO_hmmer3_tab_index ... ok 213s test_SearchIO_hmmer3_text ... ok 213s test_SearchIO_hmmer3_text_index ... ok 213s test_SearchIO_interproscan_xml ... ok 213s test_SearchIO_model ... ok 213s test_SearchIO_write ... ok 213s test_SeqFeature ... ok 227s test_SeqIO ... ok 227s test_SeqIO_AbiIO ... ok 227s test_SeqIO_FastaIO ... ok 227s test_SeqIO_Gck ... ok 228s test_SeqIO_Gfa ... ok 228s test_SeqIO_Insdc ... ok 228s test_SeqIO_NibIO ... ok 229s test_SeqIO_PdbIO ... ok 230s test_SeqIO_QualityIO ... ok 230s test_SeqIO_SeqXML ... ok 230s test_SeqIO_SffIO ... ok 230s test_SeqIO_SnapGene ... ok 231s test_SeqIO_TwoBitIO ... ok 231s test_SeqIO_UniprotIO ... ok 231s test_SeqIO_Xdna ... ok 231s test_SeqIO_features ... ok 244s test_SeqIO_index ... ok 244s test_SeqIO_online ... skipping. internet not available 244s test_SeqIO_write ... ok 244s test_SeqRecord ... ok 244s test_SeqUtils ... ok 245s test_Seq_objs ... ok 245s test_SwissProt ... ok 245s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 246s test_TogoWS ... skipping. internet not available 246s test_TreeConstruction ... ok 246s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 246s test_UniGene ... ok 246s test_UniProt ... skipping. internet not available 246s test_UniProt_GOA ... ok 246s test_align ... ok 247s test_align_substitution_matrices ... ok 249s test_bgzf ... ok 249s test_cellosaurus ... ok 253s test_codonalign ... ok 253s test_geo ... ok 253s test_kNN ... ok 253s test_motifs ... ok 253s test_motifs_online ... skipping. internet not available 253s 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. 253s warnings.warn( 253s ok 253s test_pairwise2_no_C ... ok 254s test_pairwise_aligner ... ok 254s test_pairwise_alignment_map ... ok 260s test_phenotype ... ok 260s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 260s 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. 261s test_prodoc ... ok 261s test_prosite ... ok 261s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 261s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 261s test_seq ... ok 261s test_translate ... ok 261s Skipping any tests requiring internet access 261s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 261s Operating system: posix linux 261s ---------------------------------------------------------------------- 261s Ran 218 tests in 107.979 seconds 261s 261s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 261s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 262s autopkgtest [19:38:30]: test dependencies: -----------------------] 262s dependencies PASS 262s autopkgtest [19:38:30]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 262s autopkgtest [19:38:30]: test full_suite: preparing testbed 372s autopkgtest [19:40:20]: testbed dpkg architecture: arm64 372s autopkgtest [19:40:20]: testbed apt version: 3.0.0 373s autopkgtest [19:40:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 373s autopkgtest [19:40:21]: testbed release detected to be: questing 373s autopkgtest [19:40:21]: updating testbed package index (apt update) 374s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 374s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 374s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 374s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 374s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1442 kB] 374s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [149 kB] 374s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.7 kB] 374s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [186 kB] 374s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1384 kB] 374s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [27.5 kB] 374s Fetched 3331 kB in 1s (6644 kB/s) 375s Reading package lists... 375s autopkgtest [19:40:23]: upgrading testbed (apt dist-upgrade and autopurge) 376s Reading package lists... 376s Building dependency tree... 376s Reading state information... 376s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 376s Starting 2 pkgProblemResolver with broken count: 0 376s Done 377s Entering ResolveByKeep 377s 378s Calculating upgrade... 378s The following packages will be upgraded: 378s libperl5.40 libsepol2 perl perl-base perl-modules-5.40 378s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 378s Need to get 10.4 MB of archives. 378s After this operation, 65.5 kB of additional disk space will be used. 378s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libperl5.40 arm64 5.40.1-3 [4780 kB] 378s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl arm64 5.40.1-3 [262 kB] 378s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-base arm64 5.40.1-3 [1786 kB] 378s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-modules-5.40 all 5.40.1-3 [3217 kB] 378s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 libsepol2 arm64 3.8.1-1 [312 kB] 379s Fetched 10.4 MB in 0s (22.4 MB/s) 379s (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 ... 85229 files and directories currently installed.) 379s Preparing to unpack .../libperl5.40_5.40.1-3_arm64.deb ... 379s Unpacking libperl5.40:arm64 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 379s Preparing to unpack .../perl_5.40.1-3_arm64.deb ... 379s Unpacking perl (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 379s Preparing to unpack .../perl-base_5.40.1-3_arm64.deb ... 379s Unpacking perl-base (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 379s Setting up perl-base (5.40.1-3) ... 379s (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 ... 85229 files and directories currently installed.) 379s Preparing to unpack .../perl-modules-5.40_5.40.1-3_all.deb ... 379s Unpacking perl-modules-5.40 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 380s Preparing to unpack .../libsepol2_3.8.1-1_arm64.deb ... 380s Unpacking libsepol2:arm64 (3.8.1-1) over (3.7-1) ... 380s Setting up libsepol2:arm64 (3.8.1-1) ... 380s Setting up perl-modules-5.40 (5.40.1-3) ... 380s Setting up libperl5.40:arm64 (5.40.1-3) ... 380s Setting up perl (5.40.1-3) ... 380s Processing triggers for man-db (2.13.0-1) ... 380s Processing triggers for libc-bin (2.41-6ubuntu1) ... 381s Reading package lists... 381s Building dependency tree... 381s Reading state information... 381s Starting pkgProblemResolver with broken count: 0 381s Starting 2 pkgProblemResolver with broken count: 0 381s Done 382s Solving dependencies... 382s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 385s Reading package lists... 385s Building dependency tree... 385s Reading state information... 385s Starting pkgProblemResolver with broken count: 0 385s Starting 2 pkgProblemResolver with broken count: 0 385s Done 386s The following NEW packages will be installed: 386s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 386s cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 386s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 386s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 386s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 386s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 386s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 386s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext ghostscript hevea 386s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 386s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 386s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 386s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 386s libcolamd3 libcommons-logging-java libcommons-parent-java libcups2t64 386s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 386s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 386s libgcc-14-dev libgd3 libgfortran5 libglpk40 libgomp1 libgraphite2-3 386s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 386s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhwasan0 libice6 libidn12 386s libigraph3t64 libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 386s libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 386s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 386s liblbfgsb0 liblcms2-2 liblerc4 liblqr-1-0 liblsan0 libltdl7 386s libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 libmbedtls21 386s libmbedx509-7 libmpc3 libmpfi0 libmysqlclient24 libnetpbm11t64 libopenjp2-7 386s libpaper-utils libpaper2 libpdfbox-java libpixman-1-0 libplfit0 libpotrace0 386s libpq5 libptexenc1 libpython3-all-dev libpython3-dev libpython3.13-dev 386s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 386s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 386s libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2 386s libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 386s libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft 386s mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data 386s prank preview-latex-style probcons python-biopython-doc 386s python-matplotlib-data python3-alabaster python3-all python3-all-dev 386s python3-biopython python3-biopython-sql python3-brotli python3-cairo 386s python3-contourpy python3-cycler python3-decorator python3-defusedxml 386s python3-dev python3-docutils python3-fonttools python3-freetype python3-fs 386s python3-igraph python3-imagesize python3-kiwisolver python3-lxml python3-lz4 386s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 386s python3-mysqldb python3-networkx python3-numpy python3-numpy-dev 386s python3-numpydoc python3-pil python3-pil.imagetk python3-platformdirs 386s python3-rdflib python3-reportlab python3-rlpycairo python3-roman 386s python3-roman-numerals python3-scipy python3-snowballstemmer python3-sphinx 386s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 386s python3-tabulate python3-texttable python3-tk python3-ufolib2 python3.13-dev 386s python3.13-tk sgml-base sphinx-common sphinx-rtd-theme-common t-coffee 386s t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended 386s texlive-latex-base texlive-latex-extra texlive-latex-recommended 386s texlive-pictures tk8.6-blt2.5 unicode-data w3c-sgml-lib wise wise-data 386s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 386s 0 upgraded, 257 newly installed, 0 to remove and 0 not upgraded. 386s Need to get 405 MB of archives. 386s After this operation, 1814 MB of additional disk space will be used. 386s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 m4 arm64 1.4.19-7 [244 kB] 386s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 flex arm64 2.6.4-8.2build1 [291 kB] 386s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-lato all 2.015-1 [2781 kB] 386s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 386s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 libfftw3-double3 arm64 3.3.10-2fakesync1build1 [392 kB] 386s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 386s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 386s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 386s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 386s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 386s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 386s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 386s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 386s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 386s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 386s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 libaom3 arm64 3.12.1-1 [1824 kB] 386s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 libheif-plugin-aomdec arm64 1.19.7-1 [11.4 kB] 386s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libde265-0 arm64 1.0.15-1build5 [146 kB] 386s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libheif-plugin-libde265 arm64 1.19.7-1 [8890 B] 386s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libheif1 arm64 1.19.7-1 [371 kB] 386s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 386s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 386s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 386s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 386s Get:25 http://ftpmaster.internal/ubuntu questing/universe arm64 liblqr-1-0 arm64 0.4.2-2.1build2 [27.1 kB] 386s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libltdl7 arm64 2.5.4-4 [43.0 kB] 