0s autopkgtest [17:00:36]: starting date and time: 2026-01-23 17:00:36+0000 0s autopkgtest [17:00:36]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [17:00:36]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7lcv69ao/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-s390x-2.secgroup --name adt-resolute-s390x-python-biopython-20260123-170035-juju-7f2275-prod-proposed-migration-environment-15-83b3b2f9-1a92-4a72-b2ce-9c7c9debd02c --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-python-biopython-20260123-170035-juju-7f2275-prod-proposed-migration-environment-15-83b3b2f9-1a92-4a72-b2ce-9c7c9debd02c from image adt/ubuntu-resolute-s390x-server-20260123.img (UUID 5f2e306c-5dfc-4ef6-8be2-414f657c7562)... 72s autopkgtest [17:01:48]: testbed dpkg architecture: s390x 72s autopkgtest [17:01:48]: testbed apt version: 3.1.13 72s autopkgtest [17:01:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s autopkgtest [17:01:49]: testbed release detected to be: None 73s autopkgtest [17:01:49]: updating testbed package index (apt update) 73s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 74s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 74s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 74s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 74s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1006 kB] 74s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [90.6 kB] 74s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 74s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.6 kB] 74s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [107 kB] 74s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [826 kB] 74s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [9152 B] 74s Fetched 2190 kB in 1s (2474 kB/s) 76s Reading package lists... 82s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 82s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 82s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 82s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 82s Reading package lists... 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Calculating upgrade... 82s The following packages were automatically installed and are no longer required: 82s python3.13 python3.13-minimal 82s Use 'sudo apt autoremove' to remove them. 82s The following NEW packages will be installed: 82s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 82s The following packages will be upgraded: 82s libplymouth5 libpython3-stdlib libtasn1-6 plymouth 82s plymouth-theme-ubuntu-text python3 python3-gdbm python3-jaraco.context 82s python3-minimal 82s 9 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 7066 kB of archives. 82s After this operation, 24.3 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.2-1 [917 kB] 82s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 83s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.14.2-1 [28.2 kB] 83s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.14.2-1 [22.9 kB] 83s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.2-1 [2373 kB] 83s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 83s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.14.2-1 [10.9 kB] 83s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x libtasn1-6 s390x 4.21.0-2 [48.6 kB] 83s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x libplymouth5 s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [159 kB] 83s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x plymouth-theme-ubuntu-text s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [10.2 kB] 83s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x plymouth s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [152 kB] 83s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-gdbm s390x 3.14.2-1 [11.1 kB] 83s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x python3-jaraco.context all 6.0.1-2 [8198 B] 83s dpkg-preconfigure: unable to re-open stdin: No such file or directory 83s Fetched 7066 kB in 1s (12.9 MB/s) 83s Selecting previously unselected package libpython3.14-minimal:s390x. 83s (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 ... 87685 files and directories currently installed.) 83s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_s390x.deb ... 83s Unpacking libpython3.14-minimal:s390x (3.14.2-1) ... 83s Selecting previously unselected package python3.14-minimal. 83s Preparing to unpack .../python3.14-minimal_3.14.2-1_s390x.deb ... 83s Unpacking python3.14-minimal (3.14.2-1) ... 84s Setting up libpython3.14-minimal:s390x (3.14.2-1) ... 84s Setting up python3.14-minimal (3.14.2-1) ... 87s (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 ... 88027 files and directories currently installed.) 87s Preparing to unpack .../python3-minimal_3.14.2-1_s390x.deb ... 87s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 87s Setting up python3-minimal (3.14.2-1) ... 87s (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 ... 88027 files and directories currently installed.) 87s Preparing to unpack .../0-python3_3.14.2-1_s390x.deb ... 88s running python pre-rtupdate hooks for python3.14... 88s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 88s Selecting previously unselected package libpython3.14-stdlib:s390x. 88s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_s390x.deb ... 88s Unpacking libpython3.14-stdlib:s390x (3.14.2-1) ... 88s Selecting previously unselected package python3.14. 88s Preparing to unpack .../2-python3.14_3.14.2-1_s390x.deb ... 88s Unpacking python3.14 (3.14.2-1) ... 88s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_s390x.deb ... 88s Unpacking libpython3-stdlib:s390x (3.14.2-1) over (3.13.9-3) ... 88s Preparing to unpack .../4-libtasn1-6_4.21.0-2_s390x.deb ... 88s Unpacking libtasn1-6:s390x (4.21.0-2) over (4.20.0-2ubuntu1) ... 88s Preparing to unpack .../5-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 88s Unpacking libplymouth5:s390x (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 88s Preparing to unpack .../6-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 88s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 88s Preparing to unpack .../7-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 88s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 88s Preparing to unpack .../8-python3-gdbm_3.14.2-1_s390x.deb ... 88s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 88s Preparing to unpack .../9-python3-jaraco.context_6.0.1-2_all.deb ... 89s Unpacking python3-jaraco.context (6.0.1-2) over (6.0.1-1build1) ... 89s Setting up libpython3.14-stdlib:s390x (3.14.2-1) ... 89s Setting up libplymouth5:s390x (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 89s Setting up libtasn1-6:s390x (4.21.0-2) ... 89s Setting up python3.14 (3.14.2-1) ... 92s Setting up libpython3-stdlib:s390x (3.14.2-1) ... 92s Setting up python3-gdbm (3.14.2-1) ... 92s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 92s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 93s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 93s Setting up python3 (3.14.2-1) ... 93s running python rtupdate hooks for python3.14... 93s running python post-rtupdate hooks for python3.14... 94s Setting up python3-jaraco.context (6.0.1-2) ... 94s Processing triggers for libc-bin (2.42-2ubuntu4) ... 94s Processing triggers for systemd (259-1ubuntu2) ... 94s Processing triggers for man-db (2.13.1-1) ... 96s Processing triggers for initramfs-tools (0.150ubuntu7) ... 96s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 104s Using config file '/etc/zipl.conf' 104s Building bootmap in '/boot' 104s Adding IPL section 'ubuntu' (default) 104s Preparing boot device: vda. 104s Done. 104s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 104s Processing triggers for initramfs-tools (0.150ubuntu7) ... 104s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 110s Using config file '/etc/zipl.conf' 110s Building bootmap in '/boot' 110s Adding IPL section 'ubuntu' (default) 110s Preparing boot device: vda. 110s Done. 110s autopkgtest [17:02:26]: upgrading testbed (apt dist-upgrade and autopurge) 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Calculating upgrade... 112s The following packages were automatically installed and are no longer required: 112s python3.13 python3.13-minimal 112s Use 'sudo apt autoremove' to remove them. 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Solving dependencies... 112s The following packages will be REMOVED: 112s python3.13* python3.13-minimal* 114s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 114s After this operation, 8012 kB disk space will be freed. 114s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 88454 files and directories currently installed.) 114s Removing python3.13 (3.13.11-1) ... 114s Removing python3.13-minimal (3.13.11-1) ... 116s Processing triggers for man-db (2.13.1-1) ... 116s Processing triggers for systemd (259-1ubuntu2) ... 116s (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 ... 88427 files and directories currently installed.) 116s Purging configuration files for python3.13-minimal (3.13.11-1) ... 117s autopkgtest [17:02:33]: rebooting testbed after setup commands that affected boot 145s autopkgtest [17:03:01]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP Mon Jan 12 15:39:23 UTC 2026 147s autopkgtest [17:03:03]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 152s Get:1 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (dsc) [3562 B] 152s Get:2 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (tar) [14.5 MB] 152s Get:3 http://ftpmaster.internal/ubuntu resolute/universe python-biopython 1.86+dfsg-1 (diff) [41.4 kB] 152s gpgv: Signature made Wed Oct 29 22:41:45 2025 UTC 152s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 152s gpgv: issuer "emollier@debian.org" 152s gpgv: Can't check signature: No public key 152s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.86+dfsg-1.dsc: no acceptable signature found 157s autopkgtest [17:03:10]: testing package python-biopython version 1.86+dfsg-1 159s autopkgtest [17:03:15]: build not needed 181s autopkgtest [17:03:37]: test dependencies: preparing testbed 181s Reading package lists... 182s Building dependency tree... 182s Reading state information... 182s Solving dependencies... 183s The following NEW packages will be installed: 183s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 183s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 183s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 183s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery liblapack3 183s liblcms2-2 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 183s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 183s python-biopython-doc python3-all python3-biopython python3-biopython-sql 183s python3-cairo python3-charset-normalizer python3-freetype python3-numpy 183s python3-numpy-dev python3-pil python3-reportlab python3-rlpycairo python3.13 183s python3.13-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings 183s xfonts-utils xml-core 183s 0 upgraded, 53 newly installed, 0 to remove and 0 not upgraded. 183s Need to get 53.4 MB of archives. 183s After this operation, 153 MB of additional disk space will be used. 183s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-minimal s390x 3.13.11-1 [2405 kB] 184s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.3.5+ds-3 [146 kB] 184s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7ubuntu1 [255 kB] 184s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-11ubuntu1 [629 kB] 184s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7ubuntu1 [2983 kB] 185s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.3.5+ds-3 [5305 kB] 185s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13 s390x 3.13.11-1 [758 kB] 185s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-mono all 2.37-8build1 [502 kB] 185s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-core all 2.37-8build1 [834 kB] 185s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x libfontenc1 s390x 1:1.1.8-1build2 [14.5 kB] 185s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x libfreetype6 s390x 2.14.1+dfsg-2 [443 kB] 185s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x x11-common all 1:7.7+24ubuntu1 [22.4 kB] 185s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 185s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x xfonts-utils s390x 1:7.7+7build1 [101 kB] 185s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-urw-base35 all 20200910-8build1 [10.9 MB] 186s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x fontconfig-config s390x 2.15.0-2.4ubuntu1 [38.2 kB] 186s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-extra all 2.37-8build1 [1944 kB] 186s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x libfontconfig1 s390x 2.15.0-2.4ubuntu1 [150 kB] 186s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libpixman-1-0 s390x 0.46.4-1 [217 kB] 186s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-render0 s390x 1.17.0-2build1 [16.9 kB] 186s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-shm0 s390x 1.17.0-2build1 [5916 B] 186s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libxrender1 s390x 1:0.9.12-1 [20.9 kB] 186s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x libcairo2 s390x 1.18.4-3 [578 kB] 186s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 186s Get:25 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-11ubuntu1 [154 kB] 186s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x libgraphite2-3 s390x 1.3.14-11ubuntu1 [80.5 kB] 186s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x libharfbuzz0b s390x 12.3.0-4 [569 kB] 186s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 186s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg-turbo8 s390x 2.1.5-4ubuntu2 [147 kB] 186s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 186s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 186s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x liblcms2-2 s390x 2.17-1 [176 kB] 186s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x libraqm0 s390x 0.10.3-1 [15.6 kB] 186s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x libsharpyuv0 s390x 1.5.0-0.1build1 [16.6 kB] 186s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x libjbig0 s390x 2.1-6.1ubuntu3 [32.8 kB] 186s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x libwebp7 s390x 1.5.0-0.1build1 [227 kB] 186s Get:37 http://ftpmaster.internal/ubuntu resolute/main s390x libtiff6 s390x 4.7.0-3ubuntu3 [222 kB] 186s Get:38 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpdemux2 s390x 1.5.0-0.1build1 [12.5 kB] 186s Get:39 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpmux3 s390x 1.5.0-0.1build1 [25.7 kB] 186s Get:40 http://ftpmaster.internal/ubuntu resolute/universe s390x python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 187s Get:41 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-all s390x 3.14.2-1 [890 B] 187s Get:42 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-charset-normalizer s390x 3.4.4-2 [181 kB] 187s Get:43 http://ftpmaster.internal/ubuntu resolute/main s390x libopenjp2-7 s390x 2.5.4-1 [208 kB] 187s Get:44 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pil s390x 12.0.0-1ubuntu1 [540 kB] 187s Get:45 http://ftpmaster.internal/ubuntu resolute/main s390x python3-cairo s390x 1.27.0-2build1 [140 kB] 187s Get:46 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-freetype all 2.5.1-2 [92.2 kB] 187s Get:47 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-rlpycairo all 0.3.0-4 [9332 B] 187s Get:48 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-reportlab all 4.4.9-1 [1149 kB] 187s Get:49 http://ftpmaster.internal/ubuntu resolute/main s390x sgml-base all 1.31+nmu1 [11.0 kB] 187s Get:50 http://ftpmaster.internal/ubuntu resolute/main s390x xml-core all 0.19build1 [20.3 kB] 187s Get:51 http://ftpmaster.internal/ubuntu resolute/universe s390x w3c-sgml-lib all 1.3-3build1 [278 kB] 187s Get:52 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-biopython s390x 1.86+dfsg-1 [1710 kB] 187s Get:53 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-biopython-sql all 1.86+dfsg-1 [26.4 kB] 188s Fetched 53.4 MB in 5s (11.1 MB/s) 188s Selecting previously unselected package python3.13-minimal. 188s (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 ... 88429 files and directories currently installed.) 188s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_s390x.deb ... 188s Unpacking python3.13-minimal (3.13.11-1) ... 188s Selecting previously unselected package python3-numpy-dev:s390x. 188s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_s390x.deb ... 188s Unpacking python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 188s Selecting previously unselected package libblas3:s390x. 188s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_s390x.deb ... 188s Unpacking libblas3:s390x (3.12.1-7ubuntu1) ... 189s Selecting previously unselected package libgfortran5:s390x. 189s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_s390x.deb ... 189s Unpacking libgfortran5:s390x (15.2.0-11ubuntu1) ... 189s Selecting previously unselected package liblapack3:s390x. 189s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_s390x.deb ... 189s Unpacking liblapack3:s390x (3.12.1-7ubuntu1) ... 189s Selecting previously unselected package python3-numpy. 189s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_s390x.deb ... 189s Unpacking python3-numpy (1:2.3.5+ds-3) ... 189s Selecting previously unselected package python3.13. 189s Preparing to unpack .../06-python3.13_3.13.11-1_s390x.deb ... 189s Unpacking python3.13 (3.13.11-1) ... 189s Selecting previously unselected package fonts-dejavu-mono. 189s Preparing to unpack .../07-fonts-dejavu-mono_2.37-8build1_all.deb ... 189s Unpacking fonts-dejavu-mono (2.37-8build1) ... 189s Selecting previously unselected package fonts-dejavu-core. 190s Preparing to unpack .../08-fonts-dejavu-core_2.37-8build1_all.deb ... 190s Unpacking fonts-dejavu-core (2.37-8build1) ... 190s Selecting previously unselected package libfontenc1:s390x. 190s Preparing to unpack .../09-libfontenc1_1%3a1.1.8-1build2_s390x.deb ... 190s Unpacking libfontenc1:s390x (1:1.1.8-1build2) ... 190s Selecting previously unselected package libfreetype6:s390x. 190s Preparing to unpack .../10-libfreetype6_2.14.1+dfsg-2_s390x.deb ... 190s Unpacking libfreetype6:s390x (2.14.1+dfsg-2) ... 190s Selecting previously unselected package x11-common. 190s Preparing to unpack .../11-x11-common_1%3a7.7+24ubuntu1_all.deb ... 190s Unpacking x11-common (1:7.7+24ubuntu1) ... 190s Selecting previously unselected package xfonts-encodings. 190s Preparing to unpack .../12-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 190s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 190s Selecting previously unselected package xfonts-utils. 190s Preparing to unpack .../13-xfonts-utils_1%3a7.7+7build1_s390x.deb ... 190s Unpacking xfonts-utils (1:7.7+7build1) ... 190s Selecting previously unselected package fonts-urw-base35. 190s Preparing to unpack .../14-fonts-urw-base35_20200910-8build1_all.deb ... 190s Unpacking fonts-urw-base35 (20200910-8build1) ... 190s Selecting previously unselected package fontconfig-config. 190s Preparing to unpack .../15-fontconfig-config_2.15.0-2.4ubuntu1_s390x.deb ... 190s Unpacking fontconfig-config (2.15.0-2.4ubuntu1) ... 190s Selecting previously unselected package fonts-dejavu-extra. 190s Preparing to unpack .../16-fonts-dejavu-extra_2.37-8build1_all.deb ... 190s Unpacking fonts-dejavu-extra (2.37-8build1) ... 190s Selecting previously unselected package libfontconfig1:s390x. 191s Preparing to unpack .../17-libfontconfig1_2.15.0-2.4ubuntu1_s390x.deb ... 191s Unpacking libfontconfig1:s390x (2.15.0-2.4ubuntu1) ... 