0s autopkgtest [03:40:07]: starting date and time: 2025-07-12 03:40:07+0000 0s autopkgtest [03:40:07]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [03:40:07]: host juju-7f2275-prod-proposed-migration-environment-21; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._jbq12q2/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-reportlab --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-reportlab/4.4.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-21@sto01-arm64-6.secgroup --name adt-questing-arm64-python-biopython-20250712-034007-juju-7f2275-prod-proposed-migration-environment-21-c0aec37e-2dc9-449e-a0d9-2881ea3d8291 --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-21 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-questing-arm64-python-biopython-20250712-034007-juju-7f2275-prod-proposed-migration-environment-21-c0aec37e-2dc9-449e-a0d9-2881ea3d8291 from image adt/ubuntu-questing-arm64-server-20250712.img (UUID 64e93443-6a95-4ef6-a3b4-cb2b1f0a688a)... 94s autopkgtest [03:41:41]: testbed dpkg architecture: arm64 94s autopkgtest [03:41:41]: testbed apt version: 3.1.3 94s autopkgtest [03:41:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 94s autopkgtest [03:41:41]: testbed release detected to be: None 95s autopkgtest [03:41:42]: updating testbed package index (apt update) 95s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [249 kB] 95s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 95s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 95s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 95s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [15.4 kB] 95s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [39.9 kB] 95s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [207 kB] 96s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [58.6 kB] 96s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [186 kB] 96s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [15.7 kB] 96s Fetched 772 kB in 0s (2086 kB/s) 96s Reading package lists... 97s autopkgtest [03:41:44]: upgrading testbed (apt dist-upgrade and autopurge) 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Calculating upgrade... 98s The following packages will be upgraded: 98s htop 98s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 176 kB of archives. 98s After this operation, 0 B of additional disk space will be used. 98s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 htop arm64 3.4.1-5 [176 kB] 98s Fetched 176 kB in 0s (14.4 MB/s) 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 131053 files and directories currently installed.) 98s Preparing to unpack .../htop_3.4.1-5_arm64.deb ... 98s Unpacking htop (3.4.1-5) over (3.4.1-4) ... 98s Setting up htop (3.4.1-5) ... 98s Processing triggers for man-db (2.13.1-1) ... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Solving dependencies... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s autopkgtest [03:41:49]: testbed running kernel: Linux 6.15.0-4-generic #4-Ubuntu SMP PREEMPT_DYNAMIC Fri Jul 4 14:27:49 UTC 2025 102s autopkgtest [03:41:49]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 104s Get:1 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-4 (dsc) [3070 B] 104s Get:2 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-4 (tar) [14.6 MB] 104s Get:3 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-4 (diff) [42.8 kB] 104s gpgv: Signature made Fri Apr 11 19:33:28 2025 UTC 104s gpgv: using RSA key D54C3BFAFFB042DE382DA5D741CE7F0B9F1B8B32 104s gpgv: Can't check signature: No public key 104s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-4.dsc: no acceptable signature found 105s autopkgtest [03:41:52]: testing package python-biopython version 1.85+dfsg-4 105s autopkgtest [03:41:52]: build not needed 110s autopkgtest [03:41:57]: test dependencies: preparing testbed 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Solving dependencies... 111s The following NEW packages will be installed: 111s fontconfig-config fonts-urw-base35 libblas3 libcairo2 libdeflate0 111s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 111s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 111s libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 liblerc4 libopenjp2-7 111s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 111s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 111s python3-all python3-biopython python3-biopython-sql python3-cairo 111s python3-charset-normalizer python3-freetype python3-numpy python3-numpy-dev 111s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 111s x11-common xfonts-encodings xfonts-utils xml-core 111s 0 upgraded, 50 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 44.4 MB of archives. 111s After this operation, 121 MB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 111s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2build1 [160 kB] 111s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15.1.0-8ubuntu1 [451 kB] 111s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2build1 [2308 kB] 111s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 112s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 112s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 112s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 112s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 112s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 112s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 112s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 112s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 112s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 112s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 112s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 112s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 112s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 112s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15.1.0-8ubuntu1 [147 kB] 112s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 112s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 112s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 112s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 112s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 112s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 112s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 112s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 112s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 112s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 112s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 112s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 112s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 112s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 112s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.7.0-3ubuntu1 [197 kB] 112s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 112s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 112s Get:37 http://ftpmaster.internal/ubuntu questing/universe arm64 python-biopython-doc all 1.85+dfsg-4 [18.2 MB] 112s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 python3-all arm64 3.13.5-1 [884 B] 112s Get:39 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-charset-normalizer arm64 3.4.2-1 [125 kB] 112s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 112s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 112s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 python3-cairo arm64 1.27.0-2 [122 kB] 112s Get:43 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 112s Get:44 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 112s Get:45 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 python3-reportlab all 4.4.2-1 [1145 kB] 112s Get:46 http://ftpmaster.internal/ubuntu questing/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 112s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 xml-core all 0.19 [20.3 kB] 112s Get:48 http://ftpmaster.internal/ubuntu questing/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 112s Get:49 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython arm64 1.85+dfsg-4 [1710 kB] 112s Get:50 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython-sql all 1.85+dfsg-4 [26.4 kB] 113s Fetched 44.4 MB in 1s (30.7 MB/s) 113s Selecting previously unselected package python3-numpy-dev:arm64. 113s (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 ... 131053 files and directories currently installed.) 113s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 113s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 113s Selecting previously unselected package libblas3:arm64. 113s Preparing to unpack .../01-libblas3_3.12.1-2build1_arm64.deb ... 113s Unpacking libblas3:arm64 (3.12.1-2build1) ... 113s Selecting previously unselected package libgfortran5:arm64. 113s Preparing to unpack .../02-libgfortran5_15.1.0-8ubuntu1_arm64.deb ... 113s Unpacking libgfortran5:arm64 (15.1.0-8ubuntu1) ... 113s Selecting previously unselected package liblapack3:arm64. 113s Preparing to unpack .../03-liblapack3_3.12.1-2build1_arm64.deb ... 113s Unpacking liblapack3:arm64 (3.12.1-2build1) ... 113s Selecting previously unselected package python3-numpy. 113s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 113s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 113s Selecting previously unselected package libfontenc1:arm64. 113s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 113s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 113s Selecting previously unselected package x11-common. 113s Preparing to unpack .../06-x11-common_1%3a7.7+24ubuntu1_all.deb ... 113s Unpacking x11-common (1:7.7+24ubuntu1) ... 113s Selecting previously unselected package xfonts-encodings. 113s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 113s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 113s Selecting previously unselected package xfonts-utils. 113s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_arm64.deb ... 113s Unpacking xfonts-utils (1:7.7+7) ... 113s Selecting previously unselected package fonts-urw-base35. 113s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 113s Unpacking fonts-urw-base35 (20200910-8) ... 114s Selecting previously unselected package fontconfig-config. 114s Preparing to unpack .../10-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 114s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 114s Selecting previously unselected package libfontconfig1:arm64. 114s Preparing to unpack .../11-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 114s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 114s Selecting previously unselected package libpixman-1-0:arm64. 114s Preparing to unpack .../12-libpixman-1-0_0.44.0-3_arm64.deb ... 114s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 114s Selecting previously unselected package libxcb-render0:arm64. 114s Preparing to unpack .../13-libxcb-render0_1.17.0-2_arm64.deb ... 114s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 114s Selecting previously unselected package libxcb-shm0:arm64. 114s Preparing to unpack .../14-libxcb-shm0_1.17.0-2_arm64.deb ... 114s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 114s Selecting previously unselected package libxrender1:arm64. 114s Preparing to unpack .../15-libxrender1_1%3a0.9.12-1_arm64.deb ... 114s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 114s Selecting previously unselected package libcairo2:arm64. 114s Preparing to unpack .../16-libcairo2_1.18.4-1_arm64.deb ... 114s Unpacking libcairo2:arm64 (1.18.4-1) ... 114s Selecting previously unselected package libdeflate0:arm64. 114s Preparing to unpack .../17-libdeflate0_1.23-2_arm64.deb ... 114s Unpacking libdeflate0:arm64 (1.23-2) ... 114s Selecting previously unselected package libgomp1:arm64. 114s Preparing to unpack .../18-libgomp1_15.1.0-8ubuntu1_arm64.deb ... 114s Unpacking libgomp1:arm64 (15.1.0-8ubuntu1) ... 114s Selecting previously unselected package libgraphite2-3:arm64. 114s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 114s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 114s Selecting previously unselected package libharfbuzz0b:arm64. 114s Preparing to unpack .../20-libharfbuzz0b_10.2.0-1_arm64.deb ... 114s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 114s Selecting previously unselected package libimagequant0:arm64. 114s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_arm64.deb ... 114s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 114s Selecting previously unselected package libjpeg-turbo8:arm64. 114s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 114s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 114s Selecting previously unselected package libjpeg8:arm64. 114s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_arm64.deb ... 114s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 114s Selecting previously unselected package libjs-jquery. 114s Preparing to unpack .../24-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 114s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 114s Selecting previously unselected package libjs-underscore. 114s Preparing to unpack .../25-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 114s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 114s Selecting previously unselected package libjs-sphinxdoc. 114s Preparing to unpack .../26-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 114s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 114s Selecting previously unselected package liblcms2-2:arm64. 114s Preparing to unpack .../27-liblcms2-2_2.16-2_arm64.deb ... 114s Unpacking liblcms2-2:arm64 (2.16-2) ... 114s Selecting previously unselected package liblerc4:arm64. 114s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 114s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 114s Selecting previously unselected package libraqm0:arm64. 114s Preparing to unpack .../29-libraqm0_0.10.2-1_arm64.deb ... 114s Unpacking libraqm0:arm64 (0.10.2-1) ... 114s Selecting previously unselected package libsharpyuv0:arm64. 114s Preparing to unpack .../30-libsharpyuv0_1.5.0-0.1_arm64.deb ... 114s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 114s Selecting previously unselected package libjbig0:arm64. 114s Preparing to unpack .../31-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 114s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 115s Selecting previously unselected package libwebp7:arm64. 