386s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 386s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 libraw23t64 arm64 0.21.4-2 [378 kB] 386s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 386s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 386s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 386s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.7.0-3ubuntu1 [197 kB] 386s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 386s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 386s Get:35 http://ftpmaster.internal/ubuntu questing/universe arm64 imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 386s Get:36 http://ftpmaster.internal/ubuntu questing/universe arm64 libmagickcore-7.q16-10 arm64 8:7.1.1.43+dfsg1-1 [1876 kB] 387s Get:37 http://ftpmaster.internal/ubuntu questing/universe arm64 libmagickwand-7.q16-10 arm64 8:7.1.1.43+dfsg1-1 [301 kB] 387s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 poppler-data all 0.4.12-1 [2060 kB] 387s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 387s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 387s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15-20250404-0ubuntu1 [444 kB] 387s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 387s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 387s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 sgml-base all 1.31 [11.4 kB] 387s Get:45 http://ftpmaster.internal/ubuntu questing/main arm64 autoconf all 2.72-3ubuntu1 [383 kB] 387s Get:46 http://ftpmaster.internal/ubuntu questing/main arm64 autotools-dev all 20220109.1 [44.9 kB] 387s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 automake all 1:1.17-3ubuntu1 [572 kB] 387s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 autopoint all 0.23.1-1 [619 kB] 387s Get:49 http://ftpmaster.internal/ubuntu questing/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 387s Get:50 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 387s Get:51 http://ftpmaster.internal/ubuntu questing/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 387s Get:52 http://ftpmaster.internal/ubuntu questing/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 387s Get:53 http://ftpmaster.internal/ubuntu questing/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 387s Get:54 http://ftpmaster.internal/ubuntu questing/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 387s Get:55 http://ftpmaster.internal/ubuntu questing/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 387s Get:56 http://ftpmaster.internal/ubuntu questing/main arm64 libisl23 arm64 0.27-1 [676 kB] 387s Get:57 http://ftpmaster.internal/ubuntu questing/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 387s Get:58 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [10.6 MB] 387s Get:59 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14 arm64 14.2.0-19ubuntu2 [1026 B] 387s Get:60 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 387s Get:61 http://ftpmaster.internal/ubuntu questing/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 387s Get:62 http://ftpmaster.internal/ubuntu questing/main arm64 libcc1-0 arm64 15-20250404-0ubuntu1 [49.1 kB] 387s Get:63 http://ftpmaster.internal/ubuntu questing/main arm64 libitm1 arm64 15-20250404-0ubuntu1 [27.8 kB] 387s Get:64 http://ftpmaster.internal/ubuntu questing/main arm64 libasan8 arm64 15-20250404-0ubuntu1 [2922 kB] 388s Get:65 http://ftpmaster.internal/ubuntu questing/main arm64 liblsan0 arm64 15-20250404-0ubuntu1 [1318 kB] 388s Get:66 http://ftpmaster.internal/ubuntu questing/main arm64 libtsan2 arm64 15-20250404-0ubuntu1 [2692 kB] 388s Get:67 http://ftpmaster.internal/ubuntu questing/main arm64 libubsan1 arm64 15-20250404-0ubuntu1 [1177 kB] 388s Get:68 http://ftpmaster.internal/ubuntu questing/main arm64 libhwasan0 arm64 15-20250404-0ubuntu1 [1640 kB] 388s Get:69 http://ftpmaster.internal/ubuntu questing/main arm64 libgcc-14-dev arm64 14.2.0-19ubuntu2 [2593 kB] 388s Get:70 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [20.9 MB] 388s Get:71 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14 arm64 14.2.0-19ubuntu2 [529 kB] 388s Get:72 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 388s Get:73 http://ftpmaster.internal/ubuntu questing/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 388s Get:74 http://ftpmaster.internal/ubuntu questing/main arm64 libstdc++-14-dev arm64 14.2.0-19ubuntu2 [2501 kB] 388s Get:75 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [12.1 MB] 388s Get:76 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14 arm64 14.2.0-19ubuntu2 [23.0 kB] 388s Get:77 http://ftpmaster.internal/ubuntu questing/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 388s Get:78 http://ftpmaster.internal/ubuntu questing/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 388s Get:79 http://ftpmaster.internal/ubuntu questing/main arm64 build-essential arm64 12.12ubuntu1 [5082 B] 388s Get:80 http://ftpmaster.internal/ubuntu questing/universe arm64 bwa arm64 0.7.18-1 [201 kB] 388s Get:81 http://ftpmaster.internal/ubuntu questing/universe arm64 libargtable2-0 arm64 13-3 [15.3 kB] 388s Get:82 http://ftpmaster.internal/ubuntu questing/universe arm64 clustalo arm64 1.2.4-8build1 [190 kB] 388s Get:83 http://ftpmaster.internal/ubuntu questing/main arm64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 389s Get:84 http://ftpmaster.internal/ubuntu questing/main arm64 libtool all 2.5.4-4 [168 kB] 389s Get:85 http://ftpmaster.internal/ubuntu questing/main arm64 dh-autoreconf all 20 [16.1 kB] 389s Get:86 http://ftpmaster.internal/ubuntu questing/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 389s Get:87 http://ftpmaster.internal/ubuntu questing/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 389s Get:88 http://ftpmaster.internal/ubuntu questing/main arm64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 389s Get:89 http://ftpmaster.internal/ubuntu questing/main arm64 debugedit arm64 1:5.1-2 [46.1 kB] 389s Get:90 http://ftpmaster.internal/ubuntu questing/main arm64 dwz arm64 0.15-1build6 [113 kB] 389s Get:91 http://ftpmaster.internal/ubuntu questing/main arm64 gettext arm64 0.23.1-1 [998 kB] 389s Get:92 http://ftpmaster.internal/ubuntu questing/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 389s Get:93 http://ftpmaster.internal/ubuntu questing/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 389s Get:94 http://ftpmaster.internal/ubuntu questing/main arm64 debhelper all 13.24.1ubuntu2 [895 kB] 389s Get:95 http://ftpmaster.internal/ubuntu questing/universe arm64 dh-python all 6.20250308 [118 kB] 389s Get:96 http://ftpmaster.internal/ubuntu questing/universe arm64 dialign arm64 2.2.1-13 [152 kB] 389s Get:97 http://ftpmaster.internal/ubuntu questing/main arm64 xml-core all 0.19 [20.3 kB] 389s Get:98 http://ftpmaster.internal/ubuntu questing/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 389s Get:99 http://ftpmaster.internal/ubuntu questing/universe arm64 libcifpp-data all 7.0.9-1 [481 kB] 389s Get:100 http://ftpmaster.internal/ubuntu questing/universe arm64 libcifpp7 arm64 7.0.9-1 [997 kB] 389s Get:101 http://ftpmaster.internal/ubuntu questing/universe arm64 dssp arm64 4.4.10-1 [753 kB] 389s Get:102 http://ftpmaster.internal/ubuntu questing/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 389s Get:103 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 389s Get:104 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 389s Get:105 http://ftpmaster.internal/ubuntu questing/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 389s Get:106 http://ftpmaster.internal/ubuntu questing/main arm64 libxpm4 arm64 1:3.5.17-1build2 [35.1 kB] 389s Get:107 http://ftpmaster.internal/ubuntu questing/main arm64 libgd3 arm64 2.3.3-12ubuntu3 [122 kB] 389s Get:108 http://ftpmaster.internal/ubuntu questing/universe arm64 libhpdf-2.3.0 arm64 2.3.0+dfsg-1build3 [434 kB] 389s Get:109 http://ftpmaster.internal/ubuntu questing/main arm64 mysql-common all 5.8+1.1.1ubuntu1 [6922 B] 389s Get:110 http://ftpmaster.internal/ubuntu questing/main arm64 libmysqlclient24 arm64 8.4.4-0ubuntu2 [1243 kB] 389s Get:111 http://ftpmaster.internal/ubuntu questing/main arm64 libpq5 arm64 17.4-1 [142 kB] 389s Get:112 http://ftpmaster.internal/ubuntu questing/universe arm64 emboss-lib arm64 6.6.0+dfsg-15ubuntu2 [2891 kB] 389s Get:113 http://ftpmaster.internal/ubuntu questing/universe arm64 emboss-data all 6.6.0+dfsg-15ubuntu2 [61.0 MB] 390s Get:114 http://ftpmaster.internal/ubuntu questing/universe arm64 emboss arm64 6.6.0+dfsg-15ubuntu2 [937 kB] 390s Get:115 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 390s Get:116 http://ftpmaster.internal/ubuntu questing/universe arm64 fonts-lmodern all 2.005-1 [4799 kB] 390s Get:117 http://ftpmaster.internal/ubuntu questing/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 390s Get:118 http://ftpmaster.internal/ubuntu questing/main arm64 libgs-common all 10.05.0dfsg1-0ubuntu1 [176 kB] 390s Get:119 http://ftpmaster.internal/ubuntu questing/main arm64 libgs10-common all 10.05.0dfsg1-0ubuntu1 [490 kB] 390s Get:120 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-common-data arm64 0.8-16ubuntu2 [31.0 kB] 390s Get:121 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-common3 arm64 0.8-16ubuntu2 [22.9 kB] 390s Get:122 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-client3 arm64 0.8-16ubuntu2 [26.9 kB] 390s Get:123 http://ftpmaster.internal/ubuntu questing/main arm64 libcups2t64 arm64 2.4.12-0ubuntu1 [272 kB] 390s Get:124 http://ftpmaster.internal/ubuntu questing/main arm64 libidn12 arm64 1.43-1 [58.1 kB] 390s Get:125 http://ftpmaster.internal/ubuntu questing/main arm64 libijs-0.35 arm64 0.35-15.2 [15.4 kB] 390s Get:126 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig2dec0 arm64 0.20-1build3 [63.2 kB] 390s Get:127 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 390s Get:128 http://ftpmaster.internal/ubuntu questing/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 390s Get:129 http://ftpmaster.internal/ubuntu questing/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 390s Get:130 http://ftpmaster.internal/ubuntu questing/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 390s Get:131 http://ftpmaster.internal/ubuntu questing/main arm64 libgs10 arm64 10.05.0dfsg1-0ubuntu1 [3638 kB] 390s Get:132 http://ftpmaster.internal/ubuntu questing/main arm64 ghostscript arm64 10.05.0dfsg1-0ubuntu1 [43.0 kB] 390s Get:133 http://ftpmaster.internal/ubuntu questing/universe arm64 libnetpbm11t64 arm64 2:11.09.02-2 [114 kB] 390s Get:134 http://ftpmaster.internal/ubuntu questing/universe arm64 netpbm arm64 2:11.09.02-2 [2130 kB] 390s Get:135 http://ftpmaster.internal/ubuntu questing/universe arm64 tex-common all 6.19 [29.8 kB] 390s Get:136 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 390s Get:137 http://ftpmaster.internal/ubuntu questing/universe arm64 libkpathsea6 arm64 2024.20240313.70630+ds-6 [64.4 kB] 390s Get:138 http://ftpmaster.internal/ubuntu questing/universe arm64 libptexenc1 arm64 2024.20240313.70630+ds-6 [41.7 kB] 390s Get:139 http://ftpmaster.internal/ubuntu questing/universe arm64 libsynctex2 arm64 2024.20240313.70630+ds-6 [60.4 kB] 390s Get:140 http://ftpmaster.internal/ubuntu questing/universe arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-6 [122 kB] 390s Get:141 http://ftpmaster.internal/ubuntu questing/main arm64 t1utils arm64 1.41-4build3 [61.0 kB] 390s Get:142 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 390s Get:143 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 390s Get:144 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 390s Get:145 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 390s Get:146 http://ftpmaster.internal/ubuntu questing/universe arm64 libmpfi0 arm64 1.5.4+ds-4 [35.3 kB] 390s Get:147 http://ftpmaster.internal/ubuntu questing/universe arm64 libpotrace0 arm64 1.16-2build1 [16.0 kB] 390s Get:148 http://ftpmaster.internal/ubuntu questing/universe arm64 libteckit0 arm64 2.5.12+ds1-1 [405 kB] 390s Get:149 http://ftpmaster.internal/ubuntu questing/main arm64 libxmu6 arm64 2:1.1.3-3build2 [47.5 kB] 390s Get:150 http://ftpmaster.internal/ubuntu questing/main arm64 libxaw7 arm64 2:1.0.16-1 [184 kB] 390s