191s Selecting previously unselected package libpixman-1-0:s390x. 191s Preparing to unpack .../18-libpixman-1-0_0.46.4-1_s390x.deb ... 191s Unpacking libpixman-1-0:s390x (0.46.4-1) ... 191s Selecting previously unselected package libxcb-render0:s390x. 191s Preparing to unpack .../19-libxcb-render0_1.17.0-2build1_s390x.deb ... 191s Unpacking libxcb-render0:s390x (1.17.0-2build1) ... 191s Selecting previously unselected package libxcb-shm0:s390x. 191s Preparing to unpack .../20-libxcb-shm0_1.17.0-2build1_s390x.deb ... 191s Unpacking libxcb-shm0:s390x (1.17.0-2build1) ... 191s Selecting previously unselected package libxrender1:s390x. 191s Preparing to unpack .../21-libxrender1_1%3a0.9.12-1_s390x.deb ... 191s Unpacking libxrender1:s390x (1:0.9.12-1) ... 191s Selecting previously unselected package libcairo2:s390x. 191s Preparing to unpack .../22-libcairo2_1.18.4-3_s390x.deb ... 191s Unpacking libcairo2:s390x (1.18.4-3) ... 192s Selecting previously unselected package libdeflate0:s390x. 192s Preparing to unpack .../23-libdeflate0_1.23-2_s390x.deb ... 192s Unpacking libdeflate0:s390x (1.23-2) ... 192s Selecting previously unselected package libgomp1:s390x. 192s Preparing to unpack .../24-libgomp1_15.2.0-11ubuntu1_s390x.deb ... 192s Unpacking libgomp1:s390x (15.2.0-11ubuntu1) ... 192s Selecting previously unselected package libgraphite2-3:s390x. 192s Preparing to unpack .../25-libgraphite2-3_1.3.14-11ubuntu1_s390x.deb ... 192s Unpacking libgraphite2-3:s390x (1.3.14-11ubuntu1) ... 192s Selecting previously unselected package libharfbuzz0b:s390x. 192s Preparing to unpack .../26-libharfbuzz0b_12.3.0-4_s390x.deb ... 192s Unpacking libharfbuzz0b:s390x (12.3.0-4) ... 192s Selecting previously unselected package libimagequant0:s390x. 192s Preparing to unpack .../27-libimagequant0_2.18.0-1build1_s390x.deb ... 192s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 192s Selecting previously unselected package libjpeg-turbo8:s390x. 192s Preparing to unpack .../28-libjpeg-turbo8_2.1.5-4ubuntu2_s390x.deb ... 192s Unpacking libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 192s Selecting previously unselected package libjpeg8:s390x. 192s Preparing to unpack .../29-libjpeg8_8c-2ubuntu11_s390x.deb ... 192s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 192s Selecting previously unselected package libjs-jquery. 192s Preparing to unpack .../30-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 192s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 192s Selecting previously unselected package liblcms2-2:s390x. 192s Preparing to unpack .../31-liblcms2-2_2.17-1_s390x.deb ... 192s Unpacking liblcms2-2:s390x (2.17-1) ... 192s Selecting previously unselected package libraqm0:s390x. 192s Preparing to unpack .../32-libraqm0_0.10.3-1_s390x.deb ... 192s Unpacking libraqm0:s390x (0.10.3-1) ... 192s Selecting previously unselected package libsharpyuv0:s390x. 192s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1build1_s390x.deb ... 192s Unpacking libsharpyuv0:s390x (1.5.0-0.1build1) ... 192s Selecting previously unselected package libjbig0:s390x. 192s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu3_s390x.deb ... 192s Unpacking libjbig0:s390x (2.1-6.1ubuntu3) ... 192s Selecting previously unselected package libwebp7:s390x. 192s Preparing to unpack .../35-libwebp7_1.5.0-0.1build1_s390x.deb ... 192s Unpacking libwebp7:s390x (1.5.0-0.1build1) ... 192s Selecting previously unselected package libtiff6:s390x. 192s Preparing to unpack .../36-libtiff6_4.7.0-3ubuntu3_s390x.deb ... 192s Unpacking libtiff6:s390x (4.7.0-3ubuntu3) ... 192s Selecting previously unselected package libwebpdemux2:s390x. 192s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1build1_s390x.deb ... 192s Unpacking libwebpdemux2:s390x (1.5.0-0.1build1) ... 192s Selecting previously unselected package libwebpmux3:s390x. 192s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1build1_s390x.deb ... 192s Unpacking libwebpmux3:s390x (1.5.0-0.1build1) ... 192s Selecting previously unselected package python-biopython-doc. 192s Preparing to unpack .../39-python-biopython-doc_1.86+dfsg-1_all.deb ... 192s Unpacking python-biopython-doc (1.86+dfsg-1) ... 193s Selecting previously unselected package python3-all. 193s Preparing to unpack .../40-python3-all_3.14.2-1_s390x.deb ... 193s Unpacking python3-all (3.14.2-1) ... 194s Selecting previously unselected package python3-charset-normalizer. 194s Preparing to unpack .../41-python3-charset-normalizer_3.4.4-2_s390x.deb ... 194s Unpacking python3-charset-normalizer (3.4.4-2) ... 194s Selecting previously unselected package libopenjp2-7:s390x. 194s Preparing to unpack .../42-libopenjp2-7_2.5.4-1_s390x.deb ... 194s Unpacking libopenjp2-7:s390x (2.5.4-1) ... 194s Selecting previously unselected package python3-pil:s390x. 194s Preparing to unpack .../43-python3-pil_12.0.0-1ubuntu1_s390x.deb ... 194s Unpacking python3-pil:s390x (12.0.0-1ubuntu1) ... 194s Selecting previously unselected package python3-cairo. 194s Preparing to unpack .../44-python3-cairo_1.27.0-2build1_s390x.deb ... 194s Unpacking python3-cairo (1.27.0-2build1) ... 194s Selecting previously unselected package python3-freetype. 194s Preparing to unpack .../45-python3-freetype_2.5.1-2_all.deb ... 194s Unpacking python3-freetype (2.5.1-2) ... 194s Selecting previously unselected package python3-rlpycairo. 194s Preparing to unpack .../46-python3-rlpycairo_0.3.0-4_all.deb ... 194s Unpacking python3-rlpycairo (0.3.0-4) ... 194s Selecting previously unselected package python3-reportlab. 194s Preparing to unpack .../47-python3-reportlab_4.4.9-1_all.deb ... 194s Unpacking python3-reportlab (4.4.9-1) ... 194s Selecting previously unselected package sgml-base. 194s Preparing to unpack .../48-sgml-base_1.31+nmu1_all.deb ... 194s Unpacking sgml-base (1.31+nmu1) ... 194s Selecting previously unselected package xml-core. 194s Preparing to unpack .../49-xml-core_0.19build1_all.deb ... 194s Unpacking xml-core (0.19build1) ... 194s Selecting previously unselected package w3c-sgml-lib. 194s Preparing to unpack .../50-w3c-sgml-lib_1.3-3build1_all.deb ... 194s Unpacking w3c-sgml-lib (1.3-3build1) ... 194s Selecting previously unselected package python3-biopython. 194s Preparing to unpack .../51-python3-biopython_1.86+dfsg-1_s390x.deb ... 194s Unpacking python3-biopython (1.86+dfsg-1) ... 194s Selecting previously unselected package python3-biopython-sql. 194s Preparing to unpack .../52-python3-biopython-sql_1.86+dfsg-1_all.deb ... 194s Unpacking python3-biopython-sql (1.86+dfsg-1) ... 194s Setting up libgraphite2-3:s390x (1.3.14-11ubuntu1) ... 194s Setting up liblcms2-2:s390x (2.17-1) ... 194s Setting up libpixman-1-0:s390x (0.46.4-1) ... 194s Setting up libsharpyuv0:s390x (1.5.0-0.1build1) ... 194s Setting up libxrender1:s390x (1:0.9.12-1) ... 194s Setting up libxcb-render0:s390x (1.17.0-2build1) ... 194s Setting up python3-charset-normalizer (3.4.4-2) ... 195s Setting up x11-common (1:7.7+24ubuntu1) ... 196s Setting up libdeflate0:s390x (1.23-2) ... 196s Setting up libxcb-shm0:s390x (1.17.0-2build1) ... 196s Setting up libgomp1:s390x (15.2.0-11ubuntu1) ... 196s Setting up libjbig0:s390x (2.1-6.1ubuntu3) ... 196s Setting up libfontenc1:s390x (1:1.1.8-1build2) ... 196s Setting up libblas3:s390x (3.12.1-7ubuntu1) ... 196s 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 196s Setting up libfreetype6:s390x (2.14.1+dfsg-2) ... 196s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 196s Setting up libimagequant0:s390x (2.18.0-1build1) ... 196s Setting up fonts-dejavu-mono (2.37-8build1) ... 196s Setting up python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 196s Setting up fonts-dejavu-core (2.37-8build1) ... 196s Setting up libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 196s Setting up libgfortran5:s390x (15.2.0-11ubuntu1) ... 196s Setting up libwebp7:s390x (1.5.0-0.1build1) ... 196s Setting up fonts-dejavu-extra (2.37-8build1) ... 196s Setting up libopenjp2-7:s390x (2.5.4-1) ... 196s Setting up python3.13-minimal (3.13.11-1) ... 198s Setting up libharfbuzz0b:s390x (12.3.0-4) ... 198s Setting up sgml-base (1.31+nmu1) ... 198s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 198s Setting up libwebpmux3:s390x (1.5.0-0.1build1) ... 198s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 198s Setting up liblapack3:s390x (3.12.1-7ubuntu1) ... 198s 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 198s Setting up python3.13 (3.13.11-1) ... 202s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 202s Setting up libwebpdemux2:s390x (1.5.0-0.1build1) ... 202s Setting up python3-all (3.14.2-1) ... 202s Setting up python3-freetype (2.5.1-2) ... 203s Setting up xfonts-utils (1:7.7+7build1) ... 203s Setting up libraqm0:s390x (0.10.3-1) ... 204s Setting up python3-numpy (1:2.3.5+ds-3) ... 217s Setting up python-biopython-doc (1.86+dfsg-1) ... 217s Setting up libtiff6:s390x (4.7.0-3ubuntu3) ... 217s Setting up xml-core (0.19build1) ... 217s Setting up libfontconfig1:s390x (2.15.0-2.4ubuntu1) ... 217s Setting up fonts-urw-base35 (20200910-8build1) ... 217s Setting up libcairo2:s390x (1.18.4-3) ... 217s Setting up python3-pil:s390x (12.0.0-1ubuntu1) ... 219s Setting up python3-cairo (1.27.0-2build1) ... 219s Setting up python3-rlpycairo (0.3.0-4) ... 220s Setting up python3-reportlab (4.4.9-1) ... 223s Processing triggers for libc-bin (2.42-2ubuntu4) ... 224s Processing triggers for systemd (259-1ubuntu2) ... 224s Processing triggers for man-db (2.13.1-1) ... 225s Processing triggers for sgml-base (1.31+nmu1) ... 225s Setting up w3c-sgml-lib (1.3-3build1) ... 306s Setting up python3-biopython (1.86+dfsg-1) ... 311s Setting up python3-biopython-sql (1.86+dfsg-1) ... 313s autopkgtest [17:05:49]: test dependencies: sh debian/tests/run-unit-test 313s autopkgtest [17:05:49]: test dependencies: [----------------------- 313s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 313s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 315s mkdir: created directory 'Bio' 315s mkdir: created directory 'Bio/Align' 315s mkdir: created directory 'Bio/Align/substitution_matrices' 315s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 315s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 315s test_Ace ... ok 316s test_Affy ... ok 316s test_AlignIO ... ok 316s test_AlignIO_ClustalIO ... ok 316s test_AlignIO_EmbossIO ... ok 316s test_AlignIO_FastaIO ... ok 317s test_AlignIO_MauveIO ... ok 317s test_AlignIO_PhylipIO ... ok 317s test_AlignIO_convert ... ok 317s test_Align_Alignment ... ok 318s test_Align_a2m ... ok 318s test_Align_bed ... ok 319s test_Align_bigbed ... ok 320s test_Align_bigmaf ... ok 321s test_Align_bigpsl ... ok 322s test_Align_chain ... ok 322s test_Align_clustal ... ok 336s test_Align_codonalign ... ok 336s test_Align_emboss ... ok 337s test_Align_exonerate ... ok 337s test_Align_fasta ... ok 337s test_Align_format_matrix ... ok 338s test_Align_hhr ... ok 342s test_Align_maf ... ok 342s test_Align_mauve ... ok 342s test_Align_msf ... ok 342s test_Align_nexus ... ok 343s test_Align_phylip ... ok 344s test_Align_psl ... ok 345s test_Align_sam ... ok 351s test_Align_stockholm ... ok 353s test_Align_tabular ... ok 353s test_BioSQL_MySQLdb_online ... skipping. internet not available 354s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 354s test_BioSQL_mysql_connector_online ... skipping. internet not available 354s test_BioSQL_psycopg2_online ... skipping. internet not available 364s test_BioSQL_sqlite3 ... ok 365s test_BioSQL_sqlite3_online ... skipping. internet not available 365s test_Blast_Record ... ok 367s test_Blast_parser ... ok 367s test_CAPS ... ok 367s test_Chi2 ... ok 367s test_Cluster ... ok 367s test_CodonTable ... ok 368s test_ColorSpiral ... ok 368s test_Compass ... ok 372s test_Consensus ... ok 372s test_EMBL_unittest ... ok 372s test_EmbossPrimer ... ok 376s test_Entrez ... ok 376s test_Entrez_online ... skipping. internet not available 378s test_Entrez_parser ... ok 378s test_Enzyme ... ok 378s test_ExPASy ... skipping. internet not available 378s test_File ... ok 379s test_GenBank ... ok 385s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 390s ok 393s test_GraphicsChromosome ... ok 393s test_GraphicsDistribution ... ok 395s test_GraphicsGeneral ... ok 396s test_KEGG ... ok 396s test_KEGG_online ... skipping. internet not available 414s test_KGML_graphics ... ok 414s test_KGML_graphics_online ... skipping. internet not available 415s test_KGML_nographics ... ok 416s test_KeyWList ... ok 419s test_MafIO_index ... ok 419s test_Medline ... ok 420s test_NCBIXML ... Exception ignored in: 420s Traceback (most recent call last): 420s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 420s expat_parser.Parse(NULL, True) 420s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 420s ok 420s test_NCBI_qblast ... ok 421s test_NMR ... ok 421s test_Nexus ... ok 421s test_PAML_baseml ... ok 423s test_PAML_codeml ... ok 423s test_PAML_yn00 ... ok 439s test_PDB_CEAligner ... ok 439s test_PDB_DSSP ... ok 439s test_PDB_Dice ... ok 439s test_PDB_Disordered ... ok 441s test_PDB_Exposure ... ok 441s test_PDB_FragmentMapper ... ok 445s test_PDB_KDTree ... ok 445s test_PDB_MMCIF2Dict ... ok 446s test_PDB_MMCIFIO ... ok 450s test_PDB_MMCIFParser ... ok 451s test_PDB_NACCESS ... ok 452s test_PDB_PDBIO ... ok 452s test_PDB_PDBList ... skipping. internet not available 476s test_PDB_PDBMLParser ... ok 477s test_PDB_PDBParser ... ok 477s 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 477s test_PDB_Polypeptide ... ok 477s test_PDB_QCPSuperimposer ... ok 492s test_PDB_SASA ... ok 495s test_PDB_SMCRA ... ok 495s test_PDB_Selection ... ok 496s test_PDB_StructureAlignment ... ok 497s test_PDB_Superimposer ... ok 497s test_PDB_alphafold_db ... skipping. internet not available 497s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 497s 497s test_PDB_parse_pdb_header ... ok 497s test_PDB_vectors ... ok 498s test_PQR ... ok 498s test_Pathway ... ok 498s test_Phd ... ok 499s test_Phylo ... ok 500s test_PhyloXML ... ok 500s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 500s test_Phylo_NeXML ... ok 501s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 501s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 501s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 501s test_PopGen_GenePop_nodepend ... ok 501s test_ProtParam ... ok 502s test_RCSBFormats ... ok 502s test_Restriction ... ok 502s test_SCOP_Astral ... ok 502s test_SCOP_Cla ... ok 502s test_SCOP_Des ... ok 502s test_SCOP_Dom ... ok 502s test_SCOP_Hie ... ok 502s test_SCOP_Raf ... ok 502s test_SCOP_Residues ... ok 502s test_SCOP_Scop ... ok 502s test_SVDSuperimposer ... ok 502s test_SearchIO_blast_tab ... ok 503s test_SearchIO_blast_tab_index ... ok 503s test_SearchIO_blast_xml ... ok 507s test_SearchIO_blast_xml_index ... ok 507s test_SearchIO_blat_psl ... ok 508s test_SearchIO_blat_psl_index ... ok 508s test_SearchIO_exonerate ... ok 509s test_SearchIO_exonerate_text_index ... ok 509s test_SearchIO_exonerate_vulgar_index ... ok 509s test_SearchIO_fasta_m10 ... ok 509s test_SearchIO_fasta_m10_index ... ok 510s test_SearchIO_hhsuite2_text ... ok 510s test_SearchIO_hmmer2_text ... ok 510s test_SearchIO_hmmer2_text_index ... ok 510s test_SearchIO_hmmer3_domtab ... ok 511s test_SearchIO_hmmer3_domtab_index ... ok 511s test_SearchIO_hmmer3_tab ... ok 511s test_SearchIO_hmmer3_tab_index ... ok 511s test_SearchIO_hmmer3_text ... ok 511s test_SearchIO_hmmer3_text_index ... ok 511s test_SearchIO_infernal_tab ... ok 511s test_SearchIO_infernal_tab_index ... ok 511s test_SearchIO_infernal_text ... ok 511s test_SearchIO_infernal_text_index ... ok 511s test_SearchIO_interproscan_xml ... ok 511s test_SearchIO_model ... ok 512s test_SearchIO_write ... ok 512s test_SeqFeature ... ok 564s test_SeqIO ... ok 565s test_SeqIO_AbiIO ... ok 565s test_SeqIO_FastaIO ... ok 566s test_SeqIO_Gck ... ok 566s test_SeqIO_Gfa ... ok 566s test_SeqIO_Insdc ... ok 566s test_SeqIO_NibIO ... ok 571s test_SeqIO_PdbIO ... ok 573s test_SeqIO_QualityIO ... ok 573s test_SeqIO_SeqXML ... ok 574s test_SeqIO_SffIO ... ok 574s test_SeqIO_SnapGene ... ok 577s test_SeqIO_TwoBitIO ... ok 578s test_SeqIO_UniprotIO ... ok 578s test_SeqIO_Xdna ... ok 581s test_SeqIO_features ... ok 640s test_SeqIO_index ... ok 641s test_SeqIO_online ... skipping. internet not available 641s test_SeqIO_write ... ok 641s test_SeqRecord ... ok 641s test_SeqUtils ... ok 646s test_Seq_objs ... ok 647s test_SwissProt ... ok 647s test_TogoWS ... skipping. internet not available 649s test_TreeConstruction ... ok 649s test_UniGene ... ok 649s test_UniProt ... skipping. internet not available 650s test_UniProt_GOA ... ok 650s test_align ... ok 652s test_align_substitution_matrices ... ok 663s test_bgzf ... ok 664s test_cellosaurus ... ok 685s test_codonalign ... ok 686s test_geo ... ok 687s test_motifs ... ok 687s test_motifs_online ... skipping. internet not available 687s 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. 