115s Preparing to unpack .../32-libwebp7_1.5.0-0.1_arm64.deb ... 115s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 115s Selecting previously unselected package libtiff6:arm64. 115s Preparing to unpack .../33-libtiff6_4.7.0-3ubuntu1_arm64.deb ... 115s Unpacking libtiff6:arm64 (4.7.0-3ubuntu1) ... 115s Selecting previously unselected package libwebpdemux2:arm64. 115s Preparing to unpack .../34-libwebpdemux2_1.5.0-0.1_arm64.deb ... 115s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 115s Selecting previously unselected package libwebpmux3:arm64. 115s Preparing to unpack .../35-libwebpmux3_1.5.0-0.1_arm64.deb ... 115s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 115s Selecting previously unselected package python-biopython-doc. 115s Preparing to unpack .../36-python-biopython-doc_1.85+dfsg-4_all.deb ... 115s Unpacking python-biopython-doc (1.85+dfsg-4) ... 115s Selecting previously unselected package python3-all. 115s Preparing to unpack .../37-python3-all_3.13.5-1_arm64.deb ... 115s Unpacking python3-all (3.13.5-1) ... 115s Selecting previously unselected package python3-charset-normalizer. 115s Preparing to unpack .../38-python3-charset-normalizer_3.4.2-1_arm64.deb ... 115s Unpacking python3-charset-normalizer (3.4.2-1) ... 115s Selecting previously unselected package libopenjp2-7:arm64. 115s Preparing to unpack .../39-libopenjp2-7_2.5.3-2_arm64.deb ... 115s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 115s Selecting previously unselected package python3-pil:arm64. 115s Preparing to unpack .../40-python3-pil_11.1.0-5build1_arm64.deb ... 115s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 115s Selecting previously unselected package python3-cairo. 115s Preparing to unpack .../41-python3-cairo_1.27.0-2_arm64.deb ... 115s Unpacking python3-cairo (1.27.0-2) ... 115s Selecting previously unselected package python3-freetype. 115s Preparing to unpack .../42-python3-freetype_2.5.1-1_all.deb ... 115s Unpacking python3-freetype (2.5.1-1) ... 115s Selecting previously unselected package python3-rlpycairo. 115s Preparing to unpack .../43-python3-rlpycairo_0.3.0-3_all.deb ... 115s Unpacking python3-rlpycairo (0.3.0-3) ... 115s Selecting previously unselected package python3-reportlab. 115s Preparing to unpack .../44-python3-reportlab_4.4.2-1_all.deb ... 115s Unpacking python3-reportlab (4.4.2-1) ... 115s Selecting previously unselected package sgml-base. 115s Preparing to unpack .../45-sgml-base_1.31+nmu1_all.deb ... 115s Unpacking sgml-base (1.31+nmu1) ... 115s Selecting previously unselected package xml-core. 115s Preparing to unpack .../46-xml-core_0.19_all.deb ... 115s Unpacking xml-core (0.19) ... 115s Selecting previously unselected package w3c-sgml-lib. 115s Preparing to unpack .../47-w3c-sgml-lib_1.3-3_all.deb ... 115s Unpacking w3c-sgml-lib (1.3-3) ... 115s Selecting previously unselected package python3-biopython. 115s Preparing to unpack .../48-python3-biopython_1.85+dfsg-4_arm64.deb ... 115s Unpacking python3-biopython (1.85+dfsg-4) ... 116s Selecting previously unselected package python3-biopython-sql. 116s Preparing to unpack .../49-python3-biopython-sql_1.85+dfsg-4_all.deb ... 116s Unpacking python3-biopython-sql (1.85+dfsg-4) ... 116s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 116s Setting up liblcms2-2:arm64 (2.16-2) ... 116s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 116s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 116s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 116s Setting up libxrender1:arm64 (1:0.9.12-1) ... 116s Setting up libxcb-render0:arm64 (1.17.0-2) ... 116s Setting up python3-charset-normalizer (3.4.2-1) ... 116s Setting up x11-common (1:7.7+24ubuntu1) ... 116s Setting up libdeflate0:arm64 (1.23-2) ... 116s Setting up python3-all (3.13.5-1) ... 116s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 116s Setting up libgomp1:arm64 (15.1.0-8ubuntu1) ... 116s Setting up python3-freetype (2.5.1-1) ... 116s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 116s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 116s Setting up libblas3:arm64 (3.12.1-2build1) ... 116s 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 116s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 116s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 116s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 116s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 116s Setting up libgfortran5:arm64 (15.1.0-8ubuntu1) ... 116s Setting up libwebp7:arm64 (1.5.0-0.1) ... 116s Setting up libopenjp2-7:arm64 (2.5.3-2) ... 116s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 116s Setting up sgml-base (1.31+nmu1) ... 116s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 116s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 116s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 116s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 116s Setting up liblapack3:arm64 (3.12.1-2build1) ... 116s 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 116s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 116s Setting up xfonts-utils (1:7.7+7) ... 116s Setting up libraqm0:arm64 (0.10.2-1) ... 116s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 118s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 118s Setting up python-biopython-doc (1.85+dfsg-4) ... 118s Setting up libtiff6:arm64 (4.7.0-3ubuntu1) ... 118s Setting up xml-core (0.19) ... 118s Setting up fonts-urw-base35 (20200910-8) ... 118s Setting up python3-pil:arm64 (11.1.0-5build1) ... 118s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 119s Setting up libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 119s Setting up libcairo2:arm64 (1.18.4-1) ... 119s Setting up python3-cairo (1.27.0-2) ... 119s Setting up python3-rlpycairo (0.3.0-3) ... 119s Setting up python3-reportlab (4.4.2-1) ... 119s Processing triggers for libc-bin (2.41-6ubuntu2) ... 120s Processing triggers for man-db (2.13.1-1) ... 120s Processing triggers for sgml-base (1.31+nmu1) ... 120s Setting up w3c-sgml-lib (1.3-3) ... 144s Setting up python3-biopython (1.85+dfsg-4) ... 145s Setting up python3-biopython-sql (1.85+dfsg-4) ... 146s autopkgtest [03:42:33]: test dependencies: sh debian/tests/run-unit-test 146s autopkgtest [03:42:33]: test dependencies: [----------------------- 146s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 146s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 148s mkdir: created directory 'Bio' 148s mkdir: created directory 'Bio/Align' 148s mkdir: created directory 'Bio/Align/substitution_matrices' 148s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 148s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 148s test_Ace ... ok 148s test_Affy ... ok 150s test_AlignIO ... ok 151s test_AlignIO_ClustalIO ... ok 151s test_AlignIO_EmbossIO ... ok 151s test_AlignIO_FastaIO ... ok 151s test_AlignIO_MauveIO ... ok 151s test_AlignIO_PhylipIO ... ok 151s test_AlignIO_convert ... ok 151s test_AlignInfo ... ok 151s test_Align_Alignment ... ok 151s test_Align_a2m ... ok 151s test_Align_bed ... ok 151s test_Align_bigbed ... ok 152s test_Align_bigmaf ... ok 152s test_Align_bigpsl ... ok 152s test_Align_chain ... ok 152s test_Align_clustal ... ok 155s test_Align_codonalign ... ok 155s test_Align_emboss ... ok 155s test_Align_exonerate ... ok 155s test_Align_fasta ... ok 155s test_Align_hhr ... ok 156s test_Align_maf ... ok 156s test_Align_mauve ... ok 156s test_Align_msf ... ok 156s test_Align_nexus ... ok 156s test_Align_phylip ... ok 157s test_Align_psl ... ok 157s test_Align_sam ... ok 158s test_Align_stockholm ... ok 159s test_Align_tabular ... ok 159s test_Application ... ok 159s test_BioSQL_MySQLdb_online ... skipping. internet not available 159s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 159s test_BioSQL_mysql_connector_online ... skipping. internet not available 159s test_BioSQL_psycopg2_online ... skipping. internet not available 163s test_BioSQL_sqlite3 ... ok 163s test_BioSQL_sqlite3_online ... skipping. internet not available 163s test_Blast_Record ... ok 163s test_Blast_parser ... ok 163s test_CAPS ... ok 163s test_Chi2 ... ok 163s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 163s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 164s test_Cluster ... ok 164s test_CodonTable ... ok 164s test_ColorSpiral ... ok 164s test_Compass ... ok 165s test_Consensus ... ok 165s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 165s test_EMBL_unittest ... ok 165s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 165s test_EmbossPrimer ... ok 169s test_Entrez ... ok 169s test_Entrez_online ... skipping. internet not available 169s test_Entrez_parser ... ok 169s test_Enzyme ... ok 169s test_ExPASy ... skipping. internet not available 169s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 169s test_File ... ok 170s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 170s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 170s ok 171s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 173s ok 174s test_GraphicsChromosome ... ok 174s test_GraphicsDistribution ... ok 174s test_GraphicsGeneral ... ok 175s test_HMMCasino ... ok 175s test_HMMGeneral ... ok 175s test_KEGG ... ok 175s test_KEGG_online ... skipping. internet not available 179s test_KGML_graphics ... ok 179s test_KGML_graphics_online ... skipping. internet not available 179s test_KGML_nographics ... ok 180s test_KeyWList ... ok 180s test_LogisticRegression ... ok 180s test_MafIO_index ... ok 180s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 181s test_MarkovModel ... ok 181s test_Medline ... ok 181s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 181s test_NCBIXML ... Exception ignored in: 181s Traceback (most recent call last): 181s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 181s expat_parser.Parse(NULL, True) 181s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 181s ok 181s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 181s test_NCBI_qblast ... ok 181s test_NMR ... ok 181s test_NaiveBayes ... ok 182s test_Nexus ... ok 182s test_PAML_baseml ... ok 182s test_PAML_codeml ... ok 182s test_PAML_yn00 ... ok 186s test_PDB_CEAligner ... ok 186s test_PDB_DSSP ... ok 186s test_PDB_Dice ... ok 186s test_PDB_Disordered ... ok 187s test_PDB_Exposure ... ok 187s test_PDB_FragmentMapper ... ok 188s test_PDB_KDTree ... ok 188s test_PDB_MMCIF2Dict ... ok 188s test_PDB_MMCIFIO ... ok 189s test_PDB_MMCIFParser ... ok 189s test_PDB_NACCESS ... ok 190s test_PDB_PDBIO ... ok 190s test_PDB_PDBList ... skipping. internet not available 195s test_PDB_PDBMLParser ... ok 195s test_PDB_PDBParser ... ok 196s 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 196s test_PDB_Polypeptide ... ok 196s test_PDB_QCPSuperimposer ... ok 199s test_PDB_SASA ... ok 199s test_PDB_SMCRA ... ok 199s test_PDB_Selection ... ok 199s test_PDB_StructureAlignment ... ok 199s test_PDB_Superimposer ... ok 199s test_PDB_alphafold_db ... skipping. internet not available 199s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 199s 199s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 199s 199s test_PDB_parse_pdb_header ... ok 200s test_PDB_vectors ... ok 200s test_PQR ... ok 200s test_Pathway ... ok 200s test_Phd ... ok 200s test_Phylo ... ok 200s test_PhyloXML ... ok 200s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 200s test_Phylo_NeXML ... ok 200s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 201s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 201s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 201s test_PopGen_GenePop_nodepend ... ok 201s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 201s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 201s test_ProtParam ... ok 201s test_RCSBFormats ... ok 201s test_Restriction ... ok 201s test_SCOP_Astral ... ok 201s test_SCOP_Cla ... ok 201s test_SCOP_Des ... ok 201s test_SCOP_Dom ... ok 201s test_SCOP_Hie ... ok 202s test_SCOP_Raf ... ok 202s test_SCOP_Residues ... ok 202s test_SCOP_Scop ... ok 202s test_SVDSuperimposer ... ok 202s test_SearchIO_blast_tab ... ok 202s test_SearchIO_blast_tab_index ... ok 202s test_SearchIO_blast_xml ... ok 203s test_SearchIO_blast_xml_index ... ok 203s test_SearchIO_blat_psl ... ok 203s test_SearchIO_blat_psl_index ... ok 203s test_SearchIO_exonerate ... ok 203s test_SearchIO_exonerate_text_index ... ok 204s test_SearchIO_exonerate_vulgar_index ... ok 204s test_SearchIO_fasta_m10 ... ok 204s test_SearchIO_fasta_m10_index ... ok 204s test_SearchIO_hhsuite2_text ... ok 204s test_SearchIO_hmmer2_text ... ok 204s test_SearchIO_hmmer2_text_index ... ok 204s test_SearchIO_hmmer3_domtab ... ok 204s test_SearchIO_hmmer3_domtab_index ... ok 204s test_SearchIO_hmmer3_tab ... ok 204s test_SearchIO_hmmer3_tab_index ... ok 204s test_SearchIO_hmmer3_text ... ok 204s test_SearchIO_hmmer3_text_index ... ok 205s test_SearchIO_interproscan_xml ... ok 205s test_SearchIO_model ... ok 205s test_SearchIO_write ... ok 205s test_SeqFeature ... ok 218s test_SeqIO ... ok 218s test_SeqIO_AbiIO ... ok 218s test_SeqIO_FastaIO ... ok 218s test_SeqIO_Gck ... ok 218s test_SeqIO_Gfa ... ok 218s test_SeqIO_Insdc ... ok 218s test_SeqIO_NibIO ... ok 220s test_SeqIO_PdbIO ... ok 220s test_SeqIO_QualityIO ... ok 220s test_SeqIO_SeqXML ... ok 220s test_SeqIO_SffIO ... ok 220s test_SeqIO_SnapGene ... ok 221s test_SeqIO_TwoBitIO ... ok 221s test_SeqIO_UniprotIO ... ok 222s test_SeqIO_Xdna ... ok 222s test_SeqIO_features ... ok 234s test_SeqIO_index ... ok 234s test_SeqIO_online ... skipping. internet not available 234s test_SeqIO_write ... ok 234s test_SeqRecord ... ok 234s test_SeqUtils ... ok 235s test_Seq_objs ... ok 235s test_SwissProt ... ok 235s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 235s test_TogoWS ... skipping. internet not available 236s test_TreeConstruction ... ok 236s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 236s test_UniGene ... ok 236s test_UniProt ... skipping. internet not available 236s test_UniProt_GOA ... ok 236s test_align ... ok 237s test_align_substitution_matrices ... ok 238s test_bgzf ... ok 238s test_cellosaurus ... ok 242s test_codonalign ... ok 242s test_geo ... ok 242s test_kNN ... ok 243s test_motifs ... ok 243s test_motifs_online ... skipping. internet not available 243s test_pairwise2 ... /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 243s warnings.warn( 243s ok 243s test_pairwise2_no_C ... ok 243s test_pairwise_aligner ... ok 243s test_pairwise_alignment_map ... ok 250s test_phenotype ... ok 250s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 250s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 250s test_prodoc ... ok 250s test_prosite ... ok 250s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 250s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 250s test_seq ... ok 251s test_translate ... ok 251s Skipping any tests requiring internet access 251s Python version: 3.13.5 (main, Jun 25 2025, 18:55:22) [GCC 14.3.0] 251s Operating system: posix linux 251s ---------------------------------------------------------------------- 251s Ran 218 tests in 102.283 seconds 251s 251s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 251s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 251s autopkgtest [03:44:18]: test dependencies: -----------------------] 252s dependencies PASS 252s autopkgtest [03:44:19]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 252s autopkgtest [03:44:19]: test full_suite: preparing testbed 258s Creating nova instance adt-questing-arm64-python-biopython-20250712-034007-juju-7f2275-prod-proposed-migration-environment-21-c0aec37e-2dc9-449e-a0d9-2881ea3d8291 from image adt/ubuntu-questing-arm64-server-20250712.img (UUID 64e93443-6a95-4ef6-a3b4-cb2b1f0a688a)... 