Get:151 http://ftpmaster.internal/ubuntu questing/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 390s Get:152 http://ftpmaster.internal/ubuntu questing/universe arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.1 [30.8 kB] 390s Get:153 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-binaries arm64 2024.20240313.70630+ds-6 [8349 kB] 390s Get:154 http://ftpmaster.internal/ubuntu questing/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 390s Get:155 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-base all 2024.20250309-1 [22.7 MB] 391s Get:156 http://ftpmaster.internal/ubuntu questing/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 391s Get:157 http://ftpmaster.internal/ubuntu questing/universe arm64 imagemagick-7.q16 arm64 8:7.1.1.43+dfsg1-1 [704 kB] 391s Get:158 http://ftpmaster.internal/ubuntu questing/universe arm64 imagemagick arm64 8:7.1.1.43+dfsg1-1 [14.1 kB] 391s Get:159 http://ftpmaster.internal/ubuntu questing/universe arm64 hevea arm64 2.36-2 [2333 kB] 391s Get:160 http://ftpmaster.internal/ubuntu questing/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-3 [13.2 kB] 391s Get:161 http://ftpmaster.internal/ubuntu questing/universe arm64 libamd3 arm64 1:7.8.3+dfsg-3 [26.1 kB] 391s Get:162 http://ftpmaster.internal/ubuntu questing/universe arm64 libapache-pom-java all 33-2 [5874 B] 391s Get:163 http://ftpmaster.internal/ubuntu questing/universe arm64 libarpack2t64 arm64 3.9.1-4 [94.4 kB] 391s Get:164 http://ftpmaster.internal/ubuntu questing/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-3 [18.3 kB] 391s Get:165 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 391s Get:166 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 391s Get:167 http://ftpmaster.internal/ubuntu questing/main arm64 libexpat1-dev arm64 2.7.1-1 [128 kB] 391s Get:168 http://ftpmaster.internal/ubuntu questing/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB] 391s Get:169 http://ftpmaster.internal/ubuntu questing/universe arm64 libplfit0 arm64 0.9.6+ds-2ubuntu1 [35.7 kB] 391s Get:170 http://ftpmaster.internal/ubuntu questing/universe arm64 libigraph3t64 arm64 0.10.15+ds-3 [895 kB] 391s Get:171 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 391s Get:172 http://ftpmaster.internal/ubuntu questing/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 391s Get:173 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 391s Get:174 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libjs-sphinxdoc all 8.2.3-1 [27.8 kB] 391s Get:175 http://ftpmaster.internal/ubuntu questing/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 391s Get:176 http://ftpmaster.internal/ubuntu questing/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 391s Get:177 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedcrypto16 arm64 3.6.2-3ubuntu1 [258 kB] 391s Get:178 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedx509-7 arm64 3.6.2-3ubuntu1 [35.7 kB] 391s Get:179 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedtls21 arm64 3.6.2-3ubuntu1 [122 kB] 391s Get:180 http://ftpmaster.internal/ubuntu questing/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 391s Get:181 http://ftpmaster.internal/ubuntu questing/main arm64 libpython3.13-dev arm64 3.13.3-1 [5405 kB] 391s Get:182 http://ftpmaster.internal/ubuntu questing/main arm64 libpython3-dev arm64 3.13.3-1 [10.8 kB] 391s Get:183 http://ftpmaster.internal/ubuntu questing/main arm64 libpython3-all-dev arm64 3.13.3-1 [906 B] 391s Get:184 http://ftpmaster.internal/ubuntu questing/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 391s Get:185 http://ftpmaster.internal/ubuntu questing/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu4 [168 kB] 391s Get:186 http://ftpmaster.internal/ubuntu questing/universe arm64 mafft arm64 7.505-1 [756 kB] 391s Get:187 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 391s Get:188 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6build1 [14.8 MB] 392s Get:189 http://ftpmaster.internal/ubuntu questing/universe arm64 phylip arm64 1:3.697+dfsg-4build1 [843 kB] 392s Get:190 http://ftpmaster.internal/ubuntu questing/universe arm64 prank arm64 0.0.170427+dfsg-3 [325 kB] 392s Get:191 http://ftpmaster.internal/ubuntu questing/universe arm64 preview-latex-style all 13.2-1 [347 kB] 392s Get:192 http://ftpmaster.internal/ubuntu questing/universe arm64 probcons arm64 1.12-14 [129 kB] 392s Get:193 http://ftpmaster.internal/ubuntu questing/universe arm64 python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 392s Get:194 http://ftpmaster.internal/ubuntu questing/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 392s Get:195 http://ftpmaster.internal/ubuntu questing/main arm64 python3-all arm64 3.13.3-1 [880 B] 392s Get:196 http://ftpmaster.internal/ubuntu questing/main arm64 python3.13-dev arm64 3.13.3-1 [508 kB] 392s Get:197 http://ftpmaster.internal/ubuntu questing/main arm64 python3-dev arm64 3.13.3-1 [26.7 kB] 392s Get:198 http://ftpmaster.internal/ubuntu questing/main arm64 python3-all-dev arm64 3.13.3-1 [904 B] 392s Get:199 http://ftpmaster.internal/ubuntu questing/main arm64 python3.13-tk arm64 3.13.3-1 [106 kB] 392s Get:200 http://ftpmaster.internal/ubuntu questing/main arm64 python3-tk arm64 3.13.3-1 [9856 B] 392s Get:201 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B] 392s Get:202 http://ftpmaster.internal/ubuntu questing/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 392s Get:203 http://ftpmaster.internal/ubuntu questing/main arm64 python3-cairo arm64 1.27.0-2 [122 kB] 392s Get:204 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 392s Get:205 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 392s Get:206 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 392s Get:207 http://ftpmaster.internal/ubuntu questing/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 392s Get:208 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython arm64 1.85+dfsg-2build1 [1711 kB] 392s Get:209 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 392s Get:210 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 392s Get:211 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 392s Get:212 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 392s Get:213 http://ftpmaster.internal/ubuntu questing/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 392s Get:214 http://ftpmaster.internal/ubuntu questing/main arm64 python3-defusedxml all 0.7.1-3 [42.2 kB] 392s Get:215 http://ftpmaster.internal/ubuntu questing/main arm64 python3-roman all 5.0-1 [10.3 kB] 392s Get:216 http://ftpmaster.internal/ubuntu questing/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 392s Get:217 http://ftpmaster.internal/ubuntu questing/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 392s Get:218 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 392s Get:219 http://ftpmaster.internal/ubuntu questing/main arm64 python3-lxml arm64 5.3.2-1 [1258 kB] 392s Get:220 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB] 392s Get:221 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 392s Get:222 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 392s Get:223 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 392s Get:224 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 393s Get:225 http://ftpmaster.internal/ubuntu questing/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 393s Get:226 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 393s Get:227 http://ftpmaster.internal/ubuntu questing/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 393s Get:228 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 393s Get:229 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB] 393s Get:230 http://ftpmaster.internal/ubuntu questing/main arm64 python3-msgpack arm64 1.0.3-3build4 [82.7 kB] 393s Get:231 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 393s Get:232 http://ftpmaster.internal/ubuntu questing/main arm64 python3-mysqldb arm64 1.4.6-2build6 [48.8 kB] 393s Get:233 http://ftpmaster.internal/ubuntu questing/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 393s Get:234 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 sphinx-common all 8.2.3-1 [656 kB] 393s Get:235 http://ftpmaster.internal/ubuntu questing/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 393s Get:236 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 python3-roman-numerals all 3.1.0-1ubuntu1 [8432 B] 393s Get:237 http://ftpmaster.internal/ubuntu questing/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 393s Get:238 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 python3-sphinx all 8.2.3-1 [482 kB] 393s Get:239 http://ftpmaster.internal/ubuntu questing/main arm64 python3-tabulate all 0.9.0-1 [45.3 kB] 393s Get:240 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-numpydoc all 1.8.0-1 [52.4 kB] 393s Get:241 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rdflib all 7.1.1-2 [426 kB] 393s Get:242 http://ftpmaster.internal/ubuntu questing/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 393s Get:243 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 393s Get:244 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 393s Get:245 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-texttable all 1.7.0-1 [11.2 kB] 393s Get:246 http://ftpmaster.internal/ubuntu questing/universe arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [879 kB] 393s Get:247 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-fonts-recommended all 2024.20250309-1 [4974 kB] 393s Get:248 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-latex-base all 2024.20250309-1 [1276 kB] 393s Get:249 http://ftpmaster.internal/ubuntu questing/universe arm64 libfontbox-java all 1:1.8.16-5 [208 kB] 393s Get:250 http://ftpmaster.internal/ubuntu questing/universe arm64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 393s Get:251 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-latex-recommended all 2024.20250309-1 [8727 kB] 394s Get:252 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-pictures all 2024.20250309-1 [17.0 MB] 394s Get:253 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-latex-extra all 2024.20250309-2 [24.8 MB] 394s Get:254 http://ftpmaster.internal/ubuntu questing/universe arm64 wise-data all 2.4.1-25 [83.0 kB] 394s Get:255 http://ftpmaster.internal/ubuntu questing/universe arm64 wise arm64 2.4.1-25 [802 kB] 394s Get:256 http://ftpmaster.internal/ubuntu questing/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 394s Get:257 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-igraph arm64 0.11.8+ds-1build1 [345 kB] 395s Preconfiguring packages ... 395s Fetched 405 MB in 8s (49.7 MB/s) 395s Selecting previously unselected package m4. 395s (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 ... 85229 files and directories currently installed.) 395s Preparing to unpack .../000-m4_1.4.19-7_arm64.deb ... 395s Unpacking m4 (1.4.19-7) ... 395s Selecting previously unselected package flex. 395s Preparing to unpack .../001-flex_2.6.4-8.2build1_arm64.deb ... 395s Unpacking flex (2.6.4-8.2build1) ... 395s Selecting previously unselected package fonts-lato. 395s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 395s Unpacking fonts-lato (2.015-1) ... 396s Selecting previously unselected package libgomp1:arm64. 396s Preparing to unpack .../003-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 396s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 396s Selecting previously unselected package libfftw3-double3:arm64. 396s Preparing to unpack .../004-libfftw3-double3_3.3.10-2fakesync1build1_arm64.deb ... 396s Unpacking libfftw3-double3:arm64 (3.3.10-2fakesync1build1) ... 396s Selecting previously unselected package fonts-dejavu-mono. 396s Preparing to unpack .../005-fonts-dejavu-mono_2.37-8_all.deb ... 396s Unpacking fonts-dejavu-mono (2.37-8) ... 396s Selecting previously unselected package fonts-dejavu-core. 396s Preparing to unpack .../006-fonts-dejavu-core_2.37-8_all.deb ... 396s Unpacking fonts-dejavu-core (2.37-8) ... 396s Selecting previously unselected package libfontenc1:arm64. 396s Preparing to unpack .../007-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 396s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 396s Selecting previously unselected package x11-common. 