687s warnings.warn( 688s ok 688s test_pairwise2_no_C ... ok 689s test_pairwise_aligner ... ok 690s test_pairwise_alignment_map ... ok 724s test_phenotype ... ok 724s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 725s test_prodoc ... ok 725s test_prosite ... ok 726s test_seq ... ok 726s test_translate ... ok 726s Skipping any tests requiring internet access 726s Python version: 3.13.11 (main, Dec 6 2025, 13:15:20) [GCC 15.2.0] 726s Operating system: posix linux 726s ---------------------------------------------------------------------- 726s Ran 199 tests in 411.137 seconds 726s 727s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 727s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 730s test_Ace ... ok 730s test_Affy ... ok 732s test_AlignIO ... ok 732s test_AlignIO_ClustalIO ... ok 732s test_AlignIO_EmbossIO ... ok 732s test_AlignIO_FastaIO ... ok 732s test_AlignIO_MauveIO ... ok 732s test_AlignIO_PhylipIO ... ok 733s test_AlignIO_convert ... ok 734s test_Align_Alignment ... ok 735s test_Align_a2m ... ok 736s test_Align_bed ... ok 737s test_Align_bigbed ... ok 741s test_Align_bigmaf ... ok 743s test_Align_bigpsl ... ok 744s test_Align_chain ... ok 744s test_Align_clustal ... ok 766s test_Align_codonalign ... ok 766s test_Align_emboss ... ok 767s test_Align_exonerate ... ok 767s test_Align_fasta ... ok 767s test_Align_format_matrix ... ok 769s test_Align_hhr ... ok 774s test_Align_maf ... ok 775s test_Align_mauve ... ok 775s test_Align_msf ... ok 775s test_Align_nexus ... ok 776s test_Align_phylip ... ok 777s test_Align_psl ... ok 779s test_Align_sam ... ok 790s test_Align_stockholm ... ok 793s test_Align_tabular ... ok 793s test_BioSQL_MySQLdb_online ... skipping. internet not available 793s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 793s test_BioSQL_mysql_connector_online ... skipping. internet not available 793s test_BioSQL_psycopg2_online ... skipping. internet not available 811s test_BioSQL_sqlite3 ... ok 811s test_BioSQL_sqlite3_online ... skipping. internet not available 811s test_Blast_Record ... ok 814s test_Blast_parser ... ok 814s test_CAPS ... ok 814s test_Chi2 ... ok 815s test_Cluster ... ok 815s test_CodonTable ... ok 815s test_ColorSpiral ... ok 816s test_Compass ... ok 822s test_Consensus ... ok 822s test_EMBL_unittest ... ok 822s test_EmbossPrimer ... ok 826s test_Entrez ... ok 826s test_Entrez_online ... skipping. internet not available 829s test_Entrez_parser ... ok 829s test_Enzyme ... ok 830s test_ExPASy ... skipping. internet not available 830s test_File ... ok 831s test_GenBank ... ok 842s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 850s ok 854s test_GraphicsChromosome ... ok 855s test_GraphicsDistribution ... ok 859s test_GraphicsGeneral ... ok 860s test_KEGG ... ok 860s test_KEGG_online ... skipping. internet not available 886s test_KGML_graphics ... ok 886s test_KGML_graphics_online ... skipping. internet not available 889s test_KGML_nographics ... ok 890s test_KeyWList ... ok 894s test_MafIO_index ... ok 894s test_Medline ... ok 896s test_NCBIXML ... Exception ignored while closing generator : 896s Traceback (most recent call last): 896s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 896s expat_parser.Parse(NULL, True) 896s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 896s ok 896s test_NCBI_qblast ... ok 896s test_NMR ... ok 897s test_Nexus ... ok 898s test_PAML_baseml ... ok 901s test_PAML_codeml ... ok 901s test_PAML_yn00 ... ok 921s test_PDB_CEAligner ... ok 922s test_PDB_DSSP ... ok 922s test_PDB_Dice ... ok 923s test_PDB_Disordered ... ok 923s test_PDB_Exposure ... ok 923s test_PDB_FragmentMapper ... ok 930s test_PDB_KDTree ... ok 931s test_PDB_MMCIF2Dict ... ok 932s test_PDB_MMCIFIO ... ok 937s test_PDB_MMCIFParser ... ok 938s test_PDB_NACCESS ... ok 939s test_PDB_PDBIO ... ok 940s test_PDB_PDBList ... skipping. internet not available 963s test_PDB_PDBMLParser ... ok 964s test_PDB_PDBParser ... ok 964s 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 964s test_PDB_Polypeptide ... ok 965s test_PDB_QCPSuperimposer ... ok 982s test_PDB_SASA ... ok 985s test_PDB_SMCRA ... ok 986s test_PDB_Selection ... ok 991s test_PDB_StructureAlignment ... ok 991s test_PDB_Superimposer ... ok 992s test_PDB_alphafold_db ... skipping. internet not available 992s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 992s 992s test_PDB_parse_pdb_header ... ok 993s test_PDB_vectors ... ok 993s test_PQR ... ok 994s test_Pathway ... ok 994s test_Phd ... ok 996s test_Phylo ... ok 998s test_PhyloXML ... ok 998s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 999s test_Phylo_NeXML ... ok 1000s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 1000s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 1000s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 1001s test_PopGen_GenePop_nodepend ... ok 1001s test_ProtParam ... ok 1004s test_RCSBFormats ... ok 1004s test_Restriction ... ok 1005s test_SCOP_Astral ... ok 1005s test_SCOP_Cla ... ok 1005s test_SCOP_Des ... ok 1005s test_SCOP_Dom ... ok 1006s test_SCOP_Hie ... ok 1006s test_SCOP_Raf ... ok 1006s test_SCOP_Residues ... ok 1007s test_SCOP_Scop ... ok 1007s test_SVDSuperimposer ... ok 1008s test_SearchIO_blast_tab ... ok 1009s test_SearchIO_blast_tab_index ... ok 1010s test_SearchIO_blast_xml ... ok 1015s test_SearchIO_blast_xml_index ... ok 1016s test_SearchIO_blat_psl ... ok 1016s test_SearchIO_blat_psl_index ... ok 1017s test_SearchIO_exonerate ... ok 1018s test_SearchIO_exonerate_text_index ... ok 1018s test_SearchIO_exonerate_vulgar_index ... ok 1018s test_SearchIO_fasta_m10 ... ok 1019s test_SearchIO_fasta_m10_index ... ok 1019s test_SearchIO_hhsuite2_text ... ok 1020s test_SearchIO_hmmer2_text ... ok 1020s test_SearchIO_hmmer2_text_index ... ok 1020s test_SearchIO_hmmer3_domtab ... ok 1021s test_SearchIO_hmmer3_domtab_index ... ok 1021s test_SearchIO_hmmer3_tab ... ok 1021s test_SearchIO_hmmer3_tab_index ... ok 1022s test_SearchIO_hmmer3_text ... ok 1022s test_SearchIO_hmmer3_text_index ... ok 1023s test_SearchIO_infernal_tab ... ok 1023s test_SearchIO_infernal_tab_index ... ok 1023s test_SearchIO_infernal_text ... ok 1024s test_SearchIO_infernal_text_index ... ok 1024s test_SearchIO_interproscan_xml ... ok 1025s test_SearchIO_model ... ok 1026s test_SearchIO_write ... ok 1026s test_SeqFeature ... ok 1098s test_SeqIO ... ok 1100s test_SeqIO_AbiIO ... ok 1100s test_SeqIO_FastaIO ... ok 1100s test_SeqIO_Gck ... ok 1100s test_SeqIO_Gfa ... ok 1101s test_SeqIO_Insdc ... ok 1101s test_SeqIO_NibIO ... ok 1109s test_SeqIO_PdbIO ... ok 1110s test_SeqIO_QualityIO ... ok 1111s test_SeqIO_SeqXML ... ok 1111s test_SeqIO_SffIO ... ok 1111s test_SeqIO_SnapGene ... ok 1115s test_SeqIO_TwoBitIO ... ok 1116s test_SeqIO_UniprotIO ... ok 1116s test_SeqIO_Xdna ... ok 1118s test_SeqIO_features ... ok 1167s test_SeqIO_index ... ok 1168s test_SeqIO_online ... skipping. internet not available 1168s test_SeqIO_write ... ok 1168s test_SeqRecord ... ok 1169s test_SeqUtils ... ok 1173s test_Seq_objs ... ok 1173s test_SwissProt ... ok 1174s test_TogoWS ... skipping. internet not available 1175s test_TreeConstruction ... ok 1175s test_UniGene ... ok 1175s test_UniProt ... skipping. internet not available 1175s test_UniProt_GOA ... ok 1176s test_align ... ok 1177s test_align_substitution_matrices ... ok 1186s test_bgzf ... ok 1186s test_cellosaurus ... ok 1201s test_codonalign ... ok 1202s test_geo ... ok 1203s test_motifs ... ok 1203s test_motifs_online ... skipping. internet not available 1203s 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. 1203s warnings.warn( 1203s ok 1204s test_pairwise2_no_C ... ok 1206s test_pairwise_aligner ... ok 1206s test_pairwise_alignment_map ... ok 1236s test_phenotype ... ok 1236s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 1236s test_prodoc ... ok 1237s test_prosite ... ok 1237s test_seq ... ok 1237s test_translate ... ok 1237s Skipping any tests requiring internet access 1237s Python version: 3.14.2 (main, Dec 6 2025, 13:20:08) [GCC 15.2.0] 1237s Operating system: posix linux 1237s ---------------------------------------------------------------------- 1237s Ran 199 tests in 507.611 seconds 1237s 1237s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 1237s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 1238s autopkgtest [17:21:14]: test dependencies: -----------------------] 1239s autopkgtest [17:21:15]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 1239s dependencies PASS 1240s autopkgtest [17:21:16]: test full_suite: preparing testbed 1259s Creating nova instance adt-resolute-s390x-python-biopython-20260123-170035-juju-7f2275-prod-proposed-migration-environment-15-83b3b2f9-1a92-4a72-b2ce-9c7c9debd02c from image adt/ubuntu-resolute-s390x-server-20260123.img (UUID 5f2e306c-5dfc-4ef6-8be2-414f657c7562)... 1318s autopkgtest [17:22:34]: testbed dpkg architecture: s390x 1318s autopkgtest [17:22:34]: testbed apt version: 3.1.13 1319s autopkgtest [17:22:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1319s autopkgtest [17:22:35]: testbed release detected to be: resolute 1320s autopkgtest [17:22:36]: updating testbed package index (apt update) 1320s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 1320s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 1320s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 1320s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 1320s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1006 kB] 1320s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [90.6 kB] 1320s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 1320s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.6 kB] 1320s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [107 kB] 1320s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [826 kB] 1320s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [9152 B] 1321s Fetched 2190 kB in 1s (2786 kB/s) 1323s Reading package lists... 1324s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 1324s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 1324s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 1324s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 1327s Reading package lists... 1327s Reading package lists... 1328s Building dependency tree... 1328s Reading state information... 1329s Calculating upgrade... 1329s The following packages were automatically installed and are no longer required: 1329s python3.13 python3.13-minimal 1329s Use 'sudo apt autoremove' to remove them. 1329s The following NEW packages will be installed: 1329s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 1329s The following packages will be upgraded: 1329s libplymouth5 libpython3-stdlib libtasn1-6 plymouth 1329s plymouth-theme-ubuntu-text python3 python3-gdbm python3-jaraco.context 1329s python3-minimal 1329s 9 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 1329s Need to get 7066 kB of archives. 1329s After this operation, 24.3 MB of additional disk space will be used. 1329s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.2-1 [917 kB] 1330s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 1330s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.14.2-1 [28.2 kB] 1330s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.14.2-1 [22.9 kB] 1330s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.2-1 [2373 kB] 1330s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 1330s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.14.2-1 [10.9 kB] 1330s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x libtasn1-6 s390x 4.21.0-2 [48.6 kB] 1330s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x libplymouth5 s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [159 kB] 1330s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x plymouth-theme-ubuntu-text s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [10.2 kB] 1330s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x plymouth s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [152 kB] 1330s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-gdbm s390x 3.14.2-1 [11.1 kB] 1330s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x python3-jaraco.context all 6.0.1-2 [8198 B] 1330s dpkg-preconfigure: unable to re-open stdin: No such file or directory 1331s Fetched 7066 kB in 0s (21.1 MB/s) 1331s Selecting previously unselected package libpython3.14-minimal:s390x. 1331s (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 ... 87685 files and directories currently installed.) 1331s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_s390x.deb ... 1331s Unpacking libpython3.14-minimal:s390x (3.14.2-1) ... 1331s Selecting previously unselected package python3.14-minimal. 1331s Preparing to unpack .../python3.14-minimal_3.14.2-1_s390x.deb ... 1331s Unpacking python3.14-minimal (3.14.2-1) ... 1332s Setting up libpython3.14-minimal:s390x (3.14.2-1) ... 1332s Setting up python3.14-minimal (3.14.2-1) ... 1336s (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 ... 88027 files and directories currently installed.) 1336s Preparing to unpack .../python3-minimal_3.14.2-1_s390x.deb ... 1337s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 1337s Setting up python3-minimal (3.14.2-1) ... 1337s (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 ... 88027 files and directories currently installed.) 1337s Preparing to unpack .../0-python3_3.14.2-1_s390x.deb ... 1338s running python pre-rtupdate hooks for python3.14... 1338s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 1338s Selecting previously unselected package libpython3.14-stdlib:s390x. 1338s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_s390x.deb ... 1338s Unpacking libpython3.14-stdlib:s390x (3.14.2-1) ... 1338s Selecting previously unselected package python3.14. 1338s Preparing to unpack .../2-python3.14_3.14.2-1_s390x.deb ... 1338s Unpacking python3.14 (3.14.2-1) ... 1338s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_s390x.deb ... 1338s Unpacking libpython3-stdlib:s390x (3.14.2-1) over (3.13.9-3) ... 1338s Preparing to unpack .../4-libtasn1-6_4.21.0-2_s390x.deb ... 1338s Unpacking libtasn1-6:s390x (4.21.0-2) over (4.20.0-2ubuntu1) ... 1338s Preparing to unpack .../5-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 1338s Unpacking libplymouth5:s390x (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 1338s Preparing to unpack .../6-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 1338s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 1338s Preparing to unpack .../7-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 1338s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 1339s Preparing to unpack .../8-python3-gdbm_3.14.2-1_s390x.deb ... 1339s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 1339s Preparing to unpack .../9-python3-jaraco.context_6.0.1-2_all.deb ... 1339s Unpacking python3-jaraco.context (6.0.1-2) over (6.0.1-1build1) ... 1339s Setting up libpython3.14-stdlib:s390x (3.14.2-1) ... 1339s Setting up libplymouth5:s390x (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 1339s Setting up libtasn1-6:s390x (4.21.0-2) ... 1339s Setting up python3.14 (3.14.2-1) ... 1344s Setting up libpython3-stdlib:s390x (3.14.2-1) ... 1344s Setting up python3-gdbm (3.14.2-1) ... 1344s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 1344s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 1344s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 1345s Setting up python3 (3.14.2-1) ... 1345s running python rtupdate hooks for python3.14... 1345s running python post-rtupdate hooks for python3.14... 1345s Setting up python3-jaraco.context (6.0.1-2) ... 1346s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1346s Processing triggers for systemd (259-1ubuntu2) ... 1346s Processing triggers for man-db (2.13.1-1) ... 1347s Processing triggers for initramfs-tools (0.150ubuntu7) ... 1348s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 1361s Using config file '/etc/zipl.conf' 1361s Building bootmap in '/boot' 1361s Adding IPL section 'ubuntu' (default) 1361s Preparing boot device: vda. 1361s Done. 1361s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 1361s Processing triggers for initramfs-tools (0.150ubuntu7) ... 1361s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 1373s Using config file '/etc/zipl.conf' 1373s Building bootmap in '/boot' 1373s Adding IPL section 'ubuntu' (default) 1373s Preparing boot device: vda. 1373s Done. 1374s autopkgtest [17:23:30]: upgrading testbed (apt dist-upgrade and autopurge) 1374s Reading package lists... 1374s Building dependency tree... 1374s Reading state information... 1375s Calculating upgrade... 1376s The following packages were automatically installed and are no longer required: 1376s python3.13 python3.13-minimal 1376s Use 'sudo apt autoremove' to remove them. 1376s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1376s Reading package lists... 1376s Building dependency tree... 1376s Reading state information... 1376s Solving dependencies... 1377s The following packages will be REMOVED: 1377s python3.13* python3.13-minimal* 1377s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 1377s After this operation, 8012 kB disk space will be freed. 1377s (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 ... 88454 files and directories currently installed.) 1377s Removing python3.13 (3.13.11-1) ... 1377s Removing python3.13-minimal (3.13.11-1) ... 1380s Processing triggers for man-db (2.13.1-1) ... 1381s Processing triggers for systemd (259-1ubuntu2) ... 1381s (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 ... 88427 files and directories currently installed.) 1381s Purging configuration files for python3.13-minimal (3.13.11-1) ... 1382s autopkgtest [17:23:38]: rebooting testbed after setup commands that affected boot 1423s Reading package lists... 1424s Building dependency tree... 1424s Reading state information... 1424s Solving dependencies... 1425s The following NEW packages will be installed: 1425s autoconf automake autopoint autotools-dev build-essential bwa clustalo cpp 1425s cpp-15 cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit 1425s dh-autoreconf dh-python dh-strip-nondeterminism dialign docutils-common dssp 1425s dwz fasttree flex fontconfig-config fonts-dejavu-core fonts-dejavu-extra 1425s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 1425s fonts-urw-base35 g++ g++-15 g++-15-s390x-linux-gnu g++-s390x-linux-gnu gcc 1425s gcc-15 gcc-15-s390x-linux-gnu gcc-s390x-linux-gnu gettext ghostscript hevea 1425s hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 1425s intltool-debian libamd3 libaom3 libapache-pom-java libarchive-zip-perl 1425s libargtable2-0 libarpack2t64 libasan8 libavahi-client3 libavahi-common-data 1425s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp9 1425s libcolamd3 libcommons-logging-java libcommons-parent-java libcups2t64 1425s libde265-0 libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 1425s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 1425s libfreetype6 libgcc-15-dev libgfortran5 libglpk40 libgomp1 libgraphite2-3 1425s libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 1425s libheif-plugin-libde265 libheif1 libice6 libidn12 libigraph4 libijs-0.35 1425s libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 libjpeg-turbo8 1425s libjpeg8 libjs-jquery libjson-perl libkpathsea6 liblapack3 liblcms2-2 1425s liblqr-1-0 libltdl7 libmagickcore-7.q16-10 libmagickwand-7.q16-10 1425s libmbedcrypto16 libmbedtls21 libmbedx509-7 libmpc3 libmpfi0 libmysqlclient24 1425s libnetpbm11t64 libopenjp2-7 libpaper-utils libpaper2 libpdfbox-java 1425s libpixman-1-0 libplfit0 libpotrace0 libptexenc1 libpython3-all-dev 1425s libpython3-dev libpython3.13-dev libpython3.14 libpython3.14-dev 1425s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-15-dev 1425s libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 1425s libtiff6 libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2 libwebpmux3 1425s libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 1425s libxrender1 libxslt1.1 libxss1 libxt6t64 libzopfli1 libzzip-0-13t64 lmodern 1425s m4 mafft mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf 1425s poppler-data prank preview-latex-style probcons python-biopython-doc 1425s python-matplotlib-data python3-alabaster python3-all python3-all-dev 1425s python3-biopython python3-biopython-sql python3-brotli python3-cairo 1425s python3-charset-normalizer python3-contourpy python3-cycler 1425s python3-decorator python3-defusedxml python3-dev python3-docutils 1425s python3-fonttools python3-freetype python3-igraph python3-imagesize 1425s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 1425s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 1425s python3-numpy python3-numpy-dev python3-numpydoc python3-pil 1425s python3-pil.imagetk python3-rdflib python3-reportlab python3-rlpycairo 1425s python3-roman-numerals python3-scipy python3-snowballstemmer python3-sphinx 1425s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 1425s python3-texttable python3-tk python3-ufolib2 python3-zopfli python3.13 1425s python3.13-dev python3.13-minimal python3.13-tk python3.14-dev python3.14-tk 1425s sgml-base sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 1425s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 1425s texlive-latex-extra texlive-latex-recommended texlive-luatex 1425s texlive-pictures unicode-data w3c-sgml-lib wise wise-data x11-common 1425s xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 1425s 0 upgraded, 250 newly installed, 0 to remove and 0 not upgraded. 1425s Need to get 417 MB of archives. 