0s autopkgtest [08:14:11]: starting date and time: 2025-05-02 08:14:11+0000 0s autopkgtest [08:14:11]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [08:14:11]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qlmyhs_b/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:setuptools --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/78.1.0-1.2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-8.secgroup --name adt-questing-s390x-python-biopython-20250502-081411-juju-7f2275-prod-proposed-migration-environment-15-121d5a5b-c5d7-42c9-8908-b33fdbdebf66 --image adt/ubuntu-questing-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 108s autopkgtest [08:15:59]: testbed dpkg architecture: s390x 108s autopkgtest [08:15:59]: testbed apt version: 3.0.0 108s autopkgtest [08:15:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 109s autopkgtest [08:16:00]: testbed release detected to be: None 109s autopkgtest [08:16:00]: updating testbed package index (apt update) 110s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 110s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 110s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 110s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 110s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [184 kB] 110s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [57.4 kB] 110s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2202 kB] 110s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main s390x Packages [216 kB] 110s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x Packages [1083 kB] 110s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse s390x Packages [15.9 kB] 111s Fetched 3868 kB in 1s (3135 kB/s) 111s Reading package lists... 112s autopkgtest [08:16:03]: upgrading testbed (apt dist-upgrade and autopurge) 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 112s Starting 2 pkgProblemResolver with broken count: 0 112s Done 113s Entering ResolveByKeep 113s 113s Calculating upgrade... 113s The following packages will be upgraded: 113s python3-pkg-resources python3-setuptools 113s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Need to get 805 kB of archives. 113s After this operation, 108 kB of additional disk space will be used. 113s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main s390x python3-pkg-resources all 78.1.0-1.2 [144 kB] 113s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main s390x python3-setuptools all 78.1.0-1.2 [660 kB] 114s Fetched 805 kB in 1s (1359 kB/s) 114s (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 ... 81472 files and directories currently installed.) 114s Preparing to unpack .../python3-pkg-resources_78.1.0-1.2_all.deb ... 114s Unpacking python3-pkg-resources (78.1.0-1.2) over (75.8.0-1) ... 114s Preparing to unpack .../python3-setuptools_78.1.0-1.2_all.deb ... 114s Unpacking python3-setuptools (78.1.0-1.2) over (75.8.0-1) ... 114s Setting up python3-pkg-resources (78.1.0-1.2) ... 114s Setting up python3-setuptools (78.1.0-1.2) ... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Starting pkgProblemResolver with broken count: 0 116s Starting 2 pkgProblemResolver with broken count: 0 116s Done 116s Solving dependencies... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s autopkgtest [08:16:09]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP Sun Apr 6 13:39:00 UTC 2025 118s autopkgtest [08:16:09]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 122s Get:1 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (dsc) [3406 B] 122s Get:2 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (tar) [14.6 MB] 122s Get:3 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (diff) [42.8 kB] 122s gpgv: Signature made Tue Mar 4 15:18:59 2025 UTC 122s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 122s gpgv: Can't check signature: No public key 122s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2build1.dsc: no acceptable signature found 123s autopkgtest [08:16:14]: testing package python-biopython version 1.85+dfsg-2build1 124s autopkgtest [08:16:15]: build not needed 128s autopkgtest [08:16:19]: test dependencies: preparing testbed 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Starting pkgProblemResolver with broken count: 0 129s Starting 2 pkgProblemResolver with broken count: 0 129s Done 129s The following NEW packages will be installed: 129s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 129s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 129s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 129s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 129s liblapack3 liblcms2-2 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 129s libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 129s libxrender1 python-biopython-doc python3-all python3-biopython 129s python3-biopython-sql python3-cairo python3-freetype python3-numpy 129s python3-numpy-dev python3-pil python3-reportlab python3-rlpycairo sgml-base 129s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 129s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 129s Need to get 47.4 MB of archives. 129s After this operation, 128 MB of additional disk space will be used. 129s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 130s Get:2 http://ftpmaster.internal/ubuntu questing/main s390x libblas3 s390x 3.12.1-2 [252 kB] 130s Get:3 http://ftpmaster.internal/ubuntu questing/main s390x libgfortran5 s390x 15-20250404-0ubuntu1 [621 kB] 130s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 130s Get:5 http://ftpmaster.internal/ubuntu questing/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 130s Get:6 http://ftpmaster.internal/ubuntu questing/main s390x sgml-base all 1.31 [11.4 kB] 130s Get:7 http://ftpmaster.internal/ubuntu questing/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 130s Get:8 http://ftpmaster.internal/ubuntu questing/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 130s Get:9 http://ftpmaster.internal/ubuntu questing/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 130s Get:10 http://ftpmaster.internal/ubuntu questing/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 130s Get:11 http://ftpmaster.internal/ubuntu questing/main s390x x11-common all 1:7.7+23ubuntu4 [21.8 kB] 130s Get:12 http://ftpmaster.internal/ubuntu questing/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 130s Get:13 http://ftpmaster.internal/ubuntu questing/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 130s Get:14 http://ftpmaster.internal/ubuntu questing/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 131s Get:15 http://ftpmaster.internal/ubuntu questing/main s390x fontconfig-config s390x 2.15.0-2.2ubuntu1 [37.9 kB] 131s Get:16 http://ftpmaster.internal/ubuntu questing/main s390x libfontconfig1 s390x 2.15.0-2.2ubuntu1 [150 kB] 131s Get:17 http://ftpmaster.internal/ubuntu questing/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 131s Get:18 http://ftpmaster.internal/ubuntu questing/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 131s Get:19 http://ftpmaster.internal/ubuntu questing/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 131s Get:20 http://ftpmaster.internal/ubuntu questing/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 131s Get:21 http://ftpmaster.internal/ubuntu questing/main s390x libcairo2 s390x 1.18.4-1 [580 kB] 131s Get:22 http://ftpmaster.internal/ubuntu questing/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 131s Get:23 http://ftpmaster.internal/ubuntu questing/main s390x libgomp1 s390x 15-20250404-0ubuntu1 [152 kB] 131s Get:24 http://ftpmaster.internal/ubuntu questing/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 131s Get:25 http://ftpmaster.internal/ubuntu questing/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 131s Get:26 http://ftpmaster.internal/ubuntu questing/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 131s Get:27 http://ftpmaster.internal/ubuntu questing/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 131s Get:28 http://ftpmaster.internal/ubuntu questing/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 131s Get:29 http://ftpmaster.internal/ubuntu questing/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 131s Get:30 http://ftpmaster.internal/ubuntu questing/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 131s Get:31 http://ftpmaster.internal/ubuntu questing/main s390x libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 131s Get:32 http://ftpmaster.internal/ubuntu questing/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 131s Get:33 http://ftpmaster.internal/ubuntu questing/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 131s Get:34 http://ftpmaster.internal/ubuntu questing/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 131s Get:35 http://ftpmaster.internal/ubuntu questing/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 131s Get:36 http://ftpmaster.internal/ubuntu questing/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 131s Get:37 http://ftpmaster.internal/ubuntu questing/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 131s Get:38 http://ftpmaster.internal/ubuntu questing/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 131s Get:39 http://ftpmaster.internal/ubuntu questing/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 131s Get:40 http://ftpmaster.internal/ubuntu questing/universe s390x python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 132s Get:41 http://ftpmaster.internal/ubuntu questing/main s390x python3-all s390x 3.13.3-1 [882 B] 132s Get:42 http://ftpmaster.internal/ubuntu questing/main s390x libopenjp2-7 s390x 2.5.3-2 [207 kB] 132s Get:43 http://ftpmaster.internal/ubuntu questing/main s390x python3-pil s390x 11.1.0-5build1 [498 kB] 132s Get:44 http://ftpmaster.internal/ubuntu questing/main s390x python3-cairo s390x 1.27.0-2 [120 kB] 132s Get:45 http://ftpmaster.internal/ubuntu questing/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 132s Get:46 http://ftpmaster.internal/ubuntu questing/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 132s Get:47 http://ftpmaster.internal/ubuntu questing/universe s390x python3-reportlab all 4.3.1-1 [1137 kB] 132s Get:48 http://ftpmaster.internal/ubuntu questing/main s390x xml-core all 0.19 [20.3 kB] 132s Get:49 http://ftpmaster.internal/ubuntu questing/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 132s Get:50 http://ftpmaster.internal/ubuntu questing/universe s390x python3-biopython s390x 1.85+dfsg-2build1 [1745 kB] 132s Get:51 http://ftpmaster.internal/ubuntu questing/universe s390x python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 132s Fetched 47.4 MB in 3s (17.2 MB/s) 132s Selecting previously unselected package python3-numpy-dev:s390x. 132s (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 ... 81486 files and directories currently installed.) 132s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 132s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 132s Selecting previously unselected package libblas3:s390x. 132s Preparing to unpack .../01-libblas3_3.12.1-2_s390x.deb ... 132s Unpacking libblas3:s390x (3.12.1-2) ... 132s Selecting previously unselected package libgfortran5:s390x. 132s Preparing to unpack .../02-libgfortran5_15-20250404-0ubuntu1_s390x.deb ... 132s Unpacking libgfortran5:s390x (15-20250404-0ubuntu1) ... 132s Selecting previously unselected package liblapack3:s390x. 132s Preparing to unpack .../03-liblapack3_3.12.1-2_s390x.deb ... 132s Unpacking liblapack3:s390x (3.12.1-2) ... 132s Selecting previously unselected package python3-numpy. 132s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 132s Unpacking python3-numpy (1:2.2.3+ds-5) ... 133s Selecting previously unselected package sgml-base. 133s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 133s Unpacking sgml-base (1.31) ... 133s Selecting previously unselected package fonts-dejavu-mono. 133s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 133s Unpacking fonts-dejavu-mono (2.37-8) ... 133s Selecting previously unselected package fonts-dejavu-core. 133s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 133s Unpacking fonts-dejavu-core (2.37-8) ... 133s Selecting previously unselected package libfontenc1:s390x. 133s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 133s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 133s Selecting previously unselected package libfreetype6:s390x. 133s Preparing to unpack .../09-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 133s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 133s Selecting previously unselected package x11-common. 133s Preparing to unpack .../10-x11-common_1%3a7.7+23ubuntu4_all.deb ... 133s Unpacking x11-common (1:7.7+23ubuntu4) ... 133s Selecting previously unselected package xfonts-encodings. 133s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 133s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 133s Selecting previously unselected package xfonts-utils. 133s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7_s390x.deb ... 133s Unpacking xfonts-utils (1:7.7+7) ... 133s Selecting previously unselected package fonts-urw-base35. 133s Preparing to unpack .../13-fonts-urw-base35_20200910-8_all.deb ... 133s Unpacking fonts-urw-base35 (20200910-8) ... 133s Selecting previously unselected package fontconfig-config. 133s Preparing to unpack .../14-fontconfig-config_2.15.0-2.2ubuntu1_s390x.deb ... 133s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 133s Selecting previously unselected package libfontconfig1:s390x. 133s Preparing to unpack .../15-libfontconfig1_2.15.0-2.2ubuntu1_s390x.deb ... 133s Unpacking libfontconfig1:s390x (2.15.0-2.2ubuntu1) ... 133s Selecting previously unselected package libpixman-1-0:s390x. 133s Preparing to unpack .../16-libpixman-1-0_0.44.0-3_s390x.deb ... 133s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 133s Selecting previously unselected package libxcb-render0:s390x. 133s Preparing to unpack .../17-libxcb-render0_1.17.0-2_s390x.deb ... 133s Unpacking libxcb-render0:s390x (1.17.0-2) ... 133s Selecting previously unselected package libxcb-shm0:s390x. 133s Preparing to unpack .../18-libxcb-shm0_1.17.0-2_s390x.deb ... 133s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 133s Selecting previously unselected package libxrender1:s390x. 133s Preparing to unpack .../19-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 133s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 133s Selecting previously unselected package libcairo2:s390x. 133s Preparing to unpack .../20-libcairo2_1.18.4-1_s390x.deb ... 133s Unpacking libcairo2:s390x (1.18.4-1) ... 133s Selecting previously unselected package libdeflate0:s390x. 133s Preparing to unpack .../21-libdeflate0_1.23-1_s390x.deb ... 133s Unpacking libdeflate0:s390x (1.23-1) ... 133s Selecting previously unselected package libgomp1:s390x. 133s Preparing to unpack .../22-libgomp1_15-20250404-0ubuntu1_s390x.deb ... 133s Unpacking libgomp1:s390x (15-20250404-0ubuntu1) ... 133s Selecting previously unselected package libgraphite2-3:s390x. 133s Preparing to unpack .../23-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 133s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 133s Selecting previously unselected package libharfbuzz0b:s390x. 133s Preparing to unpack .../24-libharfbuzz0b_10.2.0-1_s390x.deb ... 133s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 133s Selecting previously unselected package libimagequant0:s390x. 133s Preparing to unpack .../25-libimagequant0_2.18.0-1build1_s390x.deb ... 