396s Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu4_all.deb ... 396s Unpacking x11-common (1:7.7+23ubuntu4) ... 396s Selecting previously unselected package xfonts-encodings. 396s Preparing to unpack .../009-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 396s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 396s Selecting previously unselected package xfonts-utils. 396s Preparing to unpack .../010-xfonts-utils_1%3a7.7+7_arm64.deb ... 396s Unpacking xfonts-utils (1:7.7+7) ... 396s Selecting previously unselected package fonts-urw-base35. 396s Preparing to unpack .../011-fonts-urw-base35_20200910-8_all.deb ... 396s Unpacking fonts-urw-base35 (20200910-8) ... 396s Selecting previously unselected package fontconfig-config. 396s Preparing to unpack .../012-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 396s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 396s Selecting previously unselected package libfontconfig1:arm64. 396s Preparing to unpack .../013-libfontconfig1_2.15.0-2.2ubuntu1_arm64.deb ... 396s Unpacking libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 396s Selecting previously unselected package libsharpyuv0:arm64. 396s Preparing to unpack .../014-libsharpyuv0_1.5.0-0.1_arm64.deb ... 396s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 396s Selecting previously unselected package libaom3:arm64. 396s Preparing to unpack .../015-libaom3_3.12.1-1_arm64.deb ... 396s Unpacking libaom3:arm64 (3.12.1-1) ... 396s Selecting previously unselected package libheif-plugin-aomdec:arm64. 396s Preparing to unpack .../016-libheif-plugin-aomdec_1.19.7-1_arm64.deb ... 396s Unpacking libheif-plugin-aomdec:arm64 (1.19.7-1) ... 396s Selecting previously unselected package libde265-0:arm64. 396s Preparing to unpack .../017-libde265-0_1.0.15-1build5_arm64.deb ... 396s Unpacking libde265-0:arm64 (1.0.15-1build5) ... 396s Selecting previously unselected package libheif-plugin-libde265:arm64. 396s Preparing to unpack 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liblcms2-2:arm64 (2.16-2) ... 396s Selecting previously unselected package liblqr-1-0:arm64. 396s Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1build2_arm64.deb ... 396s Unpacking liblqr-1-0:arm64 (0.4.2-2.1build2) ... 396s Selecting previously unselected package libltdl7:arm64. 396s Preparing to unpack .../025-libltdl7_2.5.4-4_arm64.deb ... 396s Unpacking libltdl7:arm64 (2.5.4-4) ... 396s Selecting previously unselected package libopenjp2-7:arm64. 396s Preparing to unpack .../026-libopenjp2-7_2.5.3-2_arm64.deb ... 396s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 396s Selecting previously unselected package libraw23t64:arm64. 396s Preparing to unpack .../027-libraw23t64_0.21.4-2_arm64.deb ... 396s Unpacking libraw23t64:arm64 (0.21.4-2) ... 396s Selecting previously unselected package libdeflate0:arm64. 396s Preparing to unpack .../028-libdeflate0_1.23-2_arm64.deb ... 396s Unpacking libdeflate0:arm64 (1.23-2) ... 396s Selecting previously unselected package liblerc4:arm64. 396s Preparing to unpack .../029-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 396s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 396s Selecting previously unselected package libwebp7:arm64. 396s Preparing to unpack .../030-libwebp7_1.5.0-0.1_arm64.deb ... 396s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 396s Selecting previously unselected package libtiff6:arm64. 396s Preparing to unpack .../031-libtiff6_4.7.0-3ubuntu1_arm64.deb ... 396s Unpacking libtiff6:arm64 (4.7.0-3ubuntu1) ... 396s Selecting previously unselected package libwebpdemux2:arm64. 396s Preparing to unpack .../032-libwebpdemux2_1.5.0-0.1_arm64.deb ... 396s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 396s Selecting previously unselected package libwebpmux3:arm64. 397s Preparing to unpack .../033-libwebpmux3_1.5.0-0.1_arm64.deb ... 397s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 397s Selecting previously unselected package imagemagick-7-common. 397s Preparing to unpack .../034-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 397s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 397s Selecting previously unselected package libmagickcore-7.q16-10:arm64. 397s Preparing to unpack .../035-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_arm64.deb ... 397s Unpacking libmagickcore-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 397s Selecting previously unselected package libmagickwand-7.q16-10:arm64. 397s Preparing to unpack .../036-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_arm64.deb ... 397s Unpacking libmagickwand-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 397s Selecting previously unselected package poppler-data. 397s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 397s Unpacking poppler-data (0.4.12-1) ... 397s Selecting previously unselected package python3-numpy-dev:arm64. 397s Preparing to unpack .../038-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 397s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 397s Selecting previously unselected package libblas3:arm64. 397s Preparing to unpack .../039-libblas3_3.12.1-2_arm64.deb ... 397s Unpacking libblas3:arm64 (3.12.1-2) ... 397s Selecting previously unselected package libgfortran5:arm64. 397s Preparing to unpack .../040-libgfortran5_15-20250404-0ubuntu1_arm64.deb ... 397s Unpacking libgfortran5:arm64 (15-20250404-0ubuntu1) ... 397s Selecting previously unselected package liblapack3:arm64. 397s Preparing to unpack .../041-liblapack3_3.12.1-2_arm64.deb ... 397s Unpacking liblapack3:arm64 (3.12.1-2) ... 397s Selecting previously unselected package python3-numpy. 397s Preparing to unpack .../042-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 397s Unpacking python3-numpy (1:2.2.3+ds-5) ... 397s Selecting previously unselected package sgml-base. 397s Preparing to unpack .../043-sgml-base_1.31_all.deb ... 397s Unpacking sgml-base (1.31) ... 397s Selecting previously unselected package autoconf. 397s Preparing to unpack .../044-autoconf_2.72-3ubuntu1_all.deb ... 397s Unpacking autoconf (2.72-3ubuntu1) ... 397s Selecting previously unselected package autotools-dev. 397s Preparing to unpack .../045-autotools-dev_20220109.1_all.deb ... 397s Unpacking autotools-dev (20220109.1) ... 397s Selecting previously unselected package automake. 397s Preparing to unpack .../046-automake_1%3a1.17-3ubuntu1_all.deb ... 397s Unpacking automake (1:1.17-3ubuntu1) ... 397s Selecting previously unselected package autopoint. 397s Preparing to unpack .../047-autopoint_0.23.1-1_all.deb ... 397s Unpacking autopoint (0.23.1-1) ... 397s Selecting previously unselected package libtcl8.6:arm64. 397s Preparing to unpack .../048-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 397s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 397s Selecting previously unselected package libxrender1:arm64. 397s Preparing to unpack .../049-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 397s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 397s Selecting previously unselected package libxft2:arm64. 397s Preparing to unpack .../050-libxft2_2.3.6-1build1_arm64.deb ... 397s Unpacking libxft2:arm64 (2.3.6-1build1) ... 397s Selecting previously unselected package libxss1:arm64. 397s Preparing to unpack .../051-libxss1_1%3a1.2.3-1build3_arm64.deb ... 397s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 397s Selecting previously unselected package libtk8.6:arm64. 397s Preparing to unpack .../052-libtk8.6_8.6.16-1_arm64.deb ... 397s Unpacking libtk8.6:arm64 (8.6.16-1) ... 398s Selecting previously unselected package tk8.6-blt2.5. 398s Preparing to unpack .../053-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 398s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 398s Selecting previously unselected package blt. 398s Preparing to unpack .../054-blt_2.5.3+dfsg-8_arm64.deb ... 398s Unpacking blt (2.5.3+dfsg-8) ... 398s Selecting previously unselected package libisl23:arm64. 398s Preparing to unpack .../055-libisl23_0.27-1_arm64.deb ... 398s Unpacking libisl23:arm64 (0.27-1) ... 398s Selecting previously unselected package libmpc3:arm64. 398s Preparing to unpack .../056-libmpc3_1.3.1-1build2_arm64.deb ... 398s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 398s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 398s Preparing to unpack .../057-cpp-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 398s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 398s Selecting previously unselected package cpp-14. 398s Preparing to unpack .../058-cpp-14_14.2.0-19ubuntu2_arm64.deb ... 398s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 398s Selecting previously unselected package cpp-aarch64-linux-gnu. 398s Preparing to unpack .../059-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 398s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 398s Selecting previously unselected package cpp. 398s Preparing to unpack .../060-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 398s Unpacking cpp (4:14.2.0-1ubuntu1) ... 398s Selecting previously unselected package libcc1-0:arm64. 398s Preparing to unpack .../061-libcc1-0_15-20250404-0ubuntu1_arm64.deb ... 398s Unpacking libcc1-0:arm64 (15-20250404-0ubuntu1) ... 398s Selecting previously unselected package libitm1:arm64. 398s Preparing to unpack .../062-libitm1_15-20250404-0ubuntu1_arm64.deb ... 398s Unpacking libitm1:arm64 (15-20250404-0ubuntu1) ... 398s Selecting previously unselected package libasan8:arm64. 398s Preparing to unpack .../063-libasan8_15-20250404-0ubuntu1_arm64.deb ... 398s Unpacking libasan8:arm64 (15-20250404-0ubuntu1) ... 398s Selecting previously unselected package liblsan0:arm64. 398s Preparing to unpack .../064-liblsan0_15-20250404-0ubuntu1_arm64.deb ... 398s Unpacking liblsan0:arm64 (15-20250404-0ubuntu1) ... 398s Selecting previously unselected package libtsan2:arm64. 398s Preparing to unpack .../065-libtsan2_15-20250404-0ubuntu1_arm64.deb ... 398s Unpacking libtsan2:arm64 (15-20250404-0ubuntu1) ... 398s Selecting previously unselected package libubsan1:arm64. 398s Preparing to unpack .../066-libubsan1_15-20250404-0ubuntu1_arm64.deb ... 398s Unpacking libubsan1:arm64 (15-20250404-0ubuntu1) ... 398s Selecting previously unselected package libhwasan0:arm64. 398s Preparing to unpack .../067-libhwasan0_15-20250404-0ubuntu1_arm64.deb ... 398s Unpacking libhwasan0:arm64 (15-20250404-0ubuntu1) ... 398s Selecting previously unselected package libgcc-14-dev:arm64. 398s Preparing to unpack .../068-libgcc-14-dev_14.2.0-19ubuntu2_arm64.deb ... 398s Unpacking libgcc-14-dev:arm64 (14.2.0-19ubuntu2) ... 398s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 399s Preparing to unpack .../069-gcc-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 399s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 399s Selecting previously unselected package gcc-14. 399s Preparing to unpack .../070-gcc-14_14.2.0-19ubuntu2_arm64.deb ... 399s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 399s Selecting previously unselected package gcc-aarch64-linux-gnu. 399s Preparing to unpack .../071-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 399s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 399s Selecting previously unselected package gcc. 399s Preparing to unpack .../072-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 399s Unpacking gcc (4:14.2.0-1ubuntu1) ... 399s Selecting previously unselected package libstdc++-14-dev:arm64. 399s Preparing to unpack .../073-libstdc++-14-dev_14.2.0-19ubuntu2_arm64.deb ... 399s Unpacking libstdc++-14-dev:arm64 (14.2.0-19ubuntu2) ... 399s Selecting previously unselected package g++-14-aarch64-linux-gnu. 399s Preparing to unpack .../074-g++-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 399s Unpacking g++-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 399s Selecting previously unselected package g++-14. 399s Preparing to unpack .../075-g++-14_14.2.0-19ubuntu2_arm64.deb ... 399s Unpacking g++-14 (14.2.0-19ubuntu2) ... 