1425s After this operation, 1497 MB of additional disk space will be used. 1425s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-minimal s390x 3.13.11-1 [2405 kB] 1425s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x m4 s390x 1.4.20-2 [223 kB] 1425s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x flex s390x 2.6.4-8.2build2 [307 kB] 1425s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-lato all 2.015-1build1 [2779 kB] 1425s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-11ubuntu1 [154 kB] 1425s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libfftw3-double3 s390x 3.3.10-2fakesync1build2 [512 kB] 1425s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x libfreetype6 s390x 2.14.1+dfsg-2 [443 kB] 1425s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-mono all 2.37-8build1 [502 kB] 1425s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-core all 2.37-8build1 [834 kB] 1425s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x libfontenc1 s390x 1:1.1.8-1build2 [14.5 kB] 1425s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x x11-common all 1:7.7+24ubuntu1 [22.4 kB] 1425s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x xfonts-encodings all 1:1.0.5-0ubuntu3 [576 kB] 1425s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x xfonts-utils s390x 1:7.7+7build1 [101 kB] 1425s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-urw-base35 all 20200910-8build1 [10.9 MB] 1425s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x fontconfig-config s390x 2.15.0-2.4ubuntu1 [38.2 kB] 1425s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x libfontconfig1 s390x 2.15.0-2.4ubuntu1 [150 kB] 1425s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x libsharpyuv0 s390x 1.5.0-0.1build1 [16.6 kB] 1425s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x libaom3 s390x 3.13.1-2 [1513 kB] 1425s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libheif-plugin-aomdec s390x 1.21.2-1 [14.4 kB] 1425s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libde265-0 s390x 1.0.16-1build1 [182 kB] 1425s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libheif-plugin-libde265 s390x 1.21.2-1 [10.0 kB] 1425s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libheif1 s390x 1.21.2-1 [557 kB] 1425s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x libjbig0 s390x 2.1-6.1ubuntu3 [32.8 kB] 1425s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg-turbo8 s390x 2.1.5-4ubuntu2 [147 kB] 1425s Get:25 http://ftpmaster.internal/ubuntu resolute/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 1425s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x liblcms2-2 s390x 2.17-1 [176 kB] 1425s Get:27 http://ftpmaster.internal/ubuntu resolute/universe s390x liblqr-1-0 s390x 0.4.2-2.2 [32.1 kB] 1425s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x libltdl7 s390x 2.5.4-9 [44.4 kB] 1425s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x libopenjp2-7 s390x 2.5.4-1 [208 kB] 1425s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x libraw23t64 s390x 0.21.4-2 [415 kB] 1425s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 1425s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x libwebp7 s390x 1.5.0-0.1build1 [227 kB] 1425s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x libtiff6 s390x 4.7.0-3ubuntu3 [222 kB] 1425s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpdemux2 s390x 1.5.0-0.1build1 [12.5 kB] 1425s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x libwebpmux3 s390x 1.5.0-0.1build1 [25.7 kB] 1425s Get:36 http://ftpmaster.internal/ubuntu resolute/universe s390x imagemagick-7-common all 8:7.1.2.12+dfsg1-1 [71.8 kB] 1426s Get:37 http://ftpmaster.internal/ubuntu resolute/universe s390x libmagickcore-7.q16-10 s390x 8:7.1.2.12+dfsg1-1 [2051 kB] 1426s Get:38 http://ftpmaster.internal/ubuntu resolute/universe s390x libmagickwand-7.q16-10 s390x 8:7.1.2.12+dfsg1-1 [369 kB] 1426s Get:39 http://ftpmaster.internal/ubuntu resolute/main s390x poppler-data all 0.4.12-1build1 [2000 kB] 1426s Get:40 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.3.5+ds-3 [146 kB] 1426s Get:41 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7ubuntu1 [255 kB] 1426s Get:42 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-11ubuntu1 [629 kB] 1426s Get:43 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7ubuntu1 [2983 kB] 1426s Get:44 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.3.5+ds-3 [5305 kB] 1426s Get:45 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13 s390x 3.13.11-1 [758 kB] 1426s Get:46 http://ftpmaster.internal/ubuntu resolute/main s390x autoconf all 2.72-3.1ubuntu1 [384 kB] 1426s Get:47 http://ftpmaster.internal/ubuntu resolute/main s390x autotools-dev all 20240727.1 [43.4 kB] 1426s Get:48 http://ftpmaster.internal/ubuntu resolute/main s390x automake all 1:1.18.1-3build1 [582 kB] 1426s Get:49 http://ftpmaster.internal/ubuntu resolute/main s390x autopoint all 0.23.2-1 [620 kB] 1426s Get:50 http://ftpmaster.internal/ubuntu resolute/main s390x libisl23 s390x 0.27-1build1 [702 kB] 1427s Get:51 http://ftpmaster.internal/ubuntu resolute/main s390x libmpc3 s390x 1.3.1-2 [57.4 kB] 1427s Get:52 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [10.2 MB] 1427s Get:53 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15 s390x 15.2.0-11ubuntu1 [1028 B] 1427s Get:54 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [5746 B] 1427s Get:55 http://ftpmaster.internal/ubuntu resolute/main s390x cpp s390x 4:15.2.0-4ubuntu1 [22.4 kB] 1427s Get:56 http://ftpmaster.internal/ubuntu resolute/main s390x libcc1-0 s390x 15.2.0-11ubuntu1 [50.0 kB] 1427s Get:57 http://ftpmaster.internal/ubuntu resolute/main s390x libitm1 s390x 15.2.0-11ubuntu1 [30.9 kB] 1427s Get:58 http://ftpmaster.internal/ubuntu resolute/main s390x libasan8 s390x 15.2.0-11ubuntu1 [2968 kB] 1427s Get:59 http://ftpmaster.internal/ubuntu resolute/main s390x libubsan1 s390x 15.2.0-11ubuntu1 [1211 kB] 1428s Get:60 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-15-dev s390x 15.2.0-11ubuntu1 [1045 kB] 1428s Get:61 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [19.9 MB] 1429s Get:62 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15 s390x 15.2.0-11ubuntu1 [517 kB] 1429s Get:63 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [1208 B] 1429s Get:64 http://ftpmaster.internal/ubuntu resolute/main s390x gcc s390x 4:15.2.0-4ubuntu1 [5018 B] 1429s Get:65 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++-15-dev s390x 15.2.0-11ubuntu1 [2660 kB] 1429s Get:66 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [11.7 MB] 1429s Get:67 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15 s390x 15.2.0-11ubuntu1 [24.6 kB] 1429s Get:68 http://ftpmaster.internal/ubuntu resolute/main s390x g++-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [956 B] 1429s Get:69 http://ftpmaster.internal/ubuntu resolute/main s390x g++ s390x 4:15.2.0-4ubuntu1 [1078 B] 1429s Get:70 http://ftpmaster.internal/ubuntu resolute/main s390x build-essential s390x 12.12ubuntu2 [5258 B] 1429s Get:71 http://ftpmaster.internal/ubuntu resolute/universe s390x bwa s390x 0.7.19-1 [246 kB] 1429s Get:72 http://ftpmaster.internal/ubuntu resolute/universe s390x libargtable2-0 s390x 13-4 [16.7 kB] 1429s Get:73 http://ftpmaster.internal/ubuntu resolute/universe s390x clustalo s390x 1.2.4-8build2 [219 kB] 1429s Get:74 http://ftpmaster.internal/ubuntu resolute/main s390x libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 1429s Get:75 http://ftpmaster.internal/ubuntu resolute/main s390x libtool all 2.5.4-9 [169 kB] 1429s Get:76 http://ftpmaster.internal/ubuntu resolute/main s390x dh-autoreconf all 21 [12.5 kB] 1429s Get:77 http://ftpmaster.internal/ubuntu resolute/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 1429s Get:78 http://ftpmaster.internal/ubuntu resolute/main s390x libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 1429s Get:79 http://ftpmaster.internal/ubuntu resolute/main s390x dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 1429s Get:80 http://ftpmaster.internal/ubuntu resolute/main s390x debugedit s390x 1:5.2-3 [52.8 kB] 1429s Get:81 http://ftpmaster.internal/ubuntu resolute/main s390x dwz s390x 0.16-2 [121 kB] 1429s Get:82 http://ftpmaster.internal/ubuntu resolute/main s390x gettext s390x 0.23.2-1 [1062 kB] 1429s Get:83 http://ftpmaster.internal/ubuntu resolute/main s390x intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 1429s Get:84 http://ftpmaster.internal/ubuntu resolute/main s390x po-debconf all 1.0.22 [215 kB] 1429s Get:85 http://ftpmaster.internal/ubuntu resolute/main s390x debhelper all 13.28ubuntu1 [916 kB] 1429s Get:86 http://ftpmaster.internal/ubuntu resolute/universe s390x dh-python all 7.20251231 [122 kB] 1429s Get:87 http://ftpmaster.internal/ubuntu resolute/universe s390x dialign s390x 2.2.1-13build1 [156 kB] 1429s Get:88 http://ftpmaster.internal/ubuntu resolute/main s390x sgml-base all 1.31+nmu1 [11.0 kB] 1429s Get:89 http://ftpmaster.internal/ubuntu resolute/main s390x xml-core all 0.19build1 [20.3 kB] 1429s Get:90 http://ftpmaster.internal/ubuntu resolute/main s390x docutils-common all 0.22.4+dfsg-1 [130 kB] 1429s Get:91 http://ftpmaster.internal/ubuntu resolute/universe s390x libcifpp-data all 9.0.5-2 [483 kB] 1429s Get:92 http://ftpmaster.internal/ubuntu resolute/universe s390x libcifpp9 s390x 9.0.5-2 [1105 kB] 1429s Get:93 http://ftpmaster.internal/ubuntu resolute/universe s390x dssp s390x 4.5.7-1 [650 kB] 1429s Get:94 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-dejavu-extra all 2.37-8build1 [1944 kB] 1429s Get:95 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 1430s Get:96 http://ftpmaster.internal/ubuntu resolute/universe s390x fonts-lmodern all 2.005-1build1 [4788 kB] 1430s Get:97 http://ftpmaster.internal/ubuntu resolute/universe s390x fonts-lyx all 2.5.0~RC2-3 [171 kB] 1430s Get:98 http://ftpmaster.internal/ubuntu resolute/main s390x libgs-common all 10.05.0dfsg1-0ubuntu4 [176 kB] 1430s Get:99 http://ftpmaster.internal/ubuntu resolute/main s390x libgs10-common all 10.05.0dfsg1-0ubuntu4 [490 kB] 1430s Get:100 http://ftpmaster.internal/ubuntu resolute/main s390x libavahi-common-data s390x 0.8-17ubuntu1 [31.3 kB] 1430s Get:101 http://ftpmaster.internal/ubuntu resolute/main s390x libavahi-common3 s390x 0.8-17ubuntu1 [23.3 kB] 1430s Get:102 http://ftpmaster.internal/ubuntu resolute/main s390x libavahi-client3 s390x 0.8-17ubuntu1 [26.2 kB] 1430s Get:103 http://ftpmaster.internal/ubuntu resolute/main s390x libcups2t64 s390x 2.4.16-1ubuntu1 [281 kB] 1430s Get:104 http://ftpmaster.internal/ubuntu resolute/main s390x libidn12 s390x 1.43-2 [60.2 kB] 1430s Get:105 http://ftpmaster.internal/ubuntu resolute/main s390x libijs-0.35 s390x 0.35-16 [15.7 kB] 1430s Get:106 http://ftpmaster.internal/ubuntu resolute/main s390x libjbig2dec0 s390x 0.20-1build4 [69.7 kB] 1430s Get:107 http://ftpmaster.internal/ubuntu resolute/main s390x libpaper2 s390x 2.2.5-0.3build1 [17.3 kB] 1430s Get:108 http://ftpmaster.internal/ubuntu resolute/main s390x libice6 s390x 2:1.1.1-1build1 [46.2 kB] 1430s Get:109 http://ftpmaster.internal/ubuntu resolute/main s390x libsm6 s390x 2:1.2.6-1 [18.3 kB] 1430s Get:110 http://ftpmaster.internal/ubuntu resolute/main s390x libxt6t64 s390x 1:1.2.1-1.3 [180 kB] 1430s Get:111 http://ftpmaster.internal/ubuntu resolute/main s390x libgs10 s390x 10.05.0dfsg1-0ubuntu4 [3982 kB] 1430s Get:112 http://ftpmaster.internal/ubuntu resolute/main s390x ghostscript s390x 10.05.0dfsg1-0ubuntu4 [42.9 kB] 1430s Get:113 http://ftpmaster.internal/ubuntu resolute/universe s390x libnetpbm11t64 s390x 2:11.10.02-1build1 [123 kB] 1430s Get:114 http://ftpmaster.internal/ubuntu resolute/universe s390x netpbm s390x 2:11.10.02-1build1 [2215 kB] 1430s Get:115 http://ftpmaster.internal/ubuntu resolute/universe s390x tex-common all 6.20 [30.0 kB] 1430s Get:116 http://ftpmaster.internal/ubuntu resolute/main s390x libpaper-utils s390x 2.2.5-0.3build1 [15.3 kB] 1430s Get:117 http://ftpmaster.internal/ubuntu resolute/universe s390x libkpathsea6 s390x 2025.20250727.75242+ds-5build1 [68.0 kB] 1430s Get:118 http://ftpmaster.internal/ubuntu resolute/universe s390x libptexenc1 s390x 2025.20250727.75242+ds-5build1 [48.3 kB] 1430s Get:119 http://ftpmaster.internal/ubuntu resolute/universe s390x libsynctex2 s390x 2025.20250727.75242+ds-5build1 [66.6 kB] 1430s Get:120 http://ftpmaster.internal/ubuntu resolute/universe s390x libtexlua53-5 s390x 2025.20250727.75242+ds-5build1 [131 kB] 1430s Get:121 http://ftpmaster.internal/ubuntu resolute/main s390x t1utils s390x 1.41-4build4 [64.4 kB] 1430s Get:122 http://ftpmaster.internal/ubuntu resolute/main s390x libpixman-1-0 s390x 0.46.4-1 [217 kB] 1430s Get:123 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-render0 s390x 1.17.0-2build1 [16.9 kB] 1430s Get:124 http://ftpmaster.internal/ubuntu resolute/main s390x libxcb-shm0 s390x 1.17.0-2build1 [5916 B] 1430s Get:125 http://ftpmaster.internal/ubuntu resolute/main s390x libxrender1 s390x 1:0.9.12-1 [20.9 kB] 1430s Get:126 http://ftpmaster.internal/ubuntu resolute/main s390x libcairo2 s390x 1.18.4-3 [578 kB] 1430s Get:127 http://ftpmaster.internal/ubuntu resolute/main s390x libgraphite2-3 s390x 1.3.14-11ubuntu1 [80.5 kB] 1430s Get:128 http://ftpmaster.internal/ubuntu resolute/main s390x libharfbuzz0b s390x 12.3.0-4 [569 kB] 1430s Get:129 http://ftpmaster.internal/ubuntu resolute/universe s390x libmpfi0 s390x 1.5.4+ds-4 [34.1 kB] 1430s Get:130 http://ftpmaster.internal/ubuntu resolute/universe s390x libpotrace0 s390x 1.16-2build2 [18.7 kB] 1430s Get:131 http://ftpmaster.internal/ubuntu resolute/universe s390x libteckit0 s390x 2.5.13+ds-1 [438 kB] 1430s Get:132 http://ftpmaster.internal/ubuntu resolute/main s390x libxmu6 s390x 2:1.1.3-4 [51.7 kB] 1430s Get:133 http://ftpmaster.internal/ubuntu resolute/main s390x libxpm4 s390x 1:3.5.17-1build3 [41.5 kB] 1430s Get:134 http://ftpmaster.internal/ubuntu resolute/main s390x libxaw7 s390x 2:1.0.16-1build1 [201 kB] 1430s Get:135 http://ftpmaster.internal/ubuntu resolute/main s390x libxi6 s390x 2:1.8.2-2 [35.5 kB] 1430s Get:136 http://ftpmaster.internal/ubuntu resolute/universe s390x libzzip-0-13t64 s390x 0.13.78+dfsg.1-0.2 [29.8 kB] 1430s Get:137 http://ftpmaster.internal/ubuntu resolute/universe s390x texlive-binaries s390x 2025.20250727.75242+ds-5build1 [9385 kB] 1430s Get:138 http://ftpmaster.internal/ubuntu resolute/main s390x xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 1430s Get:139 http://ftpmaster.internal/ubuntu resolute/universe s390x texlive-base all 2025.20251127-1 [22.8 MB] 1430s Get:140 http://ftpmaster.internal/ubuntu resolute/main s390x hicolor-icon-theme all 0.18-2build1 [13.2 kB] 1430s Get:141 http://ftpmaster.internal/ubuntu resolute/universe s390x imagemagick-7.q16 s390x 8:7.1.2.12+dfsg1-1 [704 kB] 1430s Get:142 http://ftpmaster.internal/ubuntu resolute/universe s390x imagemagick s390x 8:7.1.2.12+dfsg1-1 [14.1 kB] 1430s Get:143 http://ftpmaster.internal/ubuntu resolute/universe s390x hevea s390x 2.36-2build3 [2413 kB] 1430s Get:144 http://ftpmaster.internal/ubuntu resolute/main s390x libsuitesparseconfig7 s390x 1:7.12.1+dfsg-1 [21.8 kB] 1430s Get:145 http://ftpmaster.internal/ubuntu resolute/universe s390x libamd3 s390x 1:7.12.1+dfsg-1 [44.0 kB] 1430s Get:146 http://ftpmaster.internal/ubuntu resolute/universe s390x libapache-pom-java all 33-2build1 [5976 B] 1430s Get:147 http://ftpmaster.internal/ubuntu resolute/universe s390x libarpack2t64 s390x 3.9.1-6 [110 kB] 1430s Get:148 http://ftpmaster.internal/ubuntu resolute/main s390x libcolamd3 s390x 1:7.12.1+dfsg-1 [31.1 kB] 1430s Get:149 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-parent-java all 56-1build1 [11.1 kB] 1430s Get:150 http://ftpmaster.internal/ubuntu resolute/universe s390x libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 1430s Get:151 http://ftpmaster.internal/ubuntu resolute/main s390x libexpat1-dev s390x 2.7.3-1 [149 kB] 1430s Get:152 http://ftpmaster.internal/ubuntu resolute/universe s390x libglpk40 s390x 5.0-2 [413 kB] 1430s Get:153 http://ftpmaster.internal/ubuntu resolute/universe s390x libplfit0 s390x 0.9.6+ds-2ubuntu1 [29.7 kB] 1431s Get:154 http://ftpmaster.internal/ubuntu resolute/universe s390x libigraph4 s390x 1.0.1+ds-3 [1398 kB] 1431s Get:155 http://ftpmaster.internal/ubuntu resolute/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 1431s Get:156 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 1431s Get:157 http://ftpmaster.internal/ubuntu resolute/main s390x libjson-perl all 4.10000-1 [81.9 kB] 1431s Get:158 http://ftpmaster.internal/ubuntu resolute/universe s390x libmbedcrypto16 s390x 3.6.5-0.1ubuntu2 [263 kB] 1431s Get:159 http://ftpmaster.internal/ubuntu resolute/universe s390x libmbedx509-7 s390x 3.6.5-0.1ubuntu2 [34.8 kB] 1431s Get:160 http://ftpmaster.internal/ubuntu resolute/universe s390x libmbedtls21 s390x 3.6.5-0.1ubuntu2 [126 kB] 1431s Get:161 http://ftpmaster.internal/ubuntu resolute/main s390x mysql-common all 5.8+1.1.1ubuntu2 [7002 B] 1431s Get:162 http://ftpmaster.internal/ubuntu resolute/main s390x libmysqlclient24 s390x 8.4.7-0ubuntu3 [1312 kB] 1431s Get:163 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14 s390x 3.14.2-1 [2651 kB] 1431s Get:164 http://ftpmaster.internal/ubuntu resolute/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu2 [897 kB] 1431s Get:165 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-dev s390x 3.14.2-1 [5938 kB] 1431s Get:166 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-dev s390x 3.14.2-1 [11.2 kB] 1431s Get:167 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.13-dev s390x 3.13.11-1 [5626 kB] 1431s Get:168 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-all-dev s390x 3.14.2-1 [916 B] 1431s Get:169 http://ftpmaster.internal/ubuntu resolute/universe s390x libqhull-r8.0 s390x 2020.2-8 [199 kB] 1431s Get:170 http://ftpmaster.internal/ubuntu resolute/main s390x libraqm0 s390x 0.10.3-1 [15.6 kB] 1431s Get:171 http://ftpmaster.internal/ubuntu resolute/main s390x libtcl8.6 s390x 8.6.17+dfsg-1 [1034 kB] 1431s Get:172 http://ftpmaster.internal/ubuntu resolute/main s390x libxft2 s390x 2.3.6-1build2 [48.0 kB] 1431s Get:173 http://ftpmaster.internal/ubuntu resolute/main s390x libxss1 s390x 1:1.2.3-1build4 [7138 B] 1431s Get:174 http://ftpmaster.internal/ubuntu resolute/main s390x libtk8.6 s390x 8.6.17-1 [828 kB] 1431s Get:175 http://ftpmaster.internal/ubuntu resolute/main s390x libxslt1.1 s390x 1.1.43-0.3 [163 kB] 1431s Get:176 http://ftpmaster.internal/ubuntu resolute/universe s390x libzopfli1 s390x 1.0.3-3 [124 kB] 1431s Get:177 http://ftpmaster.internal/ubuntu resolute/universe s390x lmodern all 2.005-1build1 [9538 kB] 1431s Get:178 http://ftpmaster.internal/ubuntu resolute/universe s390x mafft s390x 7.525-1 [1033 kB] 1431s Get:179 http://ftpmaster.internal/ubuntu resolute/universe s390x ncbi-data all 6.1.20170106+dfsg2-7 [3969 kB] 1431s Get:180 http://ftpmaster.internal/ubuntu resolute/universe s390x ncbi-blast+ s390x 2.16.0+ds-7 [15.2 MB] 1432s Get:181 http://ftpmaster.internal/ubuntu resolute/universe s390x phylip s390x 1:3.697+dfsg-4build2 [1070 kB] 1432s Get:182 http://ftpmaster.internal/ubuntu resolute/universe s390x prank s390x 250331-1 [358 kB] 1432s Get:183 http://ftpmaster.internal/ubuntu resolute/universe s390x preview-latex-style all 13.2-1.1 [347 kB] 1432s Get:184 http://ftpmaster.internal/ubuntu resolute/universe s390x probcons s390x 1.12-15 [118 kB] 1432s Get:185 http://ftpmaster.internal/ubuntu resolute/universe s390x python-biopython-doc all 1.86+dfsg-1 [18.1 MB] 1434s Get:186 http://ftpmaster.internal/ubuntu resolute/universe s390x python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 1434s Get:187 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-all s390x 3.14.2-1 [890 B] 1434s Get:188 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-dev s390x 3.14.2-1 [509 kB] 1434s Get:189 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-dev s390x 3.14.2-1 [26.6 kB] 1434s Get:190 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-dev s390x 3.13.11-1 [508 kB] 1434s Get:191 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-all-dev s390x 3.14.2-1 [916 B] 1434s Get:192 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-charset-normalizer s390x 3.4.4-2 [181 kB] 1434s Get:193 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-tk s390x 3.13.11-1 [109 kB] 1434s Get:194 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-tk s390x 3.14.2-1 [110 kB] 1434s Get:195 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-tk s390x 3.14.2-1 [11.2 kB] 1434s Get:196 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pil.imagetk s390x 12.0.0-1ubuntu1 [9884 B] 1434s Get:197 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pil s390x 12.0.0-1ubuntu1 [540 kB] 1434s Get:198 