133s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 133s Selecting previously unselected package libjpeg-turbo8:s390x. 133s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 133s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 133s Selecting previously unselected package libjpeg8:s390x. 133s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_s390x.deb ... 133s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 133s Selecting previously unselected package libjs-jquery. 133s Preparing to unpack .../28-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 133s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 133s Selecting previously unselected package libjs-underscore. 133s Preparing to unpack .../29-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 133s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 133s Selecting previously unselected package libjs-sphinxdoc. 133s Preparing to unpack .../30-libjs-sphinxdoc_8.1.3-5_all.deb ... 133s Unpacking libjs-sphinxdoc (8.1.3-5) ... 133s Selecting previously unselected package liblcms2-2:s390x. 133s Preparing to unpack .../31-liblcms2-2_2.16-2_s390x.deb ... 133s Unpacking liblcms2-2:s390x (2.16-2) ... 133s Selecting previously unselected package libraqm0:s390x. 133s Preparing to unpack .../32-libraqm0_0.10.2-1_s390x.deb ... 133s Unpacking libraqm0:s390x (0.10.2-1) ... 133s Selecting previously unselected package libsharpyuv0:s390x. 133s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1_s390x.deb ... 133s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 133s Selecting previously unselected package libjbig0:s390x. 133s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 133s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 133s Selecting previously unselected package libwebp7:s390x. 133s Preparing to unpack .../35-libwebp7_1.5.0-0.1_s390x.deb ... 133s Unpacking libwebp7:s390x (1.5.0-0.1) ... 133s Selecting previously unselected package libtiff6:s390x. 133s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 133s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 133s Selecting previously unselected package libwebpdemux2:s390x. 133s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_s390x.deb ... 133s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 133s Selecting previously unselected package libwebpmux3:s390x. 133s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_s390x.deb ... 133s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 133s Selecting previously unselected package python-biopython-doc. 133s Preparing to unpack .../39-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 133s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 133s Selecting previously unselected package python3-all. 133s Preparing to unpack .../40-python3-all_3.13.3-1_s390x.deb ... 133s Unpacking python3-all (3.13.3-1) ... 133s Selecting previously unselected package libopenjp2-7:s390x. 133s Preparing to unpack .../41-libopenjp2-7_2.5.3-2_s390x.deb ... 133s Unpacking libopenjp2-7:s390x (2.5.3-2) ... 133s Selecting previously unselected package python3-pil:s390x. 133s Preparing to unpack .../42-python3-pil_11.1.0-5build1_s390x.deb ... 133s Unpacking python3-pil:s390x (11.1.0-5build1) ... 133s Selecting previously unselected package python3-cairo. 133s Preparing to unpack .../43-python3-cairo_1.27.0-2_s390x.deb ... 133s Unpacking python3-cairo (1.27.0-2) ... 133s Selecting previously unselected package python3-freetype. 133s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 133s Unpacking python3-freetype (2.5.1-1) ... 134s Selecting previously unselected package python3-rlpycairo. 134s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 134s Unpacking python3-rlpycairo (0.3.0-3) ... 134s Selecting previously unselected package python3-reportlab. 134s Preparing to unpack .../46-python3-reportlab_4.3.1-1_all.deb ... 134s Unpacking python3-reportlab (4.3.1-1) ... 134s Selecting previously unselected package xml-core. 134s Preparing to unpack .../47-xml-core_0.19_all.deb ... 134s Unpacking xml-core (0.19) ... 134s Selecting previously unselected package w3c-sgml-lib. 134s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 134s Unpacking w3c-sgml-lib (1.3-3) ... 134s Selecting previously unselected package python3-biopython. 134s Preparing to unpack .../49-python3-biopython_1.85+dfsg-2build1_s390x.deb ... 134s Unpacking python3-biopython (1.85+dfsg-2build1) ... 134s Selecting previously unselected package python3-biopython-sql. 134s Preparing to unpack .../50-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 134s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 134s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 134s Setting up liblcms2-2:s390x (2.16-2) ... 134s Setting up libpixman-1-0:s390x (0.44.0-3) ... 134s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 134s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 134s Setting up libxcb-render0:s390x (1.17.0-2) ... 134s Setting up x11-common (1:7.7+23ubuntu4) ... 134s Setting up libdeflate0:s390x (1.23-1) ... 134s Setting up python3-all (3.13.3-1) ... 134s Setting up libxcb-shm0:s390x (1.17.0-2) ... 134s Setting up libgomp1:s390x (15-20250404-0ubuntu1) ... 134s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 134s Setting up libfontenc1:s390x (1:1.1.8-1build1) ... 134s Setting up libblas3:s390x (3.12.1-2) ... 134s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 134s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 134s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 134s Setting up libimagequant0:s390x (2.18.0-1build1) ... 134s Setting up fonts-dejavu-mono (2.37-8) ... 134s Setting up python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 134s Setting up fonts-dejavu-core (2.37-8) ... 134s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 134s Setting up libgfortran5:s390x (15-20250404-0ubuntu1) ... 134s Setting up libwebp7:s390x (1.5.0-0.1) ... 134s Setting up libopenjp2-7:s390x (2.5.3-2) ... 134s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 134s Setting up sgml-base (1.31) ... 134s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 134s Setting up libwebpmux3:s390x (1.5.0-0.1) ... 134s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 134s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 134s Setting up liblapack3:s390x (3.12.1-2) ... 134s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 134s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 134s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 134s Setting up python3-freetype (2.5.1-1) ... 134s Setting up xfonts-utils (1:7.7+7) ... 134s Setting up libraqm0:s390x (0.10.2-1) ... 134s Setting up python3-numpy (1:2.2.3+ds-5) ... 136s Setting up libjs-sphinxdoc (8.1.3-5) ... 136s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 136s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 136s Setting up xml-core (0.19) ... 136s Setting up libfontconfig1:s390x (2.15.0-2.2ubuntu1) ... 136s Setting up fonts-urw-base35 (20200910-8) ... 136s Setting up libcairo2:s390x (1.18.4-1) ... 136s Setting up python3-pil:s390x (11.1.0-5build1) ... 136s Setting up python3-cairo (1.27.0-2) ... 136s Setting up python3-rlpycairo (0.3.0-3) ... 137s Setting up python3-reportlab (4.3.1-1) ... 137s Processing triggers for libc-bin (2.41-6ubuntu1) ... 137s Processing triggers for man-db (2.13.0-1) ... 138s Processing triggers for sgml-base (1.31) ... 138s Setting up w3c-sgml-lib (1.3-3) ... 161s Setting up python3-biopython (1.85+dfsg-2build1) ... 162s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 163s autopkgtest [08:16:54]: test dependencies: sh debian/tests/run-unit-test 163s autopkgtest [08:16:54]: test dependencies: [----------------------- 164s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 164s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 164s mkdir: created directory 'Bio' 164s mkdir: created directory 'Bio/Align' 164s mkdir: created directory 'Bio/Align/substitution_matrices' 164s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 164s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 165s test_Ace ... ok 165s test_Affy ... ok 167s test_AlignIO ... ok 167s test_AlignIO_ClustalIO ... ok 167s test_AlignIO_EmbossIO ... ok 167s test_AlignIO_FastaIO ... ok 167s test_AlignIO_MauveIO ... ok 167s test_AlignIO_PhylipIO ... ok 167s test_AlignIO_convert ... ok 167s test_AlignInfo ... ok 167s test_Align_Alignment ... ok 167s test_Align_a2m ... ok 167s test_Align_bed ... ok 167s test_Align_bigbed ... ok 168s test_Align_bigmaf ... ok 168s test_Align_bigpsl ... ok 168s test_Align_chain ... ok 168s test_Align_clustal ... ok 172s test_Align_codonalign ... ok 172s test_Align_emboss ... ok 172s test_Align_exonerate ... ok 172s test_Align_fasta ... ok 172s test_Align_hhr ... ok 173s test_Align_maf ... ok 173s test_Align_mauve ... ok 173s test_Align_msf ... ok 173s test_Align_nexus ... ok 173s test_Align_phylip ... ok 174s test_Align_psl ... ok 174s test_Align_sam ... ok 175s test_Align_stockholm ... ok 176s test_Align_tabular ... ok 176s test_Application ... ok 176s test_BioSQL_MySQLdb_online ... skipping. internet not available 176s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 176s test_BioSQL_mysql_connector_online ... skipping. internet not available 176s test_BioSQL_psycopg2_online ... skipping. internet not available 179s test_BioSQL_sqlite3 ... ok 179s test_BioSQL_sqlite3_online ... skipping. internet not available 179s test_Blast_Record ... ok 179s test_Blast_parser ... ok 179s test_CAPS ... ok 179s test_Chi2 ... ok 179s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 179s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 179s test_Cluster ... ok 180s test_CodonTable ... ok 180s test_ColorSpiral ... ok 180s test_Compass ... ok 181s test_Consensus ... ok 181s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 181s test_EMBL_unittest ... ok 181s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 181s test_EmbossPrimer ... ok 185s test_Entrez ... ok 185s test_Entrez_online ... skipping. internet not available 185s test_Entrez_parser ... ok 185s test_Enzyme ... ok 185s test_ExPASy ... skipping. internet not available 185s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 185s test_File ... ok 185s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 185s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 186s ok 187s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 189s ok 190s test_GraphicsChromosome ... ok 190s test_GraphicsDistribution ... ok 191s test_GraphicsGeneral ... ok 191s test_HMMCasino ... ok 191s test_HMMGeneral ... ok 191s test_KEGG ... ok 191s test_KEGG_online ... skipping. internet not available 197s test_KGML_graphics ... ok 197s test_KGML_graphics_online ... skipping. internet not available 197s test_KGML_nographics ... ok 197s test_KeyWList ... ok 197s test_LogisticRegression ... ok 198s test_MafIO_index ... ok 198s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 198s test_MarkovModel ... ok 198s test_Medline ... ok 198s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 198s test_NCBIXML ... Exception ignored in: 198s Traceback (most recent call last): 198s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 198s expat_parser.Parse(NULL, True) 198s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 198s ok 199s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 199s test_NCBI_qblast ... ok 199s test_NMR ... ok 199s test_NaiveBayes ... ok 199s test_Nexus ... ok 199s test_PAML_baseml ... ok 200s test_PAML_codeml ... ok 200s test_PAML_yn00 ... ok 204s test_PDB_CEAligner ... ok 204s test_PDB_DSSP ... ok 204s test_PDB_Dice ... ok 204s test_PDB_Disordered ... ok 205s test_PDB_Exposure ... ok 205s test_PDB_FragmentMapper ... ok 206s test_PDB_KDTree ... ok 206s test_PDB_MMCIF2Dict ... ok 207s test_PDB_MMCIFIO ... ok 208s test_PDB_MMCIFParser ... ok 208s test_PDB_NACCESS ... ok 208s test_PDB_PDBIO ... ok 208s test_PDB_PDBList ... skipping. internet not available 218s test_PDB_PDBMLParser ... ok 218s test_PDB_PDBParser ... ok 218s 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 218s test_PDB_Polypeptide ... ok 218s test_PDB_QCPSuperimposer ... ok 222s test_PDB_SASA ... ok 222s test_PDB_SMCRA ... ok 222s test_PDB_Selection ... ok 223s test_PDB_StructureAlignment ... ok 223s test_PDB_Superimposer ... ok 223s test_PDB_alphafold_db ... skipping. internet not available 223s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 223s 223s test_PDB_parse_pdb_header ... ok 223s test_PDB_vectors ... ok 223s test_PQR ... ok 223s test_Pathway ... ok 223s test_Phd ... ok 223s test_Phylo ... ok 224s test_PhyloXML ... ok 224s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 224s test_Phylo_NeXML ... ok 224s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 224s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 224s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 224s test_PopGen_GenePop_nodepend ... ok 224s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 224s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 225s test_ProtParam ... ok 225s test_RCSBFormats ... ok 225s test_Restriction ... ok 225s test_SCOP_Astral ... ok 225s test_SCOP_Cla ... ok 225s test_SCOP_Des ... ok 225s test_SCOP_Dom ... ok 225s test_SCOP_Hie ... ok 225s test_SCOP_Raf ... ok 225s test_SCOP_Residues ... ok 225s test_SCOP_Scop ... ok 226s test_SVDSuperimposer ... ok 226s test_SearchIO_blast_tab ... ok 226s test_SearchIO_blast_tab_index ... ok 226s test_SearchIO_blast_xml ... ok 227s test_SearchIO_blast_xml_index ... ok 228s test_SearchIO_blat_psl ... ok 228s test_SearchIO_blat_psl_index ... ok 228s test_SearchIO_exonerate ... ok 228s test_SearchIO_exonerate_text_index ... ok 228s test_SearchIO_exonerate_vulgar_index ... ok 228s test_SearchIO_fasta_m10 ... ok 228s test_SearchIO_fasta_m10_index ... ok 228s test_SearchIO_hhsuite2_text ... ok 228s test_SearchIO_hmmer2_text ... ok 229s test_SearchIO_hmmer2_text_index ... ok 229s test_SearchIO_hmmer3_domtab ... ok 229s test_SearchIO_hmmer3_domtab_index ... ok 229s test_SearchIO_hmmer3_tab ... ok 229s test_SearchIO_hmmer3_tab_index ... ok 229s test_SearchIO_hmmer3_text ... ok 229s test_SearchIO_hmmer3_text_index ... ok 229s test_SearchIO_interproscan_xml ... ok 229s test_SearchIO_model ... ok 229s test_SearchIO_write ... ok 229s test_SeqFeature ... ok 247s test_SeqIO ... ok 248s test_SeqIO_AbiIO ... ok 248s test_SeqIO_FastaIO ... ok 248s test_SeqIO_Gck ... ok 248s test_SeqIO_Gfa ... ok 248s test_SeqIO_Insdc ... ok 248s test_SeqIO_NibIO ... ok 250s test_SeqIO_PdbIO ... ok 251s test_SeqIO_QualityIO ... ok 251s test_SeqIO_SeqXML ... ok 251s test_SeqIO_SffIO ... ok 251s test_SeqIO_SnapGene ... ok 252s test_SeqIO_TwoBitIO ... ok 252s test_SeqIO_UniprotIO ... ok 252s test_SeqIO_Xdna ... ok 252s test_SeqIO_features ... ok 265s test_SeqIO_index ... ok 265s test_SeqIO_online ... skipping. internet not available 265s test_SeqIO_write ... ok 265s test_SeqRecord ... ok 265s test_SeqUtils ... ok 267s test_Seq_objs ... ok 267s test_SwissProt ... ok 267s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 267s test_TogoWS ... skipping. internet not available 267s test_TreeConstruction ... ok 267s test_UniGene ... ok 267s test_UniProt ... skipping. internet not available 267s test_UniProt_GOA ... ok 267s test_align ... ok 268s test_align_substitution_matrices ... ok 270s test_bgzf ... ok 271s test_cellosaurus ... ok 275s test_codonalign ... ok 275s test_geo ... ok 275s test_kNN ... ok 275s test_motifs ... ok 275s test_motifs_online ... skipping. internet not available 275s 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. 275s warnings.warn( 275s ok 275s test_pairwise2_no_C ... ok 275s test_pairwise_aligner ... ok 275s test_pairwise_alignment_map ... ok 282s test_phenotype ... ok 282s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 282s 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. 