399s Selecting previously unselected package g++-aarch64-linux-gnu. 399s Preparing to unpack .../076-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 399s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 399s Selecting previously unselected package g++. 399s Preparing to unpack .../077-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 399s Unpacking g++ (4:14.2.0-1ubuntu1) ... 399s Selecting previously unselected package build-essential. 399s Preparing to unpack .../078-build-essential_12.12ubuntu1_arm64.deb ... 399s Unpacking build-essential (12.12ubuntu1) ... 399s Selecting previously unselected package bwa. 399s Preparing to unpack .../079-bwa_0.7.18-1_arm64.deb ... 399s Unpacking bwa (0.7.18-1) ... 400s Selecting previously unselected package libargtable2-0. 400s Preparing to unpack .../080-libargtable2-0_13-3_arm64.deb ... 400s Unpacking libargtable2-0 (13-3) ... 400s Selecting previously unselected package clustalo. 400s Preparing to unpack .../081-clustalo_1.2.4-8build1_arm64.deb ... 400s Unpacking clustalo (1.2.4-8build1) ... 400s Selecting previously unselected package libdebhelper-perl. 400s Preparing to unpack .../082-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 400s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 400s Selecting previously unselected package libtool. 400s Preparing to unpack .../083-libtool_2.5.4-4_all.deb ... 400s Unpacking libtool (2.5.4-4) ... 400s Selecting previously unselected package dh-autoreconf. 400s Preparing to unpack .../084-dh-autoreconf_20_all.deb ... 400s Unpacking dh-autoreconf (20) ... 400s Selecting previously unselected package libarchive-zip-perl. 400s Preparing to unpack .../085-libarchive-zip-perl_1.68-1_all.deb ... 400s Unpacking libarchive-zip-perl (1.68-1) ... 400s Selecting previously unselected package libfile-stripnondeterminism-perl. 400s Preparing to unpack .../086-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 400s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 400s Selecting previously unselected package dh-strip-nondeterminism. 400s Preparing to unpack .../087-dh-strip-nondeterminism_1.14.1-2_all.deb ... 400s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 400s Selecting previously unselected package debugedit. 400s Preparing to unpack .../088-debugedit_1%3a5.1-2_arm64.deb ... 400s Unpacking debugedit (1:5.1-2) ... 400s Selecting previously unselected package dwz. 400s Preparing to unpack .../089-dwz_0.15-1build6_arm64.deb ... 400s Unpacking dwz (0.15-1build6) ... 400s Selecting previously unselected package gettext. 400s Preparing to unpack .../090-gettext_0.23.1-1_arm64.deb ... 400s Unpacking gettext (0.23.1-1) ... 400s Selecting previously unselected package intltool-debian. 400s Preparing to unpack .../091-intltool-debian_0.35.0+20060710.6_all.deb ... 400s Unpacking intltool-debian (0.35.0+20060710.6) ... 400s Selecting previously unselected package po-debconf. 400s Preparing to unpack .../092-po-debconf_1.0.21+nmu1_all.deb ... 400s Unpacking po-debconf (1.0.21+nmu1) ... 400s Selecting previously unselected package debhelper. 400s Preparing to unpack .../093-debhelper_13.24.1ubuntu2_all.deb ... 400s Unpacking debhelper (13.24.1ubuntu2) ... 400s Selecting previously unselected package dh-python. 400s Preparing to unpack .../094-dh-python_6.20250308_all.deb ... 400s Unpacking dh-python (6.20250308) ... 400s Selecting previously unselected package dialign. 400s Preparing to unpack .../095-dialign_2.2.1-13_arm64.deb ... 400s Unpacking dialign (2.2.1-13) ... 400s Selecting previously unselected package xml-core. 400s Preparing to unpack .../096-xml-core_0.19_all.deb ... 400s Unpacking xml-core (0.19) ... 400s Selecting previously unselected package docutils-common. 400s Preparing to unpack .../097-docutils-common_0.21.2+dfsg-2_all.deb ... 400s Unpacking docutils-common (0.21.2+dfsg-2) ... 400s Selecting previously unselected package libcifpp-data. 400s Preparing to unpack .../098-libcifpp-data_7.0.9-1_all.deb ... 400s Unpacking libcifpp-data (7.0.9-1) ... 400s Selecting previously unselected package libcifpp7:arm64. 400s Preparing to unpack .../099-libcifpp7_7.0.9-1_arm64.deb ... 400s Unpacking libcifpp7:arm64 (7.0.9-1) ... 400s Selecting previously unselected package dssp. 400s Preparing to unpack .../100-dssp_4.4.10-1_arm64.deb ... 400s Unpacking dssp (4.4.10-1) ... 400s Selecting previously unselected package libimagequant0:arm64. 400s Preparing to unpack .../101-libimagequant0_2.18.0-1build1_arm64.deb ... 400s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 400s Selecting previously unselected package libgraphite2-3:arm64. 400s Preparing to unpack .../102-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 400s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 400s Selecting previously unselected package libharfbuzz0b:arm64. 400s Preparing to unpack .../103-libharfbuzz0b_10.2.0-1_arm64.deb ... 400s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 400s Selecting previously unselected package libraqm0:arm64. 400s Preparing to unpack .../104-libraqm0_0.10.2-1_arm64.deb ... 400s Unpacking libraqm0:arm64 (0.10.2-1) ... 400s Selecting previously unselected package libxpm4:arm64. 400s Preparing to unpack .../105-libxpm4_1%3a3.5.17-1build2_arm64.deb ... 400s Unpacking libxpm4:arm64 (1:3.5.17-1build2) ... 400s Selecting previously unselected package libgd3:arm64. 401s Preparing to unpack .../106-libgd3_2.3.3-12ubuntu3_arm64.deb ... 401s Unpacking libgd3:arm64 (2.3.3-12ubuntu3) ... 401s Selecting previously unselected package libhpdf-2.3.0:arm64. 401s Preparing to unpack .../107-libhpdf-2.3.0_2.3.0+dfsg-1build3_arm64.deb ... 401s Unpacking libhpdf-2.3.0:arm64 (2.3.0+dfsg-1build3) ... 401s Selecting previously unselected package mysql-common. 401s Preparing to unpack .../108-mysql-common_5.8+1.1.1ubuntu1_all.deb ... 401s Unpacking mysql-common (5.8+1.1.1ubuntu1) ... 401s Selecting previously unselected package libmysqlclient24:arm64. 401s Preparing to unpack .../109-libmysqlclient24_8.4.4-0ubuntu2_arm64.deb ... 401s Unpacking libmysqlclient24:arm64 (8.4.4-0ubuntu2) ... 401s Selecting previously unselected package libpq5:arm64. 401s Preparing to unpack .../110-libpq5_17.4-1_arm64.deb ... 401s Unpacking libpq5:arm64 (17.4-1) ... 401s Selecting previously unselected package emboss-lib. 401s Preparing to unpack .../111-emboss-lib_6.6.0+dfsg-15ubuntu2_arm64.deb ... 401s Unpacking emboss-lib (6.6.0+dfsg-15ubuntu2) ... 401s Selecting previously unselected package emboss-data. 401s Preparing to unpack .../112-emboss-data_6.6.0+dfsg-15ubuntu2_all.deb ... 401s Unpacking emboss-data (6.6.0+dfsg-15ubuntu2) ... 404s Selecting previously unselected package emboss. 404s Preparing to unpack .../113-emboss_6.6.0+dfsg-15ubuntu2_arm64.deb ... 404s Unpacking emboss (6.6.0+dfsg-15ubuntu2) ... 404s Selecting previously unselected package fonts-font-awesome. 404s Preparing to unpack .../114-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 404s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 404s Selecting previously unselected package fonts-lmodern. 404s Preparing to unpack .../115-fonts-lmodern_2.005-1_all.deb ... 404s Unpacking fonts-lmodern (2.005-1) ... 404s Selecting previously unselected package fonts-lyx. 404s Preparing to unpack .../116-fonts-lyx_2.4.3-1_all.deb ... 404s Unpacking fonts-lyx (2.4.3-1) ... 404s Selecting previously unselected package libgs-common. 404s Preparing to unpack .../117-libgs-common_10.05.0dfsg1-0ubuntu1_all.deb ... 404s Unpacking libgs-common (10.05.0dfsg1-0ubuntu1) ... 404s Selecting previously unselected package libgs10-common. 404s Preparing to unpack .../118-libgs10-common_10.05.0dfsg1-0ubuntu1_all.deb ... 404s Unpacking libgs10-common (10.05.0dfsg1-0ubuntu1) ... 404s Selecting previously unselected package libavahi-common-data:arm64. 404s Preparing to unpack .../119-libavahi-common-data_0.8-16ubuntu2_arm64.deb ... 404s Unpacking libavahi-common-data:arm64 (0.8-16ubuntu2) ... 404s Selecting previously unselected package libavahi-common3:arm64. 405s Preparing to unpack .../120-libavahi-common3_0.8-16ubuntu2_arm64.deb ... 405s Unpacking libavahi-common3:arm64 (0.8-16ubuntu2) ... 405s Selecting previously unselected package libavahi-client3:arm64. 405s Preparing to unpack .../121-libavahi-client3_0.8-16ubuntu2_arm64.deb ... 405s Unpacking libavahi-client3:arm64 (0.8-16ubuntu2) ... 405s Selecting previously unselected package libcups2t64:arm64. 405s Preparing to unpack .../122-libcups2t64_2.4.12-0ubuntu1_arm64.deb ... 405s Unpacking libcups2t64:arm64 (2.4.12-0ubuntu1) ... 405s Selecting previously unselected package libidn12:arm64. 405s Preparing to unpack .../123-libidn12_1.43-1_arm64.deb ... 405s Unpacking libidn12:arm64 (1.43-1) ... 405s Selecting previously unselected package libijs-0.35:arm64. 405s Preparing to unpack .../124-libijs-0.35_0.35-15.2_arm64.deb ... 405s Unpacking libijs-0.35:arm64 (0.35-15.2) ... 405s Selecting previously unselected package libjbig2dec0:arm64. 405s Preparing to unpack .../125-libjbig2dec0_0.20-1build3_arm64.deb ... 405s Unpacking libjbig2dec0:arm64 (0.20-1build3) ... 405s Selecting previously unselected package libpaper2:arm64. 405s Preparing to unpack .../126-libpaper2_2.2.5-0.3_arm64.deb ... 405s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 405s Selecting previously unselected package libice6:arm64. 405s Preparing to unpack .../127-libice6_2%3a1.1.1-1_arm64.deb ... 405s Unpacking libice6:arm64 (2:1.1.1-1) ... 405s Selecting previously unselected package libsm6:arm64. 405s Preparing to unpack .../128-libsm6_2%3a1.2.4-1_arm64.deb ... 405s Unpacking libsm6:arm64 (2:1.2.4-1) ... 405s Selecting previously unselected package libxt6t64:arm64. 405s Preparing to unpack .../129-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 405s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 405s Selecting previously unselected package libgs10:arm64. 405s Preparing to unpack .../130-libgs10_10.05.0dfsg1-0ubuntu1_arm64.deb ... 405s Unpacking libgs10:arm64 (10.05.0dfsg1-0ubuntu1) ... 405s Selecting previously unselected package ghostscript. 405s Preparing to unpack .../131-ghostscript_10.05.0dfsg1-0ubuntu1_arm64.deb ... 405s Unpacking ghostscript (10.05.0dfsg1-0ubuntu1) ... 405s Selecting previously unselected package libnetpbm11t64:arm64. 405s Preparing to unpack .../132-libnetpbm11t64_2%3a11.09.02-2_arm64.deb ... 405s Unpacking libnetpbm11t64:arm64 (2:11.09.02-2) ... 405s Selecting previously unselected package netpbm. 405s Preparing to unpack .../133-netpbm_2%3a11.09.02-2_arm64.deb ... 405s Unpacking netpbm (2:11.09.02-2) ... 405s Selecting previously unselected package tex-common. 405s Preparing to unpack .../134-tex-common_6.19_all.deb ... 405s Unpacking tex-common (6.19) ... 405s Selecting previously unselected package libpaper-utils. 405s Preparing to unpack .../135-libpaper-utils_2.2.5-0.3_arm64.deb ... 405s Unpacking libpaper-utils (2.2.5-0.3) ... 405s Selecting previously unselected package libkpathsea6:arm64. 405s Preparing to unpack .../136-libkpathsea6_2024.20240313.70630+ds-6_arm64.deb ... 405s Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-6) ... 405s Selecting previously unselected package libptexenc1:arm64. 405s Preparing to unpack .../137-libptexenc1_2024.20240313.70630+ds-6_arm64.deb ... 405s Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-6) ... 405s Selecting previously unselected package libsynctex2:arm64. 405s Preparing to unpack .../138-libsynctex2_2024.20240313.70630+ds-6_arm64.deb ... 405s Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-6) ... 405s Selecting previously unselected package libtexlua53-5:arm64. 405s Preparing to unpack .../139-libtexlua53-5_2024.20240313.70630+ds-6_arm64.deb ... 405s Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-6) ... 405s Selecting previously unselected package t1utils. 405s Preparing to unpack .../140-t1utils_1.41-4build3_arm64.deb ... 405s Unpacking t1utils (1.41-4build3) ... 405s Selecting previously unselected package libpixman-1-0:arm64. 405s Preparing to unpack .../141-libpixman-1-0_0.44.0-3_arm64.deb ... 405s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 405s Selecting previously unselected package libxcb-render0:arm64. 