304s autopkgtest [03:45:11]: testbed dpkg architecture: arm64 304s autopkgtest [03:45:11]: testbed apt version: 3.1.3 304s autopkgtest [03:45:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 304s autopkgtest [03:45:11]: testbed release detected to be: questing 305s autopkgtest [03:45:12]: updating testbed package index (apt update) 305s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [249 kB] 305s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 305s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 305s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 305s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [39.9 kB] 305s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [207 kB] 305s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [15.4 kB] 305s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [58.6 kB] 305s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [186 kB] 305s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [15.7 kB] 305s Fetched 772 kB in 0s (1930 kB/s) 306s Reading package lists... 306s autopkgtest [03:45:13]: upgrading testbed (apt dist-upgrade and autopurge) 307s Reading package lists... 307s Building dependency tree... 307s Reading state information... 307s Calculating upgrade... 307s The following packages will be upgraded: 307s htop 307s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 307s Need to get 176 kB of archives. 307s After this operation, 0 B of additional disk space will be used. 307s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 htop arm64 3.4.1-5 [176 kB] 308s Fetched 176 kB in 0s (15.2 MB/s) 308s (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 ... 131053 files and directories currently installed.) 308s Preparing to unpack .../htop_3.4.1-5_arm64.deb ... 308s Unpacking htop (3.4.1-5) over (3.4.1-4) ... 308s Setting up htop (3.4.1-5) ... 308s Processing triggers for man-db (2.13.1-1) ... 309s Reading package lists... 309s Building dependency tree... 309s Reading state information... 309s Solving dependencies... 309s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 311s Reading package lists... 312s Building dependency tree... 312s Reading state information... 312s Solving dependencies... 312s The following NEW packages will be installed: 312s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 312s cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 312s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 312s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 312s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 312s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 312s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 312s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext ghostscript hevea 312s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 312s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 312s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 312s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 312s libcolamd3 libcommons-logging-java libcommons-parent-java libcups2t64 312s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 312s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 312s libgcc-14-dev libgd3 libgfortran5 libglpk40 libgomp1 libgraphite2-3 312s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 312s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhwasan0 libice6 libidn12 312s libigraph3t64 libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 312s libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 312s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 312s liblcms2-2 liblerc4 liblqr-1-0 liblsan0 libltdl7 libmagickcore-7.q16-10 312s libmagickwand-7.q16-10 libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 312s libmpfi0 libmysqlclient24 libncbi-vdb3 libnetpbm11t64 libopenjp2-7 312s libpaper-utils libpaper2 libpdfbox-java libpixman-1-0 libplfit0 libpotrace0 312s libpq5 libptexenc1 libpython3-all-dev libpython3-dev libpython3.13-dev 312s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 312s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 312s libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2 312s libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 312s libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft 312s mysql-common ncbi-blast+ ncbi-data ncbi-vdb-data netpbm phylip po-debconf 312s poppler-data prank preview-latex-style probcons python-biopython-doc 312s python-matplotlib-data python3-alabaster python3-all python3-all-dev 312s python3-biopython python3-biopython-sql python3-brotli python3-cairo 312s python3-charset-normalizer python3-contourpy python3-cycler 312s python3-decorator python3-defusedxml python3-dev python3-docutils 312s python3-fonttools python3-freetype python3-fs python3-igraph 312s python3-imagesize python3-kiwisolver python3-lxml python3-lz4 312s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 312s python3-mysqldb python3-networkx python3-numpy python3-numpy-dev 312s python3-numpydoc python3-pil python3-pil.imagetk python3-platformdirs 312s python3-rdflib python3-reportlab python3-rlpycairo python3-roman 312s python3-scipy python3-snowballstemmer python3-sphinx 312s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 312s python3-tabulate python3-texttable python3-tk python3-ufolib2 python3.13-dev 312s python3.13-tk sgml-base sphinx-common sphinx-rtd-theme-common t-coffee 312s t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended 312s texlive-latex-base texlive-latex-extra texlive-latex-recommended 312s texlive-pictures tk8.6-blt2.5 unicode-data w3c-sgml-lib wise wise-data 312s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 312s 0 upgraded, 258 newly installed, 0 to remove and 0 not upgraded. 312s Need to get 409 MB of archives. 312s After this operation, 1834 MB of additional disk space will be used. 312s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 m4 arm64 1.4.19-8 [244 kB] 312s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 flex arm64 2.6.4-8.2build1 [291 kB] 312s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-lato all 2.015-1 [2781 kB] 312s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15.1.0-8ubuntu1 [147 kB] 312s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 libfftw3-double3 arm64 3.3.10-2fakesync1build1 [392 kB] 312s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 313s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 313s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 313s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 313s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 313s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 313s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 313s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.3ubuntu1 [38.1 kB] 313s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.3ubuntu1 [144 kB] 313s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 313s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 libaom3 arm64 3.12.1-1 [1824 kB] 313s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 libheif-plugin-aomdec arm64 1.19.8-1 [11.4 kB] 313s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libde265-0 arm64 1.0.16-1 [146 kB] 313s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libheif-plugin-libde265 arm64 1.19.8-1 [8882 B] 313s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libheif1 arm64 1.19.8-1 [372 kB] 313s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 313s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 313s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 313s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 313s Get:25 http://ftpmaster.internal/ubuntu questing/universe arm64 liblqr-1-0 arm64 0.4.2-2.1build2 [27.1 kB] 313s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libltdl7 arm64 2.5.4-4 [43.0 kB] 313s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 313s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 libraw23t64 arm64 0.21.4-2 [378 kB] 313s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 313s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 313s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 313s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.7.0-3ubuntu1 [197 kB] 313s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 313s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 313s Get:35 http://ftpmaster.internal/ubuntu questing/universe arm64 imagemagick-7-common all 8:7.1.1.43+dfsg1-1ubuntu1 [69.5 kB] 313s Get:36 http://ftpmaster.internal/ubuntu questing/universe arm64 libmagickcore-7.q16-10 arm64 8:7.1.1.43+dfsg1-1ubuntu1 [1878 kB] 313s Get:37 http://ftpmaster.internal/ubuntu questing/universe arm64 libmagickwand-7.q16-10 arm64 8:7.1.1.43+dfsg1-1ubuntu1 [300 kB] 313s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 poppler-data all 0.4.12-1 [2060 kB] 313s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 313s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2build1 [160 kB] 313s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15.1.0-8ubuntu1 [451 kB] 313s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2build1 [2308 kB] 313s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 313s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 autoconf all 2.72-3.1ubuntu1 [384 kB] 313s Get:45 http://ftpmaster.internal/ubuntu questing/main arm64 autotools-dev all 20240727.1 [43.4 kB] 313s Get:46 http://ftpmaster.internal/ubuntu questing/main arm64 automake all 1:1.17-4ubuntu1 [572 kB] 313s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 autopoint all 0.23.1-2build1 [619 kB] 313s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 313s Get:49 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 313s Get:50 http://ftpmaster.internal/ubuntu questing/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 313s Get:51 http://ftpmaster.internal/ubuntu questing/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 313s Get:52 http://ftpmaster.internal/ubuntu questing/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 313s Get:53 http://ftpmaster.internal/ubuntu questing/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 313s Get:54 http://ftpmaster.internal/ubuntu questing/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 313s Get:55 http://ftpmaster.internal/ubuntu questing/main arm64 libisl23 arm64 0.27-1 [676 kB] 313s Get:56 http://ftpmaster.internal/ubuntu questing/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 313s Get:57 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14-aarch64-linux-gnu arm64 14.3.0-1ubuntu1 [10.6 MB] 314s Get:58 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14 arm64 14.3.0-1ubuntu1 [1030 B] 314s Get:59 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 314s Get:60 http://ftpmaster.internal/ubuntu questing/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 314s Get:61 http://ftpmaster.internal/ubuntu questing/main arm64 libcc1-0 arm64 15.1.0-8ubuntu1 [49.3 kB] 314s Get:62 http://ftpmaster.internal/ubuntu questing/main arm64 libitm1 arm64 15.1.0-8ubuntu1 [28.1 kB] 314s Get:63 http://ftpmaster.internal/ubuntu questing/main arm64 libasan8 arm64 15.1.0-8ubuntu1 [2920 kB] 314s Get:64 http://ftpmaster.internal/ubuntu questing/main arm64 liblsan0 arm64 15.1.0-8ubuntu1 [1316 kB] 314s Get:65 http://ftpmaster.internal/ubuntu questing/main arm64 libtsan2 arm64 15.1.0-8ubuntu1 [2689 kB] 314s Get:66 http://ftpmaster.internal/ubuntu questing/main arm64 libubsan1 arm64 15.1.0-8ubuntu1 [1176 kB] 314s Get:67 http://ftpmaster.internal/ubuntu questing/main arm64 libhwasan0 arm64 15.1.0-8ubuntu1 [1638 kB] 314s Get:68 http://ftpmaster.internal/ubuntu questing/main arm64 libgcc-14-dev arm64 14.3.0-1ubuntu1 [2591 kB] 314s Get:69 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14-aarch64-linux-gnu arm64 14.3.0-1ubuntu1 [20.9 MB] 314s Get:70 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14 arm64 14.3.0-1ubuntu1 [538 kB] 314s Get:71 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 314s Get:72 http://ftpmaster.internal/ubuntu questing/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 314s Get:73 http://ftpmaster.internal/ubuntu questing/main arm64 libstdc++-14-dev arm64 14.3.0-1ubuntu1 [2795 kB] 314s Get:74 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14-aarch64-linux-gnu arm64 14.3.0-1ubuntu1 [12.1 MB] 314s Get:75 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14 arm64 14.3.0-1ubuntu1 [27.4 kB] 314s Get:76 http://ftpmaster.internal/ubuntu questing/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 314s Get:77 http://ftpmaster.internal/ubuntu questing/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 314s Get:78 http://ftpmaster.internal/ubuntu questing/main arm64 build-essential arm64 12.12ubuntu1 [5082 B] 314s Get:79 http://ftpmaster.internal/ubuntu questing/universe arm64 bwa arm64 0.7.18-1 [201 kB] 314s Get:80 http://ftpmaster.internal/ubuntu questing/universe arm64 libargtable2-0 arm64 13-4 [15.1 kB] 315s Get:81 http://ftpmaster.internal/ubuntu questing/universe arm64 clustalo