282s test_prodoc ... ok 282s test_prosite ... ok 282s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 282s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 282s test_seq ... ok 282s test_translate ... ok 283s Skipping any tests requiring internet access 283s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 283s Operating system: posix linux 283s ---------------------------------------------------------------------- 283s Ran 216 tests in 117.980 seconds 283s 283s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 283s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 283s autopkgtest [08:18:54]: test dependencies: -----------------------] 283s dependencies PASS 283s autopkgtest [08:18:54]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 284s autopkgtest [08:18:55]: test full_suite: preparing testbed 418s autopkgtest [08:21:09]: testbed dpkg architecture: s390x 418s autopkgtest [08:21:09]: testbed apt version: 3.0.0 419s autopkgtest [08:21:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 419s autopkgtest [08:21:10]: testbed release detected to be: questing 420s autopkgtest [08:21:11]: updating testbed package index (apt update) 420s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 420s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 420s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 421s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 421s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2202 kB] 421s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [184 kB] 421s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [57.4 kB] 421s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main s390x Packages [216 kB] 421s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x Packages [1083 kB] 422s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse s390x Packages [15.9 kB] 422s Fetched 3868 kB in 2s (2026 kB/s) 423s Reading package lists... 423s autopkgtest [08:21:14]: upgrading testbed (apt dist-upgrade and autopurge) 423s Reading package lists... 423s Building dependency tree... 423s Reading state information... 424s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 424s Starting 2 pkgProblemResolver with broken count: 0 424s Done 424s Entering ResolveByKeep 424s 424s Calculating upgrade... 424s The following packages will be upgraded: 424s python3-pkg-resources python3-setuptools 424s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 424s Need to get 805 kB of archives. 424s After this operation, 108 kB of additional disk space will be used. 424s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main s390x python3-pkg-resources all 78.1.0-1.2 [144 kB] 425s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main s390x python3-setuptools all 78.1.0-1.2 [660 kB] 425s Fetched 805 kB in 1s (1412 kB/s) 425s (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 ... 81472 files and directories currently installed.) 425s Preparing to unpack .../python3-pkg-resources_78.1.0-1.2_all.deb ... 425s Unpacking python3-pkg-resources (78.1.0-1.2) over (75.8.0-1) ... 425s Preparing to unpack .../python3-setuptools_78.1.0-1.2_all.deb ... 425s Unpacking python3-setuptools (78.1.0-1.2) over (75.8.0-1) ... 425s Setting up python3-pkg-resources (78.1.0-1.2) ... 425s Setting up python3-setuptools (78.1.0-1.2) ... 426s Reading package lists... 426s Building dependency tree... 426s Reading state information... 427s Starting pkgProblemResolver with broken count: 0 427s Starting 2 pkgProblemResolver with broken count: 0 427s Done 427s Solving dependencies... 427s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 430s Reading package lists... 430s Building dependency tree... 430s Reading state information... 430s Starting pkgProblemResolver with broken count: 0 430s Starting 2 pkgProblemResolver with broken count: 0 430s Done 430s The following NEW packages will be installed: 430s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 430s cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit 430s dh-autoreconf dh-python dh-strip-nondeterminism dialign docutils-common dssp 430s dwz fasttree flex fontconfig-config fonts-dejavu-core fonts-dejavu-mono 430s fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ 430s g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 430s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gettext ghostscript hevea 430s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 430s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 430s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 430s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 430s libcolamd3 libcommons-logging-java libcommons-parent-java libcups2t64 430s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 430s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 430s libfreetype6 libgcc-14-dev libgfortran5 libglpk40 libgomp1 libgraphite2-3 430s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 430s libheif-plugin-libde265 libheif1 libice6 libidn12 libigraph3t64 libijs-0.35 430s libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 libjpeg-turbo8 430s libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore 430s libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 liblqr-1-0 430s libltdl7 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 430s libmbedtls21 libmbedx509-7 libmpc3 libmpfi0 libmysqlclient24 libnetpbm11t64 430s libopenjp2-7 libpaper-utils libpaper2 libpdfbox-java libpixman-1-0 libplfit0 430s libpotrace0 libptexenc1 libpython3-all-dev libpython3-dev libpython3.13-dev 430s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 430s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 430s libtiff6 libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2 libwebpmux3 430s libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 430s libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft 430s mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data 430s prank preview-latex-style probcons python-biopython-doc 430s python-matplotlib-data python3-alabaster python3-all python3-all-dev 430s python3-biopython python3-biopython-sql python3-brotli python3-cairo 430s python3-contourpy python3-cycler python3-dateutil python3-decorator 430s python3-defusedxml python3-dev python3-docutils python3-fonttools 430s python3-freetype python3-fs python3-igraph python3-imagesize 430s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 430s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 430s python3-numpy python3-numpy-dev python3-numpydoc python3-packaging 430s python3-pil python3-pil.imagetk python3-platformdirs python3-rdflib 430s python3-reportlab python3-rlpycairo python3-roman python3-scipy 430s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 430s python3-sphinxcontrib.jquery python3-sympy python3-tabulate 430s python3-texttable python3-tk python3-ufolib2 python3.13-dev python3.13-tk 430s sgml-base sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 430s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 430s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 430s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 430s xfonts-encodings xfonts-utils xml-core zlib1g-dev 430s 0 upgraded, 249 newly installed, 0 to remove and 0 not upgraded. 430s Need to get 335 MB of archives. 430s After this operation, 1230 MB of additional disk space will be used. 430s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x m4 s390x 1.4.19-7 [259 kB] 431s Get:2 http://ftpmaster.internal/ubuntu questing/main s390x flex s390x 2.6.4-8.2build1 [311 kB] 431s Get:3 http://ftpmaster.internal/ubuntu questing/main s390x fonts-lato all 2.015-1 [2781 kB] 432s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x libgomp1 s390x 15-20250404-0ubuntu1 [152 kB] 433s Get:5 http://ftpmaster.internal/ubuntu questing/main s390x libfftw3-double3 s390x 3.3.10-2fakesync1build1 [511 kB] 433s Get:6 http://ftpmaster.internal/ubuntu questing/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 433s Get:7 http://ftpmaster.internal/ubuntu questing/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 433s Get:8 http://ftpmaster.internal/ubuntu questing/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 433s Get:9 http://ftpmaster.internal/ubuntu questing/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 433s Get:10 http://ftpmaster.internal/ubuntu questing/main s390x x11-common all 1:7.7+23ubuntu4 [21.8 kB] 433s Get:11 http://ftpmaster.internal/ubuntu questing/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 433s Get:12 http://ftpmaster.internal/ubuntu questing/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 433s Get:13 http://ftpmaster.internal/ubuntu questing/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 435s Get:14 http://ftpmaster.internal/ubuntu questing/main s390x fontconfig-config s390x 2.15.0-2.2ubuntu1 [37.9 kB] 435s Get:15 http://ftpmaster.internal/ubuntu questing/main s390x libfontconfig1 s390x 2.15.0-2.2ubuntu1 [150 kB] 435s Get:16 http://ftpmaster.internal/ubuntu questing/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 435s Get:17 http://ftpmaster.internal/ubuntu questing/main s390x libaom3 s390x 3.12.0-1 [1492 kB] 435s Get:18 http://ftpmaster.internal/ubuntu questing/main s390x libheif-plugin-aomdec s390x 1.19.7-1 [11.6 kB] 435s Get:19 http://ftpmaster.internal/ubuntu questing/main s390x libde265-0 s390x 1.0.15-1build5 [175 kB] 435s Get:20 http://ftpmaster.internal/ubuntu questing/main s390x libheif-plugin-libde265 s390x 1.19.7-1 [9054 B] 435s Get:21 http://ftpmaster.internal/ubuntu questing/main s390x libheif1 s390x 1.19.7-1 [415 kB] 435s Get:22 http://ftpmaster.internal/ubuntu questing/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 435s Get:23 http://ftpmaster.internal/ubuntu questing/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 435s Get:24 http://ftpmaster.internal/ubuntu questing/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 435s Get:25 http://ftpmaster.internal/ubuntu questing/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 435s Get:26 http://ftpmaster.internal/ubuntu questing/universe s390x liblqr-1-0 s390x 0.4.2-2.1build2 [32.6 kB] 435s Get:27 http://ftpmaster.internal/ubuntu questing/main s390x libltdl7 s390x 2.5.4-4 [43.8 kB] 435s Get:28 http://ftpmaster.internal/ubuntu questing/main s390x libopenjp2-7 s390x 2.5.3-2 [207 kB] 435s Get:29 http://ftpmaster.internal/ubuntu questing/main s390x libraw23t64 s390x 0.21.3-1 [415 kB] 435s Get:30 http://ftpmaster.internal/ubuntu questing/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 435s Get:31 http://ftpmaster.internal/ubuntu questing/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 435s Get:32 http://ftpmaster.internal/ubuntu questing/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 435s Get:33 http://ftpmaster.internal/ubuntu questing/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 435s Get:34 http://ftpmaster.internal/ubuntu questing/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 435s Get:35 http://ftpmaster.internal/ubuntu questing/universe s390x imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 435s Get:36 http://ftpmaster.internal/ubuntu questing/universe s390x libmagickcore-7.q16-10 s390x 8:7.1.1.43+dfsg1-1 [2040 kB] 435s Get:37 http://ftpmaster.internal/ubuntu questing/universe s390x libmagickwand-7.q16-10 s390x 8:7.1.1.43+dfsg1-1 [375 kB] 435s Get:38 http://ftpmaster.internal/ubuntu questing/main s390x poppler-data all 0.4.12-1 [2060 kB] 435s Get:39 http://ftpmaster.internal/ubuntu questing/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 435s Get:40 http://ftpmaster.internal/ubuntu questing/main s390x libblas3 s390x 3.12.1-2 [252 kB] 435s Get:41 http://ftpmaster.internal/ubuntu questing/main s390x libgfortran5 s390x 15-20250404-0ubuntu1 [621 kB] 435s Get:42 http://ftpmaster.internal/ubuntu questing/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 435s Get:43 http://ftpmaster.internal/ubuntu questing/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 436s Get:44 http://ftpmaster.internal/ubuntu questing/main s390x sgml-base all 1.31 [11.4 kB] 436s Get:45 http://ftpmaster.internal/ubuntu questing/main s390x autoconf all 2.72-3ubuntu1 [383 kB] 436s Get:46 http://ftpmaster.internal/ubuntu questing/main s390x autotools-dev all 20220109.1 [44.9 kB] 436s Get:47 http://ftpmaster.internal/ubuntu questing/main s390x automake all 1:1.17-3ubuntu1 [572 kB] 436s Get:48 http://ftpmaster.internal/ubuntu questing/main s390x autopoint all 0.23.1-1 [619 kB] 436s Get:49 http://ftpmaster.internal/ubuntu questing/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 436s Get:50 http://ftpmaster.internal/ubuntu questing/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 436s Get:51 http://ftpmaster.internal/ubuntu questing/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 436s Get:52 http://ftpmaster.internal/ubuntu questing/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 436s Get:53 http://ftpmaster.internal/ubuntu questing/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 436s Get:54 http://ftpmaster.internal/ubuntu questing/main s390x tk8.6-blt2.5 s390x 2.5.3+dfsg-8 [657 kB] 436s Get:55 http://ftpmaster.internal/ubuntu questing/main s390x blt s390x 2.5.3+dfsg-8 [4826 B] 436s Get:56 http://ftpmaster.internal/ubuntu questing/main s390x libisl23 s390x 0.27-1 [704 kB] 436s Get:57 http://ftpmaster.internal/ubuntu questing/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 436s Get:58 http://ftpmaster.internal/ubuntu questing/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-19ubuntu2 [9572 kB] 436s Get:59 http://ftpmaster.internal/ubuntu questing/main s390x cpp-14 s390x 14.2.0-19ubuntu2 [1024 B] 436s Get:60 http://ftpmaster.internal/ubuntu questing/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 436s Get:61 http://ftpmaster.internal/ubuntu questing/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 436s Get:62 http://ftpmaster.internal/ubuntu questing/main s390x libcc1-0 s390x 15-20250404-0ubuntu1 [49.6 kB] 436s Get:63 http://ftpmaster.internal/ubuntu questing/main s390x libitm1 s390x 15-20250404-0ubuntu1 [31.2 kB] 436s Get:64 http://ftpmaster.internal/ubuntu questing/main s390x libasan8 s390x 15-20250404-0ubuntu1 [2966 kB] 436s Get:65 http://ftpmaster.internal/ubuntu questing/main s390x libubsan1 s390x 15-20250404-0ubuntu1 [1210 kB] 436s Get:66 http://ftpmaster.internal/ubuntu questing/main s390x libgcc-14-dev s390x 14.2.0-19ubuntu2 [1037 kB] 436s Get:67 http://ftpmaster.internal/ubuntu questing/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-19ubuntu2 [18.7 MB] 437s Get:68 http://ftpmaster.internal/ubuntu questing/main s390x gcc-14 s390x 14.2.0-19ubuntu2 [529 kB] 437s Get:69 http://ftpmaster.internal/ubuntu questing/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 437s Get:70 http://ftpmaster.internal/ubuntu questing/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 437s Get:71 http://ftpmaster.internal/ubuntu questing/main s390x libstdc++-14-dev s390x 14.2.0-19ubuntu2 [2614 kB] 437s Get:72 http://ftpmaster.internal/ubuntu questing/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-19ubuntu2 [11.0 MB] 437s Get:73 http://ftpmaster.internal/ubuntu questing/main s390x g++-14 s390x 14.2.0-19ubuntu2 [23.0 kB] 437s Get:74 http://ftpmaster.internal/ubuntu questing/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 437s Get:75 http://ftpmaster.internal/ubuntu questing/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 437s Get:76 http://ftpmaster.internal/ubuntu questing/main s390x build-essential s390x 12.12ubuntu1 [5090 B] 437s Get:77 http://ftpmaster.internal/ubuntu questing/universe s390x bwa s390x 0.7.18-1 [249 kB] 437s Get:78 