406s Preparing to unpack .../142-libxcb-render0_1.17.0-2_arm64.deb ... 406s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 406s Selecting previously unselected package libxcb-shm0:arm64. 406s Preparing to unpack .../143-libxcb-shm0_1.17.0-2_arm64.deb ... 406s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 406s Selecting previously unselected package libcairo2:arm64. 406s Preparing to unpack .../144-libcairo2_1.18.4-1_arm64.deb ... 406s Unpacking libcairo2:arm64 (1.18.4-1) ... 406s Selecting previously unselected package libmpfi0:arm64. 406s Preparing to unpack .../145-libmpfi0_1.5.4+ds-4_arm64.deb ... 406s Unpacking libmpfi0:arm64 (1.5.4+ds-4) ... 406s Selecting previously unselected package libpotrace0:arm64. 406s Preparing to unpack .../146-libpotrace0_1.16-2build1_arm64.deb ... 406s Unpacking libpotrace0:arm64 (1.16-2build1) ... 406s Selecting previously unselected package libteckit0:arm64. 406s Preparing to unpack .../147-libteckit0_2.5.12+ds1-1_arm64.deb ... 406s Unpacking libteckit0:arm64 (2.5.12+ds1-1) ... 406s Selecting previously unselected package libxmu6:arm64. 406s Preparing to unpack .../148-libxmu6_2%3a1.1.3-3build2_arm64.deb ... 406s Unpacking libxmu6:arm64 (2:1.1.3-3build2) ... 406s Selecting previously unselected package libxaw7:arm64. 406s Preparing to unpack .../149-libxaw7_2%3a1.0.16-1_arm64.deb ... 406s Unpacking libxaw7:arm64 (2:1.0.16-1) ... 406s Selecting previously unselected package libxi6:arm64. 406s Preparing to unpack .../150-libxi6_2%3a1.8.2-1_arm64.deb ... 406s Unpacking libxi6:arm64 (2:1.8.2-1) ... 406s Selecting previously unselected package libzzip-0-13t64:arm64. 406s Preparing to unpack .../151-libzzip-0-13t64_0.13.78+dfsg.1-0.1_arm64.deb ... 406s Unpacking libzzip-0-13t64:arm64 (0.13.78+dfsg.1-0.1) ... 406s Selecting previously unselected package texlive-binaries. 406s Preparing to unpack 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libarpack2t64:arm64 (3.9.1-4) ... 407s Selecting previously unselected package libcolamd3:arm64. 407s Preparing to unpack .../163-libcolamd3_1%3a7.8.3+dfsg-3_arm64.deb ... 407s Unpacking libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 408s Selecting previously unselected package libcommons-parent-java. 408s Preparing to unpack .../164-libcommons-parent-java_56-1_all.deb ... 408s Unpacking libcommons-parent-java (56-1) ... 408s Selecting previously unselected package libcommons-logging-java. 408s Preparing to unpack .../165-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 408s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 408s Selecting previously unselected package libexpat1-dev:arm64. 408s Preparing to unpack .../166-libexpat1-dev_2.7.1-1_arm64.deb ... 408s Unpacking libexpat1-dev:arm64 (2.7.1-1) ... 408s Selecting previously unselected package libglpk40:arm64. 408s Preparing to unpack .../167-libglpk40_5.0-1build2_arm64.deb ... 408s Unpacking libglpk40:arm64 (5.0-1build2) ... 408s Selecting previously unselected package libplfit0:arm64. 408s Preparing to unpack .../168-libplfit0_0.9.6+ds-2ubuntu1_arm64.deb ... 408s Unpacking libplfit0:arm64 (0.9.6+ds-2ubuntu1) ... 408s Selecting previously unselected package libigraph3t64:arm64. 408s Preparing to unpack .../169-libigraph3t64_0.10.15+ds-3_arm64.deb ... 408s Unpacking libigraph3t64:arm64 (0.10.15+ds-3) ... 408s Selecting previously unselected package libjs-jquery. 408s Preparing to unpack .../170-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 408s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 408s Selecting previously unselected package libjs-jquery-ui. 408s Preparing to unpack .../171-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 408s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 408s Selecting previously unselected package libjs-underscore. 408s Preparing to unpack .../172-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 408s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 408s Selecting previously unselected package libjs-sphinxdoc. 408s Preparing to unpack .../173-libjs-sphinxdoc_8.2.3-1_all.deb ... 408s Unpacking libjs-sphinxdoc (8.2.3-1) ... 408s Selecting previously unselected package libjson-perl. 408s Preparing to unpack .../174-libjson-perl_4.10000-1_all.deb ... 408s Unpacking libjson-perl (4.10000-1) ... 408s Selecting previously unselected package liblbfgsb0:arm64. 408s Preparing to unpack .../175-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 408s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 408s Selecting previously unselected package libmbedcrypto16:arm64. 408s Preparing to unpack .../176-libmbedcrypto16_3.6.2-3ubuntu1_arm64.deb ... 408s Unpacking libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ... 408s Selecting previously unselected package libmbedx509-7:arm64. 408s Preparing to unpack .../177-libmbedx509-7_3.6.2-3ubuntu1_arm64.deb ... 408s Unpacking libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 408s Selecting previously unselected package libmbedtls21:arm64. 408s Preparing to unpack .../178-libmbedtls21_3.6.2-3ubuntu1_arm64.deb ... 408s Unpacking libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 408s Selecting previously unselected package zlib1g-dev:arm64. 408s Preparing to unpack .../179-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 408s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 408s Selecting previously unselected package libpython3.13-dev:arm64. 408s Preparing to unpack .../180-libpython3.13-dev_3.13.3-1_arm64.deb ... 408s Unpacking libpython3.13-dev:arm64 (3.13.3-1) ... 408s Selecting previously unselected package libpython3-dev:arm64. 408s Preparing to unpack .../181-libpython3-dev_3.13.3-1_arm64.deb ... 408s Unpacking libpython3-dev:arm64 (3.13.3-1) ... 408s Selecting previously unselected package libpython3-all-dev:arm64. 408s Preparing to unpack .../182-libpython3-all-dev_3.13.3-1_arm64.deb ... 408s Unpacking libpython3-all-dev:arm64 (3.13.3-1) ... 408s Selecting previously unselected package libqhull-r8.0:arm64. 408s Preparing to unpack .../183-libqhull-r8.0_2020.2-6build1_arm64.deb ... 408s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 408s Selecting previously unselected package libxslt1.1:arm64. 408s Preparing to unpack .../184-libxslt1.1_1.1.39-0exp1ubuntu4_arm64.deb ... 408s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu4) ... 408s Selecting previously unselected package mafft. 408s Preparing to unpack .../185-mafft_7.505-1_arm64.deb ... 408s Unpacking mafft (7.505-1) ... 408s Selecting previously unselected package ncbi-data. 408s Preparing to unpack .../186-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 408s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 409s Selecting previously unselected package ncbi-blast+. 409s Preparing to unpack .../187-ncbi-blast+_2.16.0+ds-6build1_arm64.deb ... 409s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 409s Selecting previously unselected package phylip. 409s Preparing to unpack .../188-phylip_1%3a3.697+dfsg-4build1_arm64.deb ... 409s Unpacking phylip (1:3.697+dfsg-4build1) ... 409s Selecting previously unselected package prank. 409s Preparing to unpack .../189-prank_0.0.170427+dfsg-3_arm64.deb ... 409s Unpacking prank (0.0.170427+dfsg-3) ... 409s Selecting previously unselected package preview-latex-style. 409s Preparing to unpack .../190-preview-latex-style_13.2-1_all.deb ... 409s Unpacking preview-latex-style (13.2-1) ... 409s Selecting previously unselected package probcons. 409s Preparing to unpack .../191-probcons_1.12-14_arm64.deb ... 409s Unpacking probcons (1.12-14) ... 409s Selecting previously unselected package python-biopython-doc. 409s Preparing to unpack .../192-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 409s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 409s Selecting previously unselected package python-matplotlib-data. 409s Preparing to unpack .../193-python-matplotlib-data_3.8.3-7build1_all.deb ... 409s Unpacking python-matplotlib-data (3.8.3-7build1) ... 410s Selecting previously unselected package python3-all. 410s Preparing to unpack .../194-python3-all_3.13.3-1_arm64.deb ... 410s Unpacking python3-all (3.13.3-1) ... 410s Selecting previously unselected package python3.13-dev. 410s Preparing to unpack .../195-python3.13-dev_3.13.3-1_arm64.deb ... 410s Unpacking python3.13-dev (3.13.3-1) ... 410s Selecting previously unselected package python3-dev. 410s Preparing to unpack .../196-python3-dev_3.13.3-1_arm64.deb ... 410s Unpacking python3-dev (3.13.3-1) ... 410s Selecting previously unselected package python3-all-dev. 410s Preparing to unpack .../197-python3-all-dev_3.13.3-1_arm64.deb ... 410s Unpacking python3-all-dev (3.13.3-1) ... 410s Selecting previously unselected package python3.13-tk. 410s Preparing to unpack .../198-python3.13-tk_3.13.3-1_arm64.deb ... 410s Unpacking python3.13-tk (3.13.3-1) ... 410s Selecting previously unselected package python3-tk:arm64. 410s Preparing to unpack .../199-python3-tk_3.13.3-1_arm64.deb ... 410s Unpacking python3-tk:arm64 (3.13.3-1) ... 410s Selecting previously unselected package python3-pil.imagetk:arm64. 410s Preparing to unpack .../200-python3-pil.imagetk_11.1.0-5build1_arm64.deb ... 410s Unpacking python3-pil.imagetk:arm64 (11.1.0-5build1) ... 410s Selecting previously unselected package python3-pil:arm64. 410s Preparing to unpack .../201-python3-pil_11.1.0-5build1_arm64.deb ... 410s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 410s Selecting previously unselected package python3-cairo. 410s Preparing to unpack .../202-python3-cairo_1.27.0-2_arm64.deb ... 410s Unpacking python3-cairo (1.27.0-2) ... 410s Selecting previously unselected package python3-freetype. 410s Preparing to unpack .../203-python3-freetype_2.5.1-1_all.deb ... 410s Unpacking python3-freetype (2.5.1-1) ... 410s Selecting previously unselected package python3-rlpycairo. 410s Preparing to unpack .../204-python3-rlpycairo_0.3.0-3_all.deb ... 410s Unpacking python3-rlpycairo (0.3.0-3) ... 410s Selecting previously unselected package python3-reportlab. 410s Preparing to unpack .../205-python3-reportlab_4.3.1-1_all.deb ... 410s Unpacking python3-reportlab (4.3.1-1) ... 410s Selecting previously unselected package w3c-sgml-lib. 410s Preparing to unpack .../206-w3c-sgml-lib_1.3-3_all.deb ... 410s Unpacking w3c-sgml-lib (1.3-3) ... 410s Selecting previously unselected package python3-biopython. 410s Preparing to unpack .../207-python3-biopython_1.85+dfsg-2build1_arm64.deb ... 410s Unpacking python3-biopython (1.85+dfsg-2build1) ... 410s Selecting previously unselected package python3-biopython-sql. 410s Preparing to unpack .../208-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 410s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 410s Selecting previously unselected package python3-brotli. 410s Preparing to unpack .../209-python3-brotli_1.1.0-2build4_arm64.deb ... 410s Unpacking python3-brotli (1.1.0-2build4) ... 410s Selecting previously unselected package python3-contourpy. 410s Preparing to unpack .../210-python3-contourpy_1.3.1-1build1_arm64.deb ... 410s Unpacking python3-contourpy (1.3.1-1build1) ... 410s Selecting previously unselected package python3-cycler. 410s Preparing to unpack .../211-python3-cycler_0.12.1-1_all.deb ... 410s Unpacking python3-cycler (0.12.1-1) ... 410s Selecting previously unselected package python3-decorator. 410s Preparing to unpack .../212-python3-decorator_5.1.1-5_all.deb ... 410s Unpacking python3-decorator (5.1.1-5) ... 410s Selecting previously unselected package python3-defusedxml. 410s Preparing to unpack .../213-python3-defusedxml_0.7.1-3_all.deb ... 410s Unpacking python3-defusedxml (0.7.1-3) ... 410s Selecting previously unselected package python3-roman. 410s Preparing to unpack .../214-python3-roman_5.0-1_all.deb ... 410s Unpacking python3-roman (5.0-1) ... 410s Selecting previously unselected package python3-docutils. 410s Preparing to unpack .../215-python3-docutils_0.21.2+dfsg-2_all.deb ... 410s Unpacking python3-docutils (0.21.2+dfsg-2) ... 411s Selecting previously unselected package python3-platformdirs. 411s Preparing to unpack .../216-python3-platformdirs_4.3.6-1_all.deb ... 411s Unpacking python3-platformdirs (4.3.6-1) ... 