http://ftpmaster.internal/ubuntu resolute/main s390x python3-cairo s390x 1.27.0-2build1 [140 kB] 1434s Get:199 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-freetype all 2.5.1-2 [92.2 kB] 1434s Get:200 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-rlpycairo all 0.3.0-4 [9332 B] 1434s Get:201 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-reportlab all 4.4.9-1 [1149 kB] 1434s Get:202 http://ftpmaster.internal/ubuntu resolute/universe s390x w3c-sgml-lib all 1.3-3build1 [278 kB] 1434s Get:203 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-biopython s390x 1.86+dfsg-1 [1710 kB] 1434s Get:204 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-biopython-sql all 1.86+dfsg-1 [26.4 kB] 1434s Get:205 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-brotli s390x 1.1.0-2build6 [386 kB] 1434s Get:206 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-contourpy s390x 1.3.3-1 [266 kB] 1434s Get:207 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-cycler all 0.12.1-2 [9850 B] 1434s Get:208 http://ftpmaster.internal/ubuntu resolute/main s390x python3-decorator all 5.2.1-2 [28.1 kB] 1434s Get:209 http://ftpmaster.internal/ubuntu resolute/main s390x python3-defusedxml all 0.7.1-3build1 [42.4 kB] 1434s Get:210 http://ftpmaster.internal/ubuntu resolute/main s390x python3-roman-numerals all 4.1.0-1 [8660 B] 1434s Get:211 http://ftpmaster.internal/ubuntu resolute/main s390x python3-docutils all 0.22.4+dfsg-1 [439 kB] 1434s Get:212 http://ftpmaster.internal/ubuntu resolute/main s390x python3-lxml s390x 6.0.2-1 [2478 kB] 1434s Get:213 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-lz4 s390x 4.4.5+dfsg-1 [27.5 kB] 1434s Get:214 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-scipy s390x 1.16.3-3 [19.6 MB] 1435s Get:215 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mpmath all 1.3.0-2 [423 kB] 1435s Get:216 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-sympy all 1.14.0-2 [4306 kB] 1435s Get:217 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-ufolib2 all 0.18.1+dfsg1-1 [33.7 kB] 1435s Get:218 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-zopfli s390x 0.4.0-1 [11.2 kB] 1435s Get:219 http://ftpmaster.internal/ubuntu resolute/universe s390x unicode-data all 16.0.0-1build1 [9543 kB] 1435s Get:220 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-fonttools s390x 4.61.1-3 [1788 kB] 1435s Get:221 http://ftpmaster.internal/ubuntu resolute/main s390x python3-imagesize all 1.4.1-1build1 [6900 B] 1435s Get:222 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-kiwisolver s390x 1.4.10~rc0-1 [65.0 kB] 1435s Get:223 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-matplotlib s390x 3.10.7+dfsg1-1 [17.2 MB] 1436s Get:224 http://ftpmaster.internal/ubuntu resolute/main s390x python3-msgpack s390x 1.1.2-1 [117 kB] 1436s Get:225 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mmtf all 1.1.3-1build1 [16.4 kB] 1436s Get:226 http://ftpmaster.internal/ubuntu resolute/main s390x python3-mysqldb s390x 1.4.6-2build7 [52.9 kB] 1436s Get:227 http://ftpmaster.internal/ubuntu resolute/main s390x python3-networkx all 3.2.1-4ubuntu2 [11.8 MB] 1436s Get:228 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-common all 8.2.3-12 [657 kB] 1436s Get:229 http://ftpmaster.internal/ubuntu resolute/main s390x python3-alabaster all 0.7.16-0.1build1 [18.6 kB] 1436s Get:230 http://ftpmaster.internal/ubuntu resolute/main s390x python3-snowballstemmer all 3.0.1-1 [65.9 kB] 1436s Get:231 http://ftpmaster.internal/ubuntu resolute/main s390x python3-sphinx all 8.2.3-12 [483 kB] 1436s Get:232 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-numpydoc all 1.9.0-1 [53.2 kB] 1436s Get:233 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-rdflib all 7.1.1-3 [427 kB] 1436s Get:234 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 1436s Get:235 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-sphinxcontrib.jquery all 4.1-6 [6856 B] 1436s Get:236 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [23.5 kB] 1436s Get:237 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-texttable all 1.7.0-1 [11.2 kB] 1436s Get:238 http://ftpmaster.internal/ubuntu resolute/universe s390x t-coffee s390x 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1build1 [1151 kB] 1436s Get:239 http://ftpmaster.internal/ubuntu resolute/universe s390x texlive-fonts-recommended all 2025.20251127-1 [4972 kB] 1436s Get:240 http://ftpmaster.internal/ubuntu resolute/universe s390x texlive-luatex all 2025.20251127-1 [36.0 MB] 1437s Get:241 http://ftpmaster.internal/ubuntu resolute/universe s390x texlive-latex-base all 2025.20251127-1 [1309 kB] 1437s Get:242 http://ftpmaster.internal/ubuntu resolute/universe s390x libfontbox-java all 1:1.8.16-5 [208 kB] 1437s Get:243 http://ftpmaster.internal/ubuntu resolute/universe s390x libpdfbox-java all 1:1.8.16-5 [5521 kB] 1437s Get:244 http://ftpmaster.internal/ubuntu resolute/universe s390x texlive-latex-recommended all 2025.20251127-1 [8494 kB] 1437s Get:245 http://ftpmaster.internal/ubuntu resolute/universe s390x texlive-pictures all 2025.20251127-1 [23.5 MB] 1438s Get:246 http://ftpmaster.internal/ubuntu resolute/universe s390x texlive-latex-extra all 2025.20251127-2 [32.5 MB] 1439s Get:247 http://ftpmaster.internal/ubuntu resolute/universe s390x wise-data all 2.4.1-27 [83.2 kB] 1439s Get:248 http://ftpmaster.internal/ubuntu resolute/universe s390x wise s390x 2.4.1-27 [924 kB] 1439s Get:249 http://ftpmaster.internal/ubuntu resolute/universe s390x fasttree s390x 2.1.11-2build1 [201 kB] 1439s Get:250 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-igraph s390x 1.0.0+ds-1 [348 kB] 1443s Preconfiguring packages ... 1443s Fetched 417 MB in 14s (28.8 MB/s) 1443s Selecting previously unselected package python3.13-minimal. 1444s (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 ... 88429 files and directories currently installed.) 1444s Preparing to unpack .../000-python3.13-minimal_3.13.11-1_s390x.deb ... 1444s Unpacking python3.13-minimal (3.13.11-1) ... 1444s Selecting previously unselected package m4. 1444s Preparing to unpack .../001-m4_1.4.20-2_s390x.deb ... 1444s Unpacking m4 (1.4.20-2) ... 1444s Selecting previously unselected package flex. 1444s Preparing to unpack .../002-flex_2.6.4-8.2build2_s390x.deb ... 1444s Unpacking flex (2.6.4-8.2build2) ... 1444s Selecting previously unselected package fonts-lato. 1444s Preparing to unpack .../003-fonts-lato_2.015-1build1_all.deb ... 1444s Unpacking fonts-lato (2.015-1build1) ... 1445s Selecting previously unselected package libgomp1:s390x. 1445s Preparing to unpack .../004-libgomp1_15.2.0-11ubuntu1_s390x.deb ... 1445s Unpacking libgomp1:s390x (15.2.0-11ubuntu1) ... 1445s Selecting previously unselected package libfftw3-double3:s390x. 1445s Preparing to unpack .../005-libfftw3-double3_3.3.10-2fakesync1build2_s390x.deb ... 1445s Unpacking libfftw3-double3:s390x (3.3.10-2fakesync1build2) ... 1445s Selecting previously unselected package libfreetype6:s390x. 1445s Preparing to unpack .../006-libfreetype6_2.14.1+dfsg-2_s390x.deb ... 1445s Unpacking libfreetype6:s390x (2.14.1+dfsg-2) ... 1446s Selecting previously unselected package fonts-dejavu-mono. 1446s Preparing to unpack .../007-fonts-dejavu-mono_2.37-8build1_all.deb ... 1446s Unpacking fonts-dejavu-mono (2.37-8build1) ... 1446s Selecting previously unselected package fonts-dejavu-core. 1446s Preparing to unpack .../008-fonts-dejavu-core_2.37-8build1_all.deb ... 1446s Unpacking fonts-dejavu-core (2.37-8build1) ... 1446s Selecting previously unselected package libfontenc1:s390x. 1446s Preparing to unpack .../009-libfontenc1_1%3a1.1.8-1build2_s390x.deb ... 1446s Unpacking libfontenc1:s390x (1:1.1.8-1build2) ... 1446s Selecting previously unselected package x11-common. 1446s Preparing to unpack .../010-x11-common_1%3a7.7+24ubuntu1_all.deb ... 1446s Unpacking x11-common (1:7.7+24ubuntu1) ... 1446s Selecting previously unselected package xfonts-encodings. 1446s Preparing to unpack .../011-xfonts-encodings_1%3a1.0.5-0ubuntu3_all.deb ... 1446s Unpacking xfonts-encodings (1:1.0.5-0ubuntu3) ... 1446s Selecting previously unselected package xfonts-utils. 1446s Preparing to unpack .../012-xfonts-utils_1%3a7.7+7build1_s390x.deb ... 1446s Unpacking xfonts-utils (1:7.7+7build1) ... 1446s Selecting previously unselected package fonts-urw-base35. 1446s Preparing to unpack .../013-fonts-urw-base35_20200910-8build1_all.deb ... 1446s Unpacking fonts-urw-base35 (20200910-8build1) ... 1447s Selecting previously unselected package fontconfig-config. 1447s Preparing to unpack .../014-fontconfig-config_2.15.0-2.4ubuntu1_s390x.deb ... 1448s Unpacking fontconfig-config (2.15.0-2.4ubuntu1) ... 1448s Selecting previously unselected package libfontconfig1:s390x. 1448s Preparing to unpack .../015-libfontconfig1_2.15.0-2.4ubuntu1_s390x.deb ... 1448s Unpacking libfontconfig1:s390x (2.15.0-2.4ubuntu1) ... 1448s Selecting previously unselected package libsharpyuv0:s390x. 1448s Preparing to unpack .../016-libsharpyuv0_1.5.0-0.1build1_s390x.deb ... 1448s Unpacking libsharpyuv0:s390x (1.5.0-0.1build1) ... 1448s Selecting previously unselected package libaom3:s390x. 1448s Preparing to unpack .../017-libaom3_3.13.1-2_s390x.deb ... 1448s Unpacking libaom3:s390x (3.13.1-2) ... 1449s Selecting previously unselected package libheif-plugin-aomdec:s390x. 1449s Preparing to unpack .../018-libheif-plugin-aomdec_1.21.2-1_s390x.deb ... 1449s Unpacking libheif-plugin-aomdec:s390x (1.21.2-1) ... 1449s Selecting previously unselected package libde265-0:s390x. 1449s Preparing to unpack .../019-libde265-0_1.0.16-1build1_s390x.deb ... 1449s Unpacking libde265-0:s390x (1.0.16-1build1) ... 1449s Selecting previously unselected package libheif-plugin-libde265:s390x. 1449s Preparing to unpack .../020-libheif-plugin-libde265_1.21.2-1_s390x.deb ... 1449s Unpacking libheif-plugin-libde265:s390x (1.21.2-1) ... 1450s Selecting previously unselected package libheif1:s390x. 1450s Preparing to unpack .../021-libheif1_1.21.2-1_s390x.deb ... 1450s Unpacking libheif1:s390x (1.21.2-1) ... 1450s Selecting previously unselected package libjbig0:s390x. 1450s Preparing to unpack .../022-libjbig0_2.1-6.1ubuntu3_s390x.deb ... 1450s Unpacking libjbig0:s390x (2.1-6.1ubuntu3) ... 1450s Selecting previously unselected package libjpeg-turbo8:s390x. 1450s Preparing to unpack .../023-libjpeg-turbo8_2.1.5-4ubuntu2_s390x.deb ... 1450s Unpacking libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 1450s Selecting previously unselected package libjpeg8:s390x. 1450s Preparing to unpack .../024-libjpeg8_8c-2ubuntu11_s390x.deb ... 1450s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 1450s Selecting previously unselected package liblcms2-2:s390x. 1450s Preparing to unpack .../025-liblcms2-2_2.17-1_s390x.deb ... 1450s Unpacking liblcms2-2:s390x (2.17-1) ... 1450s Selecting previously unselected package liblqr-1-0:s390x. 1450s Preparing to unpack .../026-liblqr-1-0_0.4.2-2.2_s390x.deb ... 1450s Unpacking liblqr-1-0:s390x (0.4.2-2.2) ... 1450s Selecting previously unselected package libltdl7:s390x. 1450s Preparing to unpack .../027-libltdl7_2.5.4-9_s390x.deb ... 1450s Unpacking libltdl7:s390x (2.5.4-9) ... 1450s Selecting previously unselected package libopenjp2-7:s390x. 1450s Preparing to unpack .../028-libopenjp2-7_2.5.4-1_s390x.deb ... 1450s Unpacking libopenjp2-7:s390x (2.5.4-1) ... 1450s Selecting previously unselected package libraw23t64:s390x. 1450s Preparing to unpack .../029-libraw23t64_0.21.4-2_s390x.deb ... 1450s Unpacking libraw23t64:s390x (0.21.4-2) ... 1450s Selecting previously unselected package libdeflate0:s390x. 1450s Preparing to unpack .../030-libdeflate0_1.23-2_s390x.deb ... 1450s Unpacking libdeflate0:s390x (1.23-2) ... 1450s Selecting previously unselected package libwebp7:s390x. 1450s Preparing to unpack .../031-libwebp7_1.5.0-0.1build1_s390x.deb ... 1450s Unpacking libwebp7:s390x (1.5.0-0.1build1) ... 1450s Selecting previously unselected package libtiff6:s390x. 1450s Preparing to unpack .../032-libtiff6_4.7.0-3ubuntu3_s390x.deb ... 1450s Unpacking libtiff6:s390x (4.7.0-3ubuntu3) ... 1451s Selecting previously unselected package libwebpdemux2:s390x. 1451s Preparing to unpack .../033-libwebpdemux2_1.5.0-0.1build1_s390x.deb ... 1451s Unpacking libwebpdemux2:s390x (1.5.0-0.1build1) ... 1451s Selecting previously unselected package libwebpmux3:s390x. 1451s Preparing to unpack .../034-libwebpmux3_1.5.0-0.1build1_s390x.deb ... 1451s Unpacking libwebpmux3:s390x (1.5.0-0.1build1) ... 1451s Selecting previously unselected package imagemagick-7-common. 1451s Preparing to unpack .../035-imagemagick-7-common_8%3a7.1.2.12+dfsg1-1_all.deb ... 1451s Unpacking imagemagick-7-common (8:7.1.2.12+dfsg1-1) ... 1451s Selecting previously unselected package libmagickcore-7.q16-10:s390x. 1451s Preparing to unpack .../036-libmagickcore-7.q16-10_8%3a7.1.2.12+dfsg1-1_s390x.deb ... 1451s Unpacking libmagickcore-7.q16-10:s390x (8:7.1.2.12+dfsg1-1) ... 1451s Selecting previously unselected package libmagickwand-7.q16-10:s390x. 1451s Preparing to unpack .../037-libmagickwand-7.q16-10_8%3a7.1.2.12+dfsg1-1_s390x.deb ... 1451s Unpacking libmagickwand-7.q16-10:s390x (8:7.1.2.12+dfsg1-1) ... 1451s Selecting previously unselected package poppler-data. 1451s Preparing to unpack .../038-poppler-data_0.4.12-1build1_all.deb ... 1451s Unpacking poppler-data (0.4.12-1build1) ... 1453s Selecting previously unselected package python3-numpy-dev:s390x. 1453s Preparing to unpack .../039-python3-numpy-dev_1%3a2.3.5+ds-3_s390x.deb ... 1453s Unpacking python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 1453s Selecting previously unselected package libblas3:s390x. 1453s Preparing to unpack .../040-libblas3_3.12.1-7ubuntu1_s390x.deb ... 1453s Unpacking libblas3:s390x (3.12.1-7ubuntu1) ... 1453s Selecting previously unselected package libgfortran5:s390x. 1453s Preparing to unpack .../041-libgfortran5_15.2.0-11ubuntu1_s390x.deb ... 1453s Unpacking libgfortran5:s390x (15.2.0-11ubuntu1) ... 1453s Selecting previously unselected package liblapack3:s390x. 1453s Preparing to unpack .../042-liblapack3_3.12.1-7ubuntu1_s390x.deb ... 1453s Unpacking liblapack3:s390x (3.12.1-7ubuntu1) ... 1454s Selecting previously unselected package python3-numpy. 1454s Preparing to unpack .../043-python3-numpy_1%3a2.3.5+ds-3_s390x.deb ... 1454s Unpacking python3-numpy (1:2.3.5+ds-3) ... 1456s Selecting previously unselected package python3.13. 1456s Preparing to unpack .../044-python3.13_3.13.11-1_s390x.deb ... 1456s Unpacking python3.13 (3.13.11-1) ... 1456s Selecting previously unselected package autoconf. 1456s Preparing to unpack .../045-autoconf_2.72-3.1ubuntu1_all.deb ... 1456s Unpacking autoconf (2.72-3.1ubuntu1) ... 1456s Selecting previously unselected package autotools-dev. 1456s Preparing to unpack .../046-autotools-dev_20240727.1_all.deb ... 1456s Unpacking autotools-dev (20240727.1) ... 1456s Selecting previously unselected package automake. 1456s Preparing to unpack .../047-automake_1%3a1.18.1-3build1_all.deb ... 1456s Unpacking automake (1:1.18.1-3build1) ... 1456s Selecting previously unselected package autopoint. 1456s Preparing to unpack .../048-autopoint_0.23.2-1_all.deb ... 1456s Unpacking autopoint (0.23.2-1) ... 1456s Selecting previously unselected package libisl23:s390x. 1456s Preparing to unpack .../049-libisl23_0.27-1build1_s390x.deb ... 1456s Unpacking libisl23:s390x (0.27-1build1) ... 1457s Selecting previously unselected package libmpc3:s390x. 1457s Preparing to unpack .../050-libmpc3_1.3.1-2_s390x.deb ... 1457s Unpacking libmpc3:s390x (1.3.1-2) ... 1457s Selecting previously unselected package cpp-15-s390x-linux-gnu. 1457s Preparing to unpack .../051-cpp-15-s390x-linux-gnu_15.2.0-11ubuntu1_s390x.deb ... 1457s Unpacking cpp-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 1459s Selecting previously unselected package cpp-15. 1459s Preparing to unpack .../052-cpp-15_15.2.0-11ubuntu1_s390x.deb ... 1459s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 1459s Selecting previously unselected package cpp-s390x-linux-gnu. 1459s Preparing to unpack .../053-cpp-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 1459s Unpacking cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 1459s Selecting previously unselected package cpp. 1459s Preparing to unpack .../054-cpp_4%3a15.2.0-4ubuntu1_s390x.deb ... 1459s Unpacking cpp (4:15.2.0-4ubuntu1) ... 1459s Selecting previously unselected package libcc1-0:s390x. 1459s Preparing to unpack .../055-libcc1-0_15.2.0-11ubuntu1_s390x.deb ... 1459s Unpacking libcc1-0:s390x (15.2.0-11ubuntu1) ... 1459s Selecting previously unselected package libitm1:s390x. 1459s Preparing to unpack .../056-libitm1_15.2.0-11ubuntu1_s390x.deb ... 1459s Unpacking libitm1:s390x (15.2.0-11ubuntu1) ... 1459s Selecting previously unselected package libasan8:s390x. 1459s Preparing to unpack .../057-libasan8_15.2.0-11ubuntu1_s390x.deb ... 1459s Unpacking libasan8:s390x (15.2.0-11ubuntu1) ... 1459s Selecting previously unselected package libubsan1:s390x. 1459s Preparing to unpack .../058-libubsan1_15.2.0-11ubuntu1_s390x.deb ... 1459s Unpacking libubsan1:s390x (15.2.0-11ubuntu1) ... 1460s Selecting previously unselected package libgcc-15-dev:s390x. 1460s Preparing to unpack .../059-libgcc-15-dev_15.2.0-11ubuntu1_s390x.deb ... 1460s Unpacking libgcc-15-dev:s390x (15.2.0-11ubuntu1) ... 1460s Selecting previously unselected package gcc-15-s390x-linux-gnu. 1460s Preparing to unpack .../060-gcc-15-s390x-linux-gnu_15.2.0-11ubuntu1_s390x.deb ... 1460s Unpacking gcc-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 1463s Selecting previously unselected package gcc-15. 1463s Preparing to unpack .../061-gcc-15_15.2.0-11ubuntu1_s390x.deb ... 1463s Unpacking gcc-15 (15.2.0-11ubuntu1) ... 1464s Selecting previously unselected package gcc-s390x-linux-gnu. 1464s Preparing to unpack .../062-gcc-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 1464s Unpacking gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 1464s Selecting previously unselected package gcc. 1464s Preparing to unpack .../063-gcc_4%3a15.2.0-4ubuntu1_s390x.deb ... 1464s Unpacking gcc (4:15.2.0-4ubuntu1) ... 1464s Selecting previously unselected package libstdc++-15-dev:s390x. 1464s Preparing to unpack .../064-libstdc++-15-dev_15.2.0-11ubuntu1_s390x.deb ... 1464s Unpacking libstdc++-15-dev:s390x (15.2.0-11ubuntu1) ... 1465s Selecting previously unselected package g++-15-s390x-linux-gnu. 1465s Preparing to unpack .../065-g++-15-s390x-linux-gnu_15.2.0-11ubuntu1_s390x.deb ... 1465s Unpacking g++-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 1466s Selecting previously unselected package g++-15. 1466s Preparing to unpack .../066-g++-15_15.2.0-11ubuntu1_s390x.deb ... 1466s Unpacking g++-15 (15.2.0-11ubuntu1) ... 1466s Selecting previously unselected package g++-s390x-linux-gnu. 1466s Preparing to unpack .../067-g++-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 1466s Unpacking g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 1466s Selecting previously unselected package g++. 1466s Preparing to unpack .../068-g++_4%3a15.2.0-4ubuntu1_s390x.deb ... 1466s Unpacking g++ (4:15.2.0-4ubuntu1) ... 1466s Selecting previously unselected package build-essential. 1466s Preparing to unpack .../069-build-essential_12.12ubuntu2_s390x.deb ... 1466s Unpacking build-essential (12.12ubuntu2) ... 1466s Selecting previously unselected package bwa. 1466s Preparing to unpack .../070-bwa_0.7.19-1_s390x.deb ... 1466s Unpacking bwa (0.7.19-1) ... 1466s Selecting previously unselected package libargtable2-0:s390x. 1466s Preparing to unpack .../071-libargtable2-0_13-4_s390x.deb ... 1466s Unpacking libargtable2-0:s390x (13-4) ... 1466s Selecting previously unselected package clustalo. 