http://ftpmaster.internal/ubuntu questing/universe s390x libargtable2-0 s390x 13-3 [16.9 kB] 437s Get:79 http://ftpmaster.internal/ubuntu questing/universe s390x clustalo s390x 1.2.4-8build1 [218 kB] 437s Get:80 http://ftpmaster.internal/ubuntu questing/main s390x libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 437s Get:81 http://ftpmaster.internal/ubuntu questing/main s390x libtool all 2.5.4-4 [168 kB] 437s Get:82 http://ftpmaster.internal/ubuntu questing/main s390x dh-autoreconf all 20 [16.1 kB] 437s Get:83 http://ftpmaster.internal/ubuntu questing/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 437s Get:84 http://ftpmaster.internal/ubuntu questing/main s390x libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 437s Get:85 http://ftpmaster.internal/ubuntu questing/main s390x dh-strip-nondeterminism all 1.14.1-2 [5064 B] 437s Get:86 http://ftpmaster.internal/ubuntu questing/main s390x debugedit s390x 1:5.1-2 [50.1 kB] 437s Get:87 http://ftpmaster.internal/ubuntu questing/main s390x dwz s390x 0.15-1build6 [122 kB] 437s Get:88 http://ftpmaster.internal/ubuntu questing/main s390x gettext s390x 0.23.1-1 [1065 kB] 437s Get:89 http://ftpmaster.internal/ubuntu questing/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] 437s Get:90 http://ftpmaster.internal/ubuntu questing/main s390x po-debconf all 1.0.21+nmu1 [233 kB] 437s Get:91 http://ftpmaster.internal/ubuntu questing/main s390x debhelper all 13.24.1ubuntu2 [895 kB] 437s Get:92 http://ftpmaster.internal/ubuntu questing/universe s390x dh-python all 6.20250308 [118 kB] 437s Get:93 http://ftpmaster.internal/ubuntu questing/universe s390x dialign s390x 2.2.1-13 [155 kB] 437s Get:94 http://ftpmaster.internal/ubuntu questing/main s390x xml-core all 0.19 [20.3 kB] 437s Get:95 http://ftpmaster.internal/ubuntu questing/main s390x docutils-common all 0.21.2+dfsg-2 [131 kB] 437s Get:96 http://ftpmaster.internal/ubuntu questing/universe s390x libcifpp-data all 7.0.9-1 [481 kB] 437s Get:97 http://ftpmaster.internal/ubuntu questing/universe s390x libcifpp7 s390x 7.0.9-1 [1103 kB] 437s Get:98 http://ftpmaster.internal/ubuntu questing/universe s390x dssp s390x 4.4.10-1 [784 kB] 437s Get:99 http://ftpmaster.internal/ubuntu questing/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 437s Get:100 http://ftpmaster.internal/ubuntu questing/universe s390x fonts-lmodern all 2.005-1 [4799 kB] 437s Get:101 http://ftpmaster.internal/ubuntu questing/universe s390x fonts-lyx all 2.4.3-1 [171 kB] 438s Get:102 http://ftpmaster.internal/ubuntu questing/main s390x libgs-common all 10.05.0dfsg1-0ubuntu1 [176 kB] 438s Get:103 http://ftpmaster.internal/ubuntu questing/main s390x libgs10-common all 10.05.0dfsg1-0ubuntu1 [490 kB] 438s Get:104 http://ftpmaster.internal/ubuntu questing/main s390x libavahi-common-data s390x 0.8-16ubuntu2 [31.0 kB] 438s Get:105 http://ftpmaster.internal/ubuntu questing/main s390x libavahi-common3 s390x 0.8-16ubuntu2 [23.5 kB] 438s Get:106 http://ftpmaster.internal/ubuntu questing/main s390x libavahi-client3 s390x 0.8-16ubuntu2 [26.3 kB] 438s Get:107 http://ftpmaster.internal/ubuntu questing/main s390x libcups2t64 s390x 2.4.12-0ubuntu1 [282 kB] 438s Get:108 http://ftpmaster.internal/ubuntu questing/main s390x libidn12 s390x 1.43-1 [58.9 kB] 438s Get:109 http://ftpmaster.internal/ubuntu questing/main s390x libijs-0.35 s390x 0.35-15.2 [15.4 kB] 438s Get:110 http://ftpmaster.internal/ubuntu questing/main s390x libjbig2dec0 s390x 0.20-1build3 [69.3 kB] 438s Get:111 http://ftpmaster.internal/ubuntu questing/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 438s Get:112 http://ftpmaster.internal/ubuntu questing/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 438s Get:113 http://ftpmaster.internal/ubuntu questing/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 438s Get:114 http://ftpmaster.internal/ubuntu questing/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 438s Get:115 http://ftpmaster.internal/ubuntu questing/main s390x libgs10 s390x 10.05.0dfsg1-0ubuntu1 [3974 kB] 438s Get:116 http://ftpmaster.internal/ubuntu questing/main s390x ghostscript s390x 10.05.0dfsg1-0ubuntu1 [42.8 kB] 438s Get:117 http://ftpmaster.internal/ubuntu questing/universe s390x libnetpbm11t64 s390x 2:11.09.02-2 [124 kB] 438s Get:118 http://ftpmaster.internal/ubuntu questing/universe s390x netpbm s390x 2:11.09.02-2 [2207 kB] 438s Get:119 http://ftpmaster.internal/ubuntu questing/universe s390x tex-common all 6.19 [29.8 kB] 438s Get:120 http://ftpmaster.internal/ubuntu questing/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 438s Get:121 http://ftpmaster.internal/ubuntu questing/universe s390x libkpathsea6 s390x 2024.20240313.70630+ds-6 [67.0 kB] 438s Get:122 http://ftpmaster.internal/ubuntu questing/universe s390x libptexenc1 s390x 2024.20240313.70630+ds-6 [43.4 kB] 438s Get:123 http://ftpmaster.internal/ubuntu questing/universe s390x libsynctex2 s390x 2024.20240313.70630+ds-6 [64.8 kB] 438s Get:124 http://ftpmaster.internal/ubuntu questing/universe s390x libtexlua53-5 s390x 2024.20240313.70630+ds-6 [131 kB] 438s Get:125 http://ftpmaster.internal/ubuntu questing/main s390x t1utils s390x 1.41-4build3 [65.6 kB] 438s Get:126 http://ftpmaster.internal/ubuntu questing/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 438s Get:127 http://ftpmaster.internal/ubuntu questing/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 439s Get:128 http://ftpmaster.internal/ubuntu questing/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 439s Get:129 http://ftpmaster.internal/ubuntu questing/main s390x libcairo2 s390x 1.18.4-1 [580 kB] 439s Get:130 http://ftpmaster.internal/ubuntu questing/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 439s Get:131 http://ftpmaster.internal/ubuntu questing/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 439s Get:132 http://ftpmaster.internal/ubuntu questing/universe s390x libmpfi0 s390x 1.5.4+ds-4 [34.1 kB] 439s Get:133 http://ftpmaster.internal/ubuntu questing/universe s390x libpotrace0 s390x 1.16-2build1 [18.7 kB] 439s Get:134 http://ftpmaster.internal/ubuntu questing/universe s390x libteckit0 s390x 2.5.12+ds1-1 [433 kB] 439s Get:135 http://ftpmaster.internal/ubuntu questing/main s390x libxmu6 s390x 2:1.1.3-3build2 [53.0 kB] 439s Get:136 http://ftpmaster.internal/ubuntu questing/main s390x libxpm4 s390x 1:3.5.17-1build2 [41.2 kB] 439s Get:137 http://ftpmaster.internal/ubuntu questing/main s390x libxaw7 s390x 2:1.0.16-1 [201 kB] 439s Get:138 http://ftpmaster.internal/ubuntu questing/main s390x libxi6 s390x 2:1.8.2-1 [35.4 kB] 439s Get:139 http://ftpmaster.internal/ubuntu questing/universe s390x libzzip-0-13t64 s390x 0.13.78+dfsg.1-0.1 [29.8 kB] 439s Get:140 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-binaries s390x 2024.20240313.70630+ds-6 [9170 kB] 439s Get:141 http://ftpmaster.internal/ubuntu questing/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 439s Get:142 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-base all 2024.20250309-1 [22.7 MB] 440s Get:143 http://ftpmaster.internal/ubuntu questing/main s390x hicolor-icon-theme all 0.18-2 [13.3 kB] 440s Get:144 http://ftpmaster.internal/ubuntu questing/universe s390x imagemagick-7.q16 s390x 8:7.1.1.43+dfsg1-1 [703 kB] 440s Get:145 http://ftpmaster.internal/ubuntu questing/universe s390x imagemagick s390x 8:7.1.1.43+dfsg1-1 [14.1 kB] 440s Get:146 http://ftpmaster.internal/ubuntu questing/universe s390x hevea s390x 2.36-2 [2045 kB] 440s Get:147 http://ftpmaster.internal/ubuntu questing/main s390x libsuitesparseconfig7 s390x 1:7.8.3+dfsg-3 [13.2 kB] 440s Get:148 http://ftpmaster.internal/ubuntu questing/universe s390x libamd3 s390x 1:7.8.3+dfsg-3 [35.1 kB] 440s Get:149 http://ftpmaster.internal/ubuntu questing/universe s390x libapache-pom-java all 33-2 [5874 B] 440s Get:150 http://ftpmaster.internal/ubuntu questing/universe s390x libarpack2t64 s390x 3.9.1-4 [110 kB] 440s Get:151 http://ftpmaster.internal/ubuntu questing/main s390x libcolamd3 s390x 1:7.8.3+dfsg-3 [23.4 kB] 440s Get:152 http://ftpmaster.internal/ubuntu questing/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 440s Get:153 http://ftpmaster.internal/ubuntu questing/universe s390x libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 440s Get:154 http://ftpmaster.internal/ubuntu questing/main s390x libexpat1-dev s390x 2.7.1-1 [148 kB] 440s Get:155 http://ftpmaster.internal/ubuntu questing/universe s390x libglpk40 s390x 5.0-1build2 [406 kB] 440s Get:156 http://ftpmaster.internal/ubuntu questing/universe s390x libplfit0 s390x 0.9.6+ds-2ubuntu1 [29.7 kB] 440s Get:157 http://ftpmaster.internal/ubuntu questing/universe s390x libigraph3t64 s390x 0.10.15+ds-3 [1015 kB] 440s Get:158 http://ftpmaster.internal/ubuntu questing/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 440s Get:159 http://ftpmaster.internal/ubuntu questing/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 440s Get:160 http://ftpmaster.internal/ubuntu questing/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 440s Get:161 http://ftpmaster.internal/ubuntu questing/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 440s Get:162 http://ftpmaster.internal/ubuntu questing/main s390x libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 440s Get:163 http://ftpmaster.internal/ubuntu questing/main s390x libjson-perl all 4.10000-1 [81.9 kB] 440s Get:164 http://ftpmaster.internal/ubuntu questing/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 440s Get:165 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedcrypto16 s390x 3.6.2-3ubuntu1 [261 kB] 440s Get:166 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedx509-7 s390x 3.6.2-3ubuntu1 [34.9 kB] 440s Get:167 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedtls21 s390x 3.6.2-3ubuntu1 [122 kB] 440s Get:168 http://ftpmaster.internal/ubuntu questing/main s390x mysql-common all 5.8+1.1.1ubuntu1 [6922 B] 441s Get:169 http://ftpmaster.internal/ubuntu questing/main s390x libmysqlclient24 s390x 8.4.4-0ubuntu2 [1295 kB] 441s Get:170 http://ftpmaster.internal/ubuntu questing/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 441s Get:171 http://ftpmaster.internal/ubuntu questing/main s390x libpython3.13-dev s390x 3.13.3-1 [5607 kB] 441s Get:172 http://ftpmaster.internal/ubuntu questing/main s390x libpython3-dev s390x 3.13.3-1 [10.8 kB] 441s Get:173 http://ftpmaster.internal/ubuntu questing/main s390x libpython3-all-dev s390x 3.13.3-1 [906 B] 441s Get:174 http://ftpmaster.internal/ubuntu questing/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 441s Get:175 http://ftpmaster.internal/ubuntu questing/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 441s Get:176 http://ftpmaster.internal/ubuntu questing/main s390x libxslt1.1 s390x 1.1.39-0exp1ubuntu4 [170 kB] 441s Get:177 http://ftpmaster.internal/ubuntu questing/universe s390x mafft s390x 7.505-1 [766 kB] 441s Get:178 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 441s Get:179 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-blast+ s390x 2.16.0+ds-6build1 [15.2 MB] 442s Get:180 http://ftpmaster.internal/ubuntu questing/universe s390x phylip s390x 1:3.697+dfsg-4build1 [1051 kB] 442s Get:181 http://ftpmaster.internal/ubuntu questing/universe s390x prank s390x 0.0.170427+dfsg-3 [357 kB] 442s Get:182 http://ftpmaster.internal/ubuntu questing/universe s390x preview-latex-style all 13.2-1 [347 kB] 442s Get:183 http://ftpmaster.internal/ubuntu questing/universe s390x probcons s390x 1.12-14 [109 kB] 442s Get:184 http://ftpmaster.internal/ubuntu questing/universe s390x python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 443s Get:185 http://ftpmaster.internal/ubuntu questing/universe s390x python-matplotlib-data all 3.8.3-7build1 [2934 kB] 443s Get:186 http://ftpmaster.internal/ubuntu questing/main s390x python3-all s390x 3.13.3-1 [882 B] 443s Get:187 http://ftpmaster.internal/ubuntu questing/main s390x python3.13-dev s390x 3.13.3-1 [508 kB] 443s Get:188 http://ftpmaster.internal/ubuntu questing/main s390x python3-dev s390x 3.13.3-1 [26.7 kB] 443s Get:189 http://ftpmaster.internal/ubuntu questing/main s390x python3-all-dev s390x 3.13.3-1 [904 B] 443s Get:190 http://ftpmaster.internal/ubuntu questing/main s390x python3.13-tk s390x 3.13.3-1 [108 kB] 443s Get:191 http://ftpmaster.internal/ubuntu questing/main s390x python3-tk s390x 3.13.3-1 [9854 B] 443s Get:192 http://ftpmaster.internal/ubuntu questing/universe s390x python3-pil.imagetk s390x 11.1.0-5build1 [9668 B] 443s Get:193 http://ftpmaster.internal/ubuntu questing/main s390x python3-pil s390x 11.1.0-5build1 [498 kB] 443s Get:194 http://ftpmaster.internal/ubuntu questing/main s390x python3-cairo s390x 1.27.0-2 [120 kB] 443s Get:195 http://ftpmaster.internal/ubuntu questing/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 443s Get:196 http://ftpmaster.internal/ubuntu questing/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 443s Get:197 http://ftpmaster.internal/ubuntu questing/universe s390x python3-reportlab all 4.3.1-1 [1137 kB] 443s Get:198 http://ftpmaster.internal/ubuntu questing/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 443s Get:199 http://ftpmaster.internal/ubuntu questing/universe s390x python3-biopython s390x 1.85+dfsg-2build1 [1745 kB] 443s Get:200 http://ftpmaster.internal/ubuntu questing/universe s390x python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 443s Get:201 http://ftpmaster.internal/ubuntu questing/universe s390x python3-brotli s390x 1.1.0-2build4 [380 kB] 443s Get:202 http://ftpmaster.internal/ubuntu questing/universe s390x python3-contourpy s390x 1.3.1-1build1 [197 kB] 444s Get:203 http://ftpmaster.internal/ubuntu questing/universe s390x python3-cycler all 0.12.1-1 [9716 B] 444s Get:204 http://ftpmaster.internal/ubuntu questing/main s390x python3-dateutil all 2.9.0-4 [80.3 kB] 444s Get:205 http://ftpmaster.internal/ubuntu questing/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 444s Get:206 http://ftpmaster.internal/ubuntu questing/main s390x python3-defusedxml all 0.7.1-3 [42.2 kB] 444s Get:207 http://ftpmaster.internal/ubuntu questing/main s390x python3-roman all 5.0-1 [10.3 kB] 444s Get:208 http://ftpmaster.internal/ubuntu questing/main s390x python3-docutils all 0.21.2+dfsg-2 [409 kB] 444s Get:209 http://ftpmaster.internal/ubuntu questing/main s390x python3-platformdirs all 4.3.6-1 [16.8 kB] 444s Get:210 http://ftpmaster.internal/ubuntu questing/universe s390x python3-fs all 2.4.16-7 [90.8 kB] 444s Get:211 http://ftpmaster.internal/ubuntu questing/main s390x python3-lxml s390x 5.3.2-1 [1370 kB] 444s Get:212 http://ftpmaster.internal/ubuntu questing/universe s390x python3-lz4 s390x 4.4.0+dfsg-1build1 [26.6 kB] 444s Get:213 http://ftpmaster.internal/ubuntu questing/universe s390x python3-scipy s390x 1.14.1-4ubuntu2 [18.0 MB] 445s Get:214 http://ftpmaster.internal/ubuntu questing/universe s390x python3-mpmath all 1.3.0-1 [425 kB] 446s Get:215 http://ftpmaster.internal/ubuntu questing/universe s390x python3-sympy all 1.13.3-5 [4229 kB] 446s Get:216 http://ftpmaster.internal/ubuntu questing/universe s390x python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 446s Get:217 http://ftpmaster.internal/ubuntu questing/universe s390x unicode-data all 15.1.0-1 [8878 kB] 446s Get:218 http://ftpmaster.internal/ubuntu questing/universe s390x python3-fonttools s390x 4.55.3-2build1 [1496 kB] 446s Get:219 http://ftpmaster.internal/ubuntu questing/main s390x python3-imagesize all 1.4.1-1 [6844 B] 446s Get:220 http://ftpmaster.internal/ubuntu questing/universe s390x python3-kiwisolver s390x 1.4.7-3build1 [55.0 kB] 446s Get:221 http://ftpmaster.internal/ubuntu questing/main s390x python3-packaging all 24.2-1 [51.5 kB] 446s Get:222 http://ftpmaster.internal/ubuntu questing/universe