411s Selecting previously unselected package python3-fs. 411s Preparing to unpack .../217-python3-fs_2.4.16-7_all.deb ... 411s Unpacking python3-fs (2.4.16-7) ... 411s Selecting previously unselected package python3-lxml:arm64. 411s Preparing to unpack .../218-python3-lxml_5.3.2-1_arm64.deb ... 411s Unpacking python3-lxml:arm64 (5.3.2-1) ... 411s Selecting previously unselected package python3-lz4. 411s Preparing to unpack .../219-python3-lz4_4.4.0+dfsg-1build1_arm64.deb ... 411s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 411s Selecting previously unselected package python3-scipy. 411s Preparing to unpack .../220-python3-scipy_1.14.1-4ubuntu2_arm64.deb ... 411s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 411s Selecting previously unselected package python3-mpmath. 411s 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python3-imagesize (1.4.1-1) ... 412s Selecting previously unselected package python3-kiwisolver. 412s Preparing to unpack .../227-python3-kiwisolver_1.4.7-3build1_arm64.deb ... 412s Unpacking python3-kiwisolver (1.4.7-3build1) ... 412s Selecting previously unselected package python3-matplotlib. 412s Preparing to unpack .../228-python3-matplotlib_3.8.3-7build1_arm64.deb ... 412s Unpacking python3-matplotlib (3.8.3-7build1) ... 412s Selecting previously unselected package python3-msgpack. 412s Preparing to unpack .../229-python3-msgpack_1.0.3-3build4_arm64.deb ... 412s Unpacking python3-msgpack (1.0.3-3build4) ... 412s Selecting previously unselected package python3-mmtf. 412s Preparing to unpack .../230-python3-mmtf_1.1.3-1_all.deb ... 412s Unpacking python3-mmtf (1.1.3-1) ... 412s Selecting previously unselected package python3-mysqldb. 412s Preparing to unpack .../231-python3-mysqldb_1.4.6-2build6_arm64.deb ... 412s Unpacking python3-mysqldb (1.4.6-2build6) ... 412s Selecting previously unselected package python3-networkx. 412s Preparing to unpack .../232-python3-networkx_3.2.1-4ubuntu1_all.deb ... 412s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 413s Selecting previously unselected package sphinx-common. 413s Preparing to unpack .../233-sphinx-common_8.2.3-1_all.deb ... 413s Unpacking sphinx-common (8.2.3-1) ... 413s Selecting previously unselected package python3-alabaster. 413s Preparing to unpack .../234-python3-alabaster_0.7.16-0.1_all.deb ... 413s Unpacking python3-alabaster (0.7.16-0.1) ... 413s Selecting previously unselected package python3-roman-numerals. 413s Preparing to unpack .../235-python3-roman-numerals_3.1.0-1ubuntu1_all.deb ... 413s Unpacking python3-roman-numerals (3.1.0-1ubuntu1) ... 413s Selecting previously unselected package python3-snowballstemmer. 413s Preparing to unpack .../236-python3-snowballstemmer_2.2.0-4build1_all.deb ... 413s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 413s Selecting previously unselected 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provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 420s Setting up libexpat1-dev:arm64 (2.7.1-1) ... 420s Setting up libzzip-0-13t64:arm64 (0.13.78+dfsg.1-0.1) ... 421s Setting up libjbig2dec0:arm64 (0.20-1build3) ... 421s Setting up python3-snowballstemmer (2.2.0-4build1) ... 421s Setting up libteckit0:arm64 (2.5.12+ds1-1) ... 421s Setting up python3-brotli (1.1.0-2build4) ... 421s Setting up libapache-pom-java (33-2) ... 421s Setting up libavahi-common-data:arm64 (0.8-16ubuntu2) ... 421s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 421s Setting up t1utils (1.41-4build3) ... 421s Setting up python3-cycler (0.12.1-1) ... 421s Setting up libtexlua53-5:arm64 (2024.20240313.70630+ds-6) ... 421s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 421s Setting up fonts-dejavu-mono (2.37-8) ... 421s Setting up python3-kiwisolver (1.4.7-3build1) ... 421s Setting up libmpc3:arm64 (1.3.1-1build2) ... 421s Setting up python3-numpy-dev:arm64 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422s Setting up python3-mpmath (1.3.0-1) ... 422s Setting up libisl23:arm64 (0.27-1) ... 422s Setting up libde265-0:arm64 (1.0.15-1build5) ... 422s Setting up python-matplotlib-data (3.8.3-7build1) ... 422s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 422s Setting up dialign (2.2.1-13) ... 422s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 422s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 422s Setting up xdg-utils (1.2.1-2ubuntu1) ... 422s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 422s Setting up libcc1-0:arm64 (15-20250404-0ubuntu1) ... 422s Setting up liblsan0:arm64 (15-20250404-0ubuntu1) ... 422s Setting up libitm1:arm64 (15-20250404-0ubuntu1) ... 422s Setting up libsynctex2:arm64 (2024.20240313.70630+ds-6) ... 422s Setting up prank (0.0.170427+dfsg-3) ... 422s Setting up libargtable2-0 (13-3) ... 422s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 422s Setting up python3-imagesize (1.4.1-1) ... 423s Setting up libpotrace0:arm64 (1.16-2build1) ... 423s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 423s Setting up automake (1:1.17-3ubuntu1) ... 423s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 423s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 423s Setting up python3-sympy (1.13.3-5) ... 428s Setting up libice6:arm64 (2:1.1.1-1) ... 428s Setting up flex (2.6.4-8.2build1) ... 428s Setting up liblapack3:arm64 (3.12.1-2) ... 428s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 428s Setting up gettext (0.23.1-1) ... 428s Setting up libarpack2t64:arm64 (3.9.1-4) ... 428s Setting up libamd3:arm64 (1:7.8.3+dfsg-3) ... 428s Setting up libpdfbox-java (1:1.8.16-5) ... 428s Setting up libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 428s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 429s Setting up wise (2.4.1-25) ... 429s Setting up preview-latex-style (13.2-1) ... 429s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 429s Setting up libcommons-parent-java (56-1) ... 429s Setting up libavahi-common3:arm64 (0.8-16ubuntu2) ... 429s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 429s Setting up libcifpp7:arm64 (7.0.9-1) ... 429s Setting up libpaper-utils (2.2.5-0.3) ... 429s Setting up clustalo (1.2.4-8build1) ... 429s Setting up dssp (4.4.10-1) ... 429s Setting up xfonts-utils (1:7.7+7) ... 429s Setting up intltool-debian (0.35.0+20060710.6) ... 429s Setting up libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 429s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 429s Setting up libptexenc1:arm64 (2024.20240313.70630+ds-6) ... 429s Setting up libglpk40:arm64 (5.0-1build2) ... 429s Setting up libraqm0:arm64 (0.10.2-1) ... 429s Setting up libpython3.13-dev:arm64 (3.13.3-1) ... 429s Setting up python3-numpy (1:2.2.3+ds-5) ... 430s Setting up libjs-sphinxdoc (8.2.3-1) ... 430s Setting up libraw23t64:arm64 (0.21.4-2) ... 430s Setting up libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 430s Setting up dh-strip-nondeterminism (1.14.1-2) ... 430s Setting up cpp-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 430s Setting up python3-lxml:arm64 (5.3.2-1) ... 431s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 431s Setting up libtiff6:arm64 (4.7.0-3ubuntu1) ... 431s Setting up xml-core (0.19) ... 431s Setting up python3-contourpy (1.3.1-1build1) ... 431s Setting up libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 431s Setting up libgcc-14-dev:arm64 (14.2.0-19ubuntu2) ... 431s Setting up libigraph3t64:arm64 (0.10.15+ds-3) ... 431s Setting up libstdc++-14-dev:arm64 (14.2.0-19ubuntu2) ... 431s Setting up libsm6:arm64 (2:1.2.4-1) ... 431s Setting up libavahi-client3:arm64 (0.8-16ubuntu2) ... 431s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 431s Setting up libxft2:arm64 (2.3.6-1build1) ... 431s Setting up python3-scipy (1.14.1-4ubuntu2) ... 434s Setting up libpython3-dev:arm64 (3.13.3-1) ... 434s Setting up python3.13-dev (3.13.3-1) ... 434s Setting up po-debconf (1.0.21+nmu1) ... 434s Setting up libtk8.6:arm64 (8.6.16-1) ... 434s Setting up python3-mmtf (1.1.3-1) ... 434s Setting up fonts-urw-base35 (20200910-8) ... 434s Setting up libcairo2:arm64 (1.18.4-1) ... 434s Setting up python3.13-tk (3.13.3-1) ... 434s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 434s Setting up python3-pil:arm64 (11.1.0-5build1) ... 435s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 435s Setting up libpython3-all-dev:arm64 (3.13.3-1) ... 435s Setting up sphinx-common (8.2.3-1) ... 435s Setting up python3-dev (3.13.3-1) ... 435s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 435s Setting up netpbm (2:11.09.02-2) ... 435s Setting up cpp-14 (14.2.0-19ubuntu2) ... 435s Setting up python3-igraph (0.11.8+ds-1build1) ... 435s Setting up cpp (4:14.2.0-1ubuntu1) ... 435s Setting up gcc-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 435s Setting up libcups2t64:arm64 (2.4.12-0ubuntu1) ... 435s Setting up python3-all-dev (3.13.3-1) ... 435s Setting up libgs10-common (10.05.0dfsg1-0ubuntu1) ... 435s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 435s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 435s Setting up libxmu6:arm64 (2:1.1.3-3build2) ... 435s Setting up g++-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 435s Setting up python3-cairo (1.27.0-2) ... 435s Setting up blt (2.5.3+dfsg-8) ... 435s Setting up python3-tk:arm64 (3.13.3-1) ... 435s Setting up libxaw7:arm64 (2:1.0.16-1) ... 435s Setting up gcc-14 (14.2.0-19ubuntu2) ... 435s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ... 435s Setting up python3-rlpycairo (0.3.0-3) ... 435s Setting up python3-reportlab (4.3.1-1) ... 436s Setting up texlive-binaries (2024.20240313.70630+ds-6) ... 436s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 436s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 436s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 436s Setting up g++-14 (14.2.0-19ubuntu2) ... 436s Setting up texlive-base (2024.20250309-1) ... 437s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 437s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 437s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 437s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 438s Setting up libgs10:arm64 (10.05.0dfsg1-0ubuntu1) ... 438s Setting up libtool (2.5.4-4) ... 438s Setting up ghostscript (10.05.0dfsg1-0ubuntu1) ... 438s Setting up gcc (4:14.2.0-1ubuntu1) ... 438s Setting up dh-autoreconf (20) ... 438s Setting up texlive-latex-base (2024.20250309-1) ... 438s Setting up texlive-latex-recommended (2024.20250309-1) ... 438s Setting up texlive-pictures (2024.20250309-1) ... 438s Setting up g++ (4:14.2.0-1ubuntu1) ... 438s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 438s Setting up texlive-fonts-recommended (2024.20250309-1) ... 438s Setting up build-essential (12.12ubuntu1) ... 438s Setting up debhelper (13.24.1ubuntu2) ... 438s Setting up texlive-latex-extra (2024.20250309-2) ... 438s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 438s Setting up libheif-plugin-aomdec:arm64 (1.19.7-1) ... 438s Setting up libheif-plugin-libde265:arm64 (1.19.7-1) ... 438s Setting up libheif1:arm64 (1.19.7-1) ... 438s Setting up python3-fonttools (4.55.3-2build1) ... 439s Setting up libgd3:arm64 (2.3.3-12ubuntu3) ... 439s Setting up libmagickcore-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 439s Setting up emboss-lib (6.6.0+dfsg-15ubuntu2) ... 439s Setting up python3-matplotlib (3.8.3-7build1) ... 440s Setting up libmagickwand-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1) ... 440s Setting up emboss (6.6.0+dfsg-15ubuntu2) ... 