1466s Preparing to unpack .../072-clustalo_1.2.4-8build2_s390x.deb ... 1466s Unpacking clustalo (1.2.4-8build2) ... 1467s Selecting previously unselected package libdebhelper-perl. 1467s Preparing to unpack .../073-libdebhelper-perl_13.28ubuntu1_all.deb ... 1467s Unpacking libdebhelper-perl (13.28ubuntu1) ... 1467s Selecting previously unselected package libtool. 1467s Preparing to unpack .../074-libtool_2.5.4-9_all.deb ... 1467s Unpacking libtool (2.5.4-9) ... 1467s Selecting previously unselected package dh-autoreconf. 1467s Preparing to unpack .../075-dh-autoreconf_21_all.deb ... 1467s Unpacking dh-autoreconf (21) ... 1467s Selecting previously unselected package libarchive-zip-perl. 1467s Preparing to unpack .../076-libarchive-zip-perl_1.68-1_all.deb ... 1467s Unpacking libarchive-zip-perl (1.68-1) ... 1467s Selecting previously unselected package libfile-stripnondeterminism-perl. 1467s Preparing to unpack .../077-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 1467s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 1467s Selecting previously unselected package dh-strip-nondeterminism. 1467s Preparing to unpack .../078-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 1467s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 1467s Selecting previously unselected package debugedit. 1467s Preparing to unpack .../079-debugedit_1%3a5.2-3_s390x.deb ... 1467s Unpacking debugedit (1:5.2-3) ... 1467s Selecting previously unselected package dwz. 1467s Preparing to unpack .../080-dwz_0.16-2_s390x.deb ... 1467s Unpacking dwz (0.16-2) ... 1467s Selecting previously unselected package gettext. 1467s Preparing to unpack .../081-gettext_0.23.2-1_s390x.deb ... 1467s Unpacking gettext (0.23.2-1) ... 1467s Selecting previously unselected package intltool-debian. 1467s Preparing to unpack .../082-intltool-debian_0.35.0+20060710.6build1_all.deb ... 1467s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 1467s Selecting previously unselected package po-debconf. 1467s Preparing to unpack .../083-po-debconf_1.0.22_all.deb ... 1467s Unpacking po-debconf (1.0.22) ... 1467s Selecting previously unselected package debhelper. 1467s Preparing to unpack .../084-debhelper_13.28ubuntu1_all.deb ... 1467s Unpacking debhelper (13.28ubuntu1) ... 1467s Selecting previously unselected package dh-python. 1467s Preparing to unpack .../085-dh-python_7.20251231_all.deb ... 1467s Unpacking dh-python (7.20251231) ... 1468s Selecting previously unselected package dialign. 1468s Preparing to unpack .../086-dialign_2.2.1-13build1_s390x.deb ... 1468s Unpacking dialign (2.2.1-13build1) ... 1468s Selecting previously unselected package sgml-base. 1468s Preparing to unpack .../087-sgml-base_1.31+nmu1_all.deb ... 1468s Unpacking sgml-base (1.31+nmu1) ... 1468s Selecting previously unselected package xml-core. 1468s Preparing to unpack .../088-xml-core_0.19build1_all.deb ... 1468s Unpacking xml-core (0.19build1) ... 1468s Selecting previously unselected package docutils-common. 1468s Preparing to unpack .../089-docutils-common_0.22.4+dfsg-1_all.deb ... 1468s Unpacking docutils-common (0.22.4+dfsg-1) ... 1468s Selecting previously unselected package libcifpp-data. 1468s Preparing to unpack .../090-libcifpp-data_9.0.5-2_all.deb ... 1468s Unpacking libcifpp-data (9.0.5-2) ... 1468s Selecting previously unselected package libcifpp9:s390x. 1468s Preparing to unpack .../091-libcifpp9_9.0.5-2_s390x.deb ... 1468s Unpacking libcifpp9:s390x (9.0.5-2) ... 1468s Selecting previously unselected package dssp. 1468s Preparing to unpack .../092-dssp_4.5.7-1_s390x.deb ... 1468s Unpacking dssp (4.5.7-1) ... 1469s Selecting previously unselected package fonts-dejavu-extra. 1469s Preparing to unpack .../093-fonts-dejavu-extra_2.37-8build1_all.deb ... 1469s Unpacking fonts-dejavu-extra (2.37-8build1) ... 1469s Selecting previously unselected package fonts-font-awesome. 1469s Preparing to unpack .../094-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ... 1469s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 1469s Selecting previously unselected package fonts-lmodern. 1469s Preparing to unpack .../095-fonts-lmodern_2.005-1build1_all.deb ... 1469s Unpacking fonts-lmodern (2.005-1build1) ... 1470s Selecting previously unselected package fonts-lyx. 1470s Preparing to unpack .../096-fonts-lyx_2.5.0~RC2-3_all.deb ... 1470s Unpacking fonts-lyx (2.5.0~RC2-3) ... 1470s Selecting previously unselected package libgs-common. 1470s Preparing to unpack .../097-libgs-common_10.05.0dfsg1-0ubuntu4_all.deb ... 1470s Unpacking libgs-common (10.05.0dfsg1-0ubuntu4) ... 1470s Selecting previously unselected package libgs10-common. 1470s Preparing to unpack .../098-libgs10-common_10.05.0dfsg1-0ubuntu4_all.deb ... 1470s Unpacking libgs10-common (10.05.0dfsg1-0ubuntu4) ... 1470s Selecting previously unselected package libavahi-common-data:s390x. 1470s Preparing to unpack .../099-libavahi-common-data_0.8-17ubuntu1_s390x.deb ... 1470s Unpacking libavahi-common-data:s390x (0.8-17ubuntu1) ... 1470s Selecting previously unselected package libavahi-common3:s390x. 1470s Preparing to unpack .../100-libavahi-common3_0.8-17ubuntu1_s390x.deb ... 1470s Unpacking libavahi-common3:s390x (0.8-17ubuntu1) ... 1470s Selecting previously unselected package libavahi-client3:s390x. 1470s Preparing to unpack .../101-libavahi-client3_0.8-17ubuntu1_s390x.deb ... 1470s Unpacking libavahi-client3:s390x (0.8-17ubuntu1) ... 1470s Selecting previously unselected package libcups2t64:s390x. 1470s Preparing to unpack .../102-libcups2t64_2.4.16-1ubuntu1_s390x.deb ... 1470s Unpacking libcups2t64:s390x (2.4.16-1ubuntu1) ... 1470s Selecting previously unselected package libidn12:s390x. 1470s Preparing to unpack .../103-libidn12_1.43-2_s390x.deb ... 1470s Unpacking libidn12:s390x (1.43-2) ... 1470s Selecting previously unselected package libijs-0.35:s390x. 1471s Preparing to unpack .../104-libijs-0.35_0.35-16_s390x.deb ... 1471s Unpacking libijs-0.35:s390x (0.35-16) ... 1471s Selecting previously unselected package libjbig2dec0:s390x. 1471s Preparing to unpack .../105-libjbig2dec0_0.20-1build4_s390x.deb ... 1471s Unpacking libjbig2dec0:s390x (0.20-1build4) ... 1471s Selecting previously unselected package libpaper2:s390x. 1471s Preparing to unpack .../106-libpaper2_2.2.5-0.3build1_s390x.deb ... 1471s Unpacking libpaper2:s390x (2.2.5-0.3build1) ... 1471s Selecting previously unselected package libice6:s390x. 1471s Preparing to unpack .../107-libice6_2%3a1.1.1-1build1_s390x.deb ... 1471s Unpacking libice6:s390x (2:1.1.1-1build1) ... 1471s Selecting previously unselected package libsm6:s390x. 1471s Preparing to unpack .../108-libsm6_2%3a1.2.6-1_s390x.deb ... 1471s Unpacking libsm6:s390x (2:1.2.6-1) ... 1471s Selecting previously unselected package libxt6t64:s390x. 1471s Preparing to unpack .../109-libxt6t64_1%3a1.2.1-1.3_s390x.deb ... 1471s Unpacking libxt6t64:s390x (1:1.2.1-1.3) ... 1471s Selecting previously unselected package libgs10:s390x. 1471s Preparing to unpack .../110-libgs10_10.05.0dfsg1-0ubuntu4_s390x.deb ... 1471s Unpacking libgs10:s390x (10.05.0dfsg1-0ubuntu4) ... 1472s Selecting previously unselected package ghostscript. 1472s Preparing to unpack .../111-ghostscript_10.05.0dfsg1-0ubuntu4_s390x.deb ... 1472s Unpacking ghostscript (10.05.0dfsg1-0ubuntu4) ... 1472s Selecting previously unselected package libnetpbm11t64:s390x. 1472s Preparing to unpack .../112-libnetpbm11t64_2%3a11.10.02-1build1_s390x.deb ... 1472s Unpacking libnetpbm11t64:s390x (2:11.10.02-1build1) ... 1472s Selecting previously unselected package netpbm. 1472s Preparing to unpack .../113-netpbm_2%3a11.10.02-1build1_s390x.deb ... 1472s Unpacking netpbm (2:11.10.02-1build1) ... 1473s Selecting previously unselected package tex-common. 1473s Preparing to unpack .../114-tex-common_6.20_all.deb ... 1473s Unpacking tex-common (6.20) ... 1473s Selecting previously unselected package libpaper-utils. 1473s Preparing to unpack .../115-libpaper-utils_2.2.5-0.3build1_s390x.deb ... 1473s Unpacking libpaper-utils (2.2.5-0.3build1) ... 1473s Selecting previously unselected package libkpathsea6:s390x. 1473s Preparing to unpack .../116-libkpathsea6_2025.20250727.75242+ds-5build1_s390x.deb ... 1473s Unpacking libkpathsea6:s390x (2025.20250727.75242+ds-5build1) ... 1473s Selecting previously unselected package libptexenc1:s390x. 1473s Preparing to unpack .../117-libptexenc1_2025.20250727.75242+ds-5build1_s390x.deb ... 1473s Unpacking libptexenc1:s390x (2025.20250727.75242+ds-5build1) ... 1473s Selecting previously unselected package libsynctex2:s390x. 1473s Preparing to unpack .../118-libsynctex2_2025.20250727.75242+ds-5build1_s390x.deb ... 1473s Unpacking libsynctex2:s390x (2025.20250727.75242+ds-5build1) ... 1473s Selecting previously unselected package libtexlua53-5:s390x. 1473s Preparing to unpack .../119-libtexlua53-5_2025.20250727.75242+ds-5build1_s390x.deb ... 1473s Unpacking libtexlua53-5:s390x (2025.20250727.75242+ds-5build1) ... 1473s Selecting previously unselected package t1utils. 1473s Preparing to unpack .../120-t1utils_1.41-4build4_s390x.deb ... 1473s Unpacking t1utils (1.41-4build4) ... 1474s Selecting previously unselected package libpixman-1-0:s390x. 1474s Preparing to unpack .../121-libpixman-1-0_0.46.4-1_s390x.deb ... 1474s Unpacking libpixman-1-0:s390x (0.46.4-1) ... 1474s Selecting previously unselected package libxcb-render0:s390x. 1474s Preparing to unpack .../122-libxcb-render0_1.17.0-2build1_s390x.deb ... 1474s Unpacking libxcb-render0:s390x (1.17.0-2build1) ... 1474s Selecting previously unselected package libxcb-shm0:s390x. 1474s Preparing to unpack .../123-libxcb-shm0_1.17.0-2build1_s390x.deb ... 1474s Unpacking libxcb-shm0:s390x (1.17.0-2build1) ... 1474s Selecting previously unselected package libxrender1:s390x. 1474s Preparing to unpack .../124-libxrender1_1%3a0.9.12-1_s390x.deb ... 1474s Unpacking libxrender1:s390x (1:0.9.12-1) ... 1474s Selecting previously unselected package libcairo2:s390x. 1474s Preparing to unpack .../125-libcairo2_1.18.4-3_s390x.deb ... 1474s Unpacking libcairo2:s390x (1.18.4-3) ... 1474s Selecting previously unselected package libgraphite2-3:s390x. 1474s Preparing to unpack .../126-libgraphite2-3_1.3.14-11ubuntu1_s390x.deb ... 1474s Unpacking libgraphite2-3:s390x (1.3.14-11ubuntu1) ... 1474s Selecting previously unselected package libharfbuzz0b:s390x. 1474s Preparing to unpack .../127-libharfbuzz0b_12.3.0-4_s390x.deb ... 1474s Unpacking libharfbuzz0b:s390x (12.3.0-4) ... 1474s Selecting previously unselected package libmpfi0:s390x. 1474s Preparing to unpack .../128-libmpfi0_1.5.4+ds-4_s390x.deb ... 1474s Unpacking libmpfi0:s390x (1.5.4+ds-4) ... 1474s Selecting previously unselected package libpotrace0:s390x. 1474s Preparing to unpack .../129-libpotrace0_1.16-2build2_s390x.deb ... 1474s Unpacking libpotrace0:s390x (1.16-2build2) ... 1474s Selecting previously unselected package libteckit0:s390x. 1474s Preparing to unpack .../130-libteckit0_2.5.13+ds-1_s390x.deb ... 1474s Unpacking libteckit0:s390x (2.5.13+ds-1) ... 1474s Selecting previously unselected package libxmu6:s390x. 1474s Preparing to unpack .../131-libxmu6_2%3a1.1.3-4_s390x.deb ... 1474s Unpacking libxmu6:s390x (2:1.1.3-4) ... 1474s Selecting previously unselected package libxpm4:s390x. 1474s Preparing to unpack .../132-libxpm4_1%3a3.5.17-1build3_s390x.deb ... 1474s Unpacking libxpm4:s390x (1:3.5.17-1build3) ... 1474s Selecting previously unselected package libxaw7:s390x. 1474s Preparing to unpack .../133-libxaw7_2%3a1.0.16-1build1_s390x.deb ... 1474s Unpacking libxaw7:s390x (2:1.0.16-1build1) ... 1474s Selecting previously unselected package libxi6:s390x. 1474s Preparing to unpack .../134-libxi6_2%3a1.8.2-2_s390x.deb ... 1474s Unpacking libxi6:s390x (2:1.8.2-2) ... 1475s Selecting previously unselected package libzzip-0-13t64:s390x. 1475s Preparing to unpack .../135-libzzip-0-13t64_0.13.78+dfsg.1-0.2_s390x.deb ... 1475s Unpacking libzzip-0-13t64:s390x (0.13.78+dfsg.1-0.2) ... 1475s Selecting previously unselected package texlive-binaries. 1475s Preparing to unpack .../136-texlive-binaries_2025.20250727.75242+ds-5build1_s390x.deb ... 1475s Unpacking texlive-binaries (2025.20250727.75242+ds-5build1) ... 1476s Selecting previously unselected package xdg-utils. 1476s Preparing to unpack .../137-xdg-utils_1.2.1-2ubuntu2_all.deb ... 1476s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 1476s Selecting previously unselected package texlive-base. 1476s Preparing to unpack .../138-texlive-base_2025.20251127-1_all.deb ... 1476s Unpacking texlive-base (2025.20251127-1) ... 1482s Selecting previously unselected package hicolor-icon-theme. 1482s Preparing to unpack .../139-hicolor-icon-theme_0.18-2build1_all.deb ... 1482s Unpacking hicolor-icon-theme (0.18-2build1) ... 1483s Selecting previously unselected package imagemagick-7.q16. 1483s Preparing to unpack .../140-imagemagick-7.q16_8%3a7.1.2.12+dfsg1-1_s390x.deb ... 1483s Unpacking imagemagick-7.q16 (8:7.1.2.12+dfsg1-1) ... 1483s Selecting previously unselected package imagemagick. 1483s Preparing to unpack .../141-imagemagick_8%3a7.1.2.12+dfsg1-1_s390x.deb ... 1483s Unpacking imagemagick (8:7.1.2.12+dfsg1-1) ... 1483s Selecting previously unselected package hevea. 1483s Preparing to unpack .../142-hevea_2.36-2build3_s390x.deb ... 1483s Unpacking hevea (2.36-2build3) ... 1484s Selecting previously unselected package libsuitesparseconfig7:s390x. 1484s Preparing to unpack .../143-libsuitesparseconfig7_1%3a7.12.1+dfsg-1_s390x.deb ... 1484s Unpacking libsuitesparseconfig7:s390x (1:7.12.1+dfsg-1) ... 1484s Selecting previously unselected package libamd3:s390x. 1484s Preparing to unpack .../144-libamd3_1%3a7.12.1+dfsg-1_s390x.deb ... 1484s Unpacking libamd3:s390x (1:7.12.1+dfsg-1) ... 1484s Selecting previously unselected package libapache-pom-java. 1484s Preparing to unpack .../145-libapache-pom-java_33-2build1_all.deb ... 1484s Unpacking libapache-pom-java (33-2build1) ... 1484s Selecting previously unselected package libarpack2t64:s390x. 1484s Preparing to unpack .../146-libarpack2t64_3.9.1-6_s390x.deb ... 1484s Unpacking libarpack2t64:s390x (3.9.1-6) ... 1484s Selecting previously unselected package libcolamd3:s390x. 1484s Preparing to unpack .../147-libcolamd3_1%3a7.12.1+dfsg-1_s390x.deb ... 1484s Unpacking libcolamd3:s390x (1:7.12.1+dfsg-1) ... 1484s Selecting previously unselected package libcommons-parent-java. 1484s Preparing to unpack .../148-libcommons-parent-java_56-1build1_all.deb ... 1484s Unpacking libcommons-parent-java (56-1build1) ... 1484s Selecting previously unselected package libcommons-logging-java. 1484s Preparing to unpack .../149-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 1484s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 1484s Selecting previously unselected package libexpat1-dev:s390x. 1484s Preparing to unpack .../150-libexpat1-dev_2.7.3-1_s390x.deb ... 1484s Unpacking libexpat1-dev:s390x (2.7.3-1) ... 1484s Selecting previously unselected package libglpk40:s390x. 1484s Preparing to unpack .../151-libglpk40_5.0-2_s390x.deb ... 1484s Unpacking libglpk40:s390x (5.0-2) ... 1484s Selecting previously unselected package libplfit0:s390x. 1484s Preparing to unpack .../152-libplfit0_0.9.6+ds-2ubuntu1_s390x.deb ... 1484s Unpacking libplfit0:s390x (0.9.6+ds-2ubuntu1) ... 1485s Selecting previously unselected package libigraph4:s390x. 1485s Preparing to unpack .../153-libigraph4_1.0.1+ds-3_s390x.deb ... 1485s Unpacking libigraph4:s390x (1.0.1+ds-3) ... 1485s Selecting previously unselected package libimagequant0:s390x. 1485s Preparing to unpack .../154-libimagequant0_2.18.0-1build1_s390x.deb ... 1485s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 1485s Selecting previously unselected package libjs-jquery. 1485s Preparing to unpack .../155-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 1485s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 1486s Selecting previously unselected package libjson-perl. 1486s Preparing to unpack .../156-libjson-perl_4.10000-1_all.deb ... 1486s Unpacking libjson-perl (4.10000-1) ... 1486s Selecting previously unselected package libmbedcrypto16:s390x. 1486s Preparing to unpack .../157-libmbedcrypto16_3.6.5-0.1ubuntu2_s390x.deb ... 1486s Unpacking libmbedcrypto16:s390x (3.6.5-0.1ubuntu2) ... 1486s Selecting previously unselected package libmbedx509-7:s390x. 1486s Preparing to unpack .../158-libmbedx509-7_3.6.5-0.1ubuntu2_s390x.deb ... 1486s Unpacking libmbedx509-7:s390x (3.6.5-0.1ubuntu2) ... 1486s Selecting previously unselected package libmbedtls21:s390x. 1486s Preparing to unpack .../159-libmbedtls21_3.6.5-0.1ubuntu2_s390x.deb ... 1486s Unpacking libmbedtls21:s390x (3.6.5-0.1ubuntu2) ... 1486s Selecting previously unselected package mysql-common. 1486s Preparing to unpack .../160-mysql-common_5.8+1.1.1ubuntu2_all.deb ... 1486s Unpacking mysql-common (5.8+1.1.1ubuntu2) ... 1486s Selecting previously unselected package libmysqlclient24:s390x. 1486s Preparing to unpack .../161-libmysqlclient24_8.4.7-0ubuntu3_s390x.deb ... 1486s Unpacking libmysqlclient24:s390x (8.4.7-0ubuntu3) ... 1487s Selecting previously unselected package libpython3.14:s390x. 1487s Preparing to unpack .../162-libpython3.14_3.14.2-1_s390x.deb ... 1487s Unpacking libpython3.14:s390x (3.14.2-1) ... 1487s Selecting previously unselected package zlib1g-dev:s390x. 1487s Preparing to unpack .../163-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_s390x.deb ... 1487s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 1487s Selecting previously unselected package libpython3.14-dev:s390x. 1487s Preparing to unpack .../164-libpython3.14-dev_3.14.2-1_s390x.deb ... 1487s Unpacking libpython3.14-dev:s390x (3.14.2-1) ... 1487s Selecting previously unselected package libpython3-dev:s390x. 1487s Preparing to unpack .../165-libpython3-dev_3.14.2-1_s390x.deb ... 1487s Unpacking libpython3-dev:s390x (3.14.2-1) ... 1487s Selecting previously unselected package libpython3.13-dev:s390x. 1487s Preparing to unpack .../166-libpython3.13-dev_3.13.11-1_s390x.deb ... 1487s Unpacking libpython3.13-dev:s390x (3.13.11-1) ... 1489s Selecting previously unselected package libpython3-all-dev:s390x. 1489s Preparing to unpack .../167-libpython3-all-dev_3.14.2-1_s390x.deb ... 1489s Unpacking libpython3-all-dev:s390x (3.14.2-1) ... 1489s Selecting previously unselected package libqhull-r8.0:s390x. 1489s Preparing to unpack .../168-libqhull-r8.0_2020.2-8_s390x.deb ... 1489s Unpacking libqhull-r8.0:s390x (2020.2-8) ... 1489s Selecting previously unselected package libraqm0:s390x. 1489s Preparing to unpack .../169-libraqm0_0.10.3-1_s390x.deb ... 1489s Unpacking libraqm0:s390x (0.10.3-1) ... 1489s Selecting previously unselected package libtcl8.6:s390x. 1489s Preparing to unpack .../170-libtcl8.6_8.6.17+dfsg-1_s390x.deb ... 1489s Unpacking libtcl8.6:s390x (8.6.17+dfsg-1) ... 1489s Selecting previously unselected package libxft2:s390x. 1489s Preparing to unpack .../171-libxft2_2.3.6-1build2_s390x.deb ... 1489s Unpacking libxft2:s390x (2.3.6-1build2) ... 1489s Selecting previously unselected package libxss1:s390x. 1490s Preparing to unpack .../172-libxss1_1%3a1.2.3-1build4_s390x.deb ... 1490s Unpacking libxss1:s390x (1:1.2.3-1build4) ... 1490s Selecting previously unselected package libtk8.6:s390x. 1490s Preparing to unpack .../173-libtk8.6_8.6.17-1_s390x.deb ... 1490s Unpacking libtk8.6:s390x (8.6.17-1) ... 1490s Selecting previously unselected package libxslt1.1:s390x. 1490s Preparing to unpack .../174-libxslt1.1_1.1.43-0.3_s390x.deb ... 1490s Unpacking libxslt1.1:s390x (1.1.43-0.3) ... 1490s Selecting previously unselected package libzopfli1. 1490s Preparing to unpack .../175-libzopfli1_1.0.3-3_s390x.deb ... 1490s Unpacking libzopfli1 (1.0.3-3) ... 1490s Selecting previously unselected package lmodern. 1490s Preparing to unpack .../176-lmodern_2.005-1build1_all.deb ... 1490s Unpacking lmodern (2.005-1build1) ... 1491s Selecting previously unselected package mafft. 1491s Preparing to unpack .../177-mafft_7.525-1_s390x.deb ... 1491s Unpacking mafft (7.525-1) ... 1491s Selecting previously unselected package ncbi-data. 1491s Preparing to unpack .../178-ncbi-data_6.1.20170106+dfsg2-7_all.deb ... 1491s Unpacking ncbi-data (6.1.20170106+dfsg2-7) ... 1492s Selecting previously unselected package ncbi-blast+. 1492s Preparing to unpack .../179-ncbi-blast+_2.16.0+ds-7_s390x.deb ... 1492s Unpacking ncbi-blast+ (2.16.0+ds-7) ... 1494s Selecting previously unselected package phylip. 1494s Preparing to unpack .../180-phylip_1%3a3.697+dfsg-4build2_s390x.deb ... 1494s Unpacking phylip (1:3.697+dfsg-4build2) ... 1494s Selecting previously unselected package prank. 1494s Preparing to unpack .../181-prank_250331-1_s390x.deb ... 1494s Unpacking prank (250331-1) ... 1494s Selecting previously unselected package preview-latex-style. 1494s Preparing to unpack .../182-preview-latex-style_13.2-1.1_all.deb ... 1494s Unpacking preview-latex-style (13.2-1.1) ... 1494s Selecting previously unselected package probcons. 1494s Preparing to unpack .../183-probcons_1.12-15_s390x.deb ... 1494s Unpacking probcons (1.12-15) ... 1494s Selecting previously unselected package python-biopython-doc. 1494s Preparing to unpack .../184-python-biopython-doc_1.86+dfsg-1_all.deb ... 1494s Unpacking python-biopython-doc (1.86+dfsg-1) ... 1496s Selecting previously unselected package python-matplotlib-data. 1496s Preparing to unpack .../185-python-matplotlib-data_3.10.7+dfsg1-1_all.deb ... 1496s Unpacking python-matplotlib-data (3.10.7+dfsg1-1) ... 1496s Selecting previously unselected package python3-all. 1496s Preparing to unpack .../186-python3-all_3.14.2-1_s390x.deb ... 1496s Unpacking python3-all (3.14.2-1) ... 1496s Selecting previously unselected package python3.14-dev. 1496s Preparing to unpack .../187-python3.14-dev_3.14.2-1_s390x.deb ... 1496s Unpacking python3.14-dev (3.14.2-1) ... 1496s Selecting previously unselected package python3-dev. 1497s Preparing to unpack .../188-python3-dev_3.14.2-1_s390x.deb ... 1497s Unpacking python3-dev (3.14.2-1) ... 1497s Selecting previously unselected package python3.13-dev. 1497s Preparing to unpack .../189-python3.13-dev_3.13.11-1_s390x.deb ... 1497s Unpacking python3.13-dev (3.13.11-1) ... 1497s Selecting previously unselected package python3-all-dev. 1497s Preparing to unpack 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Unpacking python3-pil.imagetk:s390x (12.0.0-1ubuntu1) ... 1497s Selecting previously unselected package python3-pil:s390x. 1497s Preparing to unpack .../196-python3-pil_12.0.0-1ubuntu1_s390x.deb ... 1497s Unpacking python3-pil:s390x (12.0.0-1ubuntu1) ... 1497s Selecting previously unselected package python3-cairo. 1497s Preparing to unpack .../197-python3-cairo_1.27.0-2build1_s390x.deb ... 1497s Unpacking python3-cairo (1.27.0-2build1) ... 1497s Selecting previously unselected package python3-freetype. 1497s Preparing to unpack .../198-python3-freetype_2.5.1-2_all.deb ... 1497s Unpacking python3-freetype (2.5.1-2) ... 1497s Selecting previously unselected package python3-rlpycairo. 1497s Preparing to unpack .../199-python3-rlpycairo_0.3.0-4_all.deb ... 1497s Unpacking python3-rlpycairo (0.3.0-4) ... 1497s Selecting previously unselected package python3-reportlab. 1497s Preparing to unpack .../200-python3-reportlab_4.4.9-1_all.deb ... 1497s Unpacking python3-reportlab (4.4.9-1) ... 1498s Selecting previously unselected package w3c-sgml-lib. 1498s Preparing to unpack .../201-w3c-sgml-lib_1.3-3build1_all.deb ... 1498s Unpacking w3c-sgml-lib (1.3-3build1) ... 1498s Selecting previously unselected package python3-biopython. 1498s Preparing to unpack .../202-python3-biopython_1.86+dfsg-1_s390x.deb ... 1498s Unpacking python3-biopython (1.86+dfsg-1) ... 1499s Selecting previously unselected package python3-biopython-sql. 1499s Preparing to unpack .../203-python3-biopython-sql_1.86+dfsg-1_all.deb ... 1499s Unpacking python3-biopython-sql (1.86+dfsg-1) ... 1499s Selecting previously unselected package python3-brotli. 1499s Preparing to unpack .../204-python3-brotli_1.1.0-2build6_s390x.deb ... 1499s Unpacking python3-brotli (1.1.0-2build6) ... 1499s Selecting previously unselected package python3-contourpy. 1499s Preparing to unpack .../205-python3-contourpy_1.3.3-1_s390x.deb ... 1499s Unpacking python3-contourpy (1.3.3-1) ... 1499s Selecting previously unselected package python3-cycler. 1499s Preparing to unpack .../206-python3-cycler_0.12.1-2_all.deb ... 1499s Unpacking python3-cycler (0.12.1-2) ... 1499s Selecting previously unselected package python3-decorator. 1499s Preparing to unpack .../207-python3-decorator_5.2.1-2_all.deb ... 1499s Unpacking python3-decorator (5.2.1-2) ... 1499s Selecting previously unselected package python3-defusedxml. 1499s Preparing to unpack .../208-python3-defusedxml_0.7.1-3build1_all.deb ... 1499s Unpacking python3-defusedxml (0.7.1-3build1) ... 1499s Selecting previously unselected package python3-roman-numerals. 1499s Preparing to unpack .../209-python3-roman-numerals_4.1.0-1_all.deb ... 1499s Unpacking python3-roman-numerals (4.1.0-1) ... 1499s Selecting previously unselected package python3-docutils. 1499s Preparing to unpack .../210-python3-docutils_0.22.4+dfsg-1_all.deb ... 1499s Unpacking python3-docutils (0.22.4+dfsg-1) ... 1499s Selecting previously unselected package python3-lxml:s390x. 1499s Preparing to unpack .../211-python3-lxml_6.0.2-1_s390x.deb ... 1499s Unpacking python3-lxml:s390x (6.0.2-1) ... 1500s Selecting previously unselected package python3-lz4. 1500s Preparing to unpack .../212-python3-lz4_4.4.5+dfsg-1_s390x.deb ... 1500s Unpacking python3-lz4 (4.4.5+dfsg-1) ... 1500s Selecting previously unselected package python3-scipy. 1500s Preparing to unpack .../213-python3-scipy_1.16.3-3_s390x.deb ... 1500s Unpacking python3-scipy (1.16.3-3) ... 1503s Selecting previously unselected package python3-mpmath. 1503s Preparing to unpack .../214-python3-mpmath_1.3.0-2_all.deb ... 1503s Unpacking python3-mpmath (1.3.0-2) ... 1503s Selecting previously unselected package python3-sympy. 1503s Preparing to unpack .../215-python3-sympy_1.14.0-2_all.deb ... 1503s Unpacking python3-sympy (1.14.0-2) ... 1504s Selecting previously unselected package python3-ufolib2. 1504s Preparing to unpack .../216-python3-ufolib2_0.18.1+dfsg1-1_all.deb ... 1504s Unpacking python3-ufolib2 (0.18.1+dfsg1-1) ... 1504s Selecting previously unselected package python3-zopfli. 1504s Preparing to unpack .../217-python3-zopfli_0.4.0-1_s390x.deb ... 1504s Unpacking python3-zopfli (0.4.0-1) ... 1504s Selecting previously unselected package unicode-data. 1504s Preparing to unpack .../218-unicode-data_16.0.0-1build1_all.deb ... 1504s Unpacking unicode-data (16.0.0-1build1) ... 1507s Selecting previously unselected package python3-fonttools. 1507s Preparing to unpack .../219-python3-fonttools_4.61.1-3_s390x.deb ... 1507s Unpacking python3-fonttools (4.61.1-3) ... 1507s Selecting previously unselected package python3-imagesize. 1508s Preparing to unpack .../220-python3-imagesize_1.4.1-1build1_all.deb ... 1508s Unpacking python3-imagesize (1.4.1-1build1) ... 1508s Selecting previously unselected package python3-kiwisolver. 1508s Preparing to unpack .../221-python3-kiwisolver_1.4.10~rc0-1_s390x.deb ... 1508s Unpacking python3-kiwisolver (1.4.10~rc0-1) ... 1508s Selecting previously unselected package python3-matplotlib. 1508s Preparing to unpack .../222-python3-matplotlib_3.10.7+dfsg1-1_s390x.deb ... 1508s Unpacking python3-matplotlib (3.10.7+dfsg1-1) ... 1510s Selecting previously unselected package python3-msgpack. 1510s Preparing to unpack .../223-python3-msgpack_1.1.2-1_s390x.deb ... 1510s Unpacking python3-msgpack (1.1.2-1) ... 1510s Selecting previously unselected package python3-mmtf. 1510s Preparing to unpack .../224-python3-mmtf_1.1.3-1build1_all.deb ... 1510s Unpacking python3-mmtf (1.1.3-1build1) ... 1510s Selecting previously unselected package python3-mysqldb. 1510s Preparing to unpack .../225-python3-mysqldb_1.4.6-2build7_s390x.deb ... 1510s Unpacking python3-mysqldb (1.4.6-2build7) ... 1510s Selecting previously unselected package python3-networkx. 1510s Preparing to unpack .../226-python3-networkx_3.2.1-4ubuntu2_all.deb ... 1510s Unpacking python3-networkx (3.2.1-4ubuntu2) ... 1513s Selecting previously unselected package sphinx-common. 1513s Preparing to unpack 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python3-rdflib (7.1.1-3) ... 1514s Selecting previously unselected package sphinx-rtd-theme-common. 1514s Preparing to unpack .../233-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 1514s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 1514s Selecting previously unselected package python3-sphinxcontrib.jquery. 1514s Preparing to unpack .../234-python3-sphinxcontrib.jquery_4.1-6_all.deb ... 1514s Unpacking python3-sphinxcontrib.jquery (4.1-6) ... 1514s Selecting previously unselected package python3-sphinx-rtd-theme. 1514s Preparing to unpack .../235-python3-sphinx-rtd-theme_3.0.2+dfsg-3_all.deb ... 1514s Unpacking python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 1514s Selecting previously unselected package python3-texttable. 1514s Preparing to unpack .../236-python3-texttable_1.7.0-1_all.deb ... 1514s Unpacking python3-texttable (1.7.0-1) ... 1514s Selecting previously unselected package t-coffee. 1514s Preparing to unpack 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wise. 1539s Preparing to unpack .../247-wise_2.4.1-27_s390x.deb ... 1539s Unpacking wise (2.4.1-27) ... 1539s Selecting previously unselected package fasttree. 1539s Preparing to unpack .../248-fasttree_2.1.11-2build1_s390x.deb ... 1539s Unpacking fasttree (2.1.11-2build1) ... 1539s Selecting previously unselected package python3-igraph. 1539s Preparing to unpack .../249-python3-igraph_1.0.0+ds-1_s390x.deb ... 1539s Unpacking python3-igraph (1.0.0+ds-1) ... 1540s Setting up dh-python (7.20251231) ... 1540s Setting up libgraphite2-3:s390x (1.3.14-11ubuntu1) ... 1540s Setting up liblcms2-2:s390x (2.17-1) ... 1540s Setting up ncbi-data (6.1.20170106+dfsg2-7) ... 1540s Setting up libpixman-1-0:s390x (0.46.4-1) ... 1540s Setting up libsharpyuv0:s390x (1.5.0-0.1build1) ... 1540s Setting up python3-texttable (1.7.0-1) ... 1541s Setting up libaom3:s390x (3.13.1-2) ... 1541s Setting up mysql-common (5.8+1.1.1ubuntu2) ... 1541s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 1541s Setting up fonts-lato (2.015-1build1) ... 1541s Setting up libxpm4:s390x (1:3.5.17-1build3) ... 1541s Setting up hicolor-icon-theme (0.18-2build1) ... 1541s Setting up libxi6:s390x (2:1.8.2-2) ... 1541s Setting up probcons (1.12-15) ... 1541s Setting up libxrender1:s390x (1:0.9.12-1) ... 1541s Setting up python3-lz4 (4.4.5+dfsg-1) ... 1541s Setting up libxcb-render0:s390x (1.17.0-2build1) ... 1541s Setting up python3-defusedxml (0.7.1-3build1) ... 1542s Setting up mafft (7.525-1) ... 1542s Setting up libarchive-zip-perl (1.68-1) ... 1542s Setting up imagemagick-7-common (8:7.1.2.12+dfsg1-1) ... 1542s Setting up python3-charset-normalizer (3.4.4-2) ... 1543s Setting up bwa (0.7.19-1) ... 1543s Setting up python3-alabaster (0.7.16-0.1build1) ... 1543s Setting up fonts-lyx (2.5.0~RC2-3) ... 1543s Setting up libijs-0.35:s390x (0.35-16) ... 1543s Setting up libdebhelper-perl (13.28ubuntu1) ... 1543s Setting up libgs-common 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doing nothing! 1554s Setting up python3-decorator (5.2.1-2) ... 1554s Setting up libfontenc1:s390x (1:1.1.8-1build2) ... 1554s Setting up autotools-dev (20240727.1) ... 1554s Setting up libblas3:s390x (3.12.1-7ubuntu1) ... 1554s 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 1554s Setting up libexpat1-dev:s390x (2.7.3-1) ... 1554s Setting up libzzip-0-13t64:s390x (0.13.78+dfsg.1-0.2) ... 1554s Setting up libzopfli1 (1.0.3-3) ... 1554s Setting up libfreetype6:s390x (2.14.1+dfsg-2) ... 1554s Setting up libjbig2dec0:s390x (0.20-1build4) ... 1554s Setting up python3-snowballstemmer (3.0.1-1) ... 1556s Setting up libteckit0:s390x (2.5.13+ds-1) ... 1556s Setting up python3-brotli (1.1.0-2build6) ... 1556s Setting up libapache-pom-java (33-2build1) ... 1556s Setting up libavahi-common-data:s390x (0.8-17ubuntu1) ... 1556s Setting up xfonts-encodings (1:1.0.5-0ubuntu3) ... 1556s Setting up t1utils (1.41-4build4) ... 1556s Setting up python3-cycler (0.12.1-2) ... 1557s Setting up libtexlua53-5:s390x (2025.20250727.75242+ds-5build1) ... 1557s Setting up libimagequant0:s390x (2.18.0-1build1) ... 1557s Setting up fonts-dejavu-mono (2.37-8build1) ... 1557s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 1558s Setting up libmpc3:s390x (1.3.1-2) ... 1558s Setting up python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 1558s Setting up libidn12:s390x (1.43-2) ... 1558s Setting up libtcl8.6:s390x (8.6.17+dfsg-1) ... 1558s Setting up autopoint (0.23.2-1) ... 1558s Setting up libmpfi0:s390x (1.5.4+ds-4) ... 1558s Setting up fonts-dejavu-core (2.37-8build1) ... 1558s Setting up wise-data (2.4.1-27) ... 1558s Setting up libjpeg-turbo8:s390x (2.1.5-4ubuntu2) ... 1558s Setting up libltdl7:s390x (2.5.4-9) ... 1558s Setting up libfftw3-double3:s390x (3.3.10-2fakesync1build2) ... 1558s Setting up libcifpp-data (9.0.5-2) ... 1558s Setting up libkpathsea6:s390x (2025.20250727.75242+ds-5build1) ... 1558s Setting up libgfortran5:s390x (15.2.0-11ubuntu1) ... 1558s Setting up autoconf (2.72-3.1ubuntu1) ... 1558s Setting up libwebp7:s390x (1.5.0-0.1build1) ... 1558s Setting up libubsan1:s390x (15.2.0-11ubuntu1) ... 1558s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 1558s Setting up fonts-dejavu-extra (2.37-8build1) ... 1558s Setting up dwz (0.16-2) ... 1558s Setting up liblqr-1-0:s390x (0.4.2-2.2) ... 1558s Setting up python3-rdflib (7.1.1-3) ... 1559s Setting up libasan8:s390x (15.2.0-11ubuntu1) ... 1559s Setting up libjson-perl (4.10000-1) ... 1559s Setting up libxslt1.1:s390x (1.1.43-0.3) ... 1559s Setting up libpython3.14:s390x (3.14.2-1) ... 1559s Setting up debugedit (1:5.2-3) ... 1559s Setting up fonts-lmodern (2.005-1build1) ... 1559s Setting up libsuitesparseconfig7:s390x (1:7.12.1+dfsg-1) ... 1559s Setting up python3-roman-numerals (4.1.0-1) ... 1560s Setting up libopenjp2-7:s390x (2.5.4-1) ... 1560s Setting up python3.13-minimal (3.13.11-1) ... 1562s Setting up libharfbuzz0b:s390x (12.3.0-4) ... 1562s Setting up fasttree (2.1.11-2build1) ... 1562s Setting up libpython3.14-dev:s390x (3.14.2-1) ... 1562s Setting up sgml-base (1.31+nmu1) ... 1562s Setting up python3-msgpack (1.1.2-1) ... 1563s Setting up libplfit0:s390x (0.9.6+ds-2ubuntu1) ... 1563s Setting up libxss1:s390x (1:1.2.3-1build4) ... 1563s Setting up libmbedcrypto16:s390x (3.6.5-0.1ubuntu2) ... 1563s Setting up libpaper2:s390x (2.2.5-0.3build1) ... 1563s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 1563s Setting up python3-mpmath (1.3.0-2) ... 1566s Setting up libisl23:s390x (0.27-1build1) ... 1566s Setting up libde265-0:s390x (1.0.16-1build1) ... 1566s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 1566s Setting up libwebpmux3:s390x (1.5.0-0.1build1) ... 1566s Setting up dialign (2.2.1-13build1) ... 1566s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ... 1566s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 1566s Setting up xdg-utils (1.2.1-2ubuntu2) ... 1566s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 1566s Setting up libcc1-0:s390x (15.2.0-11ubuntu1) ... 1566s Setting up libitm1:s390x (15.2.0-11ubuntu1) ... 1566s Setting up libsynctex2:s390x (2025.20250727.75242+ds-5build1) ... 1566s Setting up prank (250331-1) ... 1566s Setting up libargtable2-0:s390x (13-4) ... 1566s Setting up python3-imagesize (1.4.1-1build1) ... 1566s Setting up libpotrace0:s390x (1.16-2build2) ... 1566s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 1566s Setting up automake (1:1.18.1-3build1) ... 1566s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 1566s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 1566s Setting up python3-sympy (1.14.0-2) ... 1615s /usr/lib/python3/dist-packages/sympy/testing/runtests.py:283: SyntaxWarning: 'return' in a 'finally' block 1615s return p.returncode 1616s Setting up libice6:s390x (2:1.1.1-1build1) ... 1616s Setting up flex (2.6.4-8.2build2) ... 1616s Setting up liblapack3:s390x (3.12.1-7ubuntu1) ... 1616s 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 1616s Setting up gettext (0.23.2-1) ... 1616s Setting up libarpack2t64:s390x (3.9.1-6) ... 1616s Setting up libgcc-15-dev:s390x (15.2.0-11ubuntu1) ... 1616s Setting up libpython3-dev:s390x (3.14.2-1) ... 1616s Setting up libamd3:s390x (1:7.12.1+dfsg-1) ... 1616s Setting up libpdfbox-java (1:1.8.16-5) ... 1616s Setting up python3.14-dev (3.14.2-1) ... 1616s Setting up libcolamd3:s390x (1:7.12.1+dfsg-1) ... 1616s Setting up python3.13 (3.13.11-1) ... 1618s Setting up libcifpp9:s390x (9.0.5-2) ... 1618s Setting up fontconfig-config (2.15.0-2.4ubuntu1) ... 1619s Setting up wise (2.4.1-27) ... 1619s Setting up preview-latex-style (13.2-1.1) ... 1619s Setting up libwebpdemux2:s390x (1.5.0-0.1build1) ... 1619s Setting up libcommons-parent-java (56-1build1) ... 1619s Setting up libavahi-common3:s390x (0.8-17ubuntu1) ... 1619s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 1619s Setting up python3-all (3.14.2-1) ... 1619s Setting up libpaper-utils (2.2.5-0.3build1) ... 1619s Setting up clustalo (1.2.4-8build2) ... 1619s Setting up dssp (4.5.7-1) ... 1619s Setting up python3-freetype (2.5.1-2) ... 1619s Setting up xfonts-utils (1:7.7+7build1) ... 1619s Setting up python3-zopfli (0.4.0-1) ... 1620s Setting up intltool-debian (0.35.0+20060710.6build1) ... 1620s Setting up libmbedx509-7:s390x (3.6.5-0.1ubuntu2) ... 1620s Setting up libstdc++-15-dev:s390x (15.2.0-11ubuntu1) ... 1620s Setting up libptexenc1:s390x (2025.20250727.75242+ds-5build1) ... 1620s Setting up libglpk40:s390x (5.0-2) ... 1620s Setting up libraqm0:s390x (0.10.3-1) ... 1620s Setting up libpython3.13-dev:s390x (3.13.11-1) ... 1620s Setting up sphinx-common (8.2.3-12) ... 1620s Setting up python3-dev (3.14.2-1) ... 1620s Setting up python3-numpy (1:2.3.5+ds-3) ... 1636s Setting up libraw23t64:s390x (0.21.4-2) ... 1636s Setting up libmbedtls21:s390x (3.6.5-0.1ubuntu2) ... 1636s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 1636s Setting up python3-lxml:s390x (6.0.2-1) ... 1637s Setting up python-biopython-doc (1.86+dfsg-1) ... 1637s Setting up libtiff6:s390x (4.7.0-3ubuntu3) ... 1637s Setting up lmodern (2.005-1build1) ... 1637s Setting up xml-core (0.19build1) ... 1637s Setting up cpp-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 1637s Setting up python3-contourpy (1.3.3-1) ... 1638s Setting up libfontconfig1:s390x (2.15.0-2.4ubuntu1) ... 1638s Setting up libsm6:s390x (2:1.2.6-1) ... 1638s Setting up libavahi-client3:s390x (0.8-17ubuntu1) ... 1638s Setting up gcc-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 1638s Setting up g++-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 1638s Setting up libxft2:s390x (2.3.6-1build2) ... 1638s Setting up python3-scipy (1.16.3-3) ... 1671s Setting up cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 1671s Setting up python3.13-dev (3.13.11-1) ... 1671s Setting up libigraph4:s390x (1.0.1+ds-3) ... 1671s Setting up po-debconf (1.0.22) ... 1671s Setting up libtk8.6:s390x (8.6.17-1) ... 1671s Setting up python3-mmtf (1.1.3-1build1) ... 1671s Setting up fonts-urw-base35 (20200910-8build1) ... 1673s Setting up libcairo2:s390x (1.18.4-3) ... 1673s Setting up python3.13-tk (3.13.11-1) ... 