arm64 1.2.4-8build1 [190 kB] 315s Get:82 http://ftpmaster.internal/ubuntu questing/main arm64 libdebhelper-perl all 13.24.2ubuntu1 [95.7 kB] 315s Get:83 http://ftpmaster.internal/ubuntu questing/main arm64 libtool all 2.5.4-4 [168 kB] 315s Get:84 http://ftpmaster.internal/ubuntu questing/main arm64 dh-autoreconf all 20 [16.1 kB] 315s Get:85 http://ftpmaster.internal/ubuntu questing/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 315s Get:86 http://ftpmaster.internal/ubuntu questing/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 315s Get:87 http://ftpmaster.internal/ubuntu questing/main arm64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 315s Get:88 http://ftpmaster.internal/ubuntu questing/main arm64 debugedit arm64 1:5.1-2 [46.1 kB] 315s Get:89 http://ftpmaster.internal/ubuntu questing/main arm64 dwz arm64 0.15-1build6 [113 kB] 315s Get:90 http://ftpmaster.internal/ubuntu questing/main arm64 gettext arm64 0.23.1-2build1 [1456 kB] 315s Get:91 http://ftpmaster.internal/ubuntu questing/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 315s Get:92 http://ftpmaster.internal/ubuntu questing/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 315s Get:93 http://ftpmaster.internal/ubuntu questing/main arm64 debhelper all 13.24.2ubuntu1 [896 kB] 315s Get:94 http://ftpmaster.internal/ubuntu questing/universe arm64 dh-python all 6.20250414 [119 kB] 315s Get:95 http://ftpmaster.internal/ubuntu questing/universe arm64 dialign arm64 2.2.1-13 [152 kB] 315s Get:96 http://ftpmaster.internal/ubuntu questing/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 315s Get:97 http://ftpmaster.internal/ubuntu questing/main arm64 xml-core all 0.19 [20.3 kB] 315s Get:98 http://ftpmaster.internal/ubuntu questing/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 315s Get:99 http://ftpmaster.internal/ubuntu questing/universe arm64 libcifpp-data all 7.0.9-1 [481 kB] 315s Get:100 http://ftpmaster.internal/ubuntu questing/universe arm64 libcifpp7 arm64 7.0.9-1 [997 kB] 315s Get:101 http://ftpmaster.internal/ubuntu questing/universe arm64 dssp arm64 4.4.10-1 [753 kB] 315s Get:102 http://ftpmaster.internal/ubuntu questing/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 315s Get:103 http://ftpmaster.internal/ubuntu questing/main arm64 libxpm4 arm64 1:3.5.17-1build2 [35.1 kB] 315s Get:104 http://ftpmaster.internal/ubuntu questing/main arm64 libgd3 arm64 2.3.3-13ubuntu1 [124 kB] 315s Get:105 http://ftpmaster.internal/ubuntu questing/universe arm64 libhpdf-2.3.0 arm64 2.3.0+dfsg-1build3 [434 kB] 315s Get:106 http://ftpmaster.internal/ubuntu questing/main arm64 mysql-common all 5.8+1.1.1ubuntu1 [6922 B] 315s Get:107 http://ftpmaster.internal/ubuntu questing/main arm64 libmysqlclient24 arm64 8.4.5-0ubuntu3 [1245 kB] 315s Get:108 http://ftpmaster.internal/ubuntu questing/main arm64 libpq5 arm64 17.5-1build1 [252 kB] 315s Get:109 http://ftpmaster.internal/ubuntu questing/universe arm64 emboss-lib arm64 6.6.0+dfsg-15ubuntu2 [2891 kB] 315s Get:110 http://ftpmaster.internal/ubuntu questing/universe arm64 emboss-data all 6.6.0+dfsg-15ubuntu2 [61.0 MB] 316s Get:111 http://ftpmaster.internal/ubuntu questing/universe arm64 emboss arm64 6.6.0+dfsg-15ubuntu2 [937 kB] 316s Get:112 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 316s Get:113 http://ftpmaster.internal/ubuntu questing/universe arm64 fonts-lmodern all 2.005-1 [4799 kB] 316s Get:114 http://ftpmaster.internal/ubuntu questing/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 316s Get:115 http://ftpmaster.internal/ubuntu questing/main arm64 libgs-common all 10.05.0dfsg1-0ubuntu1 [176 kB] 316s Get:116 http://ftpmaster.internal/ubuntu questing/main arm64 libgs10-common all 10.05.0dfsg1-0ubuntu1 [490 kB] 316s Get:117 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-common-data arm64 0.8-16ubuntu2 [31.0 kB] 316s Get:118 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-common3 arm64 0.8-16ubuntu2 [22.9 kB] 316s Get:119 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-client3 arm64 0.8-16ubuntu2 [26.9 kB] 316s Get:120 http://ftpmaster.internal/ubuntu questing/main arm64 libcups2t64 arm64 2.4.12-0ubuntu1 [272 kB] 316s Get:121 http://ftpmaster.internal/ubuntu questing/main arm64 libidn12 arm64 1.43-1 [58.1 kB] 316s Get:122 http://ftpmaster.internal/ubuntu questing/main arm64 libijs-0.35 arm64 0.35-15.3 [15.4 kB] 316s Get:123 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig2dec0 arm64 0.20-1build3 [63.2 kB] 316s Get:124 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 316s Get:125 http://ftpmaster.internal/ubuntu questing/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 316s Get:126 http://ftpmaster.internal/ubuntu questing/main arm64 libsm6 arm64 2:1.2.6-1 [16.6 kB] 316s Get:127 http://ftpmaster.internal/ubuntu questing/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 317s Get:128 http://ftpmaster.internal/ubuntu questing/main arm64 libgs10 arm64 10.05.0dfsg1-0ubuntu1 [3638 kB] 317s Get:129 http://ftpmaster.internal/ubuntu questing/main arm64 ghostscript arm64 10.05.0dfsg1-0ubuntu1 [43.0 kB] 317s Get:130 http://ftpmaster.internal/ubuntu questing/universe arm64 libnetpbm11t64 arm64 2:11.10.02-1build1 [115 kB] 317s Get:131 http://ftpmaster.internal/ubuntu questing/universe arm64 netpbm arm64 2:11.10.02-1build1 [2146 kB] 317s Get:132 http://ftpmaster.internal/ubuntu questing/universe arm64 tex-common all 6.19 [29.8 kB] 317s Get:133 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 317s Get:134 http://ftpmaster.internal/ubuntu questing/universe arm64 libkpathsea6 arm64 2024.20240313.70630+ds-6 [64.4 kB] 317s Get:135 http://ftpmaster.internal/ubuntu questing/universe arm64 libptexenc1 arm64 2024.20240313.70630+ds-6 [41.7 kB] 317s Get:136 http://ftpmaster.internal/ubuntu questing/universe arm64 libsynctex2 arm64 2024.20240313.70630+ds-6 [60.4 kB] 317s Get:137 http://ftpmaster.internal/ubuntu questing/universe arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-6 [122 kB] 317s Get:138 http://ftpmaster.internal/ubuntu questing/main arm64 t1utils arm64 1.41-4build3 [61.0 kB] 317s Get:139 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 317s Get:140 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 317s Get:141 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 317s Get:142 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 317s Get:143 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 317s Get:144 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 317s Get:145 http://ftpmaster.internal/ubuntu questing/universe arm64 libmpfi0 arm64 1.5.4+ds-4 [35.3 kB] 317s Get:146 http://ftpmaster.internal/ubuntu questing/universe arm64 libpotrace0 arm64 1.16-2build1 [16.0 kB] 317s Get:147 http://ftpmaster.internal/ubuntu questing/universe arm64 libteckit0 arm64 2.5.12+ds1-1 [405 kB] 317s Get:148 http://ftpmaster.internal/ubuntu questing/main arm64 libxmu6 arm64 2:1.1.3-3build2 [47.5 kB] 317s Get:149 http://ftpmaster.internal/ubuntu questing/main arm64 libxaw7 arm64 2:1.0.16-1 [184 kB] 317s Get:150 http://ftpmaster.internal/ubuntu questing/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 317s Get:151 http://ftpmaster.internal/ubuntu questing/universe arm64 libzzip-0-13t64 arm64 0.13.78+dfsg.1-0.1 [30.8 kB] 317s Get:152 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-binaries arm64 2024.20240313.70630+ds-6 [8349 kB] 317s Get:153 http://ftpmaster.internal/ubuntu questing/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 317s Get:154 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-base all 2024.20250309-1 [22.7 MB] 317s Get:155 http://ftpmaster.internal/ubuntu questing/main arm64 hicolor-icon-theme all 0.18-2 [13.3 kB] 317s Get:156 http://ftpmaster.internal/ubuntu questing/universe arm64 imagemagick-7.q16 arm64 8:7.1.1.43+dfsg1-1ubuntu1 [704 kB] 317s Get:157 http://ftpmaster.internal/ubuntu questing/universe arm64 imagemagick arm64 8:7.1.1.43+dfsg1-1ubuntu1 [14.1 kB] 317s Get:158 http://ftpmaster.internal/ubuntu questing/universe arm64 hevea arm64 2.36-2 [2333 kB] 317s Get:159 http://ftpmaster.internal/ubuntu questing/main arm64 libsuitesparseconfig7 arm64 1:7.10.1+dfsg-1 [21.5 kB] 317s Get:160 http://ftpmaster.internal/ubuntu questing/universe arm64 libamd3 arm64 1:7.10.1+dfsg-1 [34.3 kB] 317s Get:161 http://ftpmaster.internal/ubuntu questing/universe arm64 libapache-pom-java all 33-2 [5874 B] 317s Get:162 http://ftpmaster.internal/ubuntu questing/universe arm64 libarpack2t64 arm64 3.9.1-6 [94.9 kB] 317s Get:163 http://ftpmaster.internal/ubuntu questing/main arm64 libcolamd3 arm64 1:7.10.1+dfsg-1 [26.5 kB] 317s Get:164 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-parent-java all 56-1 [10.7 kB] 317s Get:165 http://ftpmaster.internal/ubuntu questing/universe arm64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 317s Get:166 http://ftpmaster.internal/ubuntu questing/main arm64 libexpat1-dev arm64 2.7.1-1 [128 kB] 317s Get:167 http://ftpmaster.internal/ubuntu questing/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB] 317s Get:168 http://ftpmaster.internal/ubuntu questing/universe arm64 libplfit0 arm64 0.9.6+ds-2ubuntu1 [35.7 kB] 317s Get:169 http://ftpmaster.internal/ubuntu questing/universe arm64 libigraph3t64 arm64 0.10.15+ds-3build1 [931 kB] 317s Get:170 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 317s Get:171 http://ftpmaster.internal/ubuntu questing/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 317s Get:172 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 317s Get:173 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 317s Get:174 http://ftpmaster.internal/ubuntu questing/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 317s Get:175 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedcrypto16 arm64 3.6.2-3ubuntu1 [258 kB] 317s Get:176 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedx509-7 arm64 3.6.2-3ubuntu1 [35.7 kB] 317s Get:177 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedtls21 arm64 3.6.2-3ubuntu1 [122 kB] 317s Get:178 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [81.3 kB] 317s Get:179 http://ftpmaster.internal/ubuntu questing/universe arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1259 kB] 318s Get:180 http://ftpmaster.internal/ubuntu questing/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 318s Get:181 http://ftpmaster.internal/ubuntu questing/main arm64 libpython3.13-dev arm64 3.13.5-2 [5695 kB] 318s Get:182 http://ftpmaster.internal/ubuntu questing/main arm64 libpython3-dev arm64 3.13.5-1 [10.8 kB] 318s Get:183 http://ftpmaster.internal/ubuntu questing/main arm64 libpython3-all-dev arm64 3.13.5-1 [906 B] 318s Get:184 http://ftpmaster.internal/ubuntu questing/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 318s Get:185 http://ftpmaster.internal/ubuntu questing/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 318s Get:186 http://ftpmaster.internal/ubuntu questing/main arm64 libxslt1.1 arm64 1.1.43-0exp1 [161 kB] 318s Get:187 http://ftpmaster.internal/ubuntu questing/universe arm64 mafft arm64 7.505-1 [756 kB] 318s Get:188 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-data all 6.1.20170106+dfsg2-6 [3969 kB] 318s Get:189 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-blast+ arm64 2.16.0+ds-7 [15.4 MB] 318s Get:190 http://ftpmaster.internal/ubuntu questing/universe arm64 phylip arm64 1:3.697+dfsg-4build1 [843 kB] 318s Get:191 http://ftpmaster.internal/ubuntu questing/universe arm64 prank arm64 0.0.170427+dfsg-3 [325 kB] 318s Get:192 http://ftpmaster.internal/ubuntu questing/universe arm64 preview-latex-style all 13.2-1.1 [347 kB] 318s Get:193 http://ftpmaster.internal/ubuntu questing/universe arm64 probcons arm64 1.12-14 [129 kB] 318s Get:194 http://ftpmaster.internal/ubuntu questing/universe arm64 python-biopython-doc all 1.85+dfsg-4 [18.2 MB] 318s Get:195 http://ftpmaster.internal/ubuntu questing/universe arm64 python-matplotlib-data all 3.10.1+dfsg1-4 [2930 kB] 319s Get:196 http://ftpmaster.internal/ubuntu questing/main arm64 python3-all arm64 3.13.5-1 [884 B] 319s Get:197 http://ftpmaster.internal/ubuntu questing/main arm64 python3.13-dev arm64 3.13.5-2 [508 kB] 319s Get:198 http://ftpmaster.internal/ubuntu questing/main arm64 python3-dev arm64 3.13.5-1 [26.6 kB] 319s Get:199 http://ftpmaster.internal/ubuntu questing/main arm64 python3-all-dev arm64 3.13.5-1 [904 B] 319s Get:200 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-charset-normalizer arm64 3.4.2-1 [125 kB] 319s Get:201 http://ftpmaster.internal/ubuntu questing/main arm64 python3.13-tk arm64 3.13.5-2 [106 kB] 319s Get:202 http://ftpmaster.internal/ubuntu questing/main arm64 python3-tk arm64 3.13.4-1 [9884 B] 319s Get:203 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B] 319s Get:204 http://ftpmaster.internal/ubuntu questing/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 319s Get:205 http://ftpmaster.internal/ubuntu questing/main arm64 python3-cairo arm64 1.27.0-2 [122 kB] 319s Get:206 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 319s Get:207 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 319s Get:208 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 python3-reportlab all 4.4.2-1 [1145 kB] 319s Get:209 http://ftpmaster.internal/ubuntu questing/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 319s Get:210 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython arm64 1.85+dfsg-4 [1710 kB] 319s Get:211 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-biopython-sql all 1.85+dfsg-4 [26.4 kB] 319s Get:212 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 319s Get:213 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 319s Get:214 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 319s Get:215 http://ftpmaster.internal/ubuntu questing/main arm64 python3-decorator all 5.2.1-2 [28.1 kB] 319s Get:216 http://ftpmaster.internal/ubuntu questing/main arm64 python3-defusedxml all 0.7.1-3 [42.2 kB] 319s Get:217 http://ftpmaster.internal/ubuntu questing/main arm64 python3-roman all 5.0-1 [10.3 kB] 319s Get:218 http://ftpmaster.internal/ubuntu questing/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 319s Get:219 http://ftpmaster.internal/ubuntu questing/main arm64 python3-platformdirs all 4.3.7-1 [16.9 kB] 319s Get:220 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 319s Get:221 http://ftpmaster.internal/ubuntu questing/main arm64 python3-lxml arm64 5.4.0-1build1 [1297 kB] 319s