440s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 440s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 440s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 440s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 440s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 440s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 440s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 440s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 440s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 440s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 440s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 440s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 440s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 440s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 440s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 440s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 440s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 440s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 440s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 440s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 440s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 440s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 440s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 440s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 441s 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 441s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 441s 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 441s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 441s 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 441s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 441s 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 441s Setting up hevea (2.36-2) ... 441s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 441s Processing triggers for install-info (7.1.1-1) ... 441s Processing triggers for libc-bin (2.41-6ubuntu1) ... 441s Processing triggers for man-db (2.13.0-1) ... 442s Processing triggers for shared-mime-info (2.4-5build1) ... 442s Processing triggers for sgml-base (1.31) ... 442s Setting up w3c-sgml-lib (1.3-3) ... 467s Setting up docutils-common (0.21.2+dfsg-2) ... 467s Setting up python3-biopython (1.85+dfsg-2build1) ... 468s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 468s Processing triggers for sgml-base (1.31) ... 468s Setting up python3-docutils (0.21.2+dfsg-2) ... 469s Setting up python3-sphinx (8.2.3-1) ... 469s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 470s Setting up python3-numpydoc (1.8.0-1) ... 470s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 470s Processing triggers for tex-common (6.19) ... 470s Running updmap-sys. This may take some time... done. 470s Running mktexlsr /var/lib/texmf ... done. 470s Building format(s) --all. 542s This may take some time... done. 550s autopkgtest [19:43:18]: test full_suite: sh debian/tests/run-unit-test 550s autopkgtest [19:43:18]: test full_suite: [----------------------- 552s mkdir: created directory 'Bio' 552s mkdir: created directory 'Bio/Align' 552s mkdir: created directory 'Bio/Align/substitution_matrices' 552s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 552s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 552s test_Ace ... ok 552s test_Affy ... ok 555s test_AlignIO ... ok 555s test_AlignIO_ClustalIO ... ok 555s test_AlignIO_EmbossIO ... ok 555s test_AlignIO_FastaIO ... ok 555s test_AlignIO_MauveIO ... ok 555s test_AlignIO_PhylipIO ... ok 555s test_AlignIO_convert ... ok 555s test_AlignInfo ... ok 555s test_Align_Alignment ... ok 555s test_Align_a2m ... ok 555s test_Align_bed ... ok 555s test_Align_bigbed ... ok 556s test_Align_bigmaf ... ok 556s test_Align_bigpsl ... ok 556s test_Align_chain ... ok 556s test_Align_clustal ... ok 561s test_Align_codonalign ... ok 561s test_Align_emboss ... ok 561s test_Align_exonerate ... ok 561s test_Align_fasta ... ok 562s test_Align_hhr ... ok 562s test_Align_maf ... ok 562s test_Align_mauve ... ok 562s test_Align_msf ... ok 562s test_Align_nexus ... ok 563s test_Align_phylip ... ok 563s test_Align_psl ... ok 563s test_Align_sam ... ok 565s test_Align_stockholm ... ok 565s test_Align_tabular ... ok 565s test_Application ... ok 565s test_BioSQL_MySQLdb_online ... skipping. internet not available 565s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 565s test_BioSQL_mysql_connector_online ... skipping. internet not available 565s test_BioSQL_psycopg2_online ... skipping. internet not available 569s test_BioSQL_sqlite3 ... ok 569s test_BioSQL_sqlite3_online ... skipping. internet not available 569s test_Blast_Record ... ok 570s test_Blast_parser ... ok 570s test_CAPS ... ok 570s test_Chi2 ... ok 571s test_ClustalOmega_tool ... ok 571s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 571s test_Cluster ... ok 571s test_CodonTable ... ok 571s test_ColorSpiral ... ok 571s test_Compass ... ok 572s test_Consensus ... ok 574s test_Dialign_tool ... ok 574s test_EMBL_unittest ... ok 579s test_Emboss ... ok 579s test_EmbossPrimer ... ok 583s test_Entrez ... ok 583s test_Entrez_online ... skipping. internet not available 584s test_Entrez_parser ... ok 584s test_Enzyme ... ok 584s test_ExPASy ... skipping. internet not available 584s test_Fasttree_tool ... ok 584s test_File ... ok 584s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 584s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 584s ok 586s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 587s ok 588s test_GraphicsChromosome ... ok 588s test_GraphicsDistribution ... ok 589s test_GraphicsGeneral ... ok 589s test_HMMCasino ... ok 589s test_HMMGeneral ... ok 589s test_KEGG ... ok 589s test_KEGG_online ... skipping. internet not available 593s test_KGML_graphics ... ok 593s test_KGML_graphics_online ... skipping. internet not available 594s test_KGML_nographics ... ok 594s test_KeyWList ... ok 594s test_LogisticRegression ... ok 595s test_MafIO_index ... ok 596s test_Mafft_tool ... ok 597s test_MarkovModel ... ok 597s test_Medline ... ok 597s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 597s test_NCBIXML ... Exception ignored in: 597s Traceback (most recent call last): 597s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 597s expat_parser.Parse(NULL, True) 597s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 597s ok 599s test_NCBI_BLAST_tools ... ok 599s test_NCBI_qblast ... ok 599s test_NMR ... ok 599s test_NaiveBayes ... ok 599s test_Nexus ... ok 600s test_PAML_baseml ... ok 600s test_PAML_codeml ... ok 600s test_PAML_yn00 ... ok 604s test_PDB_CEAligner ... ok 606s test_PDB_DSSP ... ok 606s test_PDB_Dice ... ok 606s test_PDB_Disordered ... ok 606s test_PDB_Exposure ... ok 606s test_PDB_FragmentMapper ... ok 608s test_PDB_KDTree ... ok 608s test_PDB_MMCIF2Dict ... ok 608s test_PDB_MMCIFIO ... ok 609s test_PDB_MMCIFParser ... ok 609s test_PDB_NACCESS ... ok 610s test_PDB_PDBIO ... ok 610s test_PDB_PDBList ... skipping. internet not available 616s test_PDB_PDBMLParser ... ok 616s test_PDB_PDBParser ... ok 616s 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 616s test_PDB_Polypeptide ... ok 616s test_PDB_QCPSuperimposer ... ok 619s test_PDB_SASA ... ok 619s test_PDB_SMCRA ... ok 620s test_PDB_Selection ... ok 620s test_PDB_StructureAlignment ... ok 620s test_PDB_Superimposer ... ok 620s test_PDB_alphafold_db ... skipping. internet not available 622s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 622s warnings.warn( 622s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 622s warnings.warn( 622s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 622s warnings.warn( 622s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 622s warnings.warn( 622s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 622s warnings.warn( 622s ok 630s test_PDB_internal_coords ... ok 630s test_PDB_parse_pdb_header ... ok 630s test_PDB_vectors ... ok 630s test_PQR ... ok 631s test_Pathway ... ok 631s test_Phd ... ok 631s test_Phylo ... ok 632s test_PhyloXML ... ok 632s test_Phylo_CDAO ... ok 633s test_Phylo_NeXML ... ok 634s test_Phylo_igraph ... ok 636s test_Phylo_matplotlib ... ok 636s test_Phylo_networkx ... ok 637s test_PopGen_GenePop_nodepend ... ok 639s test_Prank_tool ... ok 639s test_Probcons_tool ... ok 640s test_ProtParam ... ok 641s test_RCSBFormats ... ok 641s test_Restriction ... ok 642s test_SCOP_Astral ... ok 642s test_SCOP_Cla ... ok 643s test_SCOP_Des ... ok 644s test_SCOP_Dom ... ok 644s test_SCOP_Hie ... ok 645s test_SCOP_Raf ... ok 645s test_SCOP_Residues ... ok 646s test_SCOP_Scop ... ok 646s test_SVDSuperimposer ... ok 647s test_SearchIO_blast_tab ... ok 648s test_SearchIO_blast_tab_index ... ok 648s test_SearchIO_blast_xml ... ok 650s test_SearchIO_blast_xml_index ... ok 650s test_SearchIO_blat_psl ... ok 651s test_SearchIO_blat_psl_index ... ok 652s test_SearchIO_exonerate ... ok 652s test_SearchIO_exonerate_text_index ... ok 653s test_SearchIO_exonerate_vulgar_index ... ok 653s test_SearchIO_fasta_m10 ... ok 654s test_SearchIO_fasta_m10_index ... ok 654s test_SearchIO_hhsuite2_text ... ok 655s test_SearchIO_hmmer2_text ... ok 656s test_SearchIO_hmmer2_text_index ... ok 656s test_SearchIO_hmmer3_domtab ... ok 657s test_SearchIO_hmmer3_domtab_index ... ok 657s test_SearchIO_hmmer3_tab ... ok 658s test_SearchIO_hmmer3_tab_index ... ok 659s test_SearchIO_hmmer3_text ... ok 659s test_SearchIO_hmmer3_text_index ... ok 660s test_SearchIO_interproscan_xml ... ok 660s test_SearchIO_model ... ok 661s test_SearchIO_write ... ok 661s test_SeqFeature ... ok 676s test_SeqIO ... ok 676s test_SeqIO_AbiIO ... ok 677s test_SeqIO_FastaIO ... ok 678s test_SeqIO_Gck ... ok 678s test_SeqIO_Gfa ... ok 679s test_SeqIO_Insdc ... ok 679s test_SeqIO_NibIO ... ok 681s test_SeqIO_PdbIO ... ok 682s test_SeqIO_QualityIO ... ok 683s test_SeqIO_SeqXML ... ok 683s test_SeqIO_SffIO ... ok 684s test_SeqIO_SnapGene ... ok 685s test_SeqIO_TwoBitIO ... ok 686s test_SeqIO_UniprotIO ... ok 686s test_SeqIO_Xdna ... ok 687s test_SeqIO_features ... ok 700s test_SeqIO_index ... ok 701s test_SeqIO_online ... skipping. internet not available 701s test_SeqIO_write ... ok 702s test_SeqRecord ... ok 702s test_SeqUtils ... ok 704s test_Seq_objs ... ok 704s test_SwissProt ... ok 707s test_TCoffee_tool ... ok 707s test_TogoWS ... skipping. internet not available 708s test_TreeConstruction ... ok 709s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 709s test_UniGene ... ok 710s test_UniProt ... skipping. internet not available 710s test_UniProt_GOA ... ok 711s test_align ... ok 712s test_align_substitution_matrices ... ok 714s test_bgzf ... ok 715s test_cellosaurus ... ok 720s test_codonalign ... ok 721s test_geo ... ok 722s test_kNN ... ok 722s test_motifs ... ok 723s test_motifs_online ... skipping. internet not available 724s 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. 724s warnings.warn( 724s ok 724s test_pairwise2_no_C ... ok 725s test_pairwise_aligner ... ok 726s test_pairwise_alignment_map ... ok 733s test_phenotype ... ok 733s test_phenotype_fit ... ok 734s 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. 734s test_prodoc ... ok 735s test_prosite ... ok 735s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 736s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 736s test_seq ... ok 737s test_translate ... ok 737s ---------------------------------------------------------------------- 737s Ran 218 tests in 185.126 seconds 737s 737s Skipping any tests requiring internet access 737s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 737s Operating system: posix linux 739s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 739s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 739s autopkgtest [19:46:27]: test full_suite: -----------------------] 740s full_suite PASS 740s autopkgtest [19:46:28]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 740s autopkgtest [19:46:28]: @@@@@@@@@@@@@@@@@@@@ summary 740s dependencies PASS 740s full_suite PASS 755s nova [W] Using flock in prodstack7-arm64 755s Creating nova instance adt-questing-arm64-python-biopython-20250503-193408-juju-7f2275-prod-proposed-migration-environment-2-f16a332c-bd2a-415f-9978-ca31b7805f95 from image adt/ubuntu-questing-arm64-server-20250503.img (UUID a84e47a3-c3d2-45c5-808f-b2f1d568c8b9)... 755s nova [W] Timed out waiting for 08d56bfd-b110-4d1c-b5e0-dfe22919ea62 to get deleted. 755s nova [W] Using flock in prodstack7-arm64 755s Creating nova instance adt-questing-arm64-python-biopython-20250503-193408-juju-7f2275-prod-proposed-migration-environment-2-f16a332c-bd2a-415f-9978-ca31b7805f95 from image adt/ubuntu-questing-arm64-server-20250503.img (UUID a84e47a3-c3d2-45c5-808f-b2f1d568c8b9)... 755s nova [W] Timed out waiting for df881159-a21f-4de3-b3ab-c897a798d7b6 to get deleted.