1673s Setting up ncbi-blast+ (2.16.0+ds-7) ... 1673s Setting up python3-pil:s390x (12.0.0-1ubuntu1) ... 1676s Setting up gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 1676s Setting up libpython3-all-dev:s390x (3.14.2-1) ... 1676s Setting up libxt6t64:s390x (1:1.2.1-1.3) ... 1676s Setting up netpbm (2:11.10.02-1build1) ... 1676s Setting up python3-igraph (1.0.0+ds-1) ... 1678s Setting up cpp-15 (15.2.0-11ubuntu1) ... 1678s Setting up cpp (4:15.2.0-4ubuntu1) ... 1678s Setting up libcups2t64:s390x (2.4.16-1ubuntu1) ... 1678s Setting up python3-all-dev (3.14.2-1) ... 1678s Setting up libgs10-common (10.05.0dfsg1-0ubuntu4) ... 1678s Setting up libxmu6:s390x (2:1.1.3-4) ... 1678s Setting up python3.14-tk (3.14.2-1) ... 1679s Setting up python3-cairo (1.27.0-2build1) ... 1680s Setting up python3-tk (3.14.2-1) ... 1680s Setting up g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 1680s Setting up libxaw7:s390x (2:1.0.16-1build1) ... 1680s Setting up gcc-15 (15.2.0-11ubuntu1) ... 1680s Setting up python3-pil.imagetk:s390x (12.0.0-1ubuntu1) ... 1680s Setting up python3-rlpycairo (0.3.0-4) ... 1681s Setting up python3-reportlab (4.4.9-1) ... 1687s Setting up texlive-binaries (2025.20250727.75242+ds-5build1) ... 1687s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 1687s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 1687s Setting up texlive-base (2025.20251127-1) ... 1690s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 1692s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 1693s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 1693s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 1696s Setting up g++-15 (15.2.0-11ubuntu1) ... 1696s Setting up libgs10:s390x (10.05.0dfsg1-0ubuntu4) ... 1696s Setting up libtool (2.5.4-9) ... 1696s Setting up texlive-luatex (2025.20251127-1) ... 1696s Setting up ghostscript (10.05.0dfsg1-0ubuntu4) ... 1696s Setting up gcc (4:15.2.0-4ubuntu1) ... 1696s Setting up dh-autoreconf (21) ... 1696s Setting up texlive-latex-base (2025.20251127-1) ... 1696s Setting up texlive-latex-recommended (2025.20251127-1) ... 1696s Setting up texlive-pictures (2025.20251127-1) ... 1696s Setting up g++ (4:15.2.0-4ubuntu1) ... 1696s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1696s Setting up texlive-fonts-recommended (2025.20251127-1) ... 1696s Setting up build-essential (12.12ubuntu2) ... 1696s Setting up debhelper (13.28ubuntu1) ... 1696s Setting up texlive-latex-extra (2025.20251127-2) ... 1696s Setting up python3-ufolib2 (0.18.1+dfsg1-1) ... 1697s Setting up libheif-plugin-aomdec:s390x (1.21.2-1) ... 1697s Setting up libheif-plugin-libde265:s390x (1.21.2-1) ... 1697s Setting up libheif1:s390x (1.21.2-1) ... 1697s Setting up python3-fonttools (4.61.1-3) ... 1704s Setting up libmagickcore-7.q16-10:s390x (8:7.1.2.12+dfsg1-1) ... 1704s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 1720s Setting up libmagickwand-7.q16-10:s390x (8:7.1.2.12+dfsg1-1) ... 1720s Setting up imagemagick-7.q16 (8:7.1.2.12+dfsg1-1) ... 1720s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode 1720s update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode 1720s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode 1720s update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode 1720s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode 1720s update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode 1720s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode 1720s update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode 1720s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode 1720s update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode 1720s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode 1720s update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode 1720s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode 1720s update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode 1720s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode 1720s update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode 1720s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode 1720s update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode 1720s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode 1720s update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode 1720s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 1720s update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode 1720s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode 1720s 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 1720s update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode 1720s 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 1720s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode 1720s 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 1720s update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode 1720s 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 1720s Setting up hevea (2.36-2build3) ... 1720s Setting up imagemagick (8:7.1.2.12+dfsg1-1) ... 1720s Processing triggers for install-info (7.2-5) ... 1721s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1721s Processing triggers for systemd (259-1ubuntu2) ... 1721s Processing triggers for man-db (2.13.1-1) ... 1727s Processing triggers for sgml-base (1.31+nmu1) ... 1727s Setting up docutils-common (0.22.4+dfsg-1) ... 1728s Setting up w3c-sgml-lib (1.3-3build1) ... 1845s Setting up python3-biopython (1.86+dfsg-1) ... 1852s Setting up python3-biopython-sql (1.86+dfsg-1) ... 1853s Processing triggers for sgml-base (1.31+nmu1) ... 1853s Setting up python3-docutils (0.22.4+dfsg-1) ... 1856s Setting up python3-sphinx (8.2.3-12) ... 1861s Setting up python3-sphinxcontrib.jquery (4.1-6) ... 1862s Setting up python3-numpydoc (1.9.0-1) ... 1863s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-3) ... 1864s Processing triggers for tex-common (6.20) ... 1866s Running updmap-sys. This may take some time... done. 1866s Running mktexlsr /var/lib/texmf ... done. 1866s Building format(s) --all. 2219s This may take some time... done. 2232s autopkgtest [17:37:48]: test full_suite: sh debian/tests/run-unit-test 2232s autopkgtest [17:37:48]: test full_suite: [----------------------- 2237s mkdir: created directory 'Bio' 2237s mkdir: created directory 'Bio/Align' 2237s mkdir: created directory 'Bio/Align/substitution_matrices' 2237s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 2237s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 2240s test_Ace ... ok 2240s test_Affy ... ok 2242s test_AlignIO ... ok 2242s test_AlignIO_ClustalIO ... ok 2242s test_AlignIO_EmbossIO ... ok 2242s test_AlignIO_FastaIO ... ok 2242s test_AlignIO_MauveIO ... ok 2242s test_AlignIO_PhylipIO ... ok 2242s test_AlignIO_convert ... ok 2244s test_Align_Alignment ... ok 2244s test_Align_a2m ... ok 2245s test_Align_bed ... ok 2245s test_Align_bigbed ... ok 2247s test_Align_bigmaf ... ok 2249s test_Align_bigpsl ... ok 2249s test_Align_chain ... ok 2250s test_Align_clustal ... ok 2283s test_Align_codonalign ... ok 2283s test_Align_emboss ... ok 2284s test_Align_exonerate ... ok 2284s test_Align_fasta ... ok 2285s test_Align_format_matrix ... ok 2287s test_Align_hhr ... ok 2292s test_Align_maf ... ok 2292s test_Align_mauve ... ok 2292s test_Align_msf ... ok 2293s test_Align_nexus ... ok 2293s test_Align_phylip ... ok 2296s test_Align_psl ... ok 2297s test_Align_sam ... ok 2305s test_Align_stockholm ... ok 2308s test_Align_tabular ... ok 2308s test_BioSQL_MySQLdb_online ... skipping. internet not available 2308s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 2308s test_BioSQL_mysql_connector_online ... skipping. internet not available 2308s test_BioSQL_psycopg2_online ... skipping. internet not available 2328s test_BioSQL_sqlite3 ... ok 2328s test_BioSQL_sqlite3_online ... skipping. internet not available 2328s test_Blast_Record ... ok 2331s test_Blast_parser ... ok 2331s test_CAPS ... ok 2331s test_Chi2 ... ok 2331s test_Cluster ... ok 2332s test_CodonTable ... ok 2332s test_ColorSpiral ... ok 2332s test_Compass ... ok 2335s test_Consensus ... ok 2335s test_EMBL_unittest ... ok 2335s test_EmbossPrimer ... ok 2340s test_Entrez ... ok 2340s test_Entrez_online ... skipping. internet not available 2342s test_Entrez_parser ... ok 2342s test_Enzyme ... ok 2342s test_ExPASy ... skipping. internet not available 2342s test_File ... ok 2343s test_GenBank ... ok 2354s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 2363s ok 2368s test_GraphicsChromosome ... ok 2369s test_GraphicsDistribution ... ok 2374s test_GraphicsGeneral ... ok 2374s test_KEGG ... ok 2374s test_KEGG_online ... skipping. internet not available 2403s test_KGML_graphics ... ok 2403s test_KGML_graphics_online ... skipping. internet not available 2405s test_KGML_nographics ... ok 2405s test_KeyWList ... ok 2408s test_MafIO_index ... ok 2408s test_Medline ... ok 2411s test_NCBIXML ... Exception ignored in: 2411s Traceback (most recent call last): 2411s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 2411s expat_parser.Parse(NULL, True) 2411s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 2411s ok 2411s test_NCBI_qblast ... ok 2411s test_NMR ... ok 2412s test_Nexus ... ok 2413s test_PAML_baseml ... ok 2416s test_PAML_codeml ... ok 2416s test_PAML_yn00 ... ok 2445s test_PDB_CEAligner ... ok 2452s test_PDB_DSSP ... ok 2452s test_PDB_Dice ... ok 2452s test_PDB_Disordered ... ok 2453s test_PDB_Exposure ... ok 2453s test_PDB_FragmentMapper ... ok 2461s test_PDB_KDTree ... ok 2462s test_PDB_MMCIF2Dict ... ok 2464s test_PDB_MMCIFIO ... ok 2470s test_PDB_MMCIFParser ... ok 2471s test_PDB_NACCESS ... ok 2473s test_PDB_PDBIO ... ok 2473s test_PDB_PDBList ... skipping. internet not available 2515s test_PDB_PDBMLParser ... ok 2515s test_PDB_PDBParser ... ok 2515s 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 2515s test_PDB_Polypeptide ... ok 2515s test_PDB_QCPSuperimposer ... ok 2531s test_PDB_SASA ... ok 2535s test_PDB_SMCRA ... ok 2535s test_PDB_Selection ... ok 2540s test_PDB_StructureAlignment ... ok 2540s test_PDB_Superimposer ... ok 2541s test_PDB_alphafold_db ... skipping. internet not available 2578s test_PDB_internal_coords ... ok 2579s test_PDB_parse_pdb_header ... ok 2579s test_PDB_vectors ... ok 2581s test_PQR ... ok 2582s test_Pathway ... ok 2584s test_Phd ... ok 2587s test_Phylo ... ok 2588s test_PhyloXML ... ok 2591s test_Phylo_CDAO ... ok 2593s test_Phylo_NeXML ... ok 2600s test_Phylo_igraph ... ok 2616s test_Phylo_matplotlib ... ok 2618s test_Phylo_networkx ... ok 2620s test_PopGen_GenePop_nodepend ... ok 2623s test_ProtParam ... ok 2629s test_RCSBFormats ... ok 2632s test_Restriction ... ok 2634s test_SCOP_Astral ... ok 2637s test_SCOP_Cla ... ok 2640s test_SCOP_Des ... ok 2642s test_SCOP_Dom ... ok 2644s test_SCOP_Hie ... ok 2647s test_SCOP_Raf ... ok 2650s test_SCOP_Residues ... ok 2653s test_SCOP_Scop ... ok 2656s test_SVDSuperimposer ... ok 2659s test_SearchIO_blast_tab ... ok 2662s test_SearchIO_blast_tab_index ... ok 2666s test_SearchIO_blast_xml ... ok 2673s test_SearchIO_blast_xml_index ... ok 2676s test_SearchIO_blat_psl ... ok 2679s test_SearchIO_blat_psl_index ... ok 2681s test_SearchIO_exonerate ... ok 2684s test_SearchIO_exonerate_text_index ... ok 2685s test_SearchIO_exonerate_vulgar_index ... ok 2687s test_SearchIO_fasta_m10 ... ok 2690s test_SearchIO_fasta_m10_index ... ok 2693s test_SearchIO_hhsuite2_text ... ok 2694s test_SearchIO_hmmer2_text ... ok 2697s test_SearchIO_hmmer2_text_index ... ok 2700s test_SearchIO_hmmer3_domtab ... ok 2703s test_SearchIO_hmmer3_domtab_index ... ok 2706s test_SearchIO_hmmer3_tab ... ok 2708s test_SearchIO_hmmer3_tab_index ... ok 2710s test_SearchIO_hmmer3_text ... ok 2713s test_SearchIO_hmmer3_text_index ... ok 2715s test_SearchIO_infernal_tab ... ok 2716s test_SearchIO_infernal_tab_index ... ok 2717s test_SearchIO_infernal_text ... ok 2717s test_SearchIO_infernal_text_index ... ok 2718s test_SearchIO_interproscan_xml ... ok 2720s test_SearchIO_model ... ok 2721s test_SearchIO_write ... ok 2724s test_SeqFeature ... ok 2805s test_SeqIO ... ok 2808s test_SeqIO_AbiIO ... ok 2810s test_SeqIO_FastaIO ... ok 2813s test_SeqIO_Gck ... ok 2814s test_SeqIO_Gfa ... ok 2816s test_SeqIO_Insdc ... ok 2819s test_SeqIO_NibIO ... ok 2831s test_SeqIO_PdbIO ... ok 2834s test_SeqIO_QualityIO ... ok 2837s test_SeqIO_SeqXML ... ok 2839s test_SeqIO_SffIO ... ok 2842s test_SeqIO_SnapGene ... ok 2849s test_SeqIO_TwoBitIO ... ok 2852s test_SeqIO_UniprotIO ... ok 2855s test_SeqIO_Xdna ... ok 2860s test_SeqIO_features ... ok 2933s test_SeqIO_index ... ok 2936s test_SeqIO_online ... skipping. internet not available 2938s test_SeqIO_write ... ok 2941s test_SeqRecord ... ok 2943s test_SeqUtils ... ok 2953s test_Seq_objs ... ok 2957s test_SwissProt ... ok 2959s test_TogoWS ... skipping. internet not available 2962s test_TreeConstruction ... ok 2964s test_UniGene ... ok 2966s test_UniProt ... skipping. internet not available 2970s test_UniProt_GOA ... ok 2973s test_align ... ok 2978s test_align_substitution_matrices ... ok 2993s test_bgzf ... ok 2996s test_cellosaurus ... ok 3031s test_codonalign ... ok 3034s test_geo ... ok 3039s test_motifs ... ok 3041s test_motifs_online ... skipping. internet not available 3045s 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. 3045s warnings.warn( 3045s ok 3048s test_pairwise2_no_C ... ok 3054s test_pairwise_aligner ... ok 3059s test_pairwise_alignment_map ... ok 3094s test_phenotype ... ok 3097s test_phenotype_fit ... ok 3099s test_prodoc ... ok 3103s test_prosite ... ok 3106s test_seq ... ok 3108s test_translate ... ok 3111s ---------------------------------------------------------------------- 3111s Skipping any tests requiring internet access 3111s Python version: 3.13.11 (main, Dec 6 2025, 13:15:20) [GCC 15.2.0] 3111s Operating system: posix linux 3111s Ran 199 tests in 871.300 seconds 3111s 3115s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 3115s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 3119s test_Ace ... ok 3119s test_Affy ... ok 3121s test_AlignIO ... ok 3121s test_AlignIO_ClustalIO ... ok 3121s test_AlignIO_EmbossIO ... ok 3121s test_AlignIO_FastaIO ... ok 3121s test_AlignIO_MauveIO ... ok 3121s test_AlignIO_PhylipIO ... ok 3121s test_AlignIO_convert ... ok 3122s test_Align_Alignment ... ok 3122s test_Align_a2m ... ok 3122s test_Align_bed ... ok 3123s test_Align_bigbed ... ok 3126s test_Align_bigmaf ... ok 3128s test_Align_bigpsl ... ok 3128s test_Align_chain ... ok 3128s test_Align_clustal ... ok 3157s test_Align_codonalign ... FAIL 3157s test_Align_emboss ... ok 3158s test_Align_exonerate ... ok 3159s test_Align_fasta ... ok 3159s test_Align_format_matrix ... ok 3161s test_Align_hhr ... ok 3166s test_Align_maf ... ok 3166s test_Align_mauve ... ok 3166s test_Align_msf ... ok 3167s test_Align_nexus ... ok 3168s test_Align_phylip ... ok 3170s test_Align_psl ... ok 3172s test_Align_sam ... ok 3179s test_Align_stockholm ... ok 3181s test_Align_tabular ... ok 3181s test_BioSQL_MySQLdb_online ... skipping. internet not available 3182s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 3182s test_BioSQL_mysql_connector_online ... skipping. internet not available 3182s test_BioSQL_psycopg2_online ... skipping. internet not available 3197s test_BioSQL_sqlite3 ... ok 3197s test_BioSQL_sqlite3_online ... skipping. internet not available 3197s test_Blast_Record ... ok 3200s test_Blast_parser ... ok 3200s test_CAPS ... ok 3200s test_Chi2 ... ERROR 3201s test_Cluster ... ok 3201s test_CodonTable ... ok 3201s test_ColorSpiral ... ok 3201s test_Compass ... ok 3201s test_Consensus ... ERROR 3201s test_EMBL_unittest ... ok 3201s test_EmbossPrimer ... ok 3206s test_Entrez ... ok 3206s test_Entrez_online ... skipping. internet not available 3207s test_Entrez_parser ... ok 3207s test_Enzyme ... ok 3207s test_ExPASy ... skipping. internet not available 3207s test_File ... ok 3208s test_GenBank ... ok 3217s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 3225s ok 3229s test_GraphicsChromosome ... ok 3229s test_GraphicsDistribution ... ok 3233s test_GraphicsGeneral ... ok 3234s test_KEGG ... ok 3234s test_KEGG_online ... skipping. internet not available 3257s test_KGML_graphics ... ok 3258s test_KGML_graphics_online ... skipping. internet not available 3260s test_KGML_nographics ... ok 3261s test_KeyWList ... ok 3263s test_MafIO_index ... ok 3263s test_Medline ... ok 3267s test_NCBIXML ... Exception ignored while closing generator : 3267s Traceback (most recent call last): 3267s File "/usr/lib/python3/dist-packages/Bio/Blast/NCBIXML.py", line 1319, in parse 3267s expat_parser.Parse(NULL, True) 3267s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 3267s ok 3267s test_NCBI_qblast ... ok 3267s test_NMR ... ok 3268s test_Nexus ... ok 3269s test_PAML_baseml ... ERROR 3269s test_PAML_codeml ... ERROR 3269s test_PAML_yn00 ... ERROR 3296s test_PDB_CEAligner ... ok 3302s test_PDB_DSSP ... ok 3303s test_PDB_Dice ... ok 3303s test_PDB_Disordered ... ok 3305s test_PDB_Exposure ... ok 3305s test_PDB_FragmentMapper ... ok 3311s test_PDB_KDTree ... ok 3312s test_PDB_MMCIF2Dict ... ok 3313s test_PDB_MMCIFIO ... ok 3318s test_PDB_MMCIFParser ... ok 3318s test_PDB_NACCESS ... ok 3320s test_PDB_PDBIO ... ok 3321s test_PDB_PDBList ... skipping. internet not available 3350s test_PDB_PDBMLParser ... ok 3352s test_PDB_PDBParser ... ok 3352s 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 3353s test_PDB_Polypeptide ... ok 3354s test_PDB_QCPSuperimposer ... ok 3369s test_PDB_SASA ... ok 3371s test_PDB_SMCRA ... ok 3372s test_PDB_Selection ... ok 3375s test_PDB_StructureAlignment ... ok 3376s test_PDB_Superimposer ... ok 3377s test_PDB_alphafold_db ... skipping. internet not available 3407s test_PDB_internal_coords ... ok 3409s test_PDB_parse_pdb_header ... ok 3411s test_PDB_vectors ... ok 3412s test_PQR ... ok 3413s test_Pathway ... ok 3414s test_Phd ... ok 3416s test_Phylo ... ERROR 3417s test_PhyloXML ... ERROR 3419s test_Phylo_CDAO ... ERROR 3421s test_Phylo_NeXML ... ERROR 3422s test_Phylo_igraph ... ERROR 3424s test_Phylo_matplotlib ... ERROR 3426s test_Phylo_networkx ... ERROR 3428s test_PopGen_GenePop_nodepend ... ok 3430s test_ProtParam ... ok 3434s test_RCSBFormats ... ok 3436s test_Restriction ... ok 3437s test_SCOP_Astral ... ok 3439s test_SCOP_Cla ... ok 3440s test_SCOP_Des ... ok 3441s test_SCOP_Dom ... ok 3442s test_SCOP_Hie ... ok 3444s test_SCOP_Raf ... ok 3446s test_SCOP_Residues ... ok 3447s test_SCOP_Scop ... ok 3449s test_SVDSuperimposer ... ok 3450s test_SearchIO_blast_tab ... ok 3452s test_SearchIO_blast_tab_index ... ok 3455s test_SearchIO_blast_xml ... ok 3464s test_SearchIO_blast_xml_index ... ok 3465s test_SearchIO_blat_psl ... ok 3466s test_SearchIO_blat_psl_index ... ok 3468s test_SearchIO_exonerate ... ok 3469s test_SearchIO_exonerate_text_index ... ok 3471s test_SearchIO_exonerate_vulgar_index ... ok 3473s test_SearchIO_fasta_m10 ... ok 3475s test_SearchIO_fasta_m10_index ... ok 3477s test_SearchIO_hhsuite2_text ... ok 3480s test_SearchIO_hmmer2_text ... ok 3484s test_SearchIO_hmmer2_text_index ... ok 3485s test_SearchIO_hmmer3_domtab ... ok 3486s test_SearchIO_hmmer3_domtab_index ... ok 3488s test_SearchIO_hmmer3_tab ... ok 3490s test_SearchIO_hmmer3_tab_index ... ok 3492s test_SearchIO_hmmer3_text ... ok 3494s test_SearchIO_hmmer3_text_index ... ok 3496s test_SearchIO_infernal_tab ... ok 3497s test_SearchIO_infernal_tab_index ... ok 3497s test_SearchIO_infernal_text ... ok 3497s test_SearchIO_infernal_text_index ... ok 3499s test_SearchIO_interproscan_xml ... ok 3500s test_SearchIO_model ... ok 3501s test_SearchIO_write ... ok 3502s test_SeqFeature ... ok 3590s test_SeqIO ... ok 3593s test_SeqIO_AbiIO ... ok 3594s test_SