0s autopkgtest [21:06:13]: starting date and time: 2025-05-03 21:06:13+0000 0s autopkgtest [21:06:13]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [21:06:13]: host juju-7f2275-prod-proposed-migration-environment-23; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.l2kuz5s7/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx,src:roman-numerals --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=sphinx/8.2.3-1 roman-numerals/3.1.0-1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-23@bos03-s390x-6.secgroup --name adt-questing-s390x-python-biopython-20250503-204125-juju-7f2275-prod-proposed-migration-environment-23-88002bdb-db2f-485e-8e5e-ad3a1d24f9db --image adt/ubuntu-questing-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-23 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 115s autopkgtest [21:08:08]: testbed dpkg architecture: s390x 115s autopkgtest [21:08:08]: testbed apt version: 3.0.0 115s autopkgtest [21:08:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 115s autopkgtest [21:08:08]: testbed release detected to be: None 116s autopkgtest [21:08:09]: updating testbed package index (apt update) 116s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 117s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 117s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 117s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 117s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.7 kB] 117s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [149 kB] 117s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1430 kB] 117s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main s390x Packages [178 kB] 117s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x Packages [1275 kB] 117s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse s390x Packages [26.2 kB] 117s Fetched 3202 kB in 1s (2889 kB/s) 118s Reading package lists... 119s autopkgtest [21:08:12]: upgrading testbed (apt dist-upgrade and autopurge) 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 119s Starting 2 pkgProblemResolver with broken count: 0 119s Done 119s Entering ResolveByKeep 119s 119s Calculating upgrade... 119s The following packages will be upgraded: 119s cloud-init cloud-init-base libmbim-glib4 libmbim-proxy libpython3.12-minimal 119s libpython3.12-stdlib libpython3.12t64 libqmi-glib5 libqmi-proxy libsepol2 120s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Need to get 7523 kB of archives. 120s After this operation, 158 kB disk space will be freed. 120s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x libsepol2 s390x 3.8.1-1 [332 kB] 120s Get:2 http://ftpmaster.internal/ubuntu questing/main s390x cloud-init-base all 25.2~1g7a0265d3-0ubuntu1 [619 kB] 120s Get:3 http://ftpmaster.internal/ubuntu questing/main s390x libmbim-proxy s390x 1.32.0-1 [6226 B] 120s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x libmbim-glib4 s390x 1.32.0-1 [239 kB] 120s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12t64 s390x 3.12.10-1 [2509 kB] 120s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12-stdlib s390x 3.12.10-1 [2049 kB] 120s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12-minimal s390x 3.12.10-1 [836 kB] 120s Get:8 http://ftpmaster.internal/ubuntu questing/main s390x libqmi-proxy s390x 1.36.0-1 [6190 B] 120s Get:9 http://ftpmaster.internal/ubuntu questing/main s390x libqmi-glib5 s390x 1.36.0-1 [925 kB] 120s Get:10 http://ftpmaster.internal/ubuntu questing/main s390x cloud-init all 25.2~1g7a0265d3-0ubuntu1 [2106 B] 121s Preconfiguring packages ... 121s Fetched 7523 kB in 1s (9333 kB/s) 121s (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 ... 81470 files and directories currently installed.) 121s Preparing to unpack .../libsepol2_3.8.1-1_s390x.deb ... 121s Unpacking libsepol2:s390x (3.8.1-1) over (3.7-1) ... 121s Setting up libsepol2:s390x (3.8.1-1) ... 121s (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 ... 81470 files and directories currently installed.) 121s Preparing to unpack .../0-cloud-init-base_25.2~1g7a0265d3-0ubuntu1_all.deb ... 121s Unpacking cloud-init-base (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 121s Preparing to unpack .../1-libmbim-proxy_1.32.0-1_s390x.deb ... 121s Unpacking libmbim-proxy (1.32.0-1) over (1.31.2-0ubuntu4) ... 121s Preparing to unpack .../2-libmbim-glib4_1.32.0-1_s390x.deb ... 121s Unpacking libmbim-glib4:s390x (1.32.0-1) over (1.31.2-0ubuntu4) ... 121s Preparing to unpack .../3-libpython3.12t64_3.12.10-1_s390x.deb ... 121s Unpacking libpython3.12t64:s390x (3.12.10-1) over (3.12.8-3) ... 121s Preparing to unpack .../4-libpython3.12-stdlib_3.12.10-1_s390x.deb ... 121s Unpacking libpython3.12-stdlib:s390x (3.12.10-1) over (3.12.8-3) ... 121s Preparing to unpack .../5-libpython3.12-minimal_3.12.10-1_s390x.deb ... 121s Unpacking libpython3.12-minimal:s390x (3.12.10-1) over (3.12.8-3) ... 121s Preparing to unpack .../6-libqmi-proxy_1.36.0-1_s390x.deb ... 121s Unpacking libqmi-proxy (1.36.0-1) over (1.35.6-1) ... 121s Preparing to unpack .../7-libqmi-glib5_1.36.0-1_s390x.deb ... 121s Unpacking libqmi-glib5:s390x (1.36.0-1) over (1.35.6-1) ... 121s Preparing to unpack .../8-cloud-init_25.2~1g7a0265d3-0ubuntu1_all.deb ... 121s Unpacking cloud-init (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 121s Setting up libpython3.12-minimal:s390x (3.12.10-1) ... 121s Setting up cloud-init-base (25.2~1g7a0265d3-0ubuntu1) ... 122s Setting up libmbim-glib4:s390x (1.32.0-1) ... 122s Setting up cloud-init (25.2~1g7a0265d3-0ubuntu1) ... 122s Setting up libpython3.12-stdlib:s390x (3.12.10-1) ... 122s Setting up libmbim-proxy (1.32.0-1) ... 122s Setting up libpython3.12t64:s390x (3.12.10-1) ... 122s Setting up libqmi-glib5:s390x (1.36.0-1) ... 122s Setting up libqmi-proxy (1.36.0-1) ... 122s Processing triggers for libc-bin (2.41-6ubuntu1) ... 122s Processing triggers for rsyslog (8.2412.0-2ubuntu2) ... 122s Processing triggers for man-db (2.13.0-1) ... 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 123s Starting pkgProblemResolver with broken count: 0 123s Starting 2 pkgProblemResolver with broken count: 0 123s Done 124s Solving dependencies... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s autopkgtest [21:08:17]: rebooting testbed after setup commands that affected boot 143s autopkgtest [21:08:36]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP Sun Apr 6 13:39:00 UTC 2025 145s autopkgtest [21:08:38]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 148s Get:1 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (dsc) [3406 B] 148s Get:2 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (tar) [14.6 MB] 148s Get:3 http://ftpmaster.internal/ubuntu questing/universe python-biopython 1.85+dfsg-2build1 (diff) [42.8 kB] 148s gpgv: Signature made Tue Mar 4 15:18:59 2025 UTC 148s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 148s gpgv: Can't check signature: No public key 148s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.85+dfsg-2build1.dsc: no acceptable signature found 149s autopkgtest [21:08:42]: testing package python-biopython version 1.85+dfsg-2build1 150s autopkgtest [21:08:43]: build not needed 154s autopkgtest [21:08:47]: test dependencies: preparing testbed 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Starting pkgProblemResolver with broken count: 0 155s Starting 2 pkgProblemResolver with broken count: 0 155s Done 155s The following NEW packages will be installed: 155s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 155s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 155s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 155s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 155s liblapack3 liblcms2-2 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 155s libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 155s libxrender1 python-biopython-doc python3-all python3-biopython 155s python3-biopython-sql python3-cairo python3-freetype python3-numpy 155s python3-numpy-dev python3-pil python3-reportlab python3-rlpycairo sgml-base 155s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 155s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 155s Need to get 47.4 MB of archives. 155s After this operation, 128 MB of additional disk space will be used. 155s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 155s Get:2 http://ftpmaster.internal/ubuntu questing/main s390x libblas3 s390x 3.12.1-2 [252 kB] 156s Get:3 http://ftpmaster.internal/ubuntu questing/main s390x libgfortran5 s390x 15-20250404-0ubuntu1 [621 kB] 156s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 156s Get:5 http://ftpmaster.internal/ubuntu questing/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 156s Get:6 http://ftpmaster.internal/ubuntu questing/main s390x sgml-base all 1.31 [11.4 kB] 156s Get:7 http://ftpmaster.internal/ubuntu questing/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 156s Get:8 http://ftpmaster.internal/ubuntu questing/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 156s Get:9 http://ftpmaster.internal/ubuntu questing/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 156s Get:10 http://ftpmaster.internal/ubuntu questing/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 156s Get:11 http://ftpmaster.internal/ubuntu questing/main s390x x11-common all 1:7.7+23ubuntu4 [21.8 kB] 156s Get:12 http://ftpmaster.internal/ubuntu questing/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 156s Get:13 http://ftpmaster.internal/ubuntu questing/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 156s Get:14 http://ftpmaster.internal/ubuntu questing/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 156s Get:15 http://ftpmaster.internal/ubuntu questing/main s390x fontconfig-config s390x 2.15.0-2.2ubuntu1 [37.9 kB] 156s Get:16 http://ftpmaster.internal/ubuntu questing/main s390x libfontconfig1 s390x 2.15.0-2.2ubuntu1 [150 kB] 156s Get:17 http://ftpmaster.internal/ubuntu questing/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 156s Get:18 http://ftpmaster.internal/ubuntu questing/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 156s Get:19 http://ftpmaster.internal/ubuntu questing/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 156s Get:20 http://ftpmaster.internal/ubuntu questing/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 156s Get:21 http://ftpmaster.internal/ubuntu questing/main s390x libcairo2 s390x 1.18.4-1 [580 kB] 156s Get:22 http://ftpmaster.internal/ubuntu questing/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 156s Get:23 http://ftpmaster.internal/ubuntu questing/main s390x libgomp1 s390x 15-20250404-0ubuntu1 [152 kB] 156s Get:24 http://ftpmaster.internal/ubuntu questing/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 156s Get:25 http://ftpmaster.internal/ubuntu questing/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 157s Get:26 http://ftpmaster.internal/ubuntu questing/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 157s Get:27 http://ftpmaster.internal/ubuntu questing/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 157s Get:28 http://ftpmaster.internal/ubuntu questing/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 157s Get:29 http://ftpmaster.internal/ubuntu questing/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 157s Get:30 http://ftpmaster.internal/ubuntu questing/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 157s Get:31 http://ftpmaster.internal/ubuntu questing-proposed/main s390x libjs-sphinxdoc all 8.2.3-1 [27.8 kB] 157s Get:32 http://ftpmaster.internal/ubuntu questing/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 157s Get:33 http://ftpmaster.internal/ubuntu questing/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 157s Get:34 http://ftpmaster.internal/ubuntu questing/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 157s Get:35 http://ftpmaster.internal/ubuntu questing/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 157s Get:36 http://ftpmaster.internal/ubuntu questing/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 157s Get:37 http://ftpmaster.internal/ubuntu questing/main s390x libtiff6 s390x 4.7.0-3ubuntu1 [219 kB] 157s Get:38 http://ftpmaster.internal/ubuntu questing/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 157s Get:39 http://ftpmaster.internal/ubuntu questing/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 157s Get:40 http://ftpmaster.internal/ubuntu questing/universe s390x python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 157s Get:41 http://ftpmaster.internal/ubuntu questing/main s390x python3-all s390x 3.13.3-1 [882 B] 157s Get:42 http://ftpmaster.internal/ubuntu questing/main s390x libopenjp2-7 s390x 2.5.3-2 [207 kB] 157s Get:43 http://ftpmaster.internal/ubuntu questing/main s390x python3-pil s390x 11.1.0-5build1 [498 kB] 157s Get:44 http://ftpmaster.internal/ubuntu questing/main s390x python3-cairo s390x 1.27.0-2 [120 kB] 157s Get:45 http://ftpmaster.internal/ubuntu questing/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 157s Get:46 http://ftpmaster.internal/ubuntu questing/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 157s Get:47 http://ftpmaster.internal/ubuntu questing/universe s390x python3-reportlab all 4.3.1-1 [1137 kB] 157s Get:48 http://ftpmaster.internal/ubuntu questing/main s390x xml-core all 0.19 [20.3 kB] 157s Get:49 http://ftpmaster.internal/ubuntu questing/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 157s Get:50 http://ftpmaster.internal/ubuntu questing/universe s390x python3-biopython s390x 1.85+dfsg-2build1 [1745 kB] 157s Get:51 http://ftpmaster.internal/ubuntu questing/universe s390x python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 158s Fetched 47.4 MB in 2s (19.8 MB/s) 158s Selecting previously unselected package python3-numpy-dev:s390x. 158s (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 ... 81470 files and directories currently installed.) 158s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 158s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 158s Selecting previously unselected package libblas3:s390x. 158s Preparing to unpack .../01-libblas3_3.12.1-2_s390x.deb ... 158s Unpacking libblas3:s390x (3.12.1-2) ... 158s Selecting previously unselected package libgfortran5:s390x. 158s Preparing to unpack .../02-libgfortran5_15-20250404-0ubuntu1_s390x.deb ... 158s Unpacking libgfortran5:s390x (15-20250404-0ubuntu1) ... 158s Selecting previously unselected package liblapack3:s390x. 158s Preparing to unpack .../03-liblapack3_3.12.1-2_s390x.deb ... 158s Unpacking liblapack3:s390x (3.12.1-2) ... 158s Selecting previously unselected package python3-numpy. 158s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 158s Unpacking python3-numpy (1:2.2.3+ds-5) ... 158s Selecting previously unselected package sgml-base. 158s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 158s Unpacking sgml-base (1.31) ... 158s Selecting previously unselected package fonts-dejavu-mono. 158s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-mono (2.37-8) ... 158s Selecting previously unselected package fonts-dejavu-core. 158s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-core (2.37-8) ... 158s Selecting previously unselected package libfontenc1:s390x. 158s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 158s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 158s Selecting previously unselected package libfreetype6:s390x. 158s Preparing to unpack .../09-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 158s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 158s Selecting previously unselected package x11-common. 158s Preparing to unpack .../10-x11-common_1%3a7.7+23ubuntu4_all.deb ... 158s Unpacking x11-common (1:7.7+23ubuntu4) ... 158s Selecting previously unselected package xfonts-encodings. 158s Preparing to unpack .../11-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 158s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 158s Selecting previously unselected package xfonts-utils. 158s Preparing to unpack .../12-xfonts-utils_1%3a7.7+7_s390x.deb ... 158s Unpacking xfonts-utils (1:7.7+7) ... 158s Selecting previously unselected package fonts-urw-base35. 158s Preparing to unpack .../13-fonts-urw-base35_20200910-8_all.deb ... 158s Unpacking fonts-urw-base35 (20200910-8) ... 158s Selecting previously unselected package fontconfig-config. 158s Preparing to unpack .../14-fontconfig-config_2.15.0-2.2ubuntu1_s390x.deb ... 