s390x python3-matplotlib s390x 3.8.3-7build1 [17.3 MB] 446s Get:223 http://ftpmaster.internal/ubuntu questing/main s390x python3-msgpack s390x 1.0.3-3build4 [87.7 kB] 446s Get:224 http://ftpmaster.internal/ubuntu questing/universe s390x python3-mmtf all 1.1.3-1 [16.2 kB] 446s Get:225 http://ftpmaster.internal/ubuntu questing/main s390x python3-mysqldb s390x 1.4.6-2build6 [48.4 kB] 446s Get:226 http://ftpmaster.internal/ubuntu questing/main s390x python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 446s Get:227 http://ftpmaster.internal/ubuntu questing/main s390x sphinx-common all 8.1.3-5 [663 kB] 446s Get:228 http://ftpmaster.internal/ubuntu questing/main s390x python3-alabaster all 0.7.16-0.1 [18.5 kB] 446s Get:229 http://ftpmaster.internal/ubuntu questing/main s390x python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 446s Get:230 http://ftpmaster.internal/ubuntu questing/main s390x python3-sphinx all 8.1.3-5 [474 kB] 446s Get:231 http://ftpmaster.internal/ubuntu questing/main s390x python3-tabulate all 0.9.0-1 [45.3 kB] 446s Get:232 http://ftpmaster.internal/ubuntu questing/universe s390x python3-numpydoc all 1.8.0-1 [52.4 kB] 446s Get:233 http://ftpmaster.internal/ubuntu questing/universe s390x python3-rdflib all 7.1.1-2 [426 kB] 446s Get:234 http://ftpmaster.internal/ubuntu questing/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 446s Get:235 http://ftpmaster.internal/ubuntu questing/universe s390x python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 446s Get:236 http://ftpmaster.internal/ubuntu questing/universe s390x python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 446s Get:237 http://ftpmaster.internal/ubuntu questing/universe s390x python3-texttable all 1.7.0-1 [11.2 kB] 446s Get:238 http://ftpmaster.internal/ubuntu questing/universe s390x t-coffee s390x 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [945 kB] 446s Get:239 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-fonts-recommended all 2024.20250309-1 [4974 kB] 446s Get:240 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-latex-base all 2024.20250309-1 [1276 kB] 446s Get:241 http://ftpmaster.internal/ubuntu questing/universe s390x libfontbox-java all 1:1.8.16-5 [208 kB] 446s Get:242 http://ftpmaster.internal/ubuntu questing/universe s390x libpdfbox-java all 1:1.8.16-5 [5521 kB] 446s Get:243 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-latex-recommended all 2024.20250309-1 [8727 kB] 447s Get:244 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-pictures all 2024.20250309-1 [17.0 MB] 447s Get:245 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-latex-extra all 2024.20250309-2 [24.8 MB] 448s Get:246 http://ftpmaster.internal/ubuntu questing/universe s390x wise-data all 2.4.1-25 [83.0 kB] 448s Get:247 http://ftpmaster.internal/ubuntu questing/universe s390x wise s390x 2.4.1-25 [935 kB] 448s Get:248 http://ftpmaster.internal/ubuntu questing/universe s390x fasttree s390x 2.1.11-2 [190 kB] 448s Get:249 http://ftpmaster.internal/ubuntu questing/universe s390x python3-igraph s390x 0.11.8+ds-1build1 [340 kB] 448s Preconfiguring packages ... 448s Fetched 335 MB in 18s (19.0 MB/s) 448s Selecting previously unselected package m4. 448s (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 ... 81486 files and directories currently installed.) 448s Preparing to unpack .../000-m4_1.4.19-7_s390x.deb ... 448s Unpacking m4 (1.4.19-7) ... 448s Selecting previously unselected package flex. 448s Preparing to unpack .../001-flex_2.6.4-8.2build1_s390x.deb ... 448s Unpacking flex (2.6.4-8.2build1) ... 448s Selecting previously unselected package fonts-lato. 448s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 449s Unpacking fonts-lato (2.015-1) ... 449s Selecting previously unselected package libgomp1:s390x. 449s Preparing to unpack .../003-libgomp1_15-20250404-0ubuntu1_s390x.deb ... 449s Unpacking libgomp1:s390x (15-20250404-0ubuntu1) ... 449s Selecting previously unselected package libfftw3-double3:s390x. 449s Preparing to unpack .../004-libfftw3-double3_3.3.10-2fakesync1build1_s390x.deb ... 449s Unpacking libfftw3-double3:s390x (3.3.10-2fakesync1build1) ... 449s Selecting previously unselected package libfreetype6:s390x. 449s Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 449s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 449s Selecting previously unselected package fonts-dejavu-mono. 449s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 449s Unpacking fonts-dejavu-mono (2.37-8) ... 449s Selecting previously unselected package fonts-dejavu-core. 449s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 449s Unpacking fonts-dejavu-core (2.37-8) ... 449s Selecting previously unselected package libfontenc1:s390x. 449s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 449s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 449s Selecting previously unselected package x11-common. 449s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu4_all.deb ... 449s Unpacking x11-common (1:7.7+23ubuntu4) ... 449s Selecting previously unselected package xfonts-encodings. 449s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 449s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 449s Selecting previously unselected package xfonts-utils. 449s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_s390x.deb ... 449s Unpacking xfonts-utils (1:7.7+7) ... 449s Selecting previously unselected package fonts-urw-base35. 449s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 449s Unpacking fonts-urw-base35 (20200910-8) ... 449s Selecting previously unselected package fontconfig-config. 449s Preparing to unpack .../013-fontconfig-config_2.15.0-2.2ubuntu1_s390x.deb ... 449s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 449s Selecting previously unselected package libfontconfig1:s390x. 449s Preparing to unpack .../014-libfontconfig1_2.15.0-2.2ubuntu1_s390x.deb ... 449s Unpacking libfontconfig1:s390x (2.15.0-2.2ubuntu1) ... 449s Selecting previously unselected package libsharpyuv0:s390x. 449s Preparing to unpack .../015-libsharpyuv0_1.5.0-0.1_s390x.deb ... 449s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 449s Selecting previously unselected package libaom3:s390x. 449s Preparing to unpack .../016-libaom3_3.12.0-1_s390x.deb ... 449s Unpacking libaom3:s390x (3.12.0-1) ... 449s Selecting previously unselected package libheif-plugin-aomdec:s390x. 449s Preparing to unpack .../017-libheif-plugin-aomdec_1.19.7-1_s390x.deb ... 449s Unpacking libheif-plugin-aomdec:s390x (1.19.7-1) ... 449s Selecting previously unselected package libde265-0:s390x. 449s Preparing to unpack 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... 449s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 449s Selecting previously unselected package liblcms2-2:s390x. 449s Preparing to unpack .../024-liblcms2-2_2.16-2_s390x.deb ... 449s Unpacking liblcms2-2:s390x (2.16-2) ... 449s Selecting previously unselected package liblqr-1-0:s390x. 449s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_s390x.deb ... 449s Unpacking liblqr-1-0:s390x (0.4.2-2.1build2) ... 449s Selecting previously unselected package libltdl7:s390x. 449s Preparing to unpack .../026-libltdl7_2.5.4-4_s390x.deb ... 449s Unpacking libltdl7:s390x (2.5.4-4) ... 449s Selecting previously unselected package libopenjp2-7:s390x. 449s Preparing to unpack .../027-libopenjp2-7_2.5.3-2_s390x.deb ... 449s Unpacking libopenjp2-7:s390x (2.5.3-2) ... 449s Selecting previously unselected package libraw23t64:s390x. 449s Preparing to unpack .../028-libraw23t64_0.21.3-1_s390x.deb ... 449s Unpacking libraw23t64:s390x (0.21.3-1) ... 449s Selecting previously unselected package libdeflate0:s390x. 449s Preparing to unpack .../029-libdeflate0_1.23-1_s390x.deb ... 449s Unpacking libdeflate0:s390x (1.23-1) ... 449s Selecting previously unselected package libwebp7:s390x. 449s Preparing to unpack .../030-libwebp7_1.5.0-0.1_s390x.deb ... 449s Unpacking libwebp7:s390x (1.5.0-0.1) ... 449s Selecting previously unselected package libtiff6:s390x. 449s Preparing to unpack .../031-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 449s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 449s Selecting previously unselected package libwebpdemux2:s390x. 449s Preparing to unpack .../032-libwebpdemux2_1.5.0-0.1_s390x.deb ... 449s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 449s Selecting previously unselected package libwebpmux3:s390x. 449s Preparing to unpack .../033-libwebpmux3_1.5.0-0.1_s390x.deb ... 449s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 449s Selecting previously unselected package imagemagick-7-common. 449s Preparing to unpack .../034-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 449s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 449s Selecting previously unselected package libmagickcore-7.q16-10:s390x. 449s Preparing to unpack .../035-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 449s Unpacking libmagickcore-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 449s Selecting previously unselected package libmagickwand-7.q16-10:s390x. 449s Preparing to unpack .../036-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 449s Unpacking libmagickwand-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 449s Selecting previously unselected package poppler-data. 449s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 449s Unpacking poppler-data (0.4.12-1) ... 450s Selecting previously unselected package python3-numpy-dev:s390x. 450s Preparing to unpack .../038-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 450s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 450s Selecting previously unselected package libblas3:s390x. 450s Preparing to unpack .../039-libblas3_3.12.1-2_s390x.deb ... 450s Unpacking libblas3:s390x (3.12.1-2) ... 450s Selecting previously unselected package libgfortran5:s390x. 450s Preparing to unpack .../040-libgfortran5_15-20250404-0ubuntu1_s390x.deb ... 450s Unpacking libgfortran5:s390x (15-20250404-0ubuntu1) ... 450s Selecting previously unselected package liblapack3:s390x. 450s Preparing to unpack .../041-liblapack3_3.12.1-2_s390x.deb ... 450s Unpacking liblapack3:s390x (3.12.1-2) ... 450s Selecting previously unselected package python3-numpy. 450s Preparing to unpack .../042-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 450s Unpacking python3-numpy (1:2.2.3+ds-5) ... 450s Selecting previously unselected package sgml-base. 450s Preparing to unpack .../043-sgml-base_1.31_all.deb ... 450s Unpacking sgml-base (1.31) ... 450s Selecting previously unselected package autoconf. 450s Preparing to unpack .../044-autoconf_2.72-3ubuntu1_all.deb ... 450s Unpacking autoconf (2.72-3ubuntu1) ... 450s Selecting previously unselected package autotools-dev. 450s Preparing to unpack .../045-autotools-dev_20220109.1_all.deb ... 450s Unpacking autotools-dev (20220109.1) ... 450s Selecting previously unselected package automake. 450s Preparing to unpack .../046-automake_1%3a1.17-3ubuntu1_all.deb ... 450s Unpacking automake (1:1.17-3ubuntu1) ... 450s Selecting previously unselected package autopoint. 450s Preparing to unpack .../047-autopoint_0.23.1-1_all.deb ... 450s Unpacking autopoint (0.23.1-1) ... 450s Selecting previously unselected package libtcl8.6:s390x. 450s Preparing to unpack .../048-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 450s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 450s Selecting previously unselected package libxrender1:s390x. 450s Preparing to unpack .../049-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 450s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 450s Selecting previously unselected package libxft2:s390x. 450s Preparing to unpack .../050-libxft2_2.3.6-1build1_s390x.deb ... 450s Unpacking libxft2:s390x (2.3.6-1build1) ... 450s Selecting previously unselected package libxss1:s390x. 450s Preparing to unpack .../051-libxss1_1%3a1.2.3-1build3_s390x.deb ... 450s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 450s Selecting previously unselected package libtk8.6:s390x. 450s Preparing to unpack .../052-libtk8.6_8.6.16-1_s390x.deb ... 450s Unpacking libtk8.6:s390x (8.6.16-1) ... 450s Selecting previously unselected package tk8.6-blt2.5. 450s Preparing to unpack .../053-tk8.6-blt2.5_2.5.3+dfsg-8_s390x.deb ... 450s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 450s Selecting previously unselected package blt. 450s Preparing to unpack .../054-blt_2.5.3+dfsg-8_s390x.deb ... 450s Unpacking blt (2.5.3+dfsg-8) ... 450s Selecting previously unselected package libisl23:s390x. 450s Preparing to unpack .../055-libisl23_0.27-1_s390x.deb ... 450s Unpacking libisl23:s390x (0.27-1) ... 450s Selecting previously unselected package libmpc3:s390x. 450s Preparing to unpack .../056-libmpc3_1.3.1-1build2_s390x.deb ... 450s Unpacking libmpc3:s390x (1.3.1-1build2) ... 450s Selecting previously unselected package cpp-14-s390x-linux-gnu. 450s Preparing to unpack .../057-cpp-14-s390x-linux-gnu_14.2.0-19ubuntu2_s390x.deb ... 450s Unpacking cpp-14-s390x-linux-gnu (14.2.0-19ubuntu2) ... 450s Selecting previously unselected package cpp-14. 450s Preparing to unpack .../058-cpp-14_14.2.0-19ubuntu2_s390x.deb ... 450s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 450s Selecting previously unselected package cpp-s390x-linux-gnu. 450s Preparing to unpack .../059-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 450s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 450s Selecting previously unselected package cpp. 450s Preparing to unpack .../060-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 450s Unpacking cpp (4:14.2.0-1ubuntu1) ... 450s Selecting previously unselected package libcc1-0:s390x. 450s Preparing to unpack .../061-libcc1-0_15-20250404-0ubuntu1_s390x.deb ... 450s Unpacking libcc1-0:s390x (15-20250404-0ubuntu1) ... 450s Selecting previously unselected package libitm1:s390x. 450s Preparing to unpack .../062-libitm1_15-20250404-0ubuntu1_s390x.deb ... 450s Unpacking libitm1:s390x (15-20250404-0ubuntu1) ... 450s Selecting previously unselected package libasan8:s390x. 450s Preparing to unpack .../063-libasan8_15-20250404-0ubuntu1_s390x.deb ... 450s Unpacking libasan8:s390x (15-20250404-0ubuntu1) ... 450s Selecting previously unselected package libubsan1:s390x. 450s Preparing to unpack .../064-libubsan1_15-20250404-0ubuntu1_s390x.deb ... 450s Unpacking libubsan1:s390x (15-20250404-0ubuntu1) ... 450s Selecting previously unselected package libgcc-14-dev:s390x. 450s Preparing to unpack .../065-libgcc-14-dev_14.2.0-19ubuntu2_s390x.deb ... 450s Unpacking libgcc-14-dev:s390x (14.2.0-19ubuntu2) ... 450s Selecting previously unselected package gcc-14-s390x-linux-gnu. 450s Preparing to unpack .../066-gcc-14-s390x-linux-gnu_14.2.0-19ubuntu2_s390x.deb ... 450s Unpacking gcc-14-s390x-linux-gnu (14.2.0-19ubuntu2) ... 451s Selecting previously unselected package gcc-14. 451s Preparing to unpack .../067-gcc-14_14.2.0-19ubuntu2_s390x.deb ... 451s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 451s Selecting previously unselected package gcc-s390x-linux-gnu. 451s Preparing to unpack .../068-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 451s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 451s Selecting previously unselected package gcc. 451s Preparing to unpack .../069-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ... 451s Unpacking gcc (4:14.2.0-1ubuntu1) ... 451s Selecting previously unselected package libstdc++-14-dev:s390x. 451s Preparing to unpack .../070-libstdc++-14-dev_14.2.0-19ubuntu2_s390x.deb ... 451s Unpacking libstdc++-14-dev:s390x (14.2.0-19ubuntu2) ... 