Get:222 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-lz4 arm64 4.4.0+dfsg-2 [27.1 kB] 319s Get:223 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-scipy arm64 1.15.3-1 [15.8 MB] 319s Get:224 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 319s Get:225 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 319s Get:226 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 319s Get:227 http://ftpmaster.internal/ubuntu questing/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 319s Get:228 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 319s Get:229 http://ftpmaster.internal/ubuntu questing/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 319s Get:230 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 319s Get:231 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-matplotlib arm64 3.10.1+dfsg1-4 [18.0 MB] 319s Get:232 http://ftpmaster.internal/ubuntu questing/main arm64 python3-msgpack arm64 1.0.3-3build4 [82.7 kB] 319s Get:233 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 320s Get:234 http://ftpmaster.internal/ubuntu questing/main arm64 python3-mysqldb arm64 1.4.6-2build6 [48.8 kB] 320s Get:235 http://ftpmaster.internal/ubuntu questing/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 320s Get:236 http://ftpmaster.internal/ubuntu questing/main arm64 sphinx-common all 8.2.3-1ubuntu2 [656 kB] 320s Get:237 http://ftpmaster.internal/ubuntu questing/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 320s Get:238 http://ftpmaster.internal/ubuntu questing/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 320s Get:239 http://ftpmaster.internal/ubuntu questing/main arm64 python3-sphinx all 8.2.3-1ubuntu2 [482 kB] 320s Get:240 http://ftpmaster.internal/ubuntu questing/main arm64 python3-tabulate all 0.9.0-1 [45.3 kB] 320s Get:241 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-numpydoc all 1.8.0-2 [52.4 kB] 320s Get:242 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-rdflib all 7.1.1-3 [427 kB] 320s Get:243 http://ftpmaster.internal/ubuntu questing/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 320s Get:244 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 320s Get:245 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 320s Get:246 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-texttable all 1.7.0-1 [11.2 kB] 320s Get:247 http://ftpmaster.internal/ubuntu questing/universe arm64 t-coffee arm64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [879 kB] 320s Get:248 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-fonts-recommended all 2024.20250309-1 [4974 kB] 320s Get:249 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-latex-base all 2024.20250309-1 [1276 kB] 320s Get:250 http://ftpmaster.internal/ubuntu questing/universe arm64 libfontbox-java all 1:1.8.16-5 [208 kB] 320s Get:251 http://ftpmaster.internal/ubuntu questing/universe arm64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 320s Get:252 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-latex-recommended all 2024.20250309-1 [8727 kB] 320s Get:253 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-pictures all 2024.20250309-1 [17.0 MB] 321s Get:254 http://ftpmaster.internal/ubuntu questing/universe arm64 texlive-latex-extra all 2024.20250309-2 [24.8 MB] 321s Get:255 http://ftpmaster.internal/ubuntu questing/universe arm64 wise-data all 2.4.1-27 [83.2 kB] 321s Get:256 http://ftpmaster.internal/ubuntu questing/universe arm64 wise arm64 2.4.1-27 [791 kB] 321s Get:257 http://ftpmaster.internal/ubuntu questing/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 321s Get:258 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-igraph arm64 0.11.8+ds-1build1 [345 kB] 321s Preconfiguring packages ... 322s Fetched 409 MB in 9s (46.1 MB/s) 322s Selecting previously unselected package m4. 322s (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 ... 131053 files and directories currently installed.) 322s Preparing to unpack .../000-m4_1.4.19-8_arm64.deb ... 322s Unpacking m4 (1.4.19-8) ... 322s Selecting previously unselected package flex. 322s Preparing to unpack .../001-flex_2.6.4-8.2build1_arm64.deb ... 322s Unpacking flex (2.6.4-8.2build1) ... 322s Selecting previously unselected package fonts-lato. 322s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 322s Unpacking fonts-lato (2.015-1) ... 322s Selecting previously unselected package libgomp1:arm64. 322s Preparing to unpack .../003-libgomp1_15.1.0-8ubuntu1_arm64.deb ... 322s Unpacking libgomp1:arm64 (15.1.0-8ubuntu1) ... 322s Selecting previously unselected package libfftw3-double3:arm64. 322s Preparing to unpack .../004-libfftw3-double3_3.3.10-2fakesync1build1_arm64.deb ... 322s Unpacking libfftw3-double3:arm64 (3.3.10-2fakesync1build1) ... 322s Selecting previously unselected package fonts-dejavu-mono. 322s Preparing to unpack .../005-fonts-dejavu-mono_2.37-8_all.deb ... 322s Unpacking fonts-dejavu-mono (2.37-8) ... 322s Selecting previously unselected package fonts-dejavu-core. 322s Preparing to unpack .../006-fonts-dejavu-core_2.37-8_all.deb ... 322s Unpacking fonts-dejavu-core (2.37-8) ... 322s Selecting previously unselected package libfontenc1:arm64. 322s Preparing to unpack .../007-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 322s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 322s Selecting previously unselected package x11-common. 322s Preparing to unpack .../008-x11-common_1%3a7.7+24ubuntu1_all.deb ... 322s Unpacking x11-common (1:7.7+24ubuntu1) ... 322s Selecting previously unselected package xfonts-encodings. 322s Preparing to unpack .../009-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 322s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 322s Selecting previously unselected package xfonts-utils. 322s Preparing to unpack .../010-xfonts-utils_1%3a7.7+7_arm64.deb ... 322s Unpacking xfonts-utils (1:7.7+7) ... 322s Selecting previously unselected package fonts-urw-base35. 322s Preparing to unpack .../011-fonts-urw-base35_20200910-8_all.deb ... 322s Unpacking fonts-urw-base35 (20200910-8) ... 322s Selecting previously unselected package fontconfig-config. 322s Preparing to unpack .../012-fontconfig-config_2.15.0-2.3ubuntu1_arm64.deb ... 323s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 323s Selecting previously unselected package libfontconfig1:arm64. 323s Preparing to unpack .../013-libfontconfig1_2.15.0-2.3ubuntu1_arm64.deb ... 323s Unpacking libfontconfig1:arm64 (2.15.0-2.3ubuntu1) ... 323s Selecting previously unselected package libsharpyuv0:arm64. 323s Preparing to unpack .../014-libsharpyuv0_1.5.0-0.1_arm64.deb ... 323s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 323s Selecting previously unselected package libaom3:arm64. 323s Preparing to unpack .../015-libaom3_3.12.1-1_arm64.deb ... 323s Unpacking libaom3:arm64 (3.12.1-1) ... 323s Selecting previously unselected package libheif-plugin-aomdec:arm64. 323s Preparing to unpack .../016-libheif-plugin-aomdec_1.19.8-1_arm64.deb ... 323s Unpacking libheif-plugin-aomdec:arm64 (1.19.8-1) ... 323s Selecting previously unselected package libde265-0:arm64. 323s Preparing to unpack .../017-libde265-0_1.0.16-1_arm64.deb ... 323s Unpacking libde265-0:arm64 (1.0.16-1) ... 323s Selecting previously unselected package libheif-plugin-libde265:arm64. 323s Preparing to unpack .../018-libheif-plugin-libde265_1.19.8-1_arm64.deb ... 323s Unpacking libheif-plugin-libde265:arm64 (1.19.8-1) ... 323s Selecting previously unselected package libheif1:arm64. 323s Preparing to unpack .../019-libheif1_1.19.8-1_arm64.deb ... 323s Unpacking libheif1:arm64 (1.19.8-1) ... 323s Selecting previously unselected package libjbig0:arm64. 323s Preparing to unpack .../020-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 323s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 323s Selecting previously unselected package libjpeg-turbo8:arm64. 323s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 323s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 323s Selecting previously unselected package libjpeg8:arm64. 323s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_arm64.deb ... 323s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 323s Selecting previously unselected package liblcms2-2:arm64. 323s Preparing to unpack .../023-liblcms2-2_2.16-2_arm64.deb ... 323s Unpacking liblcms2-2:arm64 (2.16-2) ... 323s Selecting previously unselected package liblqr-1-0:arm64. 323s Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1build2_arm64.deb ... 323s Unpacking liblqr-1-0:arm64 (0.4.2-2.1build2) ... 323s Selecting previously unselected package libltdl7:arm64. 323s Preparing to unpack .../025-libltdl7_2.5.4-4_arm64.deb ... 323s Unpacking libltdl7:arm64 (2.5.4-4) ... 323s Selecting previously unselected package libopenjp2-7:arm64. 323s Preparing to unpack .../026-libopenjp2-7_2.5.3-2_arm64.deb ... 323s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 323s Selecting previously unselected package libraw23t64:arm64. 323s Preparing to unpack .../027-libraw23t64_0.21.4-2_arm64.deb ... 323s Unpacking libraw23t64:arm64 (0.21.4-2) ... 323s Selecting previously unselected package libdeflate0:arm64. 323s Preparing to unpack .../028-libdeflate0_1.23-2_arm64.deb ... 323s Unpacking libdeflate0:arm64 (1.23-2) ... 323s Selecting previously unselected package liblerc4:arm64. 323s Preparing to unpack .../029-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 323s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 323s Selecting previously unselected package libwebp7:arm64. 323s Preparing to unpack .../030-libwebp7_1.5.0-0.1_arm64.deb ... 323s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 323s Selecting previously unselected package libtiff6:arm64. 323s Preparing to unpack .../031-libtiff6_4.7.0-3ubuntu1_arm64.deb ... 323s Unpacking libtiff6:arm64 (4.7.0-3ubuntu1) ... 323s Selecting previously unselected package libwebpdemux2:arm64. 323s Preparing to unpack .../032-libwebpdemux2_1.5.0-0.1_arm64.deb ... 323s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 323s Selecting previously unselected package libwebpmux3:arm64. 323s Preparing to unpack .../033-libwebpmux3_1.5.0-0.1_arm64.deb ... 323s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 323s Selecting previously unselected package imagemagick-7-common. 323s Preparing to unpack .../034-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1ubuntu1_all.deb ... 323s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1ubuntu1) ... 323s Selecting previously unselected package libmagickcore-7.q16-10:arm64. 323s Preparing to unpack .../035-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1ubuntu1_arm64.deb ... 323s Unpacking libmagickcore-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1ubuntu1) ... 323s Selecting previously unselected package libmagickwand-7.q16-10:arm64. 324s Preparing to unpack .../036-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1ubuntu1_arm64.deb ... 324s Unpacking libmagickwand-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1ubuntu1) ... 324s Selecting previously unselected package poppler-data. 324s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 324s Unpacking poppler-data (0.4.12-1) ... 324s Selecting previously unselected package python3-numpy-dev:arm64. 324s Preparing to unpack .../038-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 324s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 324s Selecting previously unselected package libblas3:arm64. 324s Preparing to unpack .../039-libblas3_3.12.1-2build1_arm64.deb ... 324s Unpacking libblas3:arm64 (3.12.1-2build1) ... 324s Selecting previously unselected package libgfortran5:arm64. 324s Preparing to unpack .../040-libgfortran5_15.1.0-8ubuntu1_arm64.deb ... 324s Unpacking libgfortran5:arm64 (15.1.0-8ubuntu1) ... 324s Selecting previously unselected package liblapack3:arm64. 324s Preparing to unpack .../041-liblapack3_3.12.1-2build1_arm64.deb ... 324s Unpacking liblapack3:arm64 (3.12.1-2build1) ... 324s Selecting previously unselected package python3-numpy. 324s Preparing to unpack .../042-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 324s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 324s Selecting previously unselected package autoconf. 324s Preparing to unpack .../043-autoconf_2.72-3.1ubuntu1_all.deb ... 324s Unpacking autoconf (2.72-3.1ubuntu1) ... 324s Selecting previously unselected package autotools-dev. 324s Preparing to unpack .../044-autotools-dev_20240727.1_all.deb ... 324s Unpacking autotools-dev (20240727.1) ... 324s Selecting previously unselected package automake. 324s Preparing to unpack .../045-automake_1%3a1.17-4ubuntu1_all.deb ... 324s Unpacking automake (1:1.17-4ubuntu1) ... 324s Selecting previously unselected package autopoint. 324s Preparing to unpack .../046-autopoint_0.23.1-2build1_all.deb ... 324s Unpacking autopoint (0.23.1-2build1) ... 324s Selecting previously unselected package libtcl8.6:arm64. 324s Preparing to unpack .../047-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 324s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 324s Selecting previously unselected package libxrender1:arm64. 324s Preparing to unpack .../048-libxrender1_1%3a0.9.12-1_arm64.deb ... 324s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 324s Selecting previously unselected package libxft2:arm64. 324s Preparing to unpack .../049-libxft2_2.3.6-1build1_arm64.deb ... 324s Unpacking libxft2:arm64 (2.3.6-1build1) ... 324s Selecting previously unselected package libxss1:arm64. 324s Preparing to unpack .../050-libxss1_1%3a1.2.3-1build3_arm64.deb ... 324s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 324s Selecting previously unselected package libtk8.6:arm64. 324s Preparing to unpack .../051-libtk8.6_8.6.16-1_arm64.deb ... 324s Unpacking libtk8.6:arm64 (8.6.16-1) ... 324s Selecting previously unselected package tk8.6-blt2.5. 324s Preparing to unpack .../052-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 324s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 324s Selecting previously unselected package blt. 324s Preparing to unpack .../053-blt_2.5.3+dfsg-8_arm64.deb ... 324s Unpacking blt (2.5.3+dfsg-8) ... 324s Selecting previously unselected package libisl23:arm64. 324s Preparing to unpack .../054-libisl23_0.27-1_arm64.deb ... 324s Unpacking libisl23:arm64 (0.27-1) ... 325s Selecting previously unselected package libmpc3:arm64. 325s Preparing to unpack .../055-libmpc3_1.3.1-1build2_arm64.deb ... 325s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 325s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 325s Preparing to unpack .../056-cpp-14-aarch64-linux-gnu_14.3.0-1ubuntu1_arm64.deb ... 325s Unpacking cpp-14-aarch64-linux-gnu (14.3.0-1ubuntu1) ... 325s Selecting previously unselected package cpp-14. 325s Preparing to unpack .../057-cpp-14_14.3.0-1ubuntu1_arm64.deb ... 325s Unpacking cpp-14 (14.3.0-1ubuntu1) ... 325s Selecting previously unselected package cpp-aarch64-linux-gnu. 325s Preparing to unpack .../058-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 325s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 325s Selecting previously unselected package cpp. 325s Preparing to unpack .../059-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 325s Unpacking cpp (4:14.2.0-1ubuntu1) ... 325s Selecting previously unselected package libcc1-0:arm64. 325s Preparing to unpack .../060-libcc1-0_15.1.0-8ubuntu1_arm64.deb ... 325s Unpacking libcc1-0:arm64 (15.1.0-8ubuntu1) ... 325s Selecting previously unselected package libitm1:arm64. 325s Preparing to unpack .../061-libitm1_15.1.0-8ubuntu1_arm64.deb ... 325s Unpacking libitm1:arm64 (15.1.0-8ubuntu1) ... 325s Selecting previously unselected package libasan8:arm64. 325s Preparing to unpack .../062-libasan8_15.1.0-8ubuntu1_arm64.deb ... 325s Unpacking libasan8:arm64 (15.1.0-8ubuntu1) ... 325s Selecting previously unselected package liblsan0:arm64. 325s Preparing to unpack .../063-liblsan0_15.1.0-8ubuntu1_arm64.deb ... 325s Unpacking liblsan0:arm64 (15.1.0-8ubuntu1) ... 325s Selecting previously unselected package libtsan2:arm64. 325s Preparing to unpack .../064-libtsan2_15.1.0-8ubuntu1_arm64.deb ... 325s Unpacking libtsan2:arm64 (15.1.0-8ubuntu1) ... 325s Selecting previously unselected package libubsan1:arm64. 325s Preparing to unpack .../065-libubsan1_15.1.0-8ubuntu1_arm64.deb ... 325s Unpacking libubsan1:arm64 (15.1.0-8ubuntu1) ... 325s Selecting previously unselected package libhwasan0:arm64. 325s Preparing to unpack .../066-libhwasan0_15.1.0-8ubuntu1_arm64.deb ... 325s Unpacking libhwasan0:arm64 (15.1.0-8ubuntu1) ... 325s Selecting previously unselected package libgcc-14-dev:arm64. 325s Preparing to unpack .../067-libgcc-14-dev_14.3.0-1ubuntu1_arm64.deb ... 325s Unpacking libgcc-14-dev:arm64 (14.3.0-1ubuntu1) ... 325s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 325s Preparing to unpack .../068-gcc-14-aarch64-linux-gnu_14.3.0-1ubuntu1_arm64.deb ... 325s Unpacking gcc-14-aarch64-linux-gnu (14.3.0-1ubuntu1) ... 326s Selecting previously unselected package gcc-14. 326s Preparing to unpack .../069-gcc-14_14.3.0-1ubuntu1_arm64.deb ... 326s Unpacking gcc-14 (14.3.0-1ubuntu1) ... 326s Selecting previously unselected package gcc-aarch64-linux-gnu. 326s Preparing to unpack .../070-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 326s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package gcc. 326s Preparing to unpack .../071-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 326s Unpacking gcc (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package libstdc++-14-dev:arm64. 326s Preparing to unpack .../072-libstdc++-14-dev_14.3.0-1ubuntu1_arm64.deb ... 326s Unpacking libstdc++-14-dev:arm64 (14.3.0-1ubuntu1) ... 326s Selecting previously unselected package g++-14-aarch64-linux-gnu. 326s Preparing to unpack .../073-g++-14-aarch64-linux-gnu_14.3.0-1ubuntu1_arm64.deb ... 326s Unpacking g++-14-aarch64-linux-gnu (14.3.0-1ubuntu1) ... 326s Selecting previously unselected package g++-14. 326s Preparing to unpack .../074-g++-14_14.3.0-1ubuntu1_arm64.deb ... 326s Unpacking g++-14 (14.3.0-1ubuntu1) ... 326s Selecting previously unselected package g++-aarch64-linux-gnu. 326s Preparing to unpack .../075-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 326s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package g++. 326s Preparing to unpack .../076-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 326s Unpacking g++ (4:14.2.0-1ubuntu1) ... 326s Selecting previously unselected package build-essential. 326s Preparing to unpack .../077-build-essential_12.12ubuntu1_arm64.deb ... 326s Unpacking build-essential (12.12ubuntu1) ... 326s Selecting previously unselected package bwa. 326s Preparing to unpack .../078-bwa_0.7.18-1_arm64.deb ... 326s Unpacking bwa (0.7.18-1) ... 326s Selecting previously unselected package libargtable2-0:arm64. 326s Preparing to unpack .../079-libargtable2-0_13-4_arm64.deb ... 326s Unpacking libargtable2-0:arm64 (13-4) ... 326s Selecting previously unselected package clustalo. 326s Preparing to unpack .../080-clustalo_1.2.4-8build1_arm64.deb ... 326s Unpacking clustalo (1.2.4-8build1) ... 326s Selecting previously unselected package libdebhelper-perl. 326s Preparing to unpack .../081-libdebhelper-perl_13.24.2ubuntu1_all.deb ... 326s Unpacking libdebhelper-perl (13.24.2ubuntu1) ... 327s Selecting previously unselected package libtool. 327s Preparing to unpack .../082-libtool_2.5.4-4_all.deb ... 327s Unpacking libtool (2.5.4-4) ... 327s Selecting previously unselected package dh-autoreconf. 327s Preparing to unpack .../083-dh-autoreconf_20_all.deb ... 327s Unpacking dh-autoreconf (20) ... 327s Selecting previously unselected package libarchive-zip-perl. 327s Preparing to unpack .../084-libarchive-zip-perl_1.68-1_all.deb ... 327s Unpacking libarchive-zip-perl (1.68-1) ... 327s Selecting previously unselected package libfile-stripnondeterminism-perl. 327s Preparing to unpack .../085-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 327s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 327s Selecting previously unselected package dh-strip-nondeterminism. 327s Preparing to unpack .../086-dh-strip-nondeterminism_1.14.1-2_all.deb ... 327s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 327s Selecting previously unselected package debugedit. 327s Preparing to unpack .../087-debugedit_1%3a5.1-2_arm64.deb ... 327s Unpacking debugedit (1:5.1-2) ... 327s Selecting previously unselected package dwz. 327s Preparing to unpack .../088-dwz_0.15-1build6_arm64.deb ... 327s Unpacking dwz (0.15-1build6) ... 327s Selecting previously unselected package gettext. 327s Preparing to unpack .../089-gettext_0.23.1-2build1_arm64.deb ... 327s Unpacking gettext (0.23.1-2build1) ... 327s Selecting previously unselected package intltool-debian. 327s Preparing to unpack .../090-intltool-debian_0.35.0+20060710.6_all.deb ... 327s Unpacking intltool-debian (0.35.0+20060710.6) ... 327s Selecting previously unselected package po-debconf. 327s Preparing to unpack .../091-po-debconf_1.0.21+nmu1_all.deb ... 327s Unpacking po-debconf (1.0.21+nmu1) ... 327s Selecting previously unselected package debhelper. 327s Preparing to unpack .../092-debhelper_13.24.2ubuntu1_all.deb ... 327s Unpacking debhelper (13.24.2ubuntu1) ... 327s Selecting previously unselected package dh-python. 327s Preparing to unpack .../093-dh-python_6.20250414_all.deb ... 327s Unpacking dh-python (6.20250414) ... 327s Selecting previously unselected package dialign. 327s Preparing to unpack .../094-dialign_2.2.1-13_arm64.deb ... 327s Unpacking dialign (2.2.1-13) ... 327s Selecting previously unselected package sgml-base. 327s Preparing to unpack .../095-sgml-base_1.31+nmu1_all.deb ... 327s Unpacking sgml-base (1.31+nmu1) ... 327s Selecting previously unselected package xml-core. 327s Preparing to unpack .../096-xml-core_0.19_all.deb ... 327s Unpacking xml-core (0.19) ... 327s Selecting previously unselected package docutils-common. 327s Preparing to unpack .../097-docutils-common_0.21.2+dfsg-2_all.deb ... 327s Unpacking docutils-common (0.21.2+dfsg-2) ... 327s Selecting previously unselected package libcifpp-data. 327s Preparing to unpack .../098-libcifpp-data_7.0.9-1_all.deb ... 327s Unpacking libcifpp-data (7.0.9-1) ... 327s Selecting previously unselected package libcifpp7:arm64. 327s Preparing to unpack .../099-libcifpp7_7.0.9-1_arm64.deb ... 327s Unpacking libcifpp7:arm64 (7.0.9-1) ... 327s Selecting previously unselected package dssp. 327s Preparing to unpack .../100-dssp_4.4.10-1_arm64.deb ... 327s Unpacking dssp (4.4.10-1) ... 327s Selecting previously unselected package libimagequant0:arm64. 327s Preparing to unpack .../101-libimagequant0_2.18.0-1build1_arm64.deb ... 327s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 327s Selecting previously unselected package libxpm4:arm64. 327s Preparing to unpack .../102-libxpm4_1%3a3.5.17-1build2_arm64.deb ... 327s Unpacking libxpm4:arm64 (1:3.5.17-1build2) ... 327s Selecting previously unselected package libgd3:arm64. 327s Preparing to unpack .../103-libgd3_2.3.3-13ubuntu1_arm64.deb ... 327s Unpacking libgd3:arm64 (2.3.3-13ubuntu1) ... 327s Selecting previously unselected package libhpdf-2.3.0:arm64. 327s Preparing to unpack .../104-libhpdf-2.3.0_2.3.0+dfsg-1build3_arm64.deb ... 327s Unpacking libhpdf-2.3.0:arm64 (2.3.0+dfsg-1build3) ... 327s Selecting previously unselected package mysql-common. 327s Preparing to unpack .../105-mysql-common_5.8+1.1.1ubuntu1_all.deb ... 327s Unpacking mysql-common (5.8+1.1.1ubuntu1) ... 328s Selecting previously unselected package libmysqlclient24:arm64. 328s Preparing to unpack .../106-libmysqlclient24_8.4.5-0ubuntu3_arm64.deb ... 328s Unpacking libmysqlclient24:arm64 (8.4.5-0ubuntu3) ... 328s Selecting previously unselected package libpq5:arm64. 328s Preparing to unpack .../107-libpq5_17.5-1build1_arm64.deb ... 328s Unpacking libpq5:arm64 (17.5-1build1) ... 328s Selecting previously unselected package emboss-lib. 328s Preparing to unpack .../108-emboss-lib_6.6.0+dfsg-15ubuntu2_arm64.deb ... 328s Unpacking emboss-lib (6.6.0+dfsg-15ubuntu2) ... 328s Selecting previously unselected package emboss-data. 328s Preparing to unpack .../109-emboss-data_6.6.0+dfsg-15ubuntu2_all.deb ... 328s Unpacking emboss-data (6.6.0+dfsg-15ubuntu2) ... 331s Selecting previously unselected package emboss. 331s Preparing to unpack .../110-emboss_6.6.0+dfsg-15ubuntu2_arm64.deb ... 331s Unpacking emboss (6.6.0+dfsg-15ubuntu2) ... 331s Selecting previously unselected package fonts-font-awesome. 331s Preparing to unpack .../111-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 331s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 331s Selecting previously unselected package fonts-lmodern. 331s Preparing to unpack .../112-fonts-lmodern_2.005-1_all.deb ... 331s Unpacking fonts-lmodern (2.005-1) ... 331s Selecting previously unselected package fonts-lyx. 331s Preparing to unpack .../113-fonts-lyx_2.4.3-1_all.deb ... 331s Unpacking fonts-lyx (2.4.3-1) ... 331s Selecting previously unselected package libgs-common. 331s Preparing to unpack .../114-libgs-common_10.05.0dfsg1-0ubuntu1_all.deb ... 331s Unpacking libgs-common (10.05.0dfsg1-0ubuntu1) ... 331s Selecting previously unselected package libgs10-common. 331s Preparing to unpack .../115-libgs10-common_10.05.0dfsg1-0ubuntu1_all.deb ... 331s Unpacking libgs10-common (10.05.0dfsg1-0ubuntu1) ... 331s Selecting previously unselected package libavahi-common-data:arm64. 331s Preparing to unpack .../116-libavahi-common-data_0.8-16ubuntu2_arm64.deb ... 331s Unpacking libavahi-common-data:arm64 (0.8-16ubuntu2) ... 331s Selecting previously unselected package libavahi-common3:arm64. 331s Preparing to unpack .../117-libavahi-common3_0.8-16ubuntu2_arm64.deb ... 331s Unpacking libavahi-common3:arm64 (0.8-16ubuntu2) ... 331s Selecting previously unselected package libavahi-client3:arm64. 331s Preparing to unpack .../118-libavahi-client3_0.8-16ubuntu2_arm64.deb ... 331s Unpacking libavahi-client3:arm64 (0.8-16ubuntu2) ... 331s Selecting previously unselected package libcups2t64:arm64. 332s Preparing to unpack .../119-libcups2t64_2.4.12-0ubuntu1_arm64.deb ... 332s Unpacking libcups2t64:arm64 (2.4.12-0ubuntu1) ... 332s Selecting previously unselected package libidn12:arm64. 332s Preparing to unpack .../120-libidn12_1.43-1_arm64.deb ... 332s Unpacking libidn12:arm64 (1.43-1) ... 332s Selecting previously unselected package libijs-0.35:arm64. 332s Preparing to unpack .../121-libijs-0.35_0.35-15.3_arm64.deb ... 332s Unpacking libijs-0.35:arm64 (0.35-15.3) ... 332s Selecting previously unselected package libjbig2dec0:arm64. 332s Preparing to unpack .../122-libjbig2dec0_0.20-1build3_arm64.deb ... 332s Unpacking libjbig2dec0:arm64 (0.20-1build3) ... 332s Selecting previously unselected package libpaper2:arm64. 332s Preparing to unpack .../123-libpaper2_2.2.5-0.3_arm64.deb ... 332s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 332s Selecting previously unselected package libice6:arm64. 332s Preparing to unpack .../124-libice6_2%3a1.1.1-1_arm64.deb ... 332s Unpacking libice6:arm64 (2:1.1.1-1) ... 332s Selecting previously unselected package libsm6:arm64. 332s Preparing to unpack .../125-libsm6_2%3a1.2.6-1_arm64.deb ... 332s Unpacking libsm6:arm64 (2:1.2.6-1) ... 332s Selecting previously unselected package libxt6t64:arm64. 332s Preparing to unpack .../126-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 332s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 332s Selecting previously unselected package libgs10:arm64. 332s Preparing to unpack .../127-libgs10_10.05.0dfsg1-0ubuntu1_arm64.deb ... 332s Unpacking libgs10:arm64 (10.05.0dfsg1-0ubuntu1) ... 332s Selecting previously unselected package ghostscript. 332s Preparing to unpack .../128-ghostscript_10.05.0dfsg1-0ubuntu1_arm64.deb ... 332s Unpacking ghostscript (10.05.0dfsg1-0ubuntu1) ... 332s Selecting previously unselected package libnetpbm11t64:arm64. 332s Preparing to unpack .../129-libnetpbm11t64_2%3a11.10.02-1build1_arm64.deb ... 332s Unpacking libnetpbm11t64:arm64 (2:11.10.02-1build1) ... 332s Selecting previously unselected package netpbm. 332s Preparing to unpack .../130-netpbm_2%3a11.10.02-1build1_arm64.deb ... 332s Unpacking netpbm (2:11.10.02-1build1) ... 332s Selecting previously unselected package tex-common. 332s Preparing to unpack .../131-tex-common_6.19_all.deb ... 332s Unpacking tex-common (6.19) ... 332s Selecting previously unselected package libpaper-utils. 332s Preparing to unpack .../132-libpaper-utils_2.2.5-0.3_arm64.deb ... 332s Unpacking libpaper-utils (2.2.5-0.3) ... 332s Selecting previously unselected package libkpathsea6:arm64. 332s Preparing to unpack .../133-libkpathsea6_2024.20240313.70630+ds-6_arm64.deb ... 