158s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 158s Selecting previously unselected package libfontconfig1:s390x. 158s Preparing to unpack .../15-libfontconfig1_2.15.0-2.2ubuntu1_s390x.deb ... 158s Unpacking libfontconfig1:s390x (2.15.0-2.2ubuntu1) ... 158s Selecting previously unselected package libpixman-1-0:s390x. 158s Preparing to unpack .../16-libpixman-1-0_0.44.0-3_s390x.deb ... 158s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 159s Selecting previously unselected package libxcb-render0:s390x. 159s Preparing to unpack .../17-libxcb-render0_1.17.0-2_s390x.deb ... 159s Unpacking libxcb-render0:s390x (1.17.0-2) ... 159s Selecting previously unselected package libxcb-shm0:s390x. 159s Preparing to unpack .../18-libxcb-shm0_1.17.0-2_s390x.deb ... 159s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 159s Selecting previously unselected package libxrender1:s390x. 159s Preparing to unpack .../19-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 159s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 159s Selecting previously unselected package libcairo2:s390x. 159s Preparing to unpack .../20-libcairo2_1.18.4-1_s390x.deb ... 159s Unpacking libcairo2:s390x (1.18.4-1) ... 159s Selecting previously unselected package libdeflate0:s390x. 159s Preparing to unpack .../21-libdeflate0_1.23-2_s390x.deb ... 159s Unpacking libdeflate0:s390x (1.23-2) ... 159s Selecting previously unselected package libgomp1:s390x. 159s Preparing to unpack .../22-libgomp1_15-20250404-0ubuntu1_s390x.deb ... 159s Unpacking libgomp1:s390x (15-20250404-0ubuntu1) ... 159s Selecting previously unselected package libgraphite2-3:s390x. 159s Preparing to unpack .../23-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 159s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 159s Selecting previously unselected package libharfbuzz0b:s390x. 159s Preparing to unpack .../24-libharfbuzz0b_10.2.0-1_s390x.deb ... 159s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 159s Selecting previously unselected package libimagequant0:s390x. 159s Preparing to unpack .../25-libimagequant0_2.18.0-1build1_s390x.deb ... 159s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 159s Selecting previously unselected package libjpeg-turbo8:s390x. 159s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 159s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 159s Selecting previously unselected package libjpeg8:s390x. 159s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_s390x.deb ... 159s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 159s Selecting previously unselected package libjs-jquery. 159s Preparing to unpack .../28-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 159s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 159s Selecting previously unselected package libjs-underscore. 159s Preparing to unpack .../29-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 159s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 159s Selecting previously unselected package libjs-sphinxdoc. 159s Preparing to unpack .../30-libjs-sphinxdoc_8.2.3-1_all.deb ... 159s Unpacking libjs-sphinxdoc (8.2.3-1) ... 159s Selecting previously unselected package liblcms2-2:s390x. 159s Preparing to unpack .../31-liblcms2-2_2.16-2_s390x.deb ... 159s Unpacking liblcms2-2:s390x (2.16-2) ... 159s Selecting previously unselected package libraqm0:s390x. 159s Preparing to unpack .../32-libraqm0_0.10.2-1_s390x.deb ... 159s Unpacking libraqm0:s390x (0.10.2-1) ... 159s Selecting previously unselected package libsharpyuv0:s390x. 159s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1_s390x.deb ... 159s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 159s Selecting previously unselected package libjbig0:s390x. 159s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 159s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 159s Selecting previously unselected package libwebp7:s390x. 159s Preparing to unpack .../35-libwebp7_1.5.0-0.1_s390x.deb ... 159s Unpacking libwebp7:s390x (1.5.0-0.1) ... 159s Selecting previously unselected package libtiff6:s390x. 159s Preparing to unpack .../36-libtiff6_4.7.0-3ubuntu1_s390x.deb ... 159s Unpacking libtiff6:s390x (4.7.0-3ubuntu1) ... 159s Selecting previously unselected package libwebpdemux2:s390x. 159s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_s390x.deb ... 159s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 159s Selecting previously unselected package libwebpmux3:s390x. 159s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_s390x.deb ... 159s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 159s Selecting previously unselected package python-biopython-doc. 159s Preparing to unpack .../39-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 159s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 159s Selecting previously unselected package python3-all. 159s Preparing to unpack .../40-python3-all_3.13.3-1_s390x.deb ... 159s Unpacking python3-all (3.13.3-1) ... 159s Selecting previously unselected package libopenjp2-7:s390x. 159s Preparing to unpack .../41-libopenjp2-7_2.5.3-2_s390x.deb ... 159s Unpacking libopenjp2-7:s390x (2.5.3-2) ... 159s Selecting previously unselected package python3-pil:s390x. 159s Preparing to unpack .../42-python3-pil_11.1.0-5build1_s390x.deb ... 159s Unpacking python3-pil:s390x (11.1.0-5build1) ... 159s Selecting previously unselected package python3-cairo. 159s Preparing to unpack .../43-python3-cairo_1.27.0-2_s390x.deb ... 159s Unpacking python3-cairo (1.27.0-2) ... 159s Selecting previously unselected package python3-freetype. 159s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 159s Unpacking python3-freetype (2.5.1-1) ... 159s Selecting previously unselected package python3-rlpycairo. 159s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 159s Unpacking python3-rlpycairo (0.3.0-3) ... 159s Selecting previously unselected package python3-reportlab. 159s Preparing to unpack .../46-python3-reportlab_4.3.1-1_all.deb ... 159s Unpacking python3-reportlab (4.3.1-1) ... 159s Selecting previously unselected package xml-core. 159s Preparing to unpack .../47-xml-core_0.19_all.deb ... 159s Unpacking xml-core (0.19) ... 159s Selecting previously unselected package w3c-sgml-lib. 159s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 159s Unpacking w3c-sgml-lib (1.3-3) ... 159s Selecting previously unselected package python3-biopython. 159s Preparing to unpack .../49-python3-biopython_1.85+dfsg-2build1_s390x.deb ... 159s Unpacking python3-biopython (1.85+dfsg-2build1) ... 159s Selecting previously unselected package python3-biopython-sql. 159s Preparing to unpack .../50-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 159s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 159s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 159s Setting up liblcms2-2:s390x (2.16-2) ... 159s Setting up libpixman-1-0:s390x (0.44.0-3) ... 159s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 159s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 159s Setting up libxcb-render0:s390x (1.17.0-2) ... 159s Setting up x11-common (1:7.7+23ubuntu4) ... 159s Setting up libdeflate0:s390x (1.23-2) ... 159s Setting up python3-all (3.13.3-1) ... 159s Setting up libxcb-shm0:s390x (1.17.0-2) ... 159s Setting up libgomp1:s390x (15-20250404-0ubuntu1) ... 159s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 159s Setting up libfontenc1:s390x (1:1.1.8-1build1) ... 159s Setting up libblas3:s390x (3.12.1-2) ... 159s 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 159s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 159s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 159s Setting up libimagequant0:s390x (2.18.0-1build1) ... 159s Setting up fonts-dejavu-mono (2.37-8) ... 159s Setting up python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 159s Setting up fonts-dejavu-core (2.37-8) ... 159s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 159s Setting up libgfortran5:s390x (15-20250404-0ubuntu1) ... 159s Setting up libwebp7:s390x (1.5.0-0.1) ... 159s Setting up libopenjp2-7:s390x (2.5.3-2) ... 159s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 159s Setting up sgml-base (1.31) ... 159s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 159s Setting up libwebpmux3:s390x (1.5.0-0.1) ... 159s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 159s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 159s Setting up liblapack3:s390x (3.12.1-2) ... 159s 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 159s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 160s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 160s Setting up python3-freetype (2.5.1-1) ... 160s Setting up xfonts-utils (1:7.7+7) ... 160s Setting up libraqm0:s390x (0.10.2-1) ... 160s Setting up python3-numpy (1:2.2.3+ds-5) ... 161s Setting up libjs-sphinxdoc (8.2.3-1) ... 161s Setting up python-biopython-doc (1.85+dfsg-2build1) ... 161s Setting up libtiff6:s390x (4.7.0-3ubuntu1) ... 161s Setting up xml-core (0.19) ... 161s Setting up libfontconfig1:s390x (2.15.0-2.2ubuntu1) ... 161s Setting up fonts-urw-base35 (20200910-8) ... 161s Setting up libcairo2:s390x (1.18.4-1) ... 161s Setting up python3-pil:s390x (11.1.0-5build1) ... 161s Setting up python3-cairo (1.27.0-2) ... 161s Setting up python3-rlpycairo (0.3.0-3) ... 162s Setting up python3-reportlab (4.3.1-1) ... 162s Processing triggers for libc-bin (2.41-6ubuntu1) ... 162s Processing triggers for man-db (2.13.0-1) ... 163s Processing triggers for sgml-base (1.31) ... 163s Setting up w3c-sgml-lib (1.3-3) ... 183s Setting up python3-biopython (1.85+dfsg-2build1) ... 183s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 185s autopkgtest [21:09:18]: test dependencies: sh debian/tests/run-unit-test 185s autopkgtest [21:09:18]: test dependencies: [----------------------- 185s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 185s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 185s mkdir: created directory 'Bio' 185s mkdir: created directory 'Bio/Align' 185s mkdir: created directory 'Bio/Align/substitution_matrices' 185s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 185s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 186s test_Ace ... ok 186s test_Affy ... ok 187s test_AlignIO ... ok 187s test_AlignIO_ClustalIO ... ok 187s test_AlignIO_EmbossIO ... ok 187s test_AlignIO_FastaIO ... ok 187s test_AlignIO_MauveIO ... ok 187s test_AlignIO_PhylipIO ... ok 188s test_AlignIO_convert ... ok 188s test_AlignInfo ... ok 188s test_Align_Alignment ... ok 188s test_Align_a2m ... ok 188s test_Align_bed ... ok 188s test_Align_bigbed ... ok 188s test_Align_bigmaf ... ok 189s test_Align_bigpsl ... ok 189s test_Align_chain ... ok 189s test_Align_clustal ... ok 192s test_Align_codonalign ... ok 192s test_Align_emboss ... ok 192s test_Align_exonerate ... ok 192s test_Align_fasta ... ok 192s test_Align_hhr ... ok 193s test_Align_maf ... ok 193s test_Align_mauve ... ok 193s test_Align_msf ... ok 193s test_Align_nexus ... ok 193s test_Align_phylip ... ok 193s test_Align_psl ... ok 193s test_Align_sam ... ok 194s test_Align_stockholm ... ok 195s test_Align_tabular ... ok 195s test_Application ... ok 195s test_BioSQL_MySQLdb_online ... skipping. internet not available 195s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 195s test_BioSQL_mysql_connector_online ... skipping. internet not available 195s test_BioSQL_psycopg2_online ... skipping. internet not available 197s test_BioSQL_sqlite3 ... ok 197s test_BioSQL_sqlite3_online ... skipping. internet not available 197s test_Blast_Record ... ok 198s test_Blast_parser ... ok 198s test_CAPS ... ok 198s test_Chi2 ... ok 198s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 198s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 198s test_Cluster ... ok 198s test_CodonTable ... ok 198s test_ColorSpiral ... ok 198s test_Compass ... ok 199s test_Consensus ... ok 199s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 199s test_EMBL_unittest ... ok 199s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 199s test_EmbossPrimer ... ok 203s test_Entrez ... ok 203s test_Entrez_online ... skipping. internet not available 203s test_Entrez_parser ... ok 203s test_Enzyme ... ok 203s test_ExPASy ... skipping. internet not available 203s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 203s test_File ... ok 203s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 203s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 203s ok 205s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 206s ok 207s test_GraphicsChromosome ... ok 207s test_GraphicsDistribution ... ok 207s test_GraphicsGeneral ... ok 208s test_HMMCasino ... ok 208s test_HMMGeneral ... ok 208s test_KEGG ... ok 208s test_KEGG_online ... skipping. internet not available 212s test_KGML_graphics ... ok 212s test_KGML_graphics_online ... skipping. internet not available 212s test_KGML_nographics ... ok 212s test_KeyWList ... ok 212s test_LogisticRegression ... ok 213s test_MafIO_index ... ok 213s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 213s test_MarkovModel ... ok 213s test_Medline ... ok 213s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 213s test_NCBIXML ... Exception ignored in: 213s Traceback (most recent call last): 213s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 213s expat_parser.Parse(NULL, True) 213s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 214s ok 214s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 214s test_NCBI_qblast ... ok 214s test_NMR ... ok 214s test_NaiveBayes ... ok 214s test_Nexus ... ok 214s test_PAML_baseml ... ok 214s test_PAML_codeml ... ok 214s test_PAML_yn00 ... ok 218s test_PDB_CEAligner ... ok 218s test_PDB_DSSP ... ok 218s test_PDB_Dice ... ok 218s test_PDB_Disordered ... ok 219s test_PDB_Exposure ... ok 219s test_PDB_FragmentMapper ... ok 220s test_PDB_KDTree ... ok 220s test_PDB_MMCIF2Dict ... ok 220s test_PDB_MMCIFIO ... ok 221s test_PDB_MMCIFParser ... ok 221s test_PDB_NACCESS ... ok 221s test_PDB_PDBIO ... ok 221s test_PDB_PDBList ... skipping. internet not available 228s test_PDB_PDBMLParser ... ok 228s test_PDB_PDBParser ... ok 228s 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 228s test_PDB_Polypeptide ... ok 228s test_PDB_QCPSuperimposer ... ok 231s test_PDB_SASA ... ok 231s test_PDB_SMCRA ... ok 231s test_PDB_Selection ... ok 231s test_PDB_StructureAlignment ... ok 231s test_PDB_Superimposer ... ok 231s test_PDB_alphafold_db ... skipping. internet not available 231s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 231s 231s test_PDB_parse_pdb_header ... ok 231s test_PDB_vectors ... ok 231s test_PQR ... ok 231s test_Pathway ... ok 231s test_Phd ... ok 231s test_Phylo ... ok 232s test_PhyloXML ... ok 232s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 232s test_Phylo_NeXML ... ok 232s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 232s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 232s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 232s test_PopGen_GenePop_nodepend ... ok 232s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 232s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 232s test_ProtParam ... ok 232s test_RCSBFormats ... ok 233s test_Restriction ... ok 233s test_SCOP_Astral ... ok 233s test_SCOP_Cla ... ok 233s test_SCOP_Des ... ok 233s test_SCOP_Dom ... ok 233s test_SCOP_Hie ... ok 233s test_SCOP_Raf ... ok 233s test_SCOP_Residues ... ok 233s test_SCOP_Scop ... ok 233s test_SVDSuperimposer ... ok 233s test_SearchIO_blast_tab ... ok 233s test_SearchIO_blast_tab_index ... ok 233s test_SearchIO_blast_xml ... ok 234s test_SearchIO_blast_xml_index ... ok 234s test_SearchIO_blat_psl ... ok 234s test_SearchIO_blat_psl_index ... ok 234s test_SearchIO_exonerate ... ok 234s test_SearchIO_exonerate_text_index ... ok 234s test_SearchIO_exonerate_vulgar_index ... ok 234s test_SearchIO_fasta_m10 ... ok 234s test_SearchIO_fasta_m10_index ... ok 235s test_SearchIO_hhsuite2_text ... ok 235s test_SearchIO_hmmer2_text ... ok 235s test_SearchIO_hmmer2_text_index ... ok 235s test_SearchIO_hmmer3_domtab ... ok 235s test_SearchIO_hmmer3_domtab_index ... ok 235s test_SearchIO_hmmer3_tab ... ok 235s test_SearchIO_hmmer3_tab_index ... ok 235s test_SearchIO_hmmer3_text ... ok 235s test_SearchIO_hmmer3_text_index ... ok 235s test_SearchIO_interproscan_xml ... ok 235s test_SearchIO_model ... ok 235s test_SearchIO_write ... ok 235s test_SeqFeature ... ok 247s test_SeqIO ... ok 247s test_SeqIO_AbiIO ... ok 247s test_SeqIO_FastaIO ... ok 247s test_SeqIO_Gck ... ok 247s test_SeqIO_Gfa ... ok 247s test_SeqIO_Insdc ... ok 247s test_SeqIO_NibIO ... ok 249s test_SeqIO_PdbIO ... ok 249s test_SeqIO_QualityIO ... ok 249s test_SeqIO_SeqXML ... ok 249s test_SeqIO_SffIO ... ok 249s test_SeqIO_SnapGene ... ok 249s test_SeqIO_TwoBitIO ... ok 250s test_SeqIO_UniprotIO ... ok 250s test_SeqIO_Xdna ... ok 250s test_SeqIO_features ... ok 259s test_SeqIO_index ... ok 259s test_SeqIO_online ... skipping. internet not available 259s test_SeqIO_write ... ok 259s test_SeqRecord ... ok 259s test_SeqUtils ... ok 260s test_Seq_objs ... ok 260s test_SwissProt ... ok 260s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 260s test_TogoWS ... skipping. internet not available 261s test_TreeConstruction ... ok 261s test_UniGene ... ok 261s test_UniProt ... skipping. internet not available 261s test_UniProt_GOA ... ok 261s test_align ... ok 261s test_align_substitution_matrices ... ok 263s test_bgzf ... ok 263s test_cellosaurus ... ok 266s test_codonalign ... ok 267s test_geo ... ok 267s test_kNN ... ok 267s test_motifs ... ok 267s test_motifs_online ... skipping. internet not available 267s 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. 