451s Selecting previously unselected package g++-14-s390x-linux-gnu. 451s Preparing to unpack .../071-g++-14-s390x-linux-gnu_14.2.0-19ubuntu2_s390x.deb ... 451s Unpacking g++-14-s390x-linux-gnu (14.2.0-19ubuntu2) ... 451s Selecting previously unselected package g++-14. 451s Preparing to unpack .../072-g++-14_14.2.0-19ubuntu2_s390x.deb ... 451s Unpacking g++-14 (14.2.0-19ubuntu2) ... 451s Selecting previously unselected package g++-s390x-linux-gnu. 451s Preparing to unpack .../073-g++-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 451s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 451s Selecting previously unselected package g++. 451s Preparing to unpack .../074-g++_4%3a14.2.0-1ubuntu1_s390x.deb ... 451s Unpacking g++ (4:14.2.0-1ubuntu1) ... 451s Selecting previously unselected package build-essential. 451s Preparing to unpack .../075-build-essential_12.12ubuntu1_s390x.deb ... 451s Unpacking build-essential (12.12ubuntu1) ... 451s Selecting previously unselected package bwa. 451s Preparing to unpack .../076-bwa_0.7.18-1_s390x.deb ... 451s Unpacking bwa (0.7.18-1) ... 451s Selecting previously unselected package libargtable2-0. 451s Preparing to unpack .../077-libargtable2-0_13-3_s390x.deb ... 451s Unpacking libargtable2-0 (13-3) ... 451s Selecting previously unselected package clustalo. 451s Preparing to unpack .../078-clustalo_1.2.4-8build1_s390x.deb ... 451s Unpacking clustalo (1.2.4-8build1) ... 451s Selecting previously unselected package libdebhelper-perl. 451s Preparing to unpack .../079-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 451s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 451s Selecting previously unselected package libtool. 451s Preparing to unpack .../080-libtool_2.5.4-4_all.deb ... 451s Unpacking libtool (2.5.4-4) ... 451s Selecting previously unselected package dh-autoreconf. 451s Preparing to unpack .../081-dh-autoreconf_20_all.deb ... 451s Unpacking dh-autoreconf (20) ... 451s Selecting previously unselected package libarchive-zip-perl. 451s Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... 451s Unpacking libarchive-zip-perl (1.68-1) ... 451s Selecting previously unselected package libfile-stripnondeterminism-perl. 451s Preparing to unpack .../083-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 451s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 451s Selecting previously unselected package dh-strip-nondeterminism. 451s Preparing to unpack .../084-dh-strip-nondeterminism_1.14.1-2_all.deb ... 451s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 451s Selecting previously unselected package debugedit. 451s Preparing to unpack .../085-debugedit_1%3a5.1-2_s390x.deb ... 451s Unpacking debugedit (1:5.1-2) ... 451s Selecting previously unselected package dwz. 451s Preparing to unpack .../086-dwz_0.15-1build6_s390x.deb ... 451s Unpacking dwz (0.15-1build6) ... 451s Selecting previously unselected package gettext. 451s Preparing to unpack .../087-gettext_0.23.1-1_s390x.deb ... 451s Unpacking gettext (0.23.1-1) ... 451s Selecting previously unselected package intltool-debian. 451s Preparing to unpack .../088-intltool-debian_0.35.0+20060710.6_all.deb ... 451s Unpacking intltool-debian (0.35.0+20060710.6) ... 451s Selecting previously unselected package po-debconf. 451s Preparing to unpack .../089-po-debconf_1.0.21+nmu1_all.deb ... 451s Unpacking po-debconf (1.0.21+nmu1) ... 451s Selecting previously unselected package debhelper. 451s Preparing to unpack .../090-debhelper_13.24.1ubuntu2_all.deb ... 451s Unpacking debhelper (13.24.1ubuntu2) ... 451s Selecting previously unselected package dh-python. 451s Preparing to unpack .../091-dh-python_6.20250308_all.deb ... 451s Unpacking dh-python (6.20250308) ... 451s Selecting previously unselected package dialign. 451s Preparing to unpack .../092-dialign_2.2.1-13_s390x.deb ... 451s Unpacking dialign (2.2.1-13) ... 451s Selecting previously unselected package xml-core. 451s Preparing to unpack .../093-xml-core_0.19_all.deb ... 451s Unpacking xml-core (0.19) ... 451s Selecting previously unselected package docutils-common. 451s Preparing to unpack .../094-docutils-common_0.21.2+dfsg-2_all.deb ... 451s Unpacking docutils-common (0.21.2+dfsg-2) ... 451s Selecting previously unselected package libcifpp-data. 451s Preparing to unpack .../095-libcifpp-data_7.0.9-1_all.deb ... 451s Unpacking libcifpp-data (7.0.9-1) ... 451s Selecting previously unselected package libcifpp7:s390x. 451s Preparing to unpack .../096-libcifpp7_7.0.9-1_s390x.deb ... 451s Unpacking libcifpp7:s390x (7.0.9-1) ... 451s Selecting previously unselected package dssp. 451s Preparing to unpack .../097-dssp_4.4.10-1_s390x.deb ... 451s Unpacking dssp (4.4.10-1) ... 451s Selecting previously unselected package fonts-font-awesome. 451s Preparing to unpack .../098-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 451s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 451s Selecting previously unselected package fonts-lmodern. 451s Preparing to unpack .../099-fonts-lmodern_2.005-1_all.deb ... 451s Unpacking fonts-lmodern (2.005-1) ... 452s Selecting previously unselected package fonts-lyx. 452s Preparing to unpack .../100-fonts-lyx_2.4.3-1_all.deb ... 452s Unpacking fonts-lyx (2.4.3-1) ... 452s Selecting previously unselected package libgs-common. 452s Preparing to unpack .../101-libgs-common_10.05.0dfsg1-0ubuntu1_all.deb ... 452s Unpacking libgs-common (10.05.0dfsg1-0ubuntu1) ... 452s Selecting previously unselected package libgs10-common. 452s Preparing to unpack .../102-libgs10-common_10.05.0dfsg1-0ubuntu1_all.deb ... 452s Unpacking libgs10-common (10.05.0dfsg1-0ubuntu1) ... 452s Selecting previously unselected package libavahi-common-data:s390x. 452s Preparing to unpack .../103-libavahi-common-data_0.8-16ubuntu2_s390x.deb ... 452s Unpacking libavahi-common-data:s390x (0.8-16ubuntu2) ... 452s Selecting previously unselected package libavahi-common3:s390x. 452s Preparing to unpack .../104-libavahi-common3_0.8-16ubuntu2_s390x.deb ... 452s Unpacking libavahi-common3:s390x (0.8-16ubuntu2) ... 452s Selecting previously unselected package libavahi-client3:s390x. 452s Preparing to unpack .../105-libavahi-client3_0.8-16ubuntu2_s390x.deb ... 452s Unpacking libavahi-client3:s390x (0.8-16ubuntu2) ... 452s Selecting previously unselected package libcups2t64:s390x. 452s Preparing to unpack .../106-libcups2t64_2.4.12-0ubuntu1_s390x.deb ... 452s Unpacking libcups2t64:s390x (2.4.12-0ubuntu1) ... 452s Selecting previously unselected package libidn12:s390x. 452s Preparing to unpack .../107-libidn12_1.43-1_s390x.deb ... 452s Unpacking libidn12:s390x (1.43-1) ... 452s Selecting previously unselected package libijs-0.35:s390x. 452s Preparing to unpack .../108-libijs-0.35_0.35-15.2_s390x.deb ... 452s Unpacking libijs-0.35:s390x (0.35-15.2) ... 452s Selecting previously unselected package libjbig2dec0:s390x. 452s Preparing to unpack .../109-libjbig2dec0_0.20-1build3_s390x.deb ... 452s Unpacking libjbig2dec0:s390x (0.20-1build3) ... 452s Selecting previously unselected package libpaper2:s390x. 452s Preparing to unpack .../110-libpaper2_2.2.5-0.3_s390x.deb ... 452s Unpacking libpaper2:s390x (2.2.5-0.3) ... 452s Selecting previously unselected package libice6:s390x. 452s Preparing to unpack .../111-libice6_2%3a1.1.1-1_s390x.deb ... 452s Unpacking libice6:s390x (2:1.1.1-1) ... 452s Selecting previously unselected package libsm6:s390x. 452s Preparing to unpack .../112-libsm6_2%3a1.2.4-1_s390x.deb ... 452s Unpacking libsm6:s390x (2:1.2.4-1) ... 452s Selecting previously unselected package libxt6t64:s390x. 452s Preparing to unpack .../113-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 452s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 452s Selecting previously unselected package libgs10:s390x. 452s Preparing to unpack .../114-libgs10_10.05.0dfsg1-0ubuntu1_s390x.deb ... 452s Unpacking libgs10:s390x (10.05.0dfsg1-0ubuntu1) ... 452s Selecting previously unselected package ghostscript. 452s Preparing to unpack .../115-ghostscript_10.05.0dfsg1-0ubuntu1_s390x.deb ... 452s Unpacking ghostscript (10.05.0dfsg1-0ubuntu1) ... 452s Selecting previously unselected package libnetpbm11t64:s390x. 452s Preparing to unpack .../116-libnetpbm11t64_2%3a11.09.02-2_s390x.deb ... 452s Unpacking libnetpbm11t64:s390x (2:11.09.02-2) ... 452s Selecting previously unselected package netpbm. 452s Preparing to unpack .../117-netpbm_2%3a11.09.02-2_s390x.deb ... 452s Unpacking netpbm (2:11.09.02-2) ... 452s Selecting previously unselected package tex-common. 452s Preparing to unpack .../118-tex-common_6.19_all.deb ... 452s Unpacking tex-common (6.19) ... 452s Selecting previously unselected package libpaper-utils. 452s Preparing to unpack .../119-libpaper-utils_2.2.5-0.3_s390x.deb ... 452s Unpacking libpaper-utils (2.2.5-0.3) ... 452s Selecting previously unselected package libkpathsea6:s390x. 452s Preparing to unpack .../120-libkpathsea6_2024.20240313.70630+ds-6_s390x.deb ... 452s Unpacking libkpathsea6:s390x (2024.20240313.70630+ds-6) ... 452s Selecting previously unselected package libptexenc1:s390x. 452s Preparing to unpack .../121-libptexenc1_2024.20240313.70630+ds-6_s390x.deb ... 452s Unpacking libptexenc1:s390x (2024.20240313.70630+ds-6) ... 452s Selecting previously unselected package libsynctex2:s390x. 452s Preparing to unpack .../122-libsynctex2_2024.20240313.70630+ds-6_s390x.deb ... 452s Unpacking libsynctex2:s390x (2024.20240313.70630+ds-6) ... 452s Selecting previously unselected package libtexlua53-5:s390x. 452s Preparing to unpack .../123-libtexlua53-5_2024.20240313.70630+ds-6_s390x.deb ... 452s Unpacking libtexlua53-5:s390x (2024.20240313.70630+ds-6) ... 452s Selecting previously unselected package t1utils. 452s Preparing to unpack .../124-t1utils_1.41-4build3_s390x.deb ... 452s Unpacking t1utils (1.41-4build3) ... 452s Selecting previously unselected package libpixman-1-0:s390x. 452s Preparing to unpack .../125-libpixman-1-0_0.44.0-3_s390x.deb ... 452s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 452s Selecting previously unselected package libxcb-render0:s390x. 452s Preparing to unpack .../126-libxcb-render0_1.17.0-2_s390x.deb ... 452s Unpacking libxcb-render0:s390x (1.17.0-2) ... 452s Selecting previously unselected package libxcb-shm0:s390x. 452s Preparing to unpack .../127-libxcb-shm0_1.17.0-2_s390x.deb ... 452s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 452s Selecting previously unselected package libcairo2:s390x. 452s Preparing to unpack .../128-libcairo2_1.18.4-1_s390x.deb ... 452s Unpacking libcairo2:s390x (1.18.4-1) ... 452s Selecting previously unselected package libgraphite2-3:s390x. 452s Preparing to unpack .../129-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 452s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 452s Selecting previously unselected package libharfbuzz0b:s390x. 452s Preparing to unpack .../130-libharfbuzz0b_10.2.0-1_s390x.deb ... 452s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 452s Selecting previously unselected package libmpfi0:s390x. 452s Preparing to unpack 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(2:1.0.16-1) ... 452s Selecting previously unselected package libxi6:s390x. 452s Preparing to unpack .../137-libxi6_2%3a1.8.2-1_s390x.deb ... 452s Unpacking libxi6:s390x (2:1.8.2-1) ... 452s Selecting previously unselected package libzzip-0-13t64:s390x. 452s Preparing to unpack .../138-libzzip-0-13t64_0.13.78+dfsg.1-0.1_s390x.deb ... 452s Unpacking libzzip-0-13t64:s390x (0.13.78+dfsg.1-0.1) ... 452s Selecting previously unselected package texlive-binaries. 452s Preparing to unpack .../139-texlive-binaries_2024.20240313.70630+ds-6_s390x.deb ... 452s Unpacking texlive-binaries (2024.20240313.70630+ds-6) ... 452s Selecting previously unselected package xdg-utils. 452s Preparing to unpack .../140-xdg-utils_1.2.1-2ubuntu1_all.deb ... 452s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 452s Selecting previously unselected package texlive-base. 452s Preparing to unpack .../141-texlive-base_2024.20250309-1_all.deb ... 452s Unpacking texlive-base (2024.20250309-1) ... 454s Selecting previously unselected package hicolor-icon-theme. 454s Preparing to unpack .../142-hicolor-icon-theme_0.18-2_all.deb ... 454s Unpacking hicolor-icon-theme (0.18-2) ... 454s Selecting previously unselected package imagemagick-7.q16. 454s Preparing to unpack .../143-imagemagick-7.q16_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 454s Unpacking imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 454s Selecting previously unselected package imagemagick. 454s Preparing to unpack .../144-imagemagick_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 454s Unpacking imagemagick (8:7.1.1.43+dfsg1-1) ... 454s Selecting previously unselected package hevea. 454s Preparing to unpack .../145-hevea_2.36-2_s390x.deb ... 454s Unpacking hevea (2.36-2) ... 454s Selecting previously unselected package libsuitesparseconfig7:s390x. 454s Preparing to unpack .../146-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_s390x.deb ... 454s Unpacking libsuitesparseconfig7:s390x (1:7.8.3+dfsg-3) ... 454s Selecting previously unselected package libamd3:s390x. 454s Preparing to unpack .../147-libamd3_1%3a7.8.3+dfsg-3_s390x.deb ... 454s Unpacking libamd3:s390x (1:7.8.3+dfsg-3) ... 454s Selecting previously unselected package libapache-pom-java. 454s Preparing to unpack .../148-libapache-pom-java_33-2_all.deb ... 454s Unpacking libapache-pom-java (33-2) ... 454s Selecting previously unselected package libarpack2t64:s390x. 454s Preparing to unpack .../149-libarpack2t64_3.9.1-4_s390x.deb ... 454s Unpacking libarpack2t64:s390x (3.9.1-4) ... 454s Selecting previously unselected package libcolamd3:s390x. 454s Preparing to unpack .../150-libcolamd3_1%3a7.8.3+dfsg-3_s390x.deb ... 454s Unpacking libcolamd3:s390x (1:7.8.3+dfsg-3) ... 454s Selecting previously unselected package libcommons-parent-java. 454s Preparing to unpack .../151-libcommons-parent-java_56-1_all.deb ... 454s Unpacking libcommons-parent-java (56-1) ... 454s Selecting previously unselected package libcommons-logging-java. 454s Preparing to unpack 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454s Unpacking libjson-perl (4.10000-1) ... 454s Selecting previously unselected package liblbfgsb0:s390x. 454s Preparing to unpack .../163-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 454s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 454s Selecting previously unselected package libmbedcrypto16:s390x. 454s Preparing to unpack .../164-libmbedcrypto16_3.6.2-3ubuntu1_s390x.deb ... 454s Unpacking libmbedcrypto16:s390x (3.6.2-3ubuntu1) ... 454s Selecting previously unselected package libmbedx509-7:s390x. 454s Preparing to unpack .../165-libmbedx509-7_3.6.2-3ubuntu1_s390x.deb ... 454s Unpacking libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 454s Selecting previously unselected package libmbedtls21:s390x. 454s Preparing to unpack .../166-libmbedtls21_3.6.2-3ubuntu1_s390x.deb ... 454s Unpacking libmbedtls21:s390x (3.6.2-3ubuntu1) ... 454s Selecting previously unselected package mysql-common. 454s Preparing to unpack .../167-mysql-common_5.8+1.1.1ubuntu1_all.deb ... 454s Unpacking mysql-common (5.8+1.1.1ubuntu1) ... 454s Selecting previously unselected package libmysqlclient24:s390x. 454s Preparing to unpack .../168-libmysqlclient24_8.4.4-0ubuntu2_s390x.deb ... 454s Unpacking libmysqlclient24:s390x (8.4.4-0ubuntu2) ... 454s Selecting previously unselected package zlib1g-dev:s390x. 454s Preparing to unpack .../169-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 454s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 454s Selecting previously unselected package libpython3.13-dev:s390x. 454s Preparing to unpack .../170-libpython3.13-dev_3.13.3-1_s390x.deb ... 454s Unpacking libpython3.13-dev:s390x (3.13.3-1) ... 454s Selecting previously unselected package libpython3-dev:s390x. 454s Preparing to unpack .../171-libpython3-dev_3.13.3-1_s390x.deb ... 454s Unpacking libpython3-dev:s390x (3.13.3-1) ... 454s Selecting previously unselected package libpython3-all-dev:s390x. 454s Preparing to unpack .../172-libpython3-all-dev_3.13.3-1_s390x.deb ... 454s Unpacking libpython3-all-dev:s390x (3.13.3-1) ... 454s Selecting previously unselected package libqhull-r8.0:s390x. 454s Preparing to unpack .../173-libqhull-r8.0_2020.2-6build1_s390x.deb ... 454s Unpacking libqhull-r8.0:s390x (2020.2-6build1) ... 454s Selecting previously unselected package libraqm0:s390x. 454s Preparing to unpack .../174-libraqm0_0.10.2-1_s390x.deb ... 454s Unpacking libraqm0:s390x (0.10.2-1) ... 454s Selecting previously unselected package libxslt1.1:s390x. 454s Preparing to unpack .../175-libxslt1.1_1.1.39-0exp1ubuntu4_s390x.deb ... 454s Unpacking libxslt1.1:s390x (1.1.39-0exp1ubuntu4) ... 454s Selecting previously unselected package mafft. 454s Preparing to unpack .../176-mafft_7.505-1_s390x.deb ... 454s Unpacking mafft (7.505-1) ... 454s Selecting previously unselected package ncbi-data. 454s Preparing to unpack .../177-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 454s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 454s Selecting previously unselected package ncbi-blast+. 454s Preparing to unpack .../178-ncbi-blast+_2.16.0+ds-6build1_s390x.deb ... 454s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 455s Selecting previously unselected package phylip. 455s Preparing to unpack .../179-phylip_1%3a3.697+dfsg-4build1_s390x.deb ... 455s Unpacking phylip (1:3.697+dfsg-4build1) ... 455s Selecting previously unselected package prank. 455s Preparing to unpack .../180-prank_0.0.170427+dfsg-3_s390x.deb ... 455s Unpacking prank (0.0.170427+dfsg-3) ... 455s Selecting previously unselected package preview-latex-style. 455s Preparing to unpack .../181-preview-latex-style_13.2-1_all.deb ... 455s Unpacking preview-latex-style (13.2-1) ... 455s Selecting previously unselected package probcons. 455s Preparing to unpack .../182-probcons_1.12-14_s390x.deb ... 455s Unpacking probcons (1.12-14) ... 455s Selecting previously unselected package python-biopython-doc. 455s Preparing to unpack .../183-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 455s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 455s Selecting previously unselected package python-matplotlib-data. 455s Preparing to unpack .../184-python-matplotlib-data_3.8.3-7build1_all.deb ... 455s Unpacking python-matplotlib-data (3.8.3-7build1) ... 455s Selecting previously unselected package python3-all. 455s Preparing to unpack .../185-python3-all_3.13.3-1_s390x.deb ... 455s Unpacking python3-all (3.13.3-1) ... 455s Selecting previously unselected package python3.13-dev. 455s Preparing to unpack .../186-python3.13-dev_3.13.3-1_s390x.deb ... 455s Unpacking python3.13-dev (3.13.3-1) ... 455s Selecting previously unselected package python3-dev. 455s Preparing to unpack .../187-python3-dev_3.13.3-1_s390x.deb ... 455s Unpacking python3-dev (3.13.3-1) ... 455s Selecting previously unselected package python3-all-dev. 455s Preparing to unpack .../188-python3-all-dev_3.13.3-1_s390x.deb ... 455s Unpacking python3-all-dev (3.13.3-1) ... 455s Selecting previously unselected package python3.13-tk. 455s Preparing to unpack .../189-python3.13-tk_3.13.3-1_s390x.deb ... 455s Unpacking python3.13-tk (3.13.3-1) ... 455s Selecting previously unselected package python3-tk:s390x. 455s Preparing to unpack .../190-python3-tk_3.13.3-1_s390x.deb ... 455s Unpacking python3-tk:s390x (3.13.3-1) ... 455s Selecting previously unselected package python3-pil.imagetk:s390x. 455s Preparing to unpack .../191-python3-pil.imagetk_11.1.0-5build1_s390x.deb ... 455s Unpacking python3-pil.imagetk:s390x (11.1.0-5build1) ... 455s Selecting previously unselected package python3-pil:s390x. 455s Preparing to unpack .../192-python3-pil_11.1.0-5build1_s390x.deb ... 455s Unpacking python3-pil:s390x (11.1.0-5build1) ... 455s Selecting previously unselected package python3-cairo. 455s Preparing to unpack .../193-python3-cairo_1.27.0-2_s390x.deb ... 455s Unpacking python3-cairo (1.27.0-2) ... 455s Selecting previously unselected package python3-freetype. 455s Preparing to unpack .../194-python3-freetype_2.5.1-1_all.deb ... 455s Unpacking python3-freetype (2.5.1-1) ... 455s Selecting previously unselected package python3-rlpycairo. 455s Preparing to unpack .../195-python3-rlpycairo_0.3.0-3_all.deb ... 455s Unpacking python3-rlpycairo (0.3.0-3) ... 455s Selecting previously unselected package python3-reportlab. 455s Preparing to unpack .../196-python3-reportlab_4.3.1-1_all.deb ... 455s Unpacking python3-reportlab (4.3.1-1) ... 455s Selecting previously unselected package w3c-sgml-lib. 455s Preparing to unpack .../197-w3c-sgml-lib_1.3-3_all.deb ... 455s Unpacking w3c-sgml-lib (1.3-3) ... 455s Selecting previously unselected package python3-biopython. 455s Preparing to unpack .../198-python3-biopython_1.85+dfsg-2build1_s390x.deb ... 455s Unpacking python3-biopython (1.85+dfsg-2build1) ... 455s Selecting previously unselected package python3-biopython-sql. 455s Preparing to unpack .../199-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 455s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 455s Selecting previously unselected package python3-brotli. 455s Preparing to unpack .../200-python3-brotli_1.1.0-2build4_s390x.deb ... 455s Unpacking python3-brotli (1.1.0-2build4) ... 455s Selecting previously unselected package python3-contourpy. 455s Preparing to unpack .../201-python3-contourpy_1.3.1-1build1_s390x.deb ... 455s Unpacking python3-contourpy (1.3.1-1build1) ... 455s Selecting previously unselected package python3-cycler. 455s Preparing to unpack .../202-python3-cycler_0.12.1-1_all.deb ... 455s Unpacking python3-cycler (0.12.1-1) ... 455s Selecting previously unselected package python3-dateutil. 455s Preparing to unpack .../203-python3-dateutil_2.9.0-4_all.deb ... 455s Unpacking python3-dateutil (2.9.0-4) ... 455s Selecting previously unselected package python3-decorator. 455s Preparing to unpack .../204-python3-decorator_5.1.1-5_all.deb ... 455s Unpacking python3-decorator (5.1.1-5) ... 455s Selecting previously unselected package python3-defusedxml. 455s Preparing to unpack .../205-python3-defusedxml_0.7.1-3_all.deb ... 455s Unpacking python3-defusedxml (0.7.1-3) ... 455s Selecting previously unselected package python3-roman. 455s Preparing to unpack .../206-python3-roman_5.0-1_all.deb ... 455s Unpacking python3-roman (5.0-1) ... 455s Selecting previously unselected package python3-docutils. 455s Preparing to unpack .../207-python3-docutils_0.21.2+dfsg-2_all.deb ... 455s Unpacking python3-docutils (0.21.2+dfsg-2) ... 455s Selecting previously unselected package python3-platformdirs. 455s Preparing to unpack .../208-python3-platformdirs_4.3.6-1_all.deb ... 455s Unpacking python3-platformdirs (4.3.6-1) ... 455s Selecting previously unselected package python3-fs. 455s Preparing to unpack .../209-python3-fs_2.4.16-7_all.deb ... 455s Unpacking python3-fs (2.4.16-7) ... 455s Selecting previously unselected package python3-lxml:s390x. 455s Preparing to unpack .../210-python3-lxml_5.3.2-1_s390x.deb ... 455s Unpacking python3-lxml:s390x (5.3.2-1) ... 456s Selecting previously unselected package python3-lz4. 456s Preparing to unpack .../211-python3-lz4_4.4.0+dfsg-1build1_s390x.deb ... 456s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 456s Selecting previously unselected package python3-scipy. 456s Preparing to unpack .../212-python3-scipy_1.14.1-4ubuntu2_s390x.deb ... 456s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 456s Selecting previously unselected package python3-mpmath. 456s Preparing to unpack .../213-python3-mpmath_1.3.0-1_all.deb ... 456s Unpacking python3-mpmath (1.3.0-1) ... 456s Selecting previously unselected package python3-sympy. 456s Preparing to unpack .../214-python3-sympy_1.13.3-5_all.deb ... 456s Unpacking python3-sympy (1.13.3-5) ... 456s Selecting previously unselected package python3-ufolib2. 456s Preparing to unpack .../215-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 456s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 456s Selecting previously unselected package unicode-data. 456s Preparing to unpack .../216-unicode-data_15.1.0-1_all.deb ... 456s Unpacking unicode-data (15.1.0-1) ... 456s Selecting previously unselected package python3-fonttools. 456s Preparing to unpack .../217-python3-fonttools_4.55.3-2build1_s390x.deb ... 456s Unpacking python3-fonttools (4.55.3-2build1) ... 456s Selecting previously unselected package python3-imagesize. 456s Preparing to unpack .../218-python3-imagesize_1.4.1-1_all.deb ... 456s Unpacking python3-imagesize (1.4.1-1) ... 456s Selecting previously unselected package python3-kiwisolver. 456s Preparing to unpack .../219-python3-kiwisolver_1.4.7-3build1_s390x.deb ... 456s Unpacking python3-kiwisolver (1.4.7-3build1) ... 456s Selecting previously unselected package python3-packaging. 456s Preparing to unpack .../220-python3-packaging_24.2-1_all.deb ... 456s Unpacking python3-packaging (24.2-1) ... 456s Selecting previously unselected package python3-matplotlib. 456s Preparing to unpack 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sphinx-common (8.1.3-5) ... 457s Selecting previously unselected package python3-alabaster. 457s Preparing to unpack .../227-python3-alabaster_0.7.16-0.1_all.deb ... 457s Unpacking python3-alabaster (0.7.16-0.1) ... 457s Selecting previously unselected package python3-snowballstemmer. 457s Preparing to unpack .../228-python3-snowballstemmer_2.2.0-4build1_all.deb ... 457s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 457s Selecting previously unselected package python3-sphinx. 457s Preparing to unpack .../229-python3-sphinx_8.1.3-5_all.deb ... 457s Unpacking python3-sphinx (8.1.3-5) ... 457s Selecting previously unselected package python3-tabulate. 457s Preparing to unpack .../230-python3-tabulate_0.9.0-1_all.deb ... 457s Unpacking python3-tabulate (0.9.0-1) ... 457s Selecting previously unselected package python3-numpydoc. 457s Preparing to unpack .../231-python3-numpydoc_1.8.0-1_all.deb ... 457s Unpacking python3-numpydoc (1.8.0-1) ... 457s Selecting previously unselected package python3-rdflib. 457s Preparing to unpack .../232-python3-rdflib_7.1.1-2_all.deb ... 457s Unpacking python3-rdflib (7.1.1-2) ... 457s Selecting previously unselected package sphinx-rtd-theme-common. 457s Preparing to unpack .../233-sphinx-rtd-theme-common_3.0.2+dfsg-2_all.deb ... 457s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 457s Selecting previously unselected package python3-sphinxcontrib.jquery. 457s Preparing to unpack .../234-python3-sphinxcontrib.jquery_4.1-5_all.deb ... 457s Unpacking python3-sphinxcontrib.jquery (4.1-5) ... 457s Selecting previously unselected package python3-sphinx-rtd-theme. 457s Preparing to unpack .../235-python3-sphinx-rtd-theme_3.0.2+dfsg-2_all.deb ... 457s Unpacking python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 457s Selecting previously unselected package python3-texttable. 457s Preparing to unpack .../236-python3-texttable_1.7.0-1_all.deb ... 457s Unpacking python3-texttable (1.7.0-1) ... 457s Selecting previously unselected package 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464s Setting up autotools-dev (20220109.1) ... 464s Setting up libblas3:s390x (3.12.1-2) ... 464s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 464s Setting up python3-packaging (24.2-1) ... 464s Setting up libexpat1-dev:s390x (2.7.1-1) ... 464s Setting up libzzip-0-13t64:s390x (0.13.78+dfsg.1-0.1) ... 464s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 464s Setting up libjbig2dec0:s390x (0.20-1build3) ... 464s Setting up python3-snowballstemmer (2.2.0-4build1) ... 464s Setting up libteckit0:s390x (2.5.12+ds1-1) ... 464s Setting up python3-brotli (1.1.0-2build4) ... 464s Setting up libapache-pom-java (33-2) ... 464s Setting up libavahi-common-data:s390x (0.8-16ubuntu2) ... 464s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 464s Setting up t1utils (1.41-4build3) ... 464s Setting up python3-cycler (0.12.1-1) ... 464s Setting up libtexlua53-5:s390x 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libmbedcrypto16:s390x (3.6.2-3ubuntu1) ... 465s Setting up libpaper2:s390x (2.2.5-0.3) ... 465s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 465s Setting up python3-mpmath (1.3.0-1) ... 465s Setting up libisl23:s390x (0.27-1) ... 465s Setting up libde265-0:s390x (1.0.15-1build5) ... 465s Setting up python-matplotlib-data (3.8.3-7build1) ... 465s Setting up libwebpmux3:s390x (1.5.0-0.1) ... 465s Setting up dialign (2.2.1-13) ... 465s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 465s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... 465s Setting up xdg-utils (1.2.1-2ubuntu1) ... 465s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 465s Setting up libcc1-0:s390x (15-20250404-0ubuntu1) ... 465s Setting up libitm1:s390x (15-20250404-0ubuntu1) ... 465s Setting up libsynctex2:s390x (2024.20240313.70630+ds-6) ... 465s Setting up prank (0.0.170427+dfsg-3) ... 465s Setting up libargtable2-0 (13-3) ... 465s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 465s Setting up python3-imagesize (1.4.1-1) ... 465s Setting up libpotrace0:s390x (1.16-2build1) ... 465s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 465s Setting up automake (1:1.17-3ubuntu1) ... 465s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 465s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 465s Setting up python3-sympy (1.13.3-5) ... 470s Setting up libice6:s390x (2:1.1.1-1) ... 470s Setting up flex (2.6.4-8.2build1) ... 470s Setting up liblapack3:s390x (3.12.1-2) ... 470s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 470s Setting up gettext (0.23.1-1) ... 470s Setting up libarpack2t64:s390x (3.9.1-4) ... 470s Setting up libamd3:s390x (1:7.8.3+dfsg-3) ... 470s Setting up libpdfbox-java (1:1.8.16-5) ... 470s Setting up libcolamd3:s390x (1:7.8.3+dfsg-3) ... 470s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 470s Setting up wise (2.4.1-25) ... 470s Setting up preview-latex-style (13.2-1) ... 470s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 470s Setting up libcommons-parent-java (56-1) ... 470s Setting up libavahi-common3:s390x (0.8-16ubuntu2) ... 470s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 470s Setting up libcifpp7:s390x (7.0.9-1) ... 470s Setting up libpaper-utils (2.2.5-0.3) ... 470s Setting up clustalo (1.2.4-8build1) ... 470s Setting up dssp (4.4.10-1) ... 470s Setting up python3-freetype (2.5.1-1) ... 470s Setting up xfonts-utils (1:7.7+7) ... 470s Setting up intltool-debian (0.35.0+20060710.6) ... 470s Setting up libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 470s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 470s Setting up libptexenc1:s390x (2024.20240313.70630+ds-6) ... 470s Setting up libglpk40:s390x (5.0-1build2) ... 470s Setting up libraqm0:s390x (0.10.2-1) ... 470s Setting up 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... 472s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 472s Setting up libxft2:s390x (2.3.6-1build1) ... 472s Setting up python3-scipy (1.14.1-4ubuntu2) ... 475s Setting up libpython3-dev:s390x (3.13.3-1) ... 475s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 475s Setting up python3.13-dev (3.13.3-1) ... 475s Setting up po-debconf (1.0.21+nmu1) ... 475s Setting up libtk8.6:s390x (8.6.16-1) ... 