332s Unpacking libkpathsea6:arm64 (2024.20240313.70630+ds-6) ... 332s Selecting previously unselected package libptexenc1:arm64. 332s Preparing to unpack .../134-libptexenc1_2024.20240313.70630+ds-6_arm64.deb ... 332s Unpacking libptexenc1:arm64 (2024.20240313.70630+ds-6) ... 332s Selecting previously unselected package libsynctex2:arm64. 332s Preparing to unpack .../135-libsynctex2_2024.20240313.70630+ds-6_arm64.deb ... 332s Unpacking libsynctex2:arm64 (2024.20240313.70630+ds-6) ... 332s Selecting previously unselected package libtexlua53-5:arm64. 332s Preparing to unpack .../136-libtexlua53-5_2024.20240313.70630+ds-6_arm64.deb ... 332s Unpacking libtexlua53-5:arm64 (2024.20240313.70630+ds-6) ... 332s Selecting previously unselected package t1utils. 332s Preparing to unpack .../137-t1utils_1.41-4build3_arm64.deb ... 332s Unpacking t1utils (1.41-4build3) ... 332s Selecting previously unselected package libpixman-1-0:arm64. 332s Preparing to unpack .../138-libpixman-1-0_0.44.0-3_arm64.deb ... 332s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 332s Selecting previously unselected package libxcb-render0:arm64. 332s Preparing to unpack .../139-libxcb-render0_1.17.0-2_arm64.deb ... 332s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 333s Selecting previously unselected package libxcb-shm0:arm64. 333s Preparing to unpack .../140-libxcb-shm0_1.17.0-2_arm64.deb ... 333s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 333s Selecting previously unselected package libcairo2:arm64. 333s Preparing to unpack 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libteckit0:arm64 (2.5.12+ds1-1) ... 333s Selecting previously unselected package libxmu6:arm64. 333s Preparing to unpack .../147-libxmu6_2%3a1.1.3-3build2_arm64.deb ... 333s Unpacking libxmu6:arm64 (2:1.1.3-3build2) ... 333s Selecting previously unselected package libxaw7:arm64. 333s Preparing to unpack .../148-libxaw7_2%3a1.0.16-1_arm64.deb ... 333s Unpacking libxaw7:arm64 (2:1.0.16-1) ... 333s Selecting previously unselected package libxi6:arm64. 333s Preparing to unpack .../149-libxi6_2%3a1.8.2-1_arm64.deb ... 333s Unpacking libxi6:arm64 (2:1.8.2-1) ... 333s Selecting previously unselected package libzzip-0-13t64:arm64. 333s Preparing to unpack .../150-libzzip-0-13t64_0.13.78+dfsg.1-0.1_arm64.deb ... 333s Unpacking libzzip-0-13t64:arm64 (0.13.78+dfsg.1-0.1) ... 333s Selecting previously unselected package texlive-binaries. 333s Preparing to unpack .../151-texlive-binaries_2024.20240313.70630+ds-6_arm64.deb ... 333s Unpacking texlive-binaries (2024.20240313.70630+ds-6) ... 333s Selecting previously unselected package xdg-utils. 333s Preparing to unpack .../152-xdg-utils_1.2.1-2ubuntu1_all.deb ... 333s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 333s Selecting previously unselected package texlive-base. 333s Preparing to unpack .../153-texlive-base_2024.20250309-1_all.deb ... 333s Unpacking texlive-base (2024.20250309-1) ... 334s Selecting previously unselected package hicolor-icon-theme. 334s Preparing to unpack .../154-hicolor-icon-theme_0.18-2_all.deb ... 334s Unpacking hicolor-icon-theme (0.18-2) ... 334s Selecting previously unselected package imagemagick-7.q16. 334s Preparing to unpack .../155-imagemagick-7.q16_8%3a7.1.1.43+dfsg1-1ubuntu1_arm64.deb ... 334s Unpacking imagemagick-7.q16 (8:7.1.1.43+dfsg1-1ubuntu1) ... 334s Selecting previously unselected package imagemagick. 334s Preparing to unpack .../156-imagemagick_8%3a7.1.1.43+dfsg1-1ubuntu1_arm64.deb ... 334s Unpacking imagemagick (8:7.1.1.43+dfsg1-1ubuntu1) ... 334s Selecting previously unselected package hevea. 334s Preparing to unpack .../157-hevea_2.36-2_arm64.deb ... 334s Unpacking hevea (2.36-2) ... 334s Selecting previously unselected package libsuitesparseconfig7:arm64. 334s Preparing to unpack .../158-libsuitesparseconfig7_1%3a7.10.1+dfsg-1_arm64.deb ... 334s Unpacking libsuitesparseconfig7:arm64 (1:7.10.1+dfsg-1) ... 334s Selecting previously unselected package libamd3:arm64. 334s Preparing to unpack .../159-libamd3_1%3a7.10.1+dfsg-1_arm64.deb ... 334s Unpacking libamd3:arm64 (1:7.10.1+dfsg-1) ... 335s Selecting previously unselected package libapache-pom-java. 335s Preparing to unpack .../160-libapache-pom-java_33-2_all.deb ... 335s Unpacking libapache-pom-java (33-2) ... 335s Selecting previously unselected package libarpack2t64:arm64. 335s Preparing to unpack .../161-libarpack2t64_3.9.1-6_arm64.deb ... 335s Unpacking libarpack2t64:arm64 (3.9.1-6) ... 335s Selecting previously unselected package libcolamd3:arm64. 335s Preparing to unpack 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.../167-libplfit0_0.9.6+ds-2ubuntu1_arm64.deb ... 335s Unpacking libplfit0:arm64 (0.9.6+ds-2ubuntu1) ... 335s Selecting previously unselected package libigraph3t64:arm64. 335s Preparing to unpack .../168-libigraph3t64_0.10.15+ds-3build1_arm64.deb ... 335s Unpacking libigraph3t64:arm64 (0.10.15+ds-3build1) ... 335s Selecting previously unselected package libjs-jquery. 335s Preparing to unpack .../169-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 335s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 335s Selecting previously unselected package libjs-jquery-ui. 335s Preparing to unpack .../170-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 335s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 335s Selecting previously unselected package libjs-underscore. 335s Preparing to unpack .../171-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 335s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 335s Selecting previously unselected package libjs-sphinxdoc. 335s Preparing to unpack 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336s Unpacking libpython3-all-dev:arm64 (3.13.5-1) ... 336s Selecting previously unselected package libqhull-r8.0:arm64. 336s Preparing to unpack .../183-libqhull-r8.0_2020.2-6build1_arm64.deb ... 336s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 336s Selecting previously unselected package libraqm0:arm64. 336s Preparing to unpack .../184-libraqm0_0.10.2-1_arm64.deb ... 336s Unpacking libraqm0:arm64 (0.10.2-1) ... 336s Selecting previously unselected package libxslt1.1:arm64. 336s Preparing to unpack .../185-libxslt1.1_1.1.43-0exp1_arm64.deb ... 336s Unpacking libxslt1.1:arm64 (1.1.43-0exp1) ... 336s Selecting previously unselected package mafft. 336s Preparing to unpack .../186-mafft_7.505-1_arm64.deb ... 336s Unpacking mafft (7.505-1) ... 336s Selecting previously unselected package ncbi-data. 336s Preparing to unpack .../187-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... 336s Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... 336s Selecting previously unselected package ncbi-blast+. 336s Preparing to unpack .../188-ncbi-blast+_2.16.0+ds-7_arm64.deb ... 336s Unpacking ncbi-blast+ (2.16.0+ds-7) ... 336s Selecting previously unselected package phylip. 336s Preparing to unpack .../189-phylip_1%3a3.697+dfsg-4build1_arm64.deb ... 336s Unpacking phylip (1:3.697+dfsg-4build1) ... 336s Selecting previously unselected package prank. 336s Preparing to unpack .../190-prank_0.0.170427+dfsg-3_arm64.deb ... 336s Unpacking prank (0.0.170427+dfsg-3) ... 336s Selecting previously unselected package preview-latex-style. 336s Preparing to unpack .../191-preview-latex-style_13.2-1.1_all.deb ... 336s Unpacking preview-latex-style (13.2-1.1) ... 336s Selecting previously unselected package probcons. 336s Preparing to unpack .../192-probcons_1.12-14_arm64.deb ... 336s Unpacking probcons (1.12-14) ... 336s Selecting previously unselected package python-biopython-doc. 336s Preparing to unpack .../193-python-biopython-doc_1.85+dfsg-4_all.deb ... 336s Unpacking python-biopython-doc (1.85+dfsg-4) ... 337s Selecting previously unselected package python-matplotlib-data. 337s Preparing to unpack .../194-python-matplotlib-data_3.10.1+dfsg1-4_all.deb ... 337s Unpacking python-matplotlib-data (3.10.1+dfsg1-4) ... 337s Selecting previously unselected package python3-all. 337s Preparing to unpack .../195-python3-all_3.13.5-1_arm64.deb ... 337s Unpacking python3-all (3.13.5-1) ... 337s Selecting previously unselected package python3.13-dev. 337s Preparing to unpack .../196-python3.13-dev_3.13.5-2_arm64.deb ... 337s Unpacking python3.13-dev (3.13.5-2) ... 337s Selecting previously unselected package python3-dev. 337s Preparing to unpack .../197-python3-dev_3.13.5-1_arm64.deb ... 337s Unpacking python3-dev (3.13.5-1) ... 337s Selecting previously unselected package python3-all-dev. 337s Preparing to unpack .../198-python3-all-dev_3.13.5-1_arm64.deb ... 337s Unpacking python3-all-dev (3.13.5-1) ... 337s Selecting previously unselected package python3-charset-normalizer. 337s Preparing to unpack .../199-python3-charset-normalizer_3.4.2-1_arm64.deb ... 337s Unpacking python3-charset-normalizer (3.4.2-1) ... 337s Selecting previously unselected package python3.13-tk. 337s Preparing to unpack .../200-python3.13-tk_3.13.5-2_arm64.deb ... 337s Unpacking python3.13-tk (3.13.5-2) ... 337s Selecting previously unselected package python3-tk:arm64. 337s Preparing to unpack .../201-python3-tk_3.13.4-1_arm64.deb ... 337s Unpacking python3-tk:arm64 (3.13.4-1) ... 337s Selecting previously unselected package python3-pil.imagetk:arm64. 337s Preparing to unpack .../202-python3-pil.imagetk_11.1.0-5build1_arm64.deb ... 337s Unpacking python3-pil.imagetk:arm64 (11.1.0-5build1) ... 337s Selecting previously unselected package python3-pil:arm64. 337s Preparing to unpack .../203-python3-pil_11.1.0-5build1_arm64.deb ... 337s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 337s Selecting previously unselected package python3-cairo. 337s Preparing to unpack .../204-python3-cairo_1.27.0-2_arm64.deb ... 337s Unpacking python3-cairo (1.27.0-2) ... 337s Selecting previously unselected package python3-freetype. 337s Preparing to unpack .../205-python3-freetype_2.5.1-1_all.deb ... 337s Unpacking python3-freetype (2.5.1-1) ... 337s Selecting previously unselected package python3-rlpycairo. 337s Preparing to unpack .../206-python3-rlpycairo_0.3.0-3_all.deb ... 337s Unpacking python3-rlpycairo (0.3.0-3) ... 337s Selecting previously unselected package python3-reportlab. 337s Preparing to unpack .../207-python3-reportlab_4.4.2-1_all.deb ... 337s Unpacking python3-reportlab (4.4.2-1) ... 337s Selecting previously unselected package w3c-sgml-lib. 337s Preparing to unpack .../208-w3c-sgml-lib_1.3-3_all.deb ... 337s Unpacking w3c-sgml-lib (1.3-3) ... 337s Selecting previously unselected package python3-biopython. 337s Preparing to unpack .../209-python3-biopython_1.85+dfsg-4_arm64.deb ... 337s Unpacking python3-biopython (1.85+dfsg-4) ... 338s Selecting previously unselected package python3-biopython-sql. 338s Preparing to unpack .../210-python3-biopython-sql_1.85+dfsg-4_all.deb ... 338s Unpacking python3-biopython-sql (1.85+dfsg-4) ... 338s Selecting previously unselected package python3-brotli. 338s Preparing to unpack .../211-python3-brotli_1.1.0-2build4_arm64.deb ... 338s Unpacking python3-brotli (1.1.0-2build4) ... 338s Selecting previously unselected package python3-contourpy. 338s Preparing to unpack .../212-python3-contourpy_1.3.1-1build1_arm64.deb ... 338s Unpacking python3-contourpy (1.3.1-1build1) ... 338s Selecting previously unselected package python3-cycler. 338s Preparing to unpack .../213-python3-cycler_0.12.1-1_all.deb ... 338s Unpacking python3-cycler (0.12.1-1) ... 338s Selecting previously unselected package python3-decorator. 338s Preparing to unpack .../214-python3-decorator_5.2.1-2_all.deb ... 338s Unpacking python3-decorator (5.2.1-2) ... 338s Selecting previously unselected package python3-defusedxml. 338s Preparing to unpack .../215-python3-defusedxml_0.7.1-3_all.deb ... 338s Unpacking python3-defusedxml (0.7.1-3) ... 338s Selecting previously unselected package python3-roman. 338s Preparing to unpack .../216-python3-roman_5.0-1_all.deb ... 338s Unpacking python3-roman (5.0-1) ... 338s Selecting previously unselected package python3-docutils. 338s Preparing to unpack .../217-python3-docutils_0.21.2+dfsg-2_all.deb ... 338s Unpacking python3-docutils (0.21.2+dfsg-2) ... 338s Selecting previously unselected package python3-platformdirs. 338s Preparing to unpack .../218-python3-platformdirs_4.3.7-1_all.deb ... 338s Unpacking python3-platformdirs (4.3.7-1) ... 338s Selecting previously unselected package python3-fs. 338s Preparing to unpack .../219-python3-fs_2.4.16-7_all.deb ... 338s Unpacking python3-fs (2.4.16-7) ... 338s Selecting previously unselected package python3-lxml:arm64. 338s Preparing to unpack .../220-python3-lxml_5.4.0-1build1_arm64.deb ... 338s Unpacking python3-lxml:arm64 (5.4.0-1build1) ... 338s Selecting previously unselected package python3-lz4. 338s Preparing to unpack .../221-python3-lz4_4.4.0+dfsg-2_arm64.deb ... 338s Unpacking python3-lz4 (4.4.0+dfsg-2) ... 338s Selecting previously unselected package python3-scipy. 338s Preparing to unpack .../222-python3-scipy_1.15.3-1_arm64.deb ... 338s Unpacking python3-scipy (1.15.3-1) ... 338s Selecting previously unselected package python3-mpmath. 338s Preparing to unpack .../223-python3-mpmath_1.3.0-1_all.deb ... 338s Unpacking python3-mpmath (1.3.0-1) ... 338s Selecting previously unselected package python3-sympy. 339s Preparing to unpack .../224-python3-sympy_1.13.3-5_all.deb ... 339s Unpacking python3-sympy (1.13.3-5) ... 339s Selecting previously unselected package python3-ufolib2. 339s Preparing to unpack .../225-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 339s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 339s Selecting previously unselected package unicode-data. 339s 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libxt6t64:arm64 (1:1.2.1-1.2build1) ... 360s Setting up netpbm (2:11.10.02-1build1) ... 360s Setting up cpp-14 (14.3.0-1ubuntu1) ... 360s Setting up python3-igraph (0.11.8+ds-1build1) ... 361s Setting up cpp (4:14.2.0-1ubuntu1) ... 361s Setting up gcc-14-aarch64-linux-gnu (14.3.0-1ubuntu1) ... 361s Setting up libcups2t64:arm64 (2.4.12-0ubuntu1) ... 361s Setting up python3-all-dev (3.13.5-1) ... 361s Setting up libgs10-common (10.05.0dfsg1-0ubuntu1) ... 361s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 361s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 361s Setting up libxmu6:arm64 (2:1.1.3-3build2) ... 361s Setting up g++-14-aarch64-linux-gnu (14.3.0-1ubuntu1) ... 361s Setting up python3-cairo (1.27.0-2) ... 361s Setting up blt (2.5.3+dfsg-8) ... 361s Setting up python3-tk:arm64 (3.13.4-1) ... 361s Setting up libxaw7:arm64 (2:1.0.16-1) ... 361s Setting up gcc-14 (14.3.0-1ubuntu1) ... 361s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ... 361s Setting up python3-rlpycairo (0.3.0-3) ... 361s Setting up python3-reportlab (4.4.2-1) ... 362s Setting up texlive-binaries (2024.20240313.70630+ds-6) ... 362s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 362s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 362s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 362s Setting up g++-14 (14.3.0-1ubuntu1) ... 362s Setting up texlive-base (2024.20250309-1) ... 362s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 362s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 363s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 363s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 363s Setting up libgs10:arm64 (10.05.0dfsg1-0ubuntu1) ... 363s Setting up libtool (2.5.4-4) ... 363s Setting up ghostscript (10.05.0dfsg1-0ubuntu1) ... 363s Setting up gcc (4:14.2.0-1ubuntu1) ... 363s Setting up dh-autoreconf (20) ... 363s Setting up texlive-latex-base (2024.20250309-1) ... 363s Setting up texlive-latex-recommended (2024.20250309-1) ... 363s Setting up texlive-pictures (2024.20250309-1) ... 363s Setting up g++ (4:14.2.0-1ubuntu1) ... 363s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 363s Setting up texlive-fonts-recommended (2024.20250309-1) ... 363s Setting up build-essential (12.12ubuntu1) ... 363s Setting up debhelper (13.24.2ubuntu1) ... 363s Setting up texlive-latex-extra (2024.20250309-2) ... 363s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 363s Setting up libheif-plugin-aomdec:arm64 (1.19.8-1) ... 363s Setting up libheif-plugin-libde265:arm64 (1.19.8-1) ... 363s Setting up libheif1:arm64 (1.19.8-1) ... 363s Setting up python3-fonttools (4.55.3-2build1) ... 364s Setting up libgd3:arm64 (2.3.3-13ubuntu1) ... 364s Setting up libmagickcore-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1ubuntu1) ... 364s Setting up emboss-lib (6.6.0+dfsg-15ubuntu2) ... 364s Setting up python3-matplotlib (3.10.1+dfsg1-4) ... 365s Setting up libmagickwand-7.q16-10:arm64 (8:7.1.1.43+dfsg1-1ubuntu1) ... 365s Setting up emboss (6.6.0+dfsg-15ubuntu2) ... 365s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1ubuntu1) ... 365s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 365s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 366s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 366s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 366s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 366s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 366s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 366s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 366s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 366s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 366s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 366s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 366s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 366s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 366s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 366s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 366s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 366s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 366s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 366s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 366s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 366s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 366s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 366s 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 366s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 366s 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 366s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 366s 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 366s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 366s 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 366s Setting up hevea (2.36-2) ... 366s Setting up imagemagick (8:7.1.1.43+dfsg1-1ubuntu1) ... 366s Processing triggers for install-info (7.1.1-1) ... 366s Processing triggers for libc-bin (2.41-6ubuntu2) ... 366s Processing triggers for man-db (2.13.1-1) ... 367s Processing triggers for shared-mime-info (2.4-5build2) ... 367s Processing triggers for sgml-base (1.31+nmu1) ... 367s Setting up w3c-sgml-lib (1.3-3) ... 390s Setting up docutils-common (0.21.2+dfsg-2) ... 391s Setting up python3-biopython (1.85+dfsg-4) ... 391s Setting up python3-biopython-sql (1.85+dfsg-4) ... 392s Processing triggers for sgml-base (1.31+nmu1) ... 392s Setting up python3-docutils (0.21.2+dfsg-2) ... 392s Setting up python3-sphinx (8.2.3-1ubuntu2) ... 393s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 393s Setting up python3-numpydoc (1.8.0-2) ... 393s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 393s Processing triggers for tex-common (6.19) ... 393s Running updmap-sys. This may take some time... done. 393s Running mktexlsr /var/lib/texmf ... done. 393s Building format(s) --all. 464s This may take some time... done. 468s autopkgtest [03:47:55]: test full_suite: sh debian/tests/run-unit-test 468s autopkgtest [03:47:55]: test full_suite: [----------------------- 470s mkdir: created directory 'Bio' 470s mkdir: created directory 'Bio/Align' 470s mkdir: created directory 'Bio/Align/substitution_matrices' 470s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 470s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 470s test_Ace ... ok 470s test_Affy ... ok 472s test_AlignIO ... ok 472s test_AlignIO_ClustalIO ... ok 472s test_AlignIO_EmbossIO ... ok 472s test_AlignIO_FastaIO ... ok 472s test_AlignIO_MauveIO ... ok 472s test_AlignIO_PhylipIO ... ok 472s test_AlignIO_convert ... ok 472s test_AlignInfo ... ok 473s test_Align_Alignment ... ok 473s test_Align_a2m ... ok 473s test_Align_bed ... ok 473s test_Align_bigbed ... ok 473s test_Align_bigmaf ... ok 474s test_Align_bigpsl ... ok 474s test_Align_chain ... ok 474s test_Align_clustal ... ok 478s test_Align_codonalign ... ok 478s test_Align_emboss ... ok 479s test_Align_exonerate ... ok 479s test_Align_fasta ... ok 479s test_Align_hhr ... ok 480s test_Align_maf ... ok 480s test_Align_mauve ... ok 480s test_Align_msf ... ok 480s test_Align_nexus ... ok 480s test_Align_phylip ... ok 480s test_Align_psl ... ok 480s test_Align_sam ... ok 482s test_Align_stockholm ... ok 482s test_Align_tabular ... ok 482s test_Application ... ok 482s test_BioSQL_MySQLdb_online ... skipping. internet not available 482s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 482s test_BioSQL_mysql_connector_online ... skipping. internet not available 482s test_BioSQL_psycopg2_online ... skipping. internet not available 486s test_BioSQL_sqlite3 ... ok 486s test_BioSQL_sqlite3_online ... skipping. internet not available 486s test_Blast_Record ... ok 487s test_Blast_parser ... ok 487s test_CAPS ... ok 487s test_Chi2 ... ok 488s test_ClustalOmega_tool ... ok 488s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 488s test_Cluster ... ok 488s test_CodonTable ... ok 488s test_ColorSpiral ... ok 488s test_Compass ... ok 489s test_Consensus ... ok 490s test_Dialign_tool ... ok 490s test_EMBL_unittest ... ok 494s test_Emboss ... ok 494s test_EmbossPrimer ... ok 499s test_Entrez ... ok 499s test_Entrez_online ... skipping. internet not available 499s test_Entrez_parser ... ok 499s test_Enzyme ... ok 499s test_ExPASy ... skipping. internet not available 499s test_Fasttree_tool ... ok 499s test_File ... ok 499s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 499s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 499s ok 501s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 503s ok 504s test_GraphicsChromosome ... ok 504s test_GraphicsDistribution ... ok 504s test_GraphicsGeneral ... ok 505s test_HMMCasino ... ok 505s test_HMMGeneral ... ok 505s test_KEGG ... ok 505s test_KEGG_online ... skipping. internet not available 509s test_KGML_graphics ... ok 509s test_KGML_graphics_online ... skipping. internet not available 509s test_KGML_nographics ... ok 510s test_KeyWList ... ok 510s test_LogisticRegression ... ok 510s test_MafIO_index ... ok 511s test_Mafft_tool ... ok 512s test_MarkovModel ... ok 512s test_Medline ... ok 512s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 512s test_NCBIXML ... Exception ignored in: 512s Traceback (most recent call last): 512s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 512s expat_parser.Parse(NULL, True) 512s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 512s ok 514s test_NCBI_BLAST_tools ... ok 514s test_NCBI_qblast ... ok 514s test_NMR ... ok 514s test_NaiveBayes ... ok 514s test_Nexus ... ok 515s test_PAML_baseml ... ok 515s test_PAML_codeml ... ok 515s test_PAML_yn00 ... ok 519s test_PDB_CEAligner ... ok 520s test_PDB_DSSP ... ok 521s test_PDB_Dice ... ok 521s test_PDB_Disordered ... ok 521s test_PDB_Exposure ... ok 521s test_PDB_FragmentMapper ... ok 523s test_PDB_KDTree ... ok 523s test_PDB_MMCIF2Dict ... ok 523s test_PDB_MMCIFIO ... ok 524s test_PDB_MMCIFParser ... ok 524s test_PDB_NACCESS ... ok 524s test_PDB_PDBIO ... ok 524s test_PDB_PDBList ... skipping. internet not available 530s test_PDB_PDBMLParser ... ok 530s test_PDB_PDBParser ... ok 530s 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 530s test_PDB_Polypeptide ... ok 530s test_PDB_QCPSuperimposer ... ok 533s test_PDB_SASA ... ok 534s test_PDB_SMCRA ... ok 534s test_PDB_Selection ... ok 534s test_PDB_StructureAlignment ... ok 534s test_PDB_Superimposer ... ok 534s test_PDB_alphafold_db ... skipping. internet not available 536s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 536s warnings.warn( 536s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 536s warnings.warn( 536s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 536s warnings.warn( 536s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 536s warnings.warn( 536s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 536s warnings.warn( 536s ok 543s test_PDB_internal_coords ... ok 543s test_PDB_parse_pdb_header ... ok 544s test_PDB_vectors ... ok 544s test_PQR ... ok 544s test_Pathway ... ok 544s test_Phd ... ok 545s test_Phylo ... ok 545s test_PhyloXML ... ok 546s test_Phylo_CDAO ... ok 546s test_Phylo_NeXML ... ok 547s test_Phylo_igraph ... ok 549s test_Phylo_matplotlib ... ok 550s test_Phylo_networkx ... ok 551s test_PopGen_GenePop_nodepend ... ok 552s test_Prank_tool ... ok 553s test_Probcons_tool ... ok 553s test_ProtParam ... ok 554s test_RCSBFormats ... ok 555s test_Restriction ... ok 555s test_SCOP_Astral ... ok 556s test_SCOP_Cla ... ok 556s test_SCOP_Des ... ok 557s test_SCOP_Dom ... ok 557s test_SCOP_Hie ... ok 558s test_SCOP_Raf ... ok 558s test_SCOP_Residues ... ok 559s test_SCOP_Scop ... ok 559s test_SVDSuperimposer ... ok 560s test_SearchIO_blast_tab ... ok 561s test_SearchIO_blast_tab_index ... ok 561s test_SearchIO_blast_xml ... ok 563s test_SearchIO_blast_xml_index ... ok 563s test_SearchIO_blat_psl ... ok 564s test_SearchIO_blat_psl_index ... ok 565s test_SearchIO_exonerate ... ok 565s test_SearchIO_exonerate_text_index ... ok 566s test_SearchIO_exonerate_vulgar_index ... ok 566s test_SearchIO_fasta_m10 ... ok 567s test_SearchIO_fasta_m10_index ... ok 567s test_SearchIO_hhsuite2_text ... ok 568s test_SearchIO_hmmer2_text ... ok 569s test_SearchIO_hmmer2_text_index ... ok 569s test_SearchIO_hmmer3_domtab ... ok 570s test_SearchIO_hmmer3_domtab_index ... ok 570s test_SearchIO_hmmer3_tab ... ok 571s test_SearchIO_hmmer3_tab_index ... ok 571s test_SearchIO_hmmer3_text ... ok 572s test_SearchIO_hmmer3_text_index ... ok 572s test_SearchIO_interproscan_xml ... ok 573s test_SearchIO_model ... ok 574s test_SearchIO_write ... ok 574s test_SeqFeature ... ok 588s test_SeqIO ... ok 589s test_SeqIO_AbiIO ... ok 589s test_SeqIO_FastaIO ... ok 590s test_SeqIO_Gck ... ok 590s test_SeqIO_Gfa ... ok 591s test_SeqIO_Insdc ... ok 591s test_SeqIO_NibIO ... ok 593s test_SeqIO_PdbIO ... ok 594s test_SeqIO_QualityIO ... ok 595s test_SeqIO_SeqXML ... ok 595s test_SeqIO_SffIO ... ok 596s test_SeqIO_SnapGene ... ok 597s test_SeqIO_TwoBitIO ... ok 598s test_SeqIO_UniprotIO ... ok 598s test_SeqIO_Xdna ... ok 599s test_SeqIO_features ... ok 611s test_SeqIO_index ... ok 612s test_SeqIO_online ... skipping. internet not available 612s test_SeqIO_write ... ok 613s test_SeqRecord ... ok 613s test_SeqUtils ... ok 615s test_Seq_objs ... ok 616s test_SwissProt ... ok 618s test_TCoffee_tool ... ok 619s test_TogoWS ... skipping. internet not available 620s test_TreeConstruction ... ok 620s test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file 621s test_UniGene ... ok 621s test_UniProt ... skipping. internet not available 622s test_UniProt_GOA ... ok 622s test_align ... ok 623s test_align_substitution_matrices ... ok 626s test_bgzf ... ok 626s test_cellosaurus ... ok 632s test_codonalign ... ok 632s test_geo ... ok 633s test_kNN ... ok 634s test_motifs ... ok 634s test_motifs_online ... skipping. internet not available 635s 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. 635s warnings.warn( 635s ok 635s test_pairwise2_no_C ... ok 636s test_pairwise_aligner ... ok 637s test_pairwise_alignment_map ... ok 644s test_phenotype ... ok 644s test_phenotype_fit ... ok 645s 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. 645s test_prodoc ... ok 646s test_prosite ... ok 646s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 647s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 647s test_seq ... ok 648s test_translate ... ok 648s Skipping any tests requiring internet access 648s Python version: 3.13.5 (main, Jun 25 2025, 18:55:22) [GCC 14.3.0] 648s Operating system: posix linux 648s ---------------------------------------------------------------------- 648s Ran 218 tests in 178.494 seconds 648s 650s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 650s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 650s autopkgtest [03:50:57]: test full_suite: -----------------------] 651s full_suite PASS 651s autopkgtest [03:50:58]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 651s autopkgtest [03:50:58]: @@@@@@@@@@@@@@@@@@@@ summary 651s dependencies PASS 651s full_suite PASS