267s warnings.warn( 267s ok 267s test_pairwise2_no_C ... ok 267s test_pairwise_aligner ... ok 267s test_pairwise_alignment_map ... ok 273s test_phenotype ... ok 273s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 273s 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. 273s test_prodoc ... ok 273s test_prosite ... ok 273s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 273s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 273s test_seq ... ok 273s test_translate ... ok 273s ---------------------------------------------------------------------- 273s Ran 216 tests in 87.594 seconds 273s 273s Skipping any tests requiring internet access 273s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 273s Operating system: posix linux 273s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 273s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 274s autopkgtest [21:10:47]: test dependencies: -----------------------] 274s autopkgtest [21:10:47]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 274s dependencies PASS 274s autopkgtest [21:10:47]: test full_suite: preparing testbed 391s autopkgtest [21:12:44]: testbed dpkg architecture: s390x 392s autopkgtest [21:12:45]: testbed apt version: 3.0.0 392s autopkgtest [21:12:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 392s autopkgtest [21:12:45]: testbed release detected to be: questing 393s autopkgtest [21:12:46]: updating testbed package index (apt update) 393s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 393s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 393s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 393s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 393s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1430 kB] 394s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.7 kB] 394s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [149 kB] 394s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main s390x Packages [178 kB] 394s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x Packages [1275 kB] 394s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse s390x Packages [26.2 kB] 394s Fetched 3202 kB in 1s (2919 kB/s) 395s Reading package lists... 395s autopkgtest [21:12:48]: upgrading testbed (apt dist-upgrade and autopurge) 395s Reading package lists... 395s Building dependency tree... 395s Reading state information... 396s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 396s Starting 2 pkgProblemResolver with broken count: 0 396s Done 396s Entering ResolveByKeep 396s 396s Calculating upgrade... 396s The following packages will be upgraded: 396s cloud-init cloud-init-base libmbim-glib4 libmbim-proxy libpython3.12-minimal 396s libpython3.12-stdlib libpython3.12t64 libqmi-glib5 libqmi-proxy libsepol2 396s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 396s Need to get 7523 kB of archives. 396s After this operation, 158 kB disk space will be freed. 396s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x libsepol2 s390x 3.8.1-1 [332 kB] 397s Get:2 http://ftpmaster.internal/ubuntu questing/main s390x cloud-init-base all 25.2~1g7a0265d3-0ubuntu1 [619 kB] 397s Get:3 http://ftpmaster.internal/ubuntu questing/main s390x libmbim-proxy s390x 1.32.0-1 [6226 B] 397s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x libmbim-glib4 s390x 1.32.0-1 [239 kB] 397s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12t64 s390x 3.12.10-1 [2509 kB] 397s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12-stdlib s390x 3.12.10-1 [2049 kB] 397s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12-minimal s390x 3.12.10-1 [836 kB] 397s Get:8 http://ftpmaster.internal/ubuntu questing/main s390x libqmi-proxy s390x 1.36.0-1 [6190 B] 397s Get:9 http://ftpmaster.internal/ubuntu questing/main s390x libqmi-glib5 s390x 1.36.0-1 [925 kB] 397s Get:10 http://ftpmaster.internal/ubuntu questing/main s390x cloud-init all 25.2~1g7a0265d3-0ubuntu1 [2106 B] 397s Preconfiguring packages ... 397s Fetched 7523 kB in 1s (9798 kB/s) 397s (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 ... 81470 files and directories currently installed.) 397s Preparing to unpack .../libsepol2_3.8.1-1_s390x.deb ... 397s Unpacking libsepol2:s390x (3.8.1-1) over (3.7-1) ... 397s Setting up libsepol2:s390x (3.8.1-1) ... 397s (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 ... 81470 files and directories currently installed.) 397s Preparing to unpack .../0-cloud-init-base_25.2~1g7a0265d3-0ubuntu1_all.deb ... 397s Unpacking cloud-init-base (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 397s Preparing to unpack .../1-libmbim-proxy_1.32.0-1_s390x.deb ... 397s Unpacking libmbim-proxy (1.32.0-1) over (1.31.2-0ubuntu4) ... 397s Preparing to unpack .../2-libmbim-glib4_1.32.0-1_s390x.deb ... 397s Unpacking libmbim-glib4:s390x (1.32.0-1) over (1.31.2-0ubuntu4) ... 397s Preparing to unpack .../3-libpython3.12t64_3.12.10-1_s390x.deb ... 397s Unpacking libpython3.12t64:s390x (3.12.10-1) over (3.12.8-3) ... 398s Preparing to unpack .../4-libpython3.12-stdlib_3.12.10-1_s390x.deb ... 398s Unpacking libpython3.12-stdlib:s390x (3.12.10-1) over (3.12.8-3) ... 398s Preparing to unpack .../5-libpython3.12-minimal_3.12.10-1_s390x.deb ... 398s Unpacking libpython3.12-minimal:s390x (3.12.10-1) over (3.12.8-3) ... 398s Preparing to unpack .../6-libqmi-proxy_1.36.0-1_s390x.deb ... 398s Unpacking libqmi-proxy (1.36.0-1) over (1.35.6-1) ... 398s Preparing to unpack .../7-libqmi-glib5_1.36.0-1_s390x.deb ... 398s Unpacking libqmi-glib5:s390x (1.36.0-1) over (1.35.6-1) ... 398s Preparing to unpack .../8-cloud-init_25.2~1g7a0265d3-0ubuntu1_all.deb ... 398s Unpacking cloud-init (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 398s Setting up libpython3.12-minimal:s390x (3.12.10-1) ... 398s Setting up cloud-init-base (25.2~1g7a0265d3-0ubuntu1) ... 399s Setting up libmbim-glib4:s390x (1.32.0-1) ... 399s Setting up cloud-init (25.2~1g7a0265d3-0ubuntu1) ... 399s Setting up libpython3.12-stdlib:s390x (3.12.10-1) ... 399s Setting up libmbim-proxy (1.32.0-1) ... 399s Setting up libpython3.12t64:s390x (3.12.10-1) ... 399s Setting up libqmi-glib5:s390x (1.36.0-1) ... 399s Setting up libqmi-proxy (1.36.0-1) ... 399s Processing triggers for libc-bin (2.41-6ubuntu1) ... 399s Processing triggers for rsyslog (8.2412.0-2ubuntu2) ... 399s Processing triggers for man-db (2.13.0-1) ... 400s Reading package lists... 400s Building dependency tree... 400s Reading state information... 400s Starting pkgProblemResolver with broken count: 0 400s Starting 2 pkgProblemResolver with broken count: 0 400s Done 400s Solving dependencies... 400s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 400s autopkgtest [21:12:53]: rebooting testbed after setup commands that affected boot 422s Reading package lists... 422s Building dependency tree... 422s Reading state information... 422s Starting pkgProblemResolver with broken count: 0 422s Starting 2 pkgProblemResolver with broken count: 0 422s Done 423s The following NEW packages will be installed: 423s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 423s cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit 423s dh-autoreconf dh-python dh-strip-nondeterminism dialign docutils-common dssp 423s dwz fasttree flex fontconfig-config fonts-dejavu-core fonts-dejavu-mono 423s fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ 423s g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 423s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gettext ghostscript hevea 423s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 423s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 423s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 423s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 423s libcolamd3 libcommons-logging-java libcommons-parent-java libcups2t64 423s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 423s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 423s libfreetype6 libgcc-14-dev libgfortran5 libglpk40 libgomp1 libgraphite2-3 423s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 423s libheif-plugin-libde265 libheif1 libice6 libidn12 libigraph3t64 libijs-0.35 423s libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 libjpeg-turbo8 423s libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore 423s libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 liblqr-1-0 423s libltdl7 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmbedcrypto16 423s libmbedtls21 libmbedx509-7 libmpc3 libmpfi0 libmysqlclient24 libnetpbm11t64 423s libopenjp2-7 libpaper-utils libpaper2 libpdfbox-java libpixman-1-0 libplfit0 423s libpotrace0 libptexenc1 libpython3-all-dev libpython3-dev libpython3.13-dev 423s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 423s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 423s libtiff6 libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2 libwebpmux3 423s libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 423s libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft 423s mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data 423s prank preview-latex-style probcons python-biopython-doc 423s python-matplotlib-data python3-alabaster python3-all python3-all-dev 423s python3-biopython python3-biopython-sql python3-brotli python3-cairo 423s python3-contourpy python3-cycler python3-dateutil python3-decorator 423s python3-defusedxml python3-dev python3-docutils python3-fonttools 423s python3-freetype python3-fs python3-igraph python3-imagesize 423s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 423s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 423s python3-numpy python3-numpy-dev python3-numpydoc python3-packaging 423s python3-pil python3-pil.imagetk python3-platformdirs python3-rdflib 423s python3-reportlab python3-rlpycairo python3-roman python3-roman-numerals 423s python3-scipy python3-snowballstemmer python3-sphinx 423s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 423s python3-tabulate python3-texttable python3-tk python3-ufolib2 python3.13-dev 423s python3.13-tk sgml-base sphinx-common sphinx-rtd-theme-common t-coffee 423s t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended 423s texlive-latex-base texlive-latex-extra texlive-latex-recommended 423s texlive-pictures tk8.6-blt2.5 unicode-data w3c-sgml-lib wise wise-data 423s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 423s 0 upgraded, 250 newly installed, 0 to remove and 0 not upgraded. 423s Need to get 335 MB of archives. 423s After this operation, 1230 MB of additional disk space will be used. 423s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x m4 s390x 1.4.19-7 [259 kB] 423s Get:2 http://ftpmaster.internal/ubuntu questing/main s390x flex s390x 2.6.4-8.2build1 [311 kB] 423s Get:3 http://ftpmaster.internal/ubuntu questing/main s390x fonts-lato all 2.015-1 [2781 kB] 423s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x libgomp1 s390x 15-20250404-0ubuntu1 [152 kB] 423s Get:5 http://ftpmaster.internal/ubuntu questing/main s390x libfftw3-double3 s390x 3.3.10-2fakesync1build1 [511 kB] 423s Get:6 http://ftpmaster.internal/ubuntu questing/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 423s Get:7 http://ftpmaster.internal/ubuntu questing/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 423s Get:8 http://ftpmaster.internal/ubuntu questing/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 423s Get:9 http://ftpmaster.internal/ubuntu questing/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 423s Get:10 http://ftpmaster.internal/ubuntu questing/main s390x x11-common all 1:7.7+23ubuntu4 [21.8 kB] 423s Get:11 http://ftpmaster.internal/ubuntu questing/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 423s Get:12 http://ftpmaster.internal/ubuntu questing/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 423s Get:13 http://ftpmaster.internal/ubuntu questing/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 424s Get:14 http://ftpmaster.internal/ubuntu questing/main s390x fontconfig-config s390x 2.15.0-2.2ubuntu1 [37.9 kB] 424s Get:15 http://ftpmaster.internal/ubuntu questing/main s390x libfontconfig1 s390x 2.15.0-2.2ubuntu1 [150 kB] 424s Get:16 http://ftpmaster.internal/ubuntu questing/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 424s Get:17 http://ftpmaster.internal/ubuntu questing/main s390x libaom3 s390x 3.12.1-1 [1491 kB] 424s Get:18 http://ftpmaster.internal/ubuntu questing/main s390x libheif-plugin-aomdec s390x 1.19.7-1 [11.6 kB] 424s Get:19 http://ftpmaster.internal/ubuntu questing/main s390x libde265-0 s390x 1.0.15-1build5 [175 kB] 424s Get:20 http://ftpmaster.internal/ubuntu questing/main s390x libheif-plugin-libde265 s390x 1.19.7-1 [9054 B] 424s Get:21 http://ftpmaster.internal/ubuntu questing/main s390x libheif1 s390x 1.19.7-1 [415 kB] 424s Get:22 http://ftpmaster.internal/ubuntu questing/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 424s Get:23 http://ftpmaster.internal/ubuntu questing/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 424s Get:24 http://ftpmaster.internal/ubuntu questing/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 424s Get:25 http://ftpmaster.internal/ubuntu questing/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 424s Get:26 http://ftpmaster.internal/ubuntu questing/universe s390x liblqr-1-0 s390x 0.4.2-2.1build2 [32.6 kB] 424s Get:27 http://ftpmaster.internal/ubuntu questing/main s390x libltdl7 s390x 2.5.4-4 [43.8 kB] 424s Get:28 http://ftpmaster.internal/ubuntu questing/main s390x libopenjp2-7 s390x 2.5.3-2 [207 kB] 424s Get:29 http://ftpmaster.internal/ubuntu questing/main s390x libraw23t64 s390x 0.21.4-2 [415 kB] 424s Get:30 http://ftpmaster.internal/ubuntu questing/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 424s Get:31 http://ftpmaster.internal/ubuntu questing/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 424s Get:32 http://ftpmaster.internal/ubuntu questing/main s390x libtiff6 s390x 4.7.0-3ubuntu1 [219 kB] 424s Get:33 http://ftpmaster.internal/ubuntu questing/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 424s Get:34 http://ftpmaster.internal/ubuntu questing/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 424s Get:35 http://ftpmaster.internal/ubuntu questing/universe s390x imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [69.7 kB] 424s Get:36 http://ftpmaster.internal/ubuntu questing/universe s390x libmagickcore-7.q16-10 s390x 8:7.1.1.43+dfsg1-1 [2040 kB] 424s Get:37 http://ftpmaster.internal/ubuntu questing/universe s390x libmagickwand-7.q16-10 s390x 8:7.1.1.43+dfsg1-1 [375 kB] 424s Get:38 http://ftpmaster.internal/ubuntu questing/main s390x poppler-data all 0.4.12-1 [2060 kB] 424s Get:39 http://ftpmaster.internal/ubuntu questing/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 424s Get:40 http://ftpmaster.internal/ubuntu questing/main s390x libblas3 s390x 3.12.1-2 [252 kB] 424s Get:41 http://ftpmaster.internal/ubuntu questing/main s390x libgfortran5 s390x 15-20250404-0ubuntu1 [621 kB] 424s Get:42 http://ftpmaster.internal/ubuntu questing/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 424s Get:43 http://ftpmaster.internal/ubuntu questing/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 424s Get:44 http://ftpmaster.internal/ubuntu questing/main s390x sgml-base all 1.31 [11.4 kB] 424s Get:45 http://ftpmaster.internal/ubuntu questing/main s390x autoconf all 2.72-3ubuntu1 [383 kB] 424s Get:46 http://ftpmaster.internal/ubuntu questing/main s390x autotools-dev all 20220109.1 [44.9 kB] 424s Get:47 http://ftpmaster.internal/ubuntu questing/main s390x automake all 1:1.17-3ubuntu1 [572 kB] 424s Get:48 http://ftpmaster.internal/ubuntu questing/main s390x autopoint all 0.23.1-1 [619 kB] 424s Get:49 http://ftpmaster.internal/ubuntu questing/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 424s Get:50 http://ftpmaster.internal/ubuntu questing/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 424s Get:51 http://ftpmaster.internal/ubuntu questing/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 424s Get:52 http://ftpmaster.internal/ubuntu questing/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 424s Get:53 http://ftpmaster.internal/ubuntu questing/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 424s Get:54 http://ftpmaster.internal/ubuntu questing/main s390x tk8.6-blt2.5 s390x 2.5.3+dfsg-8 [657 kB] 424s Get:55 http://ftpmaster.internal/ubuntu questing/main s390x blt s390x 2.5.3+dfsg-8 [4826 B] 424s Get:56 http://ftpmaster.internal/ubuntu questing/main s390x libisl23 s390x 0.27-1 [704 kB] 424s Get:57 http://ftpmaster.internal/ubuntu questing/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 424s Get:58 http://ftpmaster.internal/ubuntu questing/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-19ubuntu2 [9572 kB] 424s Get:59 http://ftpmaster.internal/ubuntu questing/main s390x cpp-14 s390x 14.2.0-19ubuntu2 [1024 B] 424s Get:60 http://ftpmaster.internal/ubuntu questing/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 424s Get:61 http://ftpmaster.internal/ubuntu questing/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 424s Get:62 http://ftpmaster.internal/ubuntu questing/main s390x libcc1-0 s390x 15-20250404-0ubuntu1 [49.6 kB] 424s Get:63 http://ftpmaster.internal/ubuntu questing/main s390x libitm1 s390x 15-20250404-0ubuntu1 [31.2 kB] 424s Get:64 http://ftpmaster.internal/ubuntu questing/main s390x libasan8 s390x 15-20250404-0ubuntu1 [2966 kB] 425s Get:65 http://ftpmaster.internal/ubuntu questing/main s390x libubsan1 s390x 15-20250404-0ubuntu1 [1210 kB] 425s Get:66 http://ftpmaster.internal/ubuntu questing/main s390x libgcc-14-dev s390x 14.2.0-19ubuntu2 [1037 kB] 425s Get:67 http://ftpmaster.internal/ubuntu questing/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-19ubuntu2 [18.7 MB] 425s Get:68 http://ftpmaster.internal/ubuntu questing/main s390x gcc-14 s390x 14.2.0-19ubuntu2 [529 kB] 425s Get:69 http://ftpmaster.internal/ubuntu questing/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 425s Get:70 http://ftpmaster.internal/ubuntu questing/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 425s Get:71 http://ftpmaster.internal/ubuntu questing/main s390x libstdc++-14-dev s390x 14.2.0-19ubuntu2 [2614 kB] 425s Get:72 http://ftpmaster.internal/ubuntu questing/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-19ubuntu2 [11.0 MB] 425s Get:73 http://ftpmaster.internal/ubuntu questing/main s390x g++-14 s390x 14.2.0-19ubuntu2 [23.0 kB] 425s Get:74 http://ftpmaster.internal/ubuntu questing/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 425s Get:75 http://ftpmaster.internal/ubuntu questing/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 425s Get:76 http://ftpmaster.internal/ubuntu questing/main s390x build-essential s390x 12.12ubuntu1 [5090 B] 425s Get:77 http://ftpmaster.internal/ubuntu questing/universe s390x bwa s390x 0.7.18-1 [249 kB] 425s Get:78 http://ftpmaster.internal/ubuntu questing/universe s390x libargtable2-0 s390x 13-3 [16.9 kB] 425s Get:79 http://ftpmaster.internal/ubuntu questing/universe s390x clustalo s390x 1.2.4-8build1 [218 kB] 425s Get:80 http://ftpmaster.internal/ubuntu questing/main s390x libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 425s Get:81 http://ftpmaster.internal/ubuntu questing/main s390x libtool all 2.5.4-4 [168 kB] 425s Get:82 http://ftpmaster.internal/ubuntu questing/main s390x dh-autoreconf all 20 [16.1 kB] 425s Get:83 http://ftpmaster.internal/ubuntu questing/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 425s Get:84 http://ftpmaster.internal/ubuntu questing/main s390x libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 425s Get:85 http://ftpmaster.internal/ubuntu questing/main s390x dh-strip-nondeterminism all 1.14.1-2 [5064 B] 425s Get:86 http://ftpmaster.internal/ubuntu questing/main s390x debugedit s390x 1:5.1-2 [50.1 kB] 425s Get:87 http://ftpmaster.internal/ubuntu questing/main s390x dwz s390x 0.15-1build6 [122 kB] 425s Get:88 http://ftpmaster.internal/ubuntu questing/main s390x gettext s390x 0.23.1-1 [1065 kB] 425s Get:89 http://ftpmaster.internal/ubuntu questing/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] 425s Get:90 http://ftpmaster.internal/ubuntu questing/main s390x po-debconf all 1.0.21+nmu1 [233 kB] 425s Get:91 http://ftpmaster.internal/ubuntu questing/main s390x debhelper all 13.24.1ubuntu2 [895 kB] 426s Get:92 http://ftpmaster.internal/ubuntu questing/universe s390x dh-python all 6.20250308 [118 kB] 426s Get:93 http://ftpmaster.internal/ubuntu questing/universe s390x dialign s390x 2.2.1-13 [155 kB] 426s Get:94 http://ftpmaster.internal/ubuntu questing/main s390x xml-core all 0.19 [20.3 kB] 426s Get:95 http://ftpmaster.internal/ubuntu questing/main s390x docutils-common all 0.21.2+dfsg-2 [131 kB] 426s Get:96 http://ftpmaster.internal/ubuntu questing/universe s390x libcifpp-data all 7.0.9-1 [481 kB] 426s Get:97 http://ftpmaster.internal/ubuntu questing/universe s390x libcifpp7 s390x 7.0.9-1 [1103 kB] 426s Get:98 http://ftpmaster.internal/ubuntu questing/universe s390x dssp s390x 4.4.10-1 [784 kB] 426s Get:99 http://ftpmaster.internal/ubuntu questing/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 426s Get:100 http://ftpmaster.internal/ubuntu questing/universe s390x fonts-lmodern all 2.005-1 [4799 kB] 426s Get:101 http://ftpmaster.internal/ubuntu questing/universe s390x fonts-lyx all 2.4.3-1 [171 kB] 426s Get:102 http://ftpmaster.internal/ubuntu questing/main s390x libgs-common all 10.05.0dfsg1-0ubuntu1 [176 kB] 426s Get:103 http://ftpmaster.internal/ubuntu questing/main s390x libgs10-common all 10.05.0dfsg1-0ubuntu1 [490 kB] 426s Get:104 http://ftpmaster.internal/ubuntu questing/main s390x libavahi-common-data s390x 0.8-16ubuntu2 [31.0 kB] 426s Get:105 http://ftpmaster.internal/ubuntu questing/main s390x libavahi-common3 s390x 0.8-16ubuntu2 [23.5 kB] 426s Get:106 http://ftpmaster.internal/ubuntu questing/main s390x libavahi-client3 s390x 0.8-16ubuntu2 [26.3 kB] 426s Get:107 http://ftpmaster.internal/ubuntu questing/main s390x libcups2t64 s390x 2.4.12-0ubuntu1 [282 kB] 426s Get:108 http://ftpmaster.internal/ubuntu questing/main s390x libidn12 s390x 1.43-1 [58.9 kB] 426s Get:109 http://ftpmaster.internal/ubuntu questing/main s390x libijs-0.35 s390x 0.35-15.2 [15.4 kB] 426s Get:110 http://ftpmaster.internal/ubuntu questing/main s390x libjbig2dec0 s390x 0.20-1build3 [69.3 kB] 426s Get:111 http://ftpmaster.internal/ubuntu questing/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 426s Get:112 http://ftpmaster.internal/ubuntu questing/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 426s Get:113 http://ftpmaster.internal/ubuntu questing/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 426s Get:114 http://ftpmaster.internal/ubuntu questing/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 426s Get:115 http://ftpmaster.internal/ubuntu questing/main s390x libgs10 s390x 10.05.0dfsg1-0ubuntu1 [3974 kB] 426s Get:116 http://ftpmaster.internal/ubuntu questing/main s390x ghostscript s390x 10.05.0dfsg1-0ubuntu1 [42.8 kB] 426s Get:117 http://ftpmaster.internal/ubuntu questing/universe s390x libnetpbm11t64 s390x 2:11.09.02-2 [124 kB] 426s Get:118 http://ftpmaster.internal/ubuntu questing/universe s390x netpbm s390x 2:11.09.02-2 [2207 kB] 427s Get:119 http://ftpmaster.internal/ubuntu questing/universe s390x tex-common all 6.19 [29.8 kB] 427s Get:120 http://ftpmaster.internal/ubuntu questing/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 427s Get:121 http://ftpmaster.internal/ubuntu questing/universe s390x libkpathsea6 s390x 2024.20240313.70630+ds-6 [67.0 kB] 427s Get:122 http://ftpmaster.internal/ubuntu questing/universe s390x libptexenc1 s390x 2024.20240313.70630+ds-6 [43.4 kB] 427s Get:123 http://ftpmaster.internal/ubuntu questing/universe s390x libsynctex2 s390x 2024.20240313.70630+ds-6 [64.8 kB] 427s Get:124 http://ftpmaster.internal/ubuntu questing/universe s390x libtexlua53-5 s390x 2024.20240313.70630+ds-6 [131 kB] 427s Get:125 http://ftpmaster.internal/ubuntu questing/main s390x t1utils s390x 1.41-4build3 [65.6 kB] 427s Get:126 http://ftpmaster.internal/ubuntu questing/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 427s Get:127 http://ftpmaster.internal/ubuntu questing/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 427s Get:128 http://ftpmaster.internal/ubuntu questing/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 427s Get:129 http://ftpmaster.internal/ubuntu questing/main s390x libcairo2 s390x 1.18.4-1 [580 kB] 427s Get:130 http://ftpmaster.internal/ubuntu questing/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 427s Get:131 http://ftpmaster.internal/ubuntu questing/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 427s Get:132 http://ftpmaster.internal/ubuntu questing/universe s390x libmpfi0 s390x 1.5.4+ds-4 [34.1 kB] 427s Get:133 http://ftpmaster.internal/ubuntu questing/universe s390x libpotrace0 s390x 1.16-2build1 [18.7 kB] 427s Get:134 http://ftpmaster.internal/ubuntu questing/universe s390x libteckit0 s390x 2.5.12+ds1-1 [433 kB] 427s Get:135 http://ftpmaster.internal/ubuntu questing/main s390x libxmu6 s390x 2:1.1.3-3build2 [53.0 kB] 427s Get:136 http://ftpmaster.internal/ubuntu questing/main s390x libxpm4 s390x 1:3.5.17-1build2 [41.2 kB] 427s Get:137 http://ftpmaster.internal/ubuntu questing/main s390x libxaw7 s390x 2:1.0.16-1 [201 kB] 427s Get:138 http://ftpmaster.internal/ubuntu questing/main s390x libxi6 s390x 2:1.8.2-1 [35.4 kB] 427s Get:139 http://ftpmaster.internal/ubuntu questing/universe s390x libzzip-0-13t64 s390x 0.13.78+dfsg.1-0.1 [29.8 kB] 427s Get:140 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-binaries s390x 2024.20240313.70630+ds-6 [9170 kB] 427s Get:141 http://ftpmaster.internal/ubuntu questing/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 427s Get:142 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-base all 2024.20250309-1 [22.7 MB] 428s Get:143 http://ftpmaster.internal/ubuntu questing/main s390x hicolor-icon-theme all 0.18-2 [13.3 kB] 428s Get:144 http://ftpmaster.internal/ubuntu questing/universe s390x imagemagick-7.q16 s390x 8:7.1.1.43+dfsg1-1 [703 kB] 428s Get:145 http://ftpmaster.internal/ubuntu questing/universe s390x imagemagick s390x 8:7.1.1.43+dfsg1-1 [14.1 kB] 428s Get:146 http://ftpmaster.internal/ubuntu questing/universe s390x hevea s390x 2.36-2 [2045 kB] 428s Get:147 http://ftpmaster.internal/ubuntu questing/main s390x libsuitesparseconfig7 s390x 1:7.8.3+dfsg-3 [13.2 kB] 428s Get:148 http://ftpmaster.internal/ubuntu questing/universe s390x libamd3 s390x 1:7.8.3+dfsg-3 [35.1 kB] 428s Get:149 http://ftpmaster.internal/ubuntu questing/universe s390x libapache-pom-java all 33-2 [5874 B] 428s Get:150 http://ftpmaster.internal/ubuntu questing/universe s390x libarpack2t64 s390x 3.9.1-4 [110 kB] 428s Get:151 http://ftpmaster.internal/ubuntu questing/main s390x libcolamd3 s390x 1:7.8.3+dfsg-3 [23.4 kB] 428s Get:152 http://ftpmaster.internal/ubuntu questing/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 428s Get:153 http://ftpmaster.internal/ubuntu questing/universe s390x libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 428s Get:154 http://ftpmaster.internal/ubuntu questing/main s390x libexpat1-dev s390x 2.7.1-1 [148 kB] 428s Get:155 http://ftpmaster.internal/ubuntu questing/universe s390x libglpk40 s390x 5.0-1build2 [406 kB] 428s Get:156 http://ftpmaster.internal/ubuntu questing/universe s390x libplfit0 s390x 0.9.6+ds-2ubuntu1 [29.7 kB] 428s Get:157 http://ftpmaster.internal/ubuntu questing/universe s390x libigraph3t64 s390x 0.10.15+ds-3 [1015 kB] 429s Get:158 http://ftpmaster.internal/ubuntu questing/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 429s Get:159 http://ftpmaster.internal/ubuntu questing/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 429s Get:160 http://ftpmaster.internal/ubuntu questing/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 429s Get:161 http://ftpmaster.internal/ubuntu questing/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 429s Get:162 http://ftpmaster.internal/ubuntu questing-proposed/main s390x libjs-sphinxdoc all 8.2.3-1 [27.8 kB] 429s Get:163 http://ftpmaster.internal/ubuntu questing/main s390x libjson-perl all 4.10000-1 [81.9 kB] 429s Get:164 http://ftpmaster.internal/ubuntu questing/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 429s Get:165 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedcrypto16 s390x 3.6.2-3ubuntu1 [261 kB] 429s Get:166 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedx509-7 s390x 3.6.2-3ubuntu1 [34.9 kB] 429s Get:167 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedtls21 s390x 3.6.2-3ubuntu1 [122 kB] 429s Get:168 http://ftpmaster.internal/ubuntu questing/main s390x mysql-common all 5.8+1.1.1ubuntu1 [6922 B] 429s Get:169 http://ftpmaster.internal/ubuntu questing/main s390x libmysqlclient24 s390x 8.4.4-0ubuntu2 [1295 kB] 429s Get:170 http://ftpmaster.internal/ubuntu questing/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 429s Get:171 http://ftpmaster.internal/ubuntu questing/main s390x libpython3.13-dev s390x 3.13.3-1 [5607 kB] 429s Get:172 http://ftpmaster.internal/ubuntu questing/main s390x libpython3-dev s390x 3.13.3-1 [10.8 kB] 429s Get:173 http://ftpmaster.internal/ubuntu questing/main s390x libpython3-all-dev s390x 3.13.3-1 [906 B] 429s Get:174 http://ftpmaster.internal/ubuntu questing/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 429s Get:175 http://ftpmaster.internal/ubuntu questing/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 429s Get:176 http://ftpmaster.internal/ubuntu questing/main s390x libxslt1.1 s390x 1.1.39-0exp1ubuntu4 [170 kB] 429s Get:177 http://ftpmaster.internal/ubuntu questing/universe s390x mafft s390x 7.505-1 [766 kB] 429s Get:178 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 429s Get:179 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-blast+ s390x 2.16.0+ds-6build1 [15.2 MB] 430s Get:180 http://ftpmaster.internal/ubuntu questing/universe s390x phylip s390x 1:3.697+dfsg-4build1 [1051 kB] 430s Get:181 http://ftpmaster.internal/ubuntu questing/universe s390x prank s390x 0.0.170427+dfsg-3 [357 kB] 430s Get:182 http://ftpmaster.internal/ubuntu questing/universe s390x preview-latex-style all 13.2-1 [347 kB] 430s Get:183 http://ftpmaster.internal/ubuntu questing/universe s390x probcons s390x 1.12-14 [109 kB] 430s Get:184 http://ftpmaster.internal/ubuntu questing/universe s390x python-biopython-doc all 1.85+dfsg-2build1 [18.2 MB] 431s Get:185 http://ftpmaster.internal/ubuntu questing/universe s390x python-matplotlib-data all 3.8.3-7build1 [2934 kB] 431s Get:186 http://ftpmaster.internal/ubuntu questing/main s390x python3-all s390x 3.13.3-1 [882 B] 431s Get:187 http://ftpmaster.internal/ubuntu questing/main s390x python3.13-dev s390x 3.13.3-1 [508 kB] 431s Get:188 http://ftpmaster.internal/ubuntu questing/main s390x python3-dev s390x 3.13.3-1 [26.7 kB] 431s Get:189 http://ftpmaster.internal/ubuntu questing/main s390x python3-all-dev s390x 3.13.3-1 [904 B] 431s Get:190 http://ftpmaster.internal/ubuntu questing/main s390x python3.13-tk s390x 3.13.3-1 [108 kB] 431s Get:191 http://ftpmaster.internal/ubuntu questing/main s390x python3-tk s390x 3.13.3-1 [9854 B] 431s Get:192 http://ftpmaster.internal/ubuntu questing/universe s390x python3-pil.imagetk s390x 11.1.0-5build1 [9668 B] 431s Get:193 http://ftpmaster.internal/ubuntu questing/main s390x python3-pil s390x 11.1.0-5build1 [498 kB] 431s Get:194 http://ftpmaster.internal/ubuntu questing/main s390x python3-cairo s390x 1.27.0-2 [120 kB] 431s Get:195 http://ftpmaster.internal/ubuntu questing/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 431s Get:196 http://ftpmaster.internal/ubuntu questing/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 431s Get:197 http://ftpmaster.internal/ubuntu questing/universe s390x python3-reportlab all 4.3.1-1 [1137 kB] 431s Get:198 http://ftpmaster.internal/ubuntu