475s Setting up python3-mmtf (1.1.3-1) ... 475s Setting up fonts-urw-base35 (20200910-8) ... 475s Setting up libcairo2:s390x (1.18.4-1) ... 475s Setting up python3.13-tk (3.13.3-1) ... 475s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 475s Setting up python3-pil:s390x (11.1.0-5build1) ... 475s Setting up gcc-14-s390x-linux-gnu (14.2.0-19ubuntu2) ... 475s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 475s Setting up libpython3-all-dev:s390x (3.13.3-1) ... 475s Setting up sphinx-common (8.1.3-5) ... 475s Setting up python3-dev (3.13.3-1) ... 475s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 475s Setting up g++-14-s390x-linux-gnu (14.2.0-19ubuntu2) ... 475s Setting up netpbm (2:11.09.02-2) ... 475s Setting up python3-igraph (0.11.8+ds-1build1) ... 475s Setting up cpp (4:14.2.0-1ubuntu1) ... 475s Setting up libcups2t64:s390x (2.4.12-0ubuntu1) ... 475s Setting up python3-all-dev (3.13.3-1) ... 475s Setting up libgs10-common (10.05.0dfsg1-0ubuntu1) ... 475s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 475s Setting up libxmu6:s390x (2:1.1.3-3build2) ... 475s Setting up python3-cairo (1.27.0-2) ... 476s Setting up blt (2.5.3+dfsg-8) ... 476s Setting up python3-tk:s390x (3.13.3-1) ... 476s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 476s Setting up libxaw7:s390x (2:1.0.16-1) ... 476s Setting up gcc-14 (14.2.0-19ubuntu2) ... 476s Setting up python3-pil.imagetk:s390x (11.1.0-5build1) ... 476s Setting up python3-rlpycairo (0.3.0-3) ... 476s Setting up python3-reportlab (4.3.1-1) ... 476s Setting up texlive-binaries (2024.20240313.70630+ds-6) ... 476s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 476s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 476s Setting up g++-14 (14.2.0-19ubuntu2) ... 476s Setting up texlive-base (2024.20250309-1) ... 477s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 477s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 477s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 477s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 478s Setting up libgs10:s390x (10.05.0dfsg1-0ubuntu1) ... 478s Setting up libtool (2.5.4-4) ... 478s Setting up ghostscript (10.05.0dfsg1-0ubuntu1) ... 478s Setting up gcc (4:14.2.0-1ubuntu1) ... 478s Setting up dh-autoreconf (20) ... 478s Setting up texlive-latex-base (2024.20250309-1) ... 478s Setting up texlive-latex-recommended (2024.20250309-1) ... 478s Setting up texlive-pictures (2024.20250309-1) ... 478s Setting up g++ (4:14.2.0-1ubuntu1) ... 478s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 478s Setting up texlive-fonts-recommended (2024.20250309-1) ... 478s Setting up build-essential (12.12ubuntu1) ... 478s Setting up debhelper (13.24.1ubuntu2) ... 478s Setting up texlive-latex-extra (2024.20250309-2) ... 478s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 478s Setting up libheif-plugin-aomdec:s390x (1.19.7-1) ... 478s Setting up libheif-plugin-libde265:s390x (1.19.7-1) ... 478s Setting up libheif1:s390x (1.19.7-1) ... 478s Setting up python3-fonttools (4.55.3-2build1) ... 478s Setting up libmagickcore-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 478s Setting up python3-matplotlib (3.8.3-7build1) ... 479s Setting up libmagickwand-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 479s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 479s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 479s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 479s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 479s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 479s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 479s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 479s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 479s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 479s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 479s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 479s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 479s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 479s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 479s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 479s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 479s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 479s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 479s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 479s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 479s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 479s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 479s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 479s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 479s 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 479s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 479s 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 479s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 479s 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 479s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 479s 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 479s Setting up hevea (2.36-2) ... 479s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 479s Processing triggers for install-info (7.1.1-1) ... 479s Processing triggers for libc-bin (2.41-6ubuntu1) ... 479s Processing triggers for man-db (2.13.0-1) ... 481s Processing triggers for sgml-base (1.31) ... 481s Setting up docutils-common (0.21.2+dfsg-2) ... 481s Setting up w3c-sgml-lib (1.3-3) ... 501s Setting up python3-biopython (1.85+dfsg-2build1) ... 502s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 502s Processing triggers for sgml-base (1.31) ... 502s Setting up python3-docutils (0.21.2+dfsg-2) ... 502s Setting up python3-sphinx (8.1.3-5) ... 503s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 503s Setting up python3-numpydoc (1.8.0-1) ... 503s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 503s Processing triggers for tex-common (6.19) ... 504s Running updmap-sys. This may take some time... done. 504s Running mktexlsr /var/lib/texmf ... done. 504s Building format(s) --all. 597s This may take some time... done. 612s autopkgtest [08:24:23]: test full_suite: sh debian/tests/run-unit-test 612s autopkgtest [08:24:23]: test full_suite: [----------------------- 613s mkdir: created directory 'Bio' 613s mkdir: created directory 'Bio/Align' 613s mkdir: created directory 'Bio/Align/substitution_matrices' 613s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 613s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 613s test_Ace ... ok 613s test_Affy ... ok 615s test_AlignIO ... ok 616s test_AlignIO_ClustalIO ... ok 616s test_AlignIO_EmbossIO ... ok 616s test_AlignIO_FastaIO ... ok 616s test_AlignIO_MauveIO ... ok 616s test_AlignIO_PhylipIO ... ok 616s test_AlignIO_convert ... ok 616s test_AlignInfo ... ok 616s test_Align_Alignment ... ok 616s test_Align_a2m ... ok 616s test_Align_bed ... ok 616s test_Align_bigbed ... ok 617s test_Align_bigmaf ... ok 617s test_Align_bigpsl ... ok 617s test_Align_chain ... ok 617s test_Align_clustal ... ok 624s test_Align_codonalign ... ok 624s test_Align_emboss ... ok 624s test_Align_exonerate ... ok 624s test_Align_fasta ... ok 625s test_Align_hhr ... ok 625s test_Align_maf ... ok 626s test_Align_mauve ... ok 626s test_Align_msf ... ok 626s test_Align_nexus ... ok 626s test_Align_phylip ... ok 626s test_Align_psl ... ok 627s test_Align_sam ... ok 628s test_Align_stockholm ... ok 628s test_Align_tabular ... ok 628s test_Application ... ok 629s test_BioSQL_MySQLdb_online ... skipping. internet not available 629s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 629s test_BioSQL_mysql_connector_online ... skipping. internet not available 629s test_BioSQL_psycopg2_online ... skipping. internet not available 632s test_BioSQL_sqlite3 ... ok 632s test_BioSQL_sqlite3_online ... skipping. internet not available 632s test_Blast_Record ... ok 633s test_Blast_parser ... ok 633s test_CAPS ... ok 633s test_Chi2 ... ok 635s test_ClustalOmega_tool ... ok 635s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 635s test_Cluster ... ok 635s test_CodonTable ... ok 635s test_ColorSpiral ... ok 635s test_Compass ... ok 636s test_Consensus ... ok 637s test_Dialign_tool ... ok 637s test_EMBL_unittest ... ok 637s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 637s test_EmbossPrimer ... ok 641s test_Entrez ... ok 641s test_Entrez_online ... skipping. internet not available 642s test_Entrez_parser ... ok 642s test_Enzyme ... ok 642s test_ExPASy ... skipping. internet not available 642s test_Fasttree_tool ... ok 642s test_File ... ok 642s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 642s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 642s ok 644s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 646s ok 647s test_GraphicsChromosome ... ok 647s test_GraphicsDistribution ... ok 647s test_GraphicsGeneral ... ok 648s test_HMMCasino ... ok 648s test_HMMGeneral ... ok 648s test_KEGG ... ok 648s test_KEGG_online ... skipping. internet not available 654s test_KGML_graphics ... ok 654s test_KGML_graphics_online ... skipping. internet not available 655s test_KGML_nographics ... ok 655s test_KeyWList ... ok 655s test_LogisticRegression ... ok 656s test_MafIO_index ... ok 657s test_Mafft_tool ... ok 657s test_MarkovModel ... ok 657s test_Medline ... ok 657s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 657s test_NCBIXML ... Exception ignored in: 657s Traceback (most recent call last): 657s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 657s expat_parser.Parse(NULL, True) 657s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 657s ok 660s test_NCBI_BLAST_tools ... ok 660s test_NCBI_qblast ... ok 660s test_NMR ... ok 660s test_NaiveBayes ... ok 660s test_Nexus ... ok 660s test_PAML_baseml ... ok 661s test_PAML_codeml ... ok 661s test_PAML_yn00 ... ok 667s test_PDB_CEAligner ... ok 669s test_PDB_DSSP ... ok 669s test_PDB_Dice ... ok 669s test_PDB_Disordered ... ok 669s test_PDB_Exposure ... ok 669s test_PDB_FragmentMapper ... ok 671s test_PDB_KDTree ... ok 671s test_PDB_MMCIF2Dict ... ok 671s test_PDB_MMCIFIO ... ok 672s test_PDB_MMCIFParser ... ok 672s test_PDB_NACCESS ... ok 673s test_PDB_PDBIO ... ok 673s test_PDB_PDBList ... skipping. internet not available 683s test_PDB_PDBMLParser ... ok 683s test_PDB_PDBParser ... ok 683s 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 683s test_PDB_Polypeptide ... ok 683s test_PDB_QCPSuperimposer ... ok 687s test_PDB_SASA ... ok 687s test_PDB_SMCRA ... ok 687s test_PDB_Selection ... ok 688s test_PDB_StructureAlignment ... ok 688s test_PDB_Superimposer ... ok 688s test_PDB_alphafold_db ... skipping. internet not available 696s test_PDB_internal_coords ... ok 696s test_PDB_parse_pdb_header ... ok 696s test_PDB_vectors ... ok 696s test_PQR ... ok 696s test_Pathway ... ok 696s test_Phd ... ok 697s test_Phylo ... ok 697s test_PhyloXML ... ok 698s test_Phylo_CDAO ... ok 698s test_Phylo_NeXML ... ok 700s test_Phylo_igraph ... ok 703s test_Phylo_matplotlib ... ok 704s test_Phylo_networkx ... ok 705s test_PopGen_GenePop_nodepend ... ok 706s test_Prank_tool ... ok 707s test_Probcons_tool ... ok 707s test_ProtParam ... ok 708s test_RCSBFormats ... ok 709s test_Restriction ... ok 709s test_SCOP_Astral ... ok 710s test_SCOP_Cla ... ok 711s test_SCOP_Des ... ok 711s test_SCOP_Dom ... ok 712s test_SCOP_Hie ... ok 712s test_SCOP_Raf ... ok 713s test_SCOP_Residues ... ok 713s test_SCOP_Scop ... ok 714s test_SVDSuperimposer ... ok 714s test_SearchIO_blast_tab ... ok 715s test_SearchIO_blast_tab_index ... ok 715s test_SearchIO_blast_xml ... ok 716s test_SearchIO_blast_xml_index ... ok 717s test_SearchIO_blat_psl ... ok 717s test_SearchIO_blat_psl_index ... ok 718s test_SearchIO_exonerate ... ok 718s test_SearchIO_exonerate_text_index ... ok 719s test_SearchIO_exonerate_vulgar_index ... ok 719s test_SearchIO_fasta_m10 ... ok 720s test_SearchIO_fasta_m10_index ... ok 720s test_SearchIO_hhsuite2_text ... ok 721s test_SearchIO_hmmer2_text ... ok 721s test_SearchIO_hmmer2_text_index ... ok 722s test_SearchIO_hmmer3_domtab ... ok 723s test_SearchIO_hmmer3_domtab_index ... ok 723s test_SearchIO_hmmer3_tab ... ok 723s test_SearchIO_hmmer3_tab_index ... ok 724s test_SearchIO_hmmer3_text ... ok 724s test_SearchIO_hmmer3_text_index ... ok 725s test_SearchIO_interproscan_xml ... ok 725s test_SearchIO_model ... ok 726s test_SearchIO_write ... ok 726s test_SeqFeature ... ok 739s test_SeqIO ... ok 740s test_SeqIO_AbiIO ... ok 741s test_SeqIO_FastaIO ... ok 741s test_SeqIO_Gck ... ok 741s test_SeqIO_Gfa ... ok 742s test_SeqIO_Insdc ... ok 742s test_SeqIO_NibIO ... ok 743s test_SeqIO_PdbIO ... ok 744s test_SeqIO_QualityIO ... ok 745s test_SeqIO_SeqXML ... ok 746s test_SeqIO_SffIO ... ok 746s test_SeqIO_SnapGene ... ok 746s test_SeqIO_TwoBitIO ... ok 746s test_SeqIO_UniprotIO ... ok 747s test_SeqIO_Xdna ... ok 747s test_SeqIO_features ... ok 757s test_SeqIO_index ... ok 758s test_SeqIO_online ... skipping. internet not available 758s test_SeqIO_write ... ok 758s test_SeqRecord ... ok 759s test_SeqUtils ... ok 760s test_Seq_objs ... ok 760s test_SwissProt ... ok 762s test_TCoffee_tool ... ok 763s test_TogoWS ... skipping. internet not available 764s test_TreeConstruction ... ok 764s test_UniGene ... ok 764s test_UniProt ... skipping. internet not available 765s test_UniProt_GOA ... ok 765s test_align ... ok 766s test_align_substitution_matrices ... ok 768s test_bgzf ... ok 768s test_cellosaurus ... ok 773s test_codonalign ... ok 773s test_geo ... ok 774s test_kNN ... ok 774s test_motifs ... ok 775s test_motifs_online ... skipping. internet not available 775s 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. 775s warnings.warn( 775s ok 775s test_pairwise2_no_C ... ok 776s test_pairwise_aligner ... ok 776s test_pairwise_alignment_map ... ok 782s test_phenotype ... ok 783s test_phenotype_fit ... ok 783s 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. 783s test_prodoc ... ok 784s test_prosite ... ok 784s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 784s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 785s test_seq ... ok 785s test_translate ... ok 786s ---------------------------------------------------------------------- 786s Skipping any tests requiring internet access 786s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 786s Operating system: posix linux 786s Ran 216 tests in 172.188 seconds 786s 786s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 786s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 787s autopkgtest [08:27:18]: test full_suite: -----------------------] 787s full_suite PASS 787s autopkgtest [08:27:18]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 788s autopkgtest [08:27:19]: @@@@@@@@@@@@@@@@@@@@ summary 788s dependencies PASS 788s full_suite PASS 805s nova [W] Using flock in prodstack6-s390x 805s Creating nova instance adt-questing-s390x-python-biopython-20250502-081411-juju-7f2275-prod-proposed-migration-environment-15-121d5a5b-c5d7-42c9-8908-b33fdbdebf66 from image adt/ubuntu-questing-s390x-server-20250502.img (UUID 632ecfca-a19d-4f3a-af48-b7883fa0ccf2)... 805s nova [W] Timed out waiting for b8ff3ea7-2d2e-484a-84c2-14966af84783 to get deleted. 805s nova [W] Using flock in prodstack6-s390x 805s flock: timeout while waiting to get lock 805s Creating nova instance adt-questing-s390x-python-biopython-20250502-081411-juju-7f2275-prod-proposed-migration-environment-15-121d5a5b-c5d7-42c9-8908-b33fdbdebf66 from image adt/ubuntu-questing-s390x-server-20250502.img (UUID 632ecfca-a19d-4f3a-af48-b7883fa0ccf2)... 805s nova [W] Timed out waiting for 34d86230-6830-48f7-b9e9-21d4a893f4d5 to get deleted.