questing/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 431s Get:199 http://ftpmaster.internal/ubuntu questing/universe s390x python3-biopython s390x 1.85+dfsg-2build1 [1745 kB] 431s Get:200 http://ftpmaster.internal/ubuntu questing/universe s390x python3-biopython-sql all 1.85+dfsg-2build1 [26.4 kB] 431s Get:201 http://ftpmaster.internal/ubuntu questing/universe s390x python3-brotli s390x 1.1.0-2build4 [380 kB] 431s Get:202 http://ftpmaster.internal/ubuntu questing/universe s390x python3-contourpy s390x 1.3.1-1build1 [197 kB] 431s Get:203 http://ftpmaster.internal/ubuntu questing/universe s390x python3-cycler all 0.12.1-1 [9716 B] 431s Get:204 http://ftpmaster.internal/ubuntu questing/main s390x python3-dateutil all 2.9.0-4 [80.3 kB] 431s Get:205 http://ftpmaster.internal/ubuntu questing/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 431s Get:206 http://ftpmaster.internal/ubuntu questing/main s390x python3-defusedxml all 0.7.1-3 [42.2 kB] 431s Get:207 http://ftpmaster.internal/ubuntu questing/main s390x python3-roman all 5.0-1 [10.3 kB] 431s Get:208 http://ftpmaster.internal/ubuntu questing/main s390x python3-docutils all 0.21.2+dfsg-2 [409 kB] 432s Get:209 http://ftpmaster.internal/ubuntu questing/main s390x python3-platformdirs all 4.3.6-1 [16.8 kB] 432s Get:210 http://ftpmaster.internal/ubuntu questing/universe s390x python3-fs all 2.4.16-7 [90.8 kB] 432s Get:211 http://ftpmaster.internal/ubuntu questing/main s390x python3-lxml s390x 5.3.2-1 [1370 kB] 432s Get:212 http://ftpmaster.internal/ubuntu questing/universe s390x python3-lz4 s390x 4.4.0+dfsg-1build1 [26.6 kB] 432s Get:213 http://ftpmaster.internal/ubuntu questing/universe s390x python3-scipy s390x 1.14.1-4ubuntu2 [18.0 MB] 432s Get:214 http://ftpmaster.internal/ubuntu questing/universe s390x python3-mpmath all 1.3.0-1 [425 kB] 432s Get:215 http://ftpmaster.internal/ubuntu questing/universe s390x python3-sympy all 1.13.3-5 [4229 kB] 433s Get:216 http://ftpmaster.internal/ubuntu questing/universe s390x python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 433s Get:217 http://ftpmaster.internal/ubuntu questing/universe s390x unicode-data all 15.1.0-1 [8878 kB] 433s Get:218 http://ftpmaster.internal/ubuntu questing/universe s390x python3-fonttools s390x 4.55.3-2build1 [1496 kB] 433s Get:219 http://ftpmaster.internal/ubuntu questing/main s390x python3-imagesize all 1.4.1-1 [6844 B] 433s Get:220 http://ftpmaster.internal/ubuntu questing/universe s390x python3-kiwisolver s390x 1.4.7-3build1 [55.0 kB] 433s Get:221 http://ftpmaster.internal/ubuntu questing/main s390x python3-packaging all 24.2-1 [51.5 kB] 433s Get:222 http://ftpmaster.internal/ubuntu questing/universe s390x python3-matplotlib s390x 3.8.3-7build1 [17.3 MB] 434s Get:223 http://ftpmaster.internal/ubuntu questing/main s390x python3-msgpack s390x 1.0.3-3build4 [87.7 kB] 434s Get:224 http://ftpmaster.internal/ubuntu questing/universe s390x python3-mmtf all 1.1.3-1 [16.2 kB] 434s Get:225 http://ftpmaster.internal/ubuntu questing/main s390x python3-mysqldb s390x 1.4.6-2build6 [48.4 kB] 434s Get:226 http://ftpmaster.internal/ubuntu questing/main s390x python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 434s Get:227 http://ftpmaster.internal/ubuntu questing-proposed/main s390x sphinx-common all 8.2.3-1 [656 kB] 434s Get:228 http://ftpmaster.internal/ubuntu questing/main s390x python3-alabaster all 0.7.16-0.1 [18.5 kB] 434s Get:229 http://ftpmaster.internal/ubuntu questing/universe s390x python3-roman-numerals all 3.1.0-1ubuntu1 [8432 B] 434s Get:230 http://ftpmaster.internal/ubuntu questing/main s390x python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 434s Get:231 http://ftpmaster.internal/ubuntu questing-proposed/main s390x python3-sphinx all 8.2.3-1 [482 kB] 434s Get:232 http://ftpmaster.internal/ubuntu questing/main s390x python3-tabulate all 0.9.0-1 [45.3 kB] 434s Get:233 http://ftpmaster.internal/ubuntu questing/universe s390x python3-numpydoc all 1.8.0-1 [52.4 kB] 434s Get:234 http://ftpmaster.internal/ubuntu questing/universe s390x python3-rdflib all 7.1.1-2 [426 kB] 434s Get:235 http://ftpmaster.internal/ubuntu questing/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 434s Get:236 http://ftpmaster.internal/ubuntu questing/universe s390x python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 434s Get:237 http://ftpmaster.internal/ubuntu questing/universe s390x python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 434s Get:238 http://ftpmaster.internal/ubuntu questing/universe s390x python3-texttable all 1.7.0-1 [11.2 kB] 434s Get:239 http://ftpmaster.internal/ubuntu questing/universe s390x t-coffee s390x 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [945 kB] 434s Get:240 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-fonts-recommended all 2024.20250309-1 [4974 kB] 435s Get:241 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-latex-base all 2024.20250309-1 [1276 kB] 435s Get:242 http://ftpmaster.internal/ubuntu questing/universe s390x libfontbox-java all 1:1.8.16-5 [208 kB] 435s Get:243 http://ftpmaster.internal/ubuntu questing/universe s390x libpdfbox-java all 1:1.8.16-5 [5521 kB] 435s Get:244 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-latex-recommended all 2024.20250309-1 [8727 kB] 435s Get:245 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-pictures all 2024.20250309-1 [17.0 MB] 436s Get:246 http://ftpmaster.internal/ubuntu questing/universe s390x texlive-latex-extra all 2024.20250309-2 [24.8 MB] 437s Get:247 http://ftpmaster.internal/ubuntu questing/universe s390x wise-data all 2.4.1-25 [83.0 kB] 437s Get:248 http://ftpmaster.internal/ubuntu questing/universe s390x wise s390x 2.4.1-25 [935 kB] 437s Get:249 http://ftpmaster.internal/ubuntu questing/universe s390x fasttree s390x 2.1.11-2 [190 kB] 437s Get:250 http://ftpmaster.internal/ubuntu questing/universe s390x python3-igraph s390x 0.11.8+ds-1build1 [340 kB] 438s Preconfiguring packages ... 438s Fetched 335 MB in 14s (23.2 MB/s) 438s Selecting previously unselected package m4. 438s (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 ... 81470 files and directories currently installed.) 438s Preparing to unpack .../000-m4_1.4.19-7_s390x.deb ... 438s Unpacking m4 (1.4.19-7) ... 438s Selecting previously unselected package flex. 438s Preparing to unpack .../001-flex_2.6.4-8.2build1_s390x.deb ... 438s Unpacking flex (2.6.4-8.2build1) ... 438s Selecting previously unselected package fonts-lato. 438s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 438s Unpacking fonts-lato (2.015-1) ... 438s Selecting previously unselected package libgomp1:s390x. 438s Preparing to unpack .../003-libgomp1_15-20250404-0ubuntu1_s390x.deb ... 438s Unpacking libgomp1:s390x (15-20250404-0ubuntu1) ... 438s Selecting previously unselected package libfftw3-double3:s390x. 438s Preparing to unpack .../004-libfftw3-double3_3.3.10-2fakesync1build1_s390x.deb ... 438s Unpacking libfftw3-double3:s390x (3.3.10-2fakesync1build1) ... 438s Selecting previously unselected package libfreetype6:s390x. 438s Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 438s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 438s Selecting previously unselected package fonts-dejavu-mono. 438s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 438s Unpacking fonts-dejavu-mono (2.37-8) ... 438s Selecting previously unselected package fonts-dejavu-core. 438s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 438s Unpacking fonts-dejavu-core (2.37-8) ... 438s Selecting previously unselected package libfontenc1:s390x. 438s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 438s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 438s Selecting previously unselected package x11-common. 438s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu4_all.deb ... 438s Unpacking x11-common (1:7.7+23ubuntu4) ... 438s Selecting previously unselected package xfonts-encodings. 438s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 438s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 438s Selecting previously unselected package xfonts-utils. 438s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_s390x.deb ... 438s Unpacking xfonts-utils (1:7.7+7) ... 438s Selecting previously unselected package fonts-urw-base35. 438s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 438s Unpacking fonts-urw-base35 (20200910-8) ... 438s Selecting previously unselected package fontconfig-config. 438s Preparing to unpack .../013-fontconfig-config_2.15.0-2.2ubuntu1_s390x.deb ... 439s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 439s Selecting previously unselected package libfontconfig1:s390x. 439s Preparing to unpack .../014-libfontconfig1_2.15.0-2.2ubuntu1_s390x.deb ... 439s Unpacking libfontconfig1:s390x (2.15.0-2.2ubuntu1) ... 439s Selecting previously unselected package libsharpyuv0:s390x. 439s Preparing to unpack .../015-libsharpyuv0_1.5.0-0.1_s390x.deb ... 439s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 439s Selecting previously unselected package libaom3:s390x. 439s Preparing to unpack .../016-libaom3_3.12.1-1_s390x.deb ... 439s Unpacking libaom3:s390x (3.12.1-1) ... 439s Selecting previously unselected package libheif-plugin-aomdec:s390x. 439s Preparing to unpack .../017-libheif-plugin-aomdec_1.19.7-1_s390x.deb ... 439s Unpacking libheif-plugin-aomdec:s390x (1.19.7-1) ... 439s Selecting previously unselected package libde265-0:s390x. 439s Preparing to unpack .../018-libde265-0_1.0.15-1build5_s390x.deb ... 439s Unpacking libde265-0:s390x (1.0.15-1build5) ... 439s Selecting previously unselected package libheif-plugin-libde265:s390x. 439s Preparing to unpack .../019-libheif-plugin-libde265_1.19.7-1_s390x.deb ... 439s Unpacking libheif-plugin-libde265:s390x (1.19.7-1) ... 439s Selecting previously unselected package libheif1:s390x. 439s Preparing to unpack .../020-libheif1_1.19.7-1_s390x.deb ... 439s Unpacking libheif1:s390x (1.19.7-1) ... 439s Selecting previously unselected package libjbig0:s390x. 439s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 439s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 439s Selecting previously unselected package libjpeg-turbo8:s390x. 439s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 439s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 439s Selecting previously unselected package libjpeg8:s390x. 439s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_s390x.deb ... 439s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 439s Selecting previously unselected package liblcms2-2:s390x. 439s Preparing to unpack .../024-liblcms2-2_2.16-2_s390x.deb ... 439s Unpacking liblcms2-2:s390x (2.16-2) ... 439s Selecting previously unselected package liblqr-1-0:s390x. 439s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_s390x.deb ... 439s Unpacking liblqr-1-0:s390x (0.4.2-2.1build2) ... 439s Selecting previously unselected package libltdl7:s390x. 439s Preparing to unpack .../026-libltdl7_2.5.4-4_s390x.deb ... 439s Unpacking libltdl7:s390x (2.5.4-4) ... 439s Selecting previously unselected package libopenjp2-7:s390x. 439s Preparing to unpack .../027-libopenjp2-7_2.5.3-2_s390x.deb ... 439s Unpacking libopenjp2-7:s390x (2.5.3-2) ... 439s Selecting previously unselected package libraw23t64:s390x. 439s Preparing to unpack .../028-libraw23t64_0.21.4-2_s390x.deb ... 439s Unpacking libraw23t64:s390x (0.21.4-2) ... 439s Selecting previously unselected package libdeflate0:s390x. 439s Preparing to unpack .../029-libdeflate0_1.23-2_s390x.deb ... 439s Unpacking libdeflate0:s390x (1.23-2) ... 439s Selecting previously unselected package libwebp7:s390x. 439s Preparing to unpack .../030-libwebp7_1.5.0-0.1_s390x.deb ... 439s Unpacking libwebp7:s390x (1.5.0-0.1) ... 439s Selecting previously unselected package libtiff6:s390x. 439s Preparing to unpack .../031-libtiff6_4.7.0-3ubuntu1_s390x.deb ... 439s Unpacking libtiff6:s390x (4.7.0-3ubuntu1) ... 439s Selecting previously unselected package libwebpdemux2:s390x. 439s Preparing to unpack .../032-libwebpdemux2_1.5.0-0.1_s390x.deb ... 439s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 439s Selecting previously unselected package libwebpmux3:s390x. 439s Preparing to unpack .../033-libwebpmux3_1.5.0-0.1_s390x.deb ... 439s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 439s Selecting previously unselected package imagemagick-7-common. 439s Preparing to unpack .../034-imagemagick-7-common_8%3a7.1.1.43+dfsg1-1_all.deb ... 439s Unpacking imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 439s Selecting previously unselected package libmagickcore-7.q16-10:s390x. 439s Preparing to unpack .../035-libmagickcore-7.q16-10_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 439s Unpacking libmagickcore-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 439s Selecting previously unselected package libmagickwand-7.q16-10:s390x. 439s Preparing to unpack .../036-libmagickwand-7.q16-10_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 439s Unpacking libmagickwand-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 439s Selecting previously unselected package poppler-data. 439s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 439s Unpacking poppler-data (0.4.12-1) ... 439s Selecting previously unselected package python3-numpy-dev:s390x. 439s Preparing to unpack .../038-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 439s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 439s Selecting previously unselected package libblas3:s390x. 439s Preparing to unpack .../039-libblas3_3.12.1-2_s390x.deb ... 439s Unpacking libblas3:s390x (3.12.1-2) ... 439s Selecting previously unselected package libgfortran5:s390x. 439s Preparing to unpack .../040-libgfortran5_15-20250404-0ubuntu1_s390x.deb ... 439s Unpacking libgfortran5:s390x (15-20250404-0ubuntu1) ... 439s Selecting previously unselected package liblapack3:s390x. 439s Preparing to unpack .../041-liblapack3_3.12.1-2_s390x.deb ... 439s Unpacking liblapack3:s390x (3.12.1-2) ... 439s Selecting previously unselected package python3-numpy. 439s Preparing to unpack .../042-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 439s Unpacking python3-numpy (1:2.2.3+ds-5) ... 439s Selecting previously unselected package sgml-base. 439s Preparing to unpack .../043-sgml-base_1.31_all.deb ... 439s Unpacking sgml-base (1.31) ... 439s Selecting previously unselected package autoconf. 439s Preparing to unpack .../044-autoconf_2.72-3ubuntu1_all.deb ... 439s Unpacking autoconf (2.72-3ubuntu1) ... 439s Selecting previously unselected package autotools-dev. 439s Preparing to unpack .../045-autotools-dev_20220109.1_all.deb ... 439s Unpacking autotools-dev (20220109.1) ... 439s Selecting previously unselected package automake. 439s Preparing to unpack .../046-automake_1%3a1.17-3ubuntu1_all.deb ... 439s Unpacking automake (1:1.17-3ubuntu1) ... 439s Selecting previously unselected package autopoint. 439s Preparing to unpack .../047-autopoint_0.23.1-1_all.deb ... 439s Unpacking autopoint (0.23.1-1) ... 439s Selecting previously unselected package libtcl8.6:s390x. 439s Preparing to unpack .../048-libtcl8.6_8.6.16+dfsg-1_s390x.deb ... 439s Unpacking libtcl8.6:s390x (8.6.16+dfsg-1) ... 439s Selecting previously unselected package libxrender1:s390x. 439s Preparing to unpack .../049-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 439s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 439s Selecting previously unselected package libxft2:s390x. 439s Preparing to unpack .../050-libxft2_2.3.6-1build1_s390x.deb ... 439s Unpacking libxft2:s390x (2.3.6-1build1) ... 439s Selecting previously unselected package libxss1:s390x. 439s Preparing to unpack .../051-libxss1_1%3a1.2.3-1build3_s390x.deb ... 439s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 439s Selecting previously unselected package libtk8.6:s390x. 439s Preparing to unpack .../052-libtk8.6_8.6.16-1_s390x.deb ... 439s Unpacking libtk8.6:s390x (8.6.16-1) ... 439s Selecting previously unselected package tk8.6-blt2.5. 439s Preparing to unpack .../053-tk8.6-blt2.5_2.5.3+dfsg-8_s390x.deb ... 439s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 439s Selecting previously unselected package blt. 439s Preparing to unpack .../054-blt_2.5.3+dfsg-8_s390x.deb ... 439s Unpacking blt (2.5.3+dfsg-8) ... 439s Selecting previously unselected package libisl23:s390x. 439s Preparing to unpack .../055-libisl23_0.27-1_s390x.deb ... 439s Unpacking libisl23:s390x (0.27-1) ... 439s Selecting previously unselected package libmpc3:s390x. 439s Preparing to unpack .../056-libmpc3_1.3.1-1build2_s390x.deb ... 439s Unpacking libmpc3:s390x (1.3.1-1build2) ... 439s Selecting previously unselected package cpp-14-s390x-linux-gnu. 439s Preparing to unpack .../057-cpp-14-s390x-linux-gnu_14.2.0-19ubuntu2_s390x.deb ... 439s Unpacking cpp-14-s390x-linux-gnu (14.2.0-19ubuntu2) ... 440s Selecting previously unselected package cpp-14. 440s Preparing to unpack .../058-cpp-14_14.2.0-19ubuntu2_s390x.deb ... 440s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 440s Selecting previously unselected package cpp-s390x-linux-gnu. 440s Preparing to unpack .../059-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 440s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 440s Selecting previously unselected package cpp. 440s Preparing to unpack .../060-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 440s Unpacking cpp (4:14.2.0-1ubuntu1) ... 440s Selecting previously unselected package libcc1-0:s390x. 440s Preparing to unpack .../061-libcc1-0_15-20250404-0ubuntu1_s390x.deb ... 440s Unpacking libcc1-0:s390x (15-20250404-0ubuntu1) ... 440s Selecting previously unselected package libitm1:s390x. 440s Preparing to unpack .../062-libitm1_15-20250404-0ubuntu1_s390x.deb ... 440s Unpacking libitm1:s390x (15-20250404-0ubuntu1) ... 440s Selecting previously unselected package libasan8:s390x. 440s Preparing to unpack .../063-libasan8_15-20250404-0ubuntu1_s390x.deb ... 440s Unpacking libasan8:s390x (15-20250404-0ubuntu1) ... 440s Selecting previously unselected package libubsan1:s390x. 440s Preparing to unpack .../064-libubsan1_15-20250404-0ubuntu1_s390x.deb ... 440s Unpacking libubsan1:s390x (15-20250404-0ubuntu1) ... 440s Selecting previously unselected package libgcc-14-dev:s390x. 440s Preparing to unpack .../065-libgcc-14-dev_14.2.0-19ubuntu2_s390x.deb ... 440s Unpacking libgcc-14-dev:s390x (14.2.0-19ubuntu2) ... 440s Selecting previously unselected package gcc-14-s390x-linux-gnu. 440s Preparing to unpack .../066-gcc-14-s390x-linux-gnu_14.2.0-19ubuntu2_s390x.deb ... 440s Unpacking gcc-14-s390x-linux-gnu (14.2.0-19ubuntu2) ... 440s Selecting previously unselected package gcc-14. 440s Preparing to unpack .../067-gcc-14_14.2.0-19ubuntu2_s390x.deb ... 440s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 440s Selecting previously unselected package gcc-s390x-linux-gnu. 440s Preparing to unpack .../068-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 440s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 440s Selecting previously unselected package gcc. 440s Preparing to unpack .../069-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ... 440s Unpacking gcc (4:14.2.0-1ubuntu1) ... 440s Selecting previously unselected package libstdc++-14-dev:s390x. 440s Preparing to unpack .../070-libstdc++-14-dev_14.2.0-19ubuntu2_s390x.deb ... 440s Unpacking libstdc++-14-dev:s390x (14.2.0-19ubuntu2) ... 440s Selecting previously unselected package g++-14-s390x-linux-gnu. 440s Preparing to unpack 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440s Selecting previously unselected package libargtable2-0. 440s Preparing to unpack .../077-libargtable2-0_13-3_s390x.deb ... 440s Unpacking libargtable2-0 (13-3) ... 440s Selecting previously unselected package clustalo. 440s Preparing to unpack .../078-clustalo_1.2.4-8build1_s390x.deb ... 440s Unpacking clustalo (1.2.4-8build1) ... 440s Selecting previously unselected package libdebhelper-perl. 440s Preparing to unpack .../079-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 440s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 440s Selecting previously unselected package libtool. 440s Preparing to unpack .../080-libtool_2.5.4-4_all.deb ... 440s Unpacking libtool (2.5.4-4) ... 440s Selecting previously unselected package dh-autoreconf. 440s Preparing to unpack .../081-dh-autoreconf_20_all.deb ... 440s Unpacking dh-autoreconf (20) ... 440s Selecting previously unselected package libarchive-zip-perl. 440s Preparing to unpack .../082-libarchive-zip-perl_1.68-1_all.deb ... 440s Unpacking libarchive-zip-perl (1.68-1) ... 440s Selecting previously unselected package libfile-stripnondeterminism-perl. 440s Preparing to unpack .../083-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 440s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 440s Selecting previously unselected package dh-strip-nondeterminism. 440s Preparing to unpack .../084-dh-strip-nondeterminism_1.14.1-2_all.deb ... 440s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 440s Selecting previously unselected package debugedit. 440s Preparing to unpack .../085-debugedit_1%3a5.1-2_s390x.deb ... 440s Unpacking debugedit (1:5.1-2) ... 440s Selecting previously unselected package dwz. 440s Preparing to unpack .../086-dwz_0.15-1build6_s390x.deb ... 440s Unpacking dwz (0.15-1build6) ... 440s Selecting previously unselected package gettext. 440s Preparing to unpack .../087-gettext_0.23.1-1_s390x.deb ... 440s Unpacking gettext (0.23.1-1) ... 441s Selecting previously unselected package intltool-debian. 441s 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(2.005-1) ... 441s Selecting previously unselected package fonts-lyx. 441s Preparing to unpack .../100-fonts-lyx_2.4.3-1_all.deb ... 441s Unpacking fonts-lyx (2.4.3-1) ... 441s Selecting previously unselected package libgs-common. 441s Preparing to unpack .../101-libgs-common_10.05.0dfsg1-0ubuntu1_all.deb ... 441s Unpacking libgs-common (10.05.0dfsg1-0ubuntu1) ... 441s Selecting previously unselected package libgs10-common. 441s Preparing to unpack .../102-libgs10-common_10.05.0dfsg1-0ubuntu1_all.deb ... 441s Unpacking libgs10-common (10.05.0dfsg1-0ubuntu1) ... 441s Selecting previously unselected package libavahi-common-data:s390x. 441s Preparing to unpack .../103-libavahi-common-data_0.8-16ubuntu2_s390x.deb ... 441s Unpacking libavahi-common-data:s390x (0.8-16ubuntu2) ... 441s Selecting previously unselected package libavahi-common3:s390x. 441s Preparing to unpack .../104-libavahi-common3_0.8-16ubuntu2_s390x.deb ... 441s Unpacking libavahi-common3:s390x (0.8-16ubuntu2) ... 441s Selecting previously unselected package libavahi-client3:s390x. 441s Preparing to unpack .../105-libavahi-client3_0.8-16ubuntu2_s390x.deb ... 441s Unpacking libavahi-client3:s390x (0.8-16ubuntu2) ... 441s Selecting previously unselected package libcups2t64:s390x. 441s Preparing to unpack .../106-libcups2t64_2.4.12-0ubuntu1_s390x.deb ... 441s Unpacking libcups2t64:s390x (2.4.12-0ubuntu1) ... 441s Selecting previously unselected package libidn12:s390x. 441s Preparing to unpack .../107-libidn12_1.43-1_s390x.deb ... 441s Unpacking libidn12:s390x (1.43-1) ... 441s Selecting previously unselected package libijs-0.35:s390x. 441s Preparing to unpack .../108-libijs-0.35_0.35-15.2_s390x.deb ... 441s Unpacking libijs-0.35:s390x (0.35-15.2) ... 441s Selecting previously unselected package libjbig2dec0:s390x. 441s Preparing to unpack .../109-libjbig2dec0_0.20-1build3_s390x.deb ... 441s Unpacking libjbig2dec0:s390x (0.20-1build3) ... 441s Selecting previously unselected package libpaper2:s390x. 441s Preparing to unpack .../110-libpaper2_2.2.5-0.3_s390x.deb ... 441s Unpacking libpaper2:s390x (2.2.5-0.3) ... 441s Selecting previously unselected package libice6:s390x. 441s Preparing to unpack .../111-libice6_2%3a1.1.1-1_s390x.deb ... 441s Unpacking libice6:s390x (2:1.1.1-1) ... 441s Selecting previously unselected package libsm6:s390x. 441s Preparing to unpack .../112-libsm6_2%3a1.2.4-1_s390x.deb ... 441s Unpacking libsm6:s390x (2:1.2.4-1) ... 441s Selecting previously unselected package libxt6t64:s390x. 441s Preparing to unpack .../113-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 441s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 441s Selecting previously unselected package libgs10:s390x. 441s Preparing to unpack .../114-libgs10_10.05.0dfsg1-0ubuntu1_s390x.deb ... 441s Unpacking libgs10:s390x (10.05.0dfsg1-0ubuntu1) ... 441s Selecting previously unselected package ghostscript. 441s Preparing to unpack .../115-ghostscript_10.05.0dfsg1-0ubuntu1_s390x.deb ... 441s Unpacking ghostscript (10.05.0dfsg1-0ubuntu1) ... 441s Selecting previously unselected package libnetpbm11t64:s390x. 441s Preparing to unpack .../116-libnetpbm11t64_2%3a11.09.02-2_s390x.deb ... 441s Unpacking libnetpbm11t64:s390x (2:11.09.02-2) ... 441s Selecting previously unselected package netpbm. 441s Preparing to unpack .../117-netpbm_2%3a11.09.02-2_s390x.deb ... 441s Unpacking netpbm (2:11.09.02-2) ... 441s Selecting previously unselected package tex-common. 441s Preparing to unpack .../118-tex-common_6.19_all.deb ... 441s Unpacking tex-common (6.19) ... 441s Selecting previously unselected package libpaper-utils. 441s Preparing to unpack .../119-libpaper-utils_2.2.5-0.3_s390x.deb ... 441s Unpacking libpaper-utils (2.2.5-0.3) ... 441s Selecting previously unselected package libkpathsea6:s390x. 441s Preparing to unpack .../120-libkpathsea6_2024.20240313.70630+ds-6_s390x.deb ... 441s Unpacking libkpathsea6:s390x (2024.20240313.70630+ds-6) ... 441s Selecting previously unselected package libptexenc1:s390x. 441s Preparing to unpack .../121-libptexenc1_2024.20240313.70630+ds-6_s390x.deb ... 441s Unpacking libptexenc1:s390x (2024.20240313.70630+ds-6) ... 441s Selecting previously unselected package libsynctex2:s390x. 441s Preparing to unpack .../122-libsynctex2_2024.20240313.70630+ds-6_s390x.deb ... 441s Unpacking libsynctex2:s390x (2024.20240313.70630+ds-6) ... 441s Selecting previously unselected package libtexlua53-5:s390x. 441s Preparing to unpack .../123-libtexlua53-5_2024.20240313.70630+ds-6_s390x.deb ... 441s Unpacking libtexlua53-5:s390x (2024.20240313.70630+ds-6) ... 441s Selecting previously unselected package t1utils. 441s Preparing to unpack .../124-t1utils_1.41-4build3_s390x.deb ... 441s Unpacking t1utils (1.41-4build3) ... 441s Selecting previously unselected package libpixman-1-0:s390x. 441s Preparing to unpack .../125-libpixman-1-0_0.44.0-3_s390x.deb ... 441s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 441s Selecting previously unselected package libxcb-render0:s390x. 441s Preparing to unpack .../126-libxcb-render0_1.17.0-2_s390x.deb ... 441s Unpacking libxcb-render0:s390x (1.17.0-2) ... 441s Selecting previously unselected package libxcb-shm0:s390x. 441s Preparing to unpack .../127-libxcb-shm0_1.17.0-2_s390x.deb ... 441s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 441s Selecting previously unselected package libcairo2:s390x. 441s Preparing to unpack .../128-libcairo2_1.18.4-1_s390x.deb ... 441s Unpacking libcairo2:s390x (1.18.4-1) ... 441s Selecting previously unselected package libgraphite2-3:s390x. 441s Preparing to unpack .../129-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 441s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 441s Selecting previously unselected package libharfbuzz0b:s390x. 441s Preparing to unpack .../130-libharfbuzz0b_10.2.0-1_s390x.deb ... 441s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 441s Selecting previously unselected package libmpfi0:s390x. 441s Preparing to unpack .../131-libmpfi0_1.5.4+ds-4_s390x.deb ... 441s Unpacking libmpfi0:s390x (1.5.4+ds-4) ... 441s Selecting previously unselected package libpotrace0:s390x. 441s Preparing to unpack .../132-libpotrace0_1.16-2build1_s390x.deb ... 441s Unpacking libpotrace0:s390x (1.16-2build1) ... 441s Selecting previously unselected package libteckit0:s390x. 441s Preparing to unpack .../133-libteckit0_2.5.12+ds1-1_s390x.deb ... 441s Unpacking libteckit0:s390x (2.5.12+ds1-1) ... 441s Selecting previously unselected package libxmu6:s390x. 441s Preparing to unpack .../134-libxmu6_2%3a1.1.3-3build2_s390x.deb ... 441s Unpacking libxmu6:s390x (2:1.1.3-3build2) ... 441s Selecting previously unselected package libxpm4:s390x. 442s Preparing to unpack .../135-libxpm4_1%3a3.5.17-1build2_s390x.deb ... 442s Unpacking libxpm4:s390x (1:3.5.17-1build2) ... 442s Selecting previously unselected package libxaw7:s390x. 442s Preparing to unpack .../136-libxaw7_2%3a1.0.16-1_s390x.deb ... 442s Unpacking libxaw7:s390x (2:1.0.16-1) ... 442s Selecting previously unselected package libxi6:s390x. 442s Preparing to unpack .../137-libxi6_2%3a1.8.2-1_s390x.deb ... 442s Unpacking libxi6:s390x (2:1.8.2-1) ... 442s Selecting previously unselected package libzzip-0-13t64:s390x. 442s Preparing to unpack .../138-libzzip-0-13t64_0.13.78+dfsg.1-0.1_s390x.deb ... 442s Unpacking libzzip-0-13t64:s390x (0.13.78+dfsg.1-0.1) ... 442s Selecting previously unselected package texlive-binaries. 442s Preparing to unpack .../139-texlive-binaries_2024.20240313.70630+ds-6_s390x.deb ... 442s Unpacking texlive-binaries (2024.20240313.70630+ds-6) ... 442s Selecting previously unselected package xdg-utils. 442s Preparing to unpack .../140-xdg-utils_1.2.1-2ubuntu1_all.deb ... 442s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 442s Selecting previously unselected package texlive-base. 442s Preparing to unpack .../141-texlive-base_2024.20250309-1_all.deb ... 442s Unpacking texlive-base (2024.20250309-1) ... 443s Selecting previously unselected package hicolor-icon-theme. 443s Preparing to unpack .../142-hicolor-icon-theme_0.18-2_all.deb ... 443s Unpacking hicolor-icon-theme (0.18-2) ... 443s Selecting previously unselected package imagemagick-7.q16. 443s Preparing to unpack .../143-imagemagick-7.q16_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 443s Unpacking imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 443s Selecting previously unselected package imagemagick. 443s Preparing to unpack .../144-imagemagick_8%3a7.1.1.43+dfsg1-1_s390x.deb ... 443s Unpacking imagemagick (8:7.1.1.43+dfsg1-1) ... 443s Selecting previously unselected package hevea. 443s Preparing to unpack .../145-hevea_2.36-2_s390x.deb ... 443s Unpacking hevea (2.36-2) ... 443s Selecting previously unselected package libsuitesparseconfig7:s390x. 443s Preparing to unpack .../146-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_s390x.deb ... 443s Unpacking libsuitesparseconfig7:s390x (1:7.8.3+dfsg-3) ... 443s Selecting previously unselected package libamd3:s390x. 443s Preparing to unpack .../147-libamd3_1%3a7.8.3+dfsg-3_s390x.deb ... 443s Unpacking libamd3:s390x (1:7.8.3+dfsg-3) ... 443s Selecting previously unselected package libapache-pom-java. 443s Preparing to unpack .../148-libapache-pom-java_33-2_all.deb ... 443s Unpacking libapache-pom-java (33-2) ... 443s Selecting previously unselected package libarpack2t64:s390x. 443s Preparing to unpack .../149-libarpack2t64_3.9.1-4_s390x.deb ... 443s Unpacking libarpack2t64:s390x (3.9.1-4) ... 443s Selecting previously unselected package libcolamd3:s390x. 443s Preparing to unpack .../150-libcolamd3_1%3a7.8.3+dfsg-3_s390x.deb ... 443s Unpacking libcolamd3:s390x (1:7.8.3+dfsg-3) ... 443s Selecting previously unselected package libcommons-parent-java. 443s Preparing to unpack .../151-libcommons-parent-java_56-1_all.deb ... 443s Unpacking libcommons-parent-java (56-1) ... 443s Selecting previously unselected package libcommons-logging-java. 443s Preparing to unpack .../152-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 443s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 443s Selecting previously unselected package libexpat1-dev:s390x. 443s Preparing to unpack .../153-libexpat1-dev_2.7.1-1_s390x.deb ... 443s Unpacking libexpat1-dev:s390x (2.7.1-1) ... 443s Selecting previously unselected package libglpk40:s390x. 443s Preparing to unpack .../154-libglpk40_5.0-1build2_s390x.deb ... 443s Unpacking libglpk40:s390x (5.0-1build2) ... 443s Selecting previously unselected package libplfit0:s390x. 443s Preparing to unpack .../155-libplfit0_0.9.6+ds-2ubuntu1_s390x.deb ... 443s Unpacking libplfit0:s390x (0.9.6+ds-2ubuntu1) ... 443s Selecting previously unselected package libigraph3t64:s390x. 443s Preparing to unpack .../156-libigraph3t64_0.10.15+ds-3_s390x.deb ... 443s Unpacking libigraph3t64:s390x (0.10.15+ds-3) ... 443s Selecting previously unselected package libimagequant0:s390x. 443s Preparing to unpack .../157-libimagequant0_2.18.0-1build1_s390x.deb ... 443s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 443s Selecting previously unselected package libjs-jquery. 443s Preparing to unpack .../158-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 443s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 443s Selecting previously unselected package libjs-jquery-ui. 443s Preparing to unpack .../159-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 443s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 443s Selecting previously unselected package libjs-underscore. 443s Preparing to unpack .../160-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 443s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 443s Selecting previously unselected package libjs-sphinxdoc. 443s Preparing to unpack .../161-libjs-sphinxdoc_8.2.3-1_all.deb ... 443s Unpacking libjs-sphinxdoc (8.2.3-1) ... 443s Selecting previously unselected package libjson-perl. 443s Preparing to unpack .../162-libjson-perl_4.10000-1_all.deb ... 443s Unpacking libjson-perl (4.10000-1) ... 443s Selecting previously unselected package liblbfgsb0:s390x. 443s Preparing to unpack .../163-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 443s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 443s Selecting previously unselected package libmbedcrypto16:s390x. 443s Preparing to unpack .../164-libmbedcrypto16_3.6.2-3ubuntu1_s390x.deb ... 443s Unpacking libmbedcrypto16:s390x (3.6.2-3ubuntu1) ... 443s Selecting previously unselected package libmbedx509-7:s390x. 443s Preparing to unpack .../165-libmbedx509-7_3.6.2-3ubuntu1_s390x.deb ... 443s Unpacking libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 443s Selecting previously unselected package libmbedtls21:s390x. 443s Preparing to unpack .../166-libmbedtls21_3.6.2-3ubuntu1_s390x.deb ... 443s Unpacking libmbedtls21:s390x (3.6.2-3ubuntu1) ... 443s Selecting previously unselected package mysql-common. 443s Preparing to unpack .../167-mysql-common_5.8+1.1.1ubuntu1_all.deb ... 443s Unpacking mysql-common (5.8+1.1.1ubuntu1) ... 443s Selecting previously unselected package libmysqlclient24:s390x. 443s Preparing to unpack .../168-libmysqlclient24_8.4.4-0ubuntu2_s390x.deb ... 443s Unpacking libmysqlclient24:s390x (8.4.4-0ubuntu2) ... 443s Selecting previously unselected package zlib1g-dev:s390x. 443s Preparing to unpack .../169-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 443s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 443s Selecting previously unselected package libpython3.13-dev:s390x. 443s Preparing to unpack .../170-libpython3.13-dev_3.13.3-1_s390x.deb ... 443s Unpacking libpython3.13-dev:s390x (3.13.3-1) ... 443s Selecting previously unselected package libpython3-dev:s390x. 443s Preparing to unpack .../171-libpython3-dev_3.13.3-1_s390x.deb ... 443s Unpacking libpython3-dev:s390x (3.13.3-1) ... 443s Selecting previously unselected package libpython3-all-dev:s390x. 443s Preparing to unpack .../172-libpython3-all-dev_3.13.3-1_s390x.deb ... 443s Unpacking libpython3-all-dev:s390x (3.13.3-1) ... 443s Selecting previously unselected package libqhull-r8.0:s390x. 443s Preparing to unpack .../173-libqhull-r8.0_2020.2-6build1_s390x.deb ... 443s Unpacking libqhull-r8.0:s390x (2020.2-6build1) ... 443s Selecting previously unselected package libraqm0:s390x. 443s Preparing to unpack .../174-libraqm0_0.10.2-1_s390x.deb ... 443s Unpacking libraqm0:s390x (0.10.2-1) ... 444s Selecting previously unselected package libxslt1.1:s390x. 444s Preparing to unpack .../175-libxslt1.1_1.1.39-0exp1ubuntu4_s390x.deb ... 444s Unpacking libxslt1.1:s390x (1.1.39-0exp1ubuntu4) ... 444s Selecting previously unselected package mafft. 444s Preparing to unpack .../176-mafft_7.505-1_s390x.deb ... 444s Unpacking mafft (7.505-1) ... 444s Selecting previously unselected package ncbi-data. 444s Preparing to unpack .../177-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 444s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 444s Selecting previously unselected package ncbi-blast+. 444s Preparing to unpack .../178-ncbi-blast+_2.16.0+ds-6build1_s390x.deb ... 444s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 444s Selecting previously unselected package phylip. 444s Preparing to unpack .../179-phylip_1%3a3.697+dfsg-4build1_s390x.deb ... 444s Unpacking phylip (1:3.697+dfsg-4build1) ... 444s Selecting previously unselected package prank. 444s Preparing to unpack .../180-prank_0.0.170427+dfsg-3_s390x.deb ... 444s Unpacking prank (0.0.170427+dfsg-3) ... 444s Selecting previously unselected package preview-latex-style. 444s Preparing to unpack .../181-preview-latex-style_13.2-1_all.deb ... 444s Unpacking preview-latex-style (13.2-1) ... 444s Selecting previously unselected package probcons. 444s Preparing to unpack .../182-probcons_1.12-14_s390x.deb ... 444s Unpacking probcons (1.12-14) ... 444s Selecting previously unselected package python-biopython-doc. 444s Preparing to unpack .../183-python-biopython-doc_1.85+dfsg-2build1_all.deb ... 444s Unpacking python-biopython-doc (1.85+dfsg-2build1) ... 444s Selecting previously unselected package python-matplotlib-data. 444s Preparing to unpack .../184-python-matplotlib-data_3.8.3-7build1_all.deb ... 444s Unpacking python-matplotlib-data (3.8.3-7build1) ... 444s Selecting previously unselected package python3-all. 444s Preparing to unpack .../185-python3-all_3.13.3-1_s390x.deb ... 444s Unpacking python3-all (3.13.3-1) ... 444s Selecting previously unselected package python3.13-dev. 444s Preparing to unpack .../186-python3.13-dev_3.13.3-1_s390x.deb ... 444s Unpacking python3.13-dev (3.13.3-1) ... 444s Selecting previously unselected package python3-dev. 444s Preparing to unpack .../187-python3-dev_3.13.3-1_s390x.deb ... 444s Unpacking python3-dev (3.13.3-1) ... 444s Selecting previously unselected package python3-all-dev. 444s Preparing to unpack .../188-python3-all-dev_3.13.3-1_s390x.deb ... 444s Unpacking python3-all-dev (3.13.3-1) ... 444s Selecting previously unselected package python3.13-tk. 444s Preparing to unpack .../189-python3.13-tk_3.13.3-1_s390x.deb ... 444s Unpacking python3.13-tk (3.13.3-1) ... 444s Selecting previously unselected package python3-tk:s390x. 444s Preparing to unpack .../190-python3-tk_3.13.3-1_s390x.deb ... 444s Unpacking python3-tk:s390x (3.13.3-1) ... 444s Selecting previously unselected package python3-pil.imagetk:s390x. 444s Preparing to unpack .../191-python3-pil.imagetk_11.1.0-5build1_s390x.deb ... 444s Unpacking python3-pil.imagetk:s390x (11.1.0-5build1) ... 444s Selecting previously unselected package python3-pil:s390x. 444s Preparing to unpack .../192-python3-pil_11.1.0-5build1_s390x.deb ... 444s Unpacking python3-pil:s390x (11.1.0-5build1) ... 444s Selecting previously unselected package python3-cairo. 444s Preparing to unpack .../193-python3-cairo_1.27.0-2_s390x.deb ... 444s Unpacking python3-cairo (1.27.0-2) ... 444s Selecting previously unselected package python3-freetype. 444s Preparing to unpack .../194-python3-freetype_2.5.1-1_all.deb ... 444s Unpacking python3-freetype (2.5.1-1) ... 444s Selecting previously unselected package python3-rlpycairo. 444s Preparing to unpack .../195-python3-rlpycairo_0.3.0-3_all.deb ... 444s Unpacking python3-rlpycairo (0.3.0-3) ... 444s Selecting previously unselected package python3-reportlab. 444s Preparing to unpack .../196-python3-reportlab_4.3.1-1_all.deb ... 444s Unpacking python3-reportlab (4.3.1-1) ... 445s Selecting previously unselected package w3c-sgml-lib. 445s Preparing to unpack .../197-w3c-sgml-lib_1.3-3_all.deb ... 445s Unpacking w3c-sgml-lib (1.3-3) ... 445s Selecting previously unselected package python3-biopython. 445s Preparing to unpack .../198-python3-biopython_1.85+dfsg-2build1_s390x.deb ... 445s Unpacking python3-biopython (1.85+dfsg-2build1) ... 445s Selecting previously unselected package python3-biopython-sql. 445s Preparing to unpack .../199-python3-biopython-sql_1.85+dfsg-2build1_all.deb ... 445s Unpacking python3-biopython-sql (1.85+dfsg-2build1) ... 445s Selecting previously unselected package python3-brotli. 445s Preparing to unpack .../200-python3-brotli_1.1.0-2build4_s390x.deb ... 445s Unpacking python3-brotli (1.1.0-2build4) ... 445s Selecting previously unselected package python3-contourpy. 445s Preparing to unpack .../201-python3-contourpy_1.3.1-1build1_s390x.deb ... 445s Unpacking python3-contourpy (1.3.1-1build1) ... 445s Selecting previously unselected package python3-cycler. 445s Preparing to unpack .../202-python3-cycler_0.12.1-1_all.deb ... 445s Unpacking python3-cycler (0.12.1-1) ... 445s Selecting previously unselected package python3-dateutil. 445s Preparing to unpack .../203-python3-dateutil_2.9.0-4_all.deb ... 445s Unpacking python3-dateutil (2.9.0-4) ... 445s Selecting previously unselected package python3-decorator. 445s Preparing to unpack .../204-python3-decorator_5.1.1-5_all.deb ... 445s Unpacking python3-decorator (5.1.1-5) ... 445s Selecting previously unselected package python3-defusedxml. 445s Preparing to unpack .../205-python3-defusedxml_0.7.1-3_all.deb ... 445s Unpacking python3-defusedxml (0.7.1-3) ... 445s Selecting previously unselected package python3-roman. 445s Preparing to unpack .../206-python3-roman_5.0-1_all.deb ... 445s Unpacking python3-roman (5.0-1) ... 445s Selecting previously unselected package python3-docutils. 445s Preparing to unpack .../207-python3-docutils_0.21.2+dfsg-2_all.deb ... 445s Unpacking python3-docutils (0.21.2+dfsg-2) ... 445s Selecting previously unselected package python3-platformdirs. 445s Preparing to unpack .../208-python3-platformdirs_4.3.6-1_all.deb ... 445s Unpacking python3-platformdirs (4.3.6-1) ... 445s Selecting previously unselected package python3-fs. 445s Preparing to unpack .../209-python3-fs_2.4.16-7_all.deb ... 445s Unpacking python3-fs (2.4.16-7) ... 445s Selecting previously unselected package python3-lxml:s390x. 445s Preparing to unpack .../210-python3-lxml_5.3.2-1_s390x.deb 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package unicode-data. 445s Preparing to unpack .../216-unicode-data_15.1.0-1_all.deb ... 445s Unpacking unicode-data (15.1.0-1) ... 446s Selecting previously unselected package python3-fonttools. 446s Preparing to unpack .../217-python3-fonttools_4.55.3-2build1_s390x.deb ... 446s Unpacking python3-fonttools (4.55.3-2build1) ... 446s Selecting previously unselected package python3-imagesize. 446s Preparing to unpack .../218-python3-imagesize_1.4.1-1_all.deb ... 446s Unpacking python3-imagesize (1.4.1-1) ... 446s Selecting previously unselected package python3-kiwisolver. 446s Preparing to unpack .../219-python3-kiwisolver_1.4.7-3build1_s390x.deb ... 446s Unpacking python3-kiwisolver (1.4.7-3build1) ... 446s Selecting previously unselected package python3-packaging. 446s Preparing to unpack .../220-python3-packaging_24.2-1_all.deb ... 446s Unpacking python3-packaging (24.2-1) ... 446s Selecting previously unselected package python3-matplotlib. 446s Preparing to unpack .../221-python3-matplotlib_3.8.3-7build1_s390x.deb ... 446s Unpacking python3-matplotlib (3.8.3-7build1) ... 446s Selecting previously unselected package python3-msgpack. 446s Preparing to unpack .../222-python3-msgpack_1.0.3-3build4_s390x.deb ... 446s Unpacking python3-msgpack (1.0.3-3build4) ... 446s Selecting previously unselected package python3-mmtf. 446s Preparing to unpack .../223-python3-mmtf_1.1.3-1_all.deb ... 446s Unpacking python3-mmtf (1.1.3-1) ... 446s Selecting previously unselected package python3-mysqldb. 446s Preparing to unpack .../224-python3-mysqldb_1.4.6-2build6_s390x.deb ... 446s Unpacking python3-mysqldb (1.4.6-2build6) ... 446s Selecting previously unselected package python3-networkx. 446s Preparing to unpack .../225-python3-networkx_3.2.1-4ubuntu1_all.deb ... 446s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 446s Selecting previously unselected package sphinx-common. 446s Preparing to unpack .../226-sphinx-common_8.2.3-1_all.deb ... 446s Unpacking sphinx-common (8.2.3-1) ... 446s Selecting previously unselected package python3-alabaster. 446s Preparing to unpack .../227-python3-alabaster_0.7.16-0.1_all.deb ... 446s Unpacking python3-alabaster (0.7.16-0.1) ... 446s Selecting previously unselected package python3-roman-numerals. 446s Preparing to unpack .../228-python3-roman-numerals_3.1.0-1ubuntu1_all.deb ... 446s Unpacking python3-roman-numerals (3.1.0-1ubuntu1) ... 446s Selecting previously unselected package python3-snowballstemmer. 446s Preparing to unpack .../229-python3-snowballstemmer_2.2.0-4build1_all.deb ... 446s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 446s Selecting previously unselected package python3-sphinx. 446s Preparing to unpack .../230-python3-sphinx_8.2.3-1_all.deb ... 446s Unpacking python3-sphinx (8.2.3-1) ... 446s Selecting previously unselected package python3-tabulate. 446s Preparing to unpack .../231-python3-tabulate_0.9.0-1_all.deb ... 446s Unpacking python3-tabulate (0.9.0-1) ... 446s 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previously unselected package python3-texttable. 447s Preparing to unpack .../237-python3-texttable_1.7.0-1_all.deb ... 447s Unpacking python3-texttable (1.7.0-1) ... 447s Selecting previously unselected package t-coffee. 447s Preparing to unpack .../238-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_s390x.deb ... 447s Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 447s Selecting previously unselected package texlive-fonts-recommended. 447s Preparing to unpack .../239-texlive-fonts-recommended_2024.20250309-1_all.deb ... 447s Unpacking texlive-fonts-recommended (2024.20250309-1) ... 447s Selecting previously unselected package texlive-latex-base. 447s Preparing to unpack .../240-texlive-latex-base_2024.20250309-1_all.deb ... 447s Unpacking texlive-latex-base (2024.20250309-1) ... 447s Selecting previously unselected package libfontbox-java. 447s Preparing to unpack .../241-libfontbox-java_1%3a1.8.16-5_all.deb ... 447s Unpacking libfontbox-java (1:1.8.16-5) ... 447s Selecting previously unselected package libpdfbox-java. 447s Preparing to unpack .../242-libpdfbox-java_1%3a1.8.16-5_all.deb ... 447s Unpacking libpdfbox-java (1:1.8.16-5) ... 447s Selecting previously unselected package texlive-latex-recommended. 447s Preparing to unpack .../243-texlive-latex-recommended_2024.20250309-1_all.deb ... 447s Unpacking texlive-latex-recommended (2024.20250309-1) ... 448s Selecting previously unselected package texlive-pictures. 448s Preparing to unpack .../244-texlive-pictures_2024.20250309-1_all.deb ... 448s Unpacking texlive-pictures (2024.20250309-1) ... 449s Selecting previously unselected package texlive-latex-extra. 449s Preparing to unpack .../245-texlive-latex-extra_2024.20250309-2_all.deb ... 449s Unpacking texlive-latex-extra (2024.20250309-2) ... 450s Selecting previously unselected package wise-data. 450s Preparing to unpack .../246-wise-data_2.4.1-25_all.deb ... 450s Unpacking wise-data (2.4.1-25) ... 450s Selecting previously unselected package wise. 450s Preparing to unpack .../247-wise_2.4.1-25_s390x.deb ... 450s Unpacking wise (2.4.1-25) ... 450s Selecting previously unselected package fasttree. 450s Preparing to unpack .../248-fasttree_2.1.11-2_s390x.deb ... 450s Unpacking fasttree (2.1.11-2) ... 450s Selecting previously unselected package python3-igraph. 450s Preparing to unpack .../249-python3-igraph_0.11.8+ds-1build1_s390x.deb ... 450s Unpacking python3-igraph (0.11.8+ds-1build1) ... 450s Setting up dh-python (6.20250308) ... 450s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 450s Setting up liblcms2-2:s390x (2.16-2) ... 450s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 450s Setting up libpixman-1-0:s390x (0.44.0-3) ... 450s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 450s Setting up python3-texttable (1.7.0-1) ... 450s Setting up libaom3:s390x (3.12.1-1) ... 450s Setting up mysql-common (5.8+1.1.1ubuntu1) ... 450s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 450s Setting up fonts-lato (2.015-1) ... 450s Setting up libxpm4:s390x (1:3.5.17-1build2) ... 450s Setting up hicolor-icon-theme (0.18-2) ... 450s Setting up libxi6:s390x (2:1.8.2-1) ... 450s Setting up probcons (1.12-14) ... 450s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 450s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 450s Setting up libxcb-render0:s390x (1.17.0-2) ... 450s Setting up python3-defusedxml (0.7.1-3) ... 451s Setting up mafft (7.505-1) ... 451s Setting up libarchive-zip-perl (1.68-1) ... 451s Setting up imagemagick-7-common (8:7.1.1.43+dfsg1-1) ... 451s Setting up bwa (0.7.18-1) ... 451s Setting up python3-alabaster (0.7.16-0.1) ... 451s Setting up fonts-lyx (2.4.3-1) ... 451s Setting up libijs-0.35:s390x (0.35-15.2) ... 451s Setting up libdebhelper-perl (13.24.1ubuntu2) ... 451s Setting up libgs-common (10.05.0dfsg1-0ubuntu1) ... 451s Setting up libfontbox-java (1:1.8.16-5) ... 451s Setting up phylip (1:3.697+dfsg-4build1) ... 451s Setting up x11-common (1:7.7+23ubuntu4) ... 451s Setting up libdeflate0:s390x (1.23-2) ... 451s Setting up python3-tabulate (0.9.0-1) ... 451s Setting up m4 (1.4.19-7) ... 451s Setting up libqhull-r8.0:s390x (2020.2-6build1) ... 451s Setting up python3-all (3.13.3-1) ... 451s Setting up libxcb-shm0:s390x (1.17.0-2) ... 451s Setting up libgomp1:s390x (15-20250404-0ubuntu1) ... 451s Setting up python3-networkx (3.2.1-4ubuntu1) ... 452s Setting up libmysqlclient24:s390x (8.4.4-0ubuntu2) ... 452s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 452s Setting up libnetpbm11t64:s390x (2:11.09.02-2) ... 452s Setting up python3-platformdirs (4.3.6-1) ... 452s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 452s Setting up poppler-data (0.4.12-1) ... 452s Setting up python3-fs (2.4.16-7) ... 452s Setting up unicode-data (15.1.0-1) ... 452s Setting up python3-mysqldb (1.4.6-2build6) ... 452s Setting up tex-common (6.19) ... 452s update-language: texlive-base not installed and configured, doing nothing! 452s Setting up python3-roman (5.0-1) ... 452s Setting up python3-decorator (5.1.1-5) ... 452s Setting up libfontenc1:s390x (1:1.1.8-1build1) ... 452s Setting up autotools-dev (20220109.1) ... 452s Setting up libblas3:s390x (3.12.1-2) ... 452s 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 452s Setting up python3-packaging (24.2-1) ... 453s Setting up libexpat1-dev:s390x (2.7.1-1) ... 453s Setting up libzzip-0-13t64:s390x (0.13.78+dfsg.1-0.1) ... 453s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 453s Setting up libjbig2dec0:s390x (0.20-1build3) ... 453s Setting up python3-snowballstemmer (2.2.0-4build1) ... 453s Setting up libteckit0:s390x (2.5.12+ds1-1) ... 453s Setting up python3-brotli (1.1.0-2build4) ... 453s Setting up libapache-pom-java (33-2) ... 453s Setting up libavahi-common-data:s390x (0.8-16ubuntu2) ... 453s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 453s Setting up t1utils (1.41-4build3) ... 453s Setting up python3-cycler (0.12.1-1) ... 453s Setting up libtexlua53-5:s390x (2024.20240313.70630+ds-6) ... 453s Setting up libimagequant0:s390x (2.18.0-1build1) ... 453s Setting up fonts-dejavu-mono (2.37-8) ... 453s Setting up python3-kiwisolver (1.4.7-3build1) ... 453s Setting up libmpc3:s390x (1.3.1-1build2) ... 453s Setting up python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 453s Setting up libidn12:s390x (1.43-1) ... 453s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ... 453s Setting up autopoint (0.23.1-1) ... 453s Setting up libmpfi0:s390x (1.5.4+ds-4) ... 453s Setting up fonts-dejavu-core (2.37-8) ... 453s Setting up wise-data (2.4.1-25) ... 453s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 453s Setting up libltdl7:s390x (2.5.4-4) ... 453s Setting up libfftw3-double3:s390x (3.3.10-2fakesync1build1) ... 453s Setting up 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libxaw7:s390x (2:1.0.16-1) ... 464s Setting up gcc-14 (14.2.0-19ubuntu2) ... 464s Setting up python3-pil.imagetk:s390x (11.1.0-5build1) ... 464s Setting up python3-rlpycairo (0.3.0-3) ... 464s Setting up python3-reportlab (4.3.1-1) ... 464s Setting up texlive-binaries (2024.20240313.70630+ds-6) ... 464s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 464s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 464s Setting up g++-14 (14.2.0-19ubuntu2) ... 464s Setting up texlive-base (2024.20250309-1) ... 465s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 465s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 465s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 465s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 466s 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python3-fonttools (4.55.3-2build1) ... 466s Setting up libmagickcore-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 466s Setting up python3-matplotlib (3.8.3-7build1) ... 467s Setting up libmagickwand-7.q16-10:s390x (8:7.1.1.43+dfsg1-1) ... 467s Setting up imagemagick-7.q16 (8:7.1.1.43+dfsg1-1) ... 467s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 467s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 467s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 467s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 467s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 467s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 467s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 467s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 467s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 467s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 467s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 467s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 467s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 467s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 467s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 467s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 467s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 467s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 467s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 467s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 467s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 467s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 467s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 467s 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 467s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 467s 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 467s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 467s 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 467s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 467s 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 467s Setting up hevea (2.36-2) ... 467s Setting up imagemagick (8:7.1.1.43+dfsg1-1) ... 467s Processing triggers for install-info (7.1.1-1) ... 467s Processing triggers for libc-bin (2.41-6ubuntu1) ... 467s Processing triggers for man-db (2.13.0-1) ... 469s Processing triggers for sgml-base (1.31) ... 469s Setting up docutils-common (0.21.2+dfsg-2) ... 469s Setting up w3c-sgml-lib (1.3-3) ... 489s Setting up python3-biopython (1.85+dfsg-2build1) ... 490s Setting up python3-biopython-sql (1.85+dfsg-2build1) ... 490s Processing triggers for sgml-base (1.31) ... 490s Setting up python3-docutils (0.21.2+dfsg-2) ... 490s Setting up python3-sphinx (8.2.3-1) ... 491s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 491s Setting up python3-numpydoc (1.8.0-1) ... 491s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... 491s Processing triggers for tex-common (6.19) ... 491s Running updmap-sys. This may take some time... done. 491s Running mktexlsr /var/lib/texmf ... done. 491s Building format(s) --all. 568s This may take some time... done. 576s autopkgtest [21:15:49]: test full_suite: sh debian/tests/run-unit-test 576s autopkgtest [21:15:49]: test full_suite: [----------------------- 576s mkdir: created directory 'Bio' 576s mkdir: created directory 'Bio/Align' 576s mkdir: created directory 'Bio/Align/substitution_matrices' 576s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 576s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 577s test_Ace ... ok 577s test_Affy ... ok 578s test_AlignIO ... ok 578s test_AlignIO_ClustalIO ... ok 578s test_AlignIO_EmbossIO ... ok 578s test_AlignIO_FastaIO ... ok 578s test_AlignIO_MauveIO ... ok 578s test_AlignIO_PhylipIO ... ok 578s test_AlignIO_convert ... ok 579s test_AlignInfo ... ok 579s test_Align_Alignment ... ok 579s test_Align_a2m ... ok 579s test_Align_bed ... ok 579s test_Align_bigbed ... ok 579s test_Align_bigmaf ... ok 579s test_Align_bigpsl ... ok 580s test_Align_chain ... ok 580s test_Align_clustal ... ok 584s test_Align_codonalign ... ok 584s test_Align_emboss ... ok 584s test_Align_exonerate ... ok 584s test_Align_fasta ... ok 585s test_Align_hhr ... ok 585s test_Align_maf ... ok 585s test_Align_mauve ... ok 585s test_Align_msf ... ok 585s test_Align_nexus ... ok 585s test_Align_phylip ... ok 586s test_Align_psl ... ok 586s test_Align_sam ... ok 587s test_Align_stockholm ... ok 587s test_Align_tabular ... ok 587s test_Application ... ok 587s test_BioSQL_MySQLdb_online ... skipping. internet not available 587s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 587s test_BioSQL_mysql_connector_online ... skipping. internet not available 587s test_BioSQL_psycopg2_online ... skipping. internet not available 590s test_BioSQL_sqlite3 ... ok 590s test_BioSQL_sqlite3_online ... skipping. internet not available 590s test_Blast_Record ... ok 590s test_Blast_parser ... ok 590s test_CAPS ... ok 590s test_Chi2 ... ok 592s test_ClustalOmega_tool ... ok 592s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 592s test_Cluster ... ok 592s test_CodonTable ... ok 592s test_ColorSpiral ... ok 592s test_Compass ... ok 593s test_Consensus ... ok 594s test_Dialign_tool ... ok 594s test_EMBL_unittest ... ok 594s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 594s test_EmbossPrimer ... ok 598s test_Entrez ... ok 598s test_Entrez_online ... skipping. internet not available 599s test_Entrez_parser ... ok 599s test_Enzyme ... ok 599s test_ExPASy ... skipping. internet not available 599s test_Fasttree_tool ... ok 599s test_File ... ok 599s test_GenBank ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:600: BiopythonWarning: Annotation 'Sequence Read Archive: SRX001885, SRX001121, SRX001531, SRX001530, SRX001529' too long 599s warnings.warn(f"Annotation {text!r} too long", BiopythonWarning) 599s ok 601s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 602s ok 602s test_GraphicsChromosome ... ok 602s test_GraphicsDistribution ... ok 603s test_GraphicsGeneral ... ok 603s test_HMMCasino ... ok 603s test_HMMGeneral ... ok 603s test_KEGG ... ok 603s test_KEGG_online ... skipping. internet not available 607s test_KGML_graphics ... ok 607s test_KGML_graphics_online ... skipping. internet not available 608s test_KGML_nographics ... ok 608s test_KeyWList ... ok 608s test_LogisticRegression ... ok 609s test_MafIO_index ... ok 609s test_Mafft_tool ... ok 609s test_MarkovModel ... ok 610s test_Medline ... ok 610s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 610s test_NCBIXML ... Exception ignored in: 610s Traceback (most recent call last): 610s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 610s expat_parser.Parse(NULL, True) 610s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 610s ok 612s test_NCBI_BLAST_tools ... ok 612s test_NCBI_qblast ... ok 612s test_NMR ... ok 612s test_NaiveBayes ... ok 612s test_Nexus ... ok 612s test_PAML_baseml ... ok 613s test_PAML_codeml ... ok 613s test_PAML_yn00 ... ok 617s test_PDB_CEAligner ... ok 618s test_PDB_DSSP ... ok 618s test_PDB_Dice ... ok 618s test_PDB_Disordered ... ok 618s test_PDB_Exposure ... ok 618s test_PDB_FragmentMapper ... ok 620s test_PDB_KDTree ... ok 620s test_PDB_MMCIF2Dict ... ok 620s test_PDB_MMCIFIO ... ok 621s test_PDB_MMCIFParser ... ok 621s test_PDB_NACCESS ... ok 621s test_PDB_PDBIO ... ok 621s test_PDB_PDBList ... skipping. internet not available 628s test_PDB_PDBMLParser ... ok 629s test_PDB_PDBParser ... ok 629s 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 629s test_PDB_Polypeptide ... ok 629s test_PDB_QCPSuperimposer ... ok 632s test_PDB_SASA ... ok 632s test_PDB_SMCRA ... ok 632s test_PDB_Selection ... ok 632s test_PDB_StructureAlignment ... ok 632s test_PDB_Superimposer ... ok 632s test_PDB_alphafold_db ... skipping. internet not available 638s test_PDB_internal_coords ... ok 638s test_PDB_parse_pdb_header ... ok 639s test_PDB_vectors ... ok 639s test_PQR ... ok 639s test_Pathway ... ok 639s test_Phd ... ok 640s test_Phylo ... ok 640s test_PhyloXML ... ok 640s test_Phylo_CDAO ... ok 641s test_Phylo_NeXML ... ok 641s test_Phylo_igraph ... ok 643s test_Phylo_matplotlib ... ok 644s test_Phylo_networkx ... ok 644s test_PopGen_GenePop_nodepend ... ok 645s test_Prank_tool ... ok 646s test_Probcons_tool ... ok 646s test_ProtParam ... ok 647s test_RCSBFormats ... ok 647s test_Restriction ... ok 648s test_SCOP_Astral ... ok 648s test_SCOP_Cla ... ok 649s test_SCOP_Des ... ok 649s test_SCOP_Dom ... ok 649s test_SCOP_Hie ... ok 650s test_SCOP_Raf ... ok 650s test_SCOP_Residues ... ok 650s test_SCOP_Scop ... ok 651s test_SVDSuperimposer ... ok 651s test_SearchIO_blast_tab ... ok 651s test_SearchIO_blast_tab_index ... ok 652s test_SearchIO_blast_xml ... ok 653s test_SearchIO_blast_xml_index ... ok 654s test_SearchIO_blat_psl ... ok 654s test_SearchIO_blat_psl_index ... ok 655s test_SearchIO_exonerate ... ok 655s test_SearchIO_exonerate_text_index ... ok 655s test_SearchIO_exonerate_vulgar_index ... ok 656s test_SearchIO_fasta_m10 ... ok 656s test_SearchIO_fasta_m10_index ... ok 657s test_SearchIO_hhsuite2_text ... ok 657s test_SearchIO_hmmer2_text ... ok 658s test_SearchIO_hmmer2_text_index ... ok 658s test_SearchIO_hmmer3_domtab ... ok 659s test_SearchIO_hmmer3_domtab_index ... ok 659s test_SearchIO_hmmer3_tab ... ok 660s test_SearchIO_hmmer3_tab_index ... ok 660s test_SearchIO_hmmer3_text ... ok 661s test_SearchIO_hmmer3_text_index ... ok 661s test_SearchIO_interproscan_xml ... ok 662s test_SearchIO_model ... ok 663s test_SearchIO_write ... ok 663s test_SeqFeature ... ok 676s test_SeqIO ... ok 677s test_SeqIO_AbiIO ... ok 677s test_SeqIO_FastaIO ... ok 677s test_SeqIO_Gck ... ok 678s test_SeqIO_Gfa ... ok 678s test_SeqIO_Insdc ... ok 679s test_SeqIO_NibIO ... ok 680s test_SeqIO_PdbIO ... ok 681s test_SeqIO_QualityIO ... ok 681s test_SeqIO_SeqXML ... ok 682s test_SeqIO_SffIO ... ok 682s test_SeqIO_SnapGene ... ok 683s test_SeqIO_TwoBitIO ... ok 684s test_SeqIO_UniprotIO ... ok 684s test_SeqIO_Xdna ... ok 685s test_SeqIO_features ... ok 695s test_SeqIO_index ... ok 695s test_SeqIO_online ... skipping. internet not available 696s test_SeqIO_write ... ok 696s test_SeqRecord ... ok 697s test_SeqUtils ... ok 698s test_Seq_objs ... ok 698s test_SwissProt ... ok 700s test_TCoffee_tool ... ok 701s test_TogoWS ... skipping. internet not available 702s test_TreeConstruction ... ok 702s test_UniGene ... ok 702s test_UniProt ... skipping. internet not available 703s test_UniProt_GOA ... ok 703s test_align ... ok 704s test_align_substitution_matrices ... ok 706s test_bgzf ... ok 707s test_cellosaurus ... ok 712s test_codonalign ... ok 712s test_geo ... ok 712s test_kNN ... ok 713s test_motifs ... ok 713s test_motifs_online ... skipping. internet not available 714s 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. 714s warnings.warn( 714s ok 714s test_pairwise2_no_C ... ok 715s test_pairwise_aligner ... ok 715s test_pairwise_alignment_map ... ok 721s test_phenotype ... ok 722s test_phenotype_fit ... ok 722s 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. 723s test_prodoc ... ok 723s test_prosite ... ok 724s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 724s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 725s test_seq ... ok 725s test_translate ... ok 725s ---------------------------------------------------------------------- 725s Ran 216 tests in 148.714 seconds 725s 725s Skipping any tests requiring internet access 725s Python version: 3.13.3 (main, Apr 8 2025, 19:55:40) [GCC 14.2.0] 725s Operating system: posix linux 726s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 726s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 727s autopkgtest [21:18:20]: test full_suite: -----------------------] 727s autopkgtest [21:18:20]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 727s full_suite PASS 727s autopkgtest [21:18:20]: @@@@@@@@@@@@@@@@@@@@ summary 727s dependencies PASS 727s full_suite PASS 744s nova [W] Using flock in prodstack6-s390x 744s Creating nova instance adt-questing-s390x-python-biopython-20250503-204125-juju-7f2275-prod-proposed-migration-environment-23-88002bdb-db2f-485e-8e5e-ad3a1d24f9db from image adt/ubuntu-questing-s390x-server-20250503.img (UUID 28f9c1a1-7734-4b43-83da-146791cb698d)... 744s nova [W] Timed out waiting for fe403871-97dc-4ff9-a248-e3c08449ada0 to get deleted. 744s nova [W] Using flock in prodstack6-s390x 744s Creating nova instance adt-questing-s390x-python-biopython-20250503-204125-juju-7f2275-prod-proposed-migration-environment-23-88002bdb-db2f-485e-8e5e-ad3a1d24f9db from image adt/ubuntu-questing-s390x-server-20250503.img (UUID 28f9c1a1-7734-4b43-83da-146791cb698d)... 744s nova [W] Timed out waiting for 84692bd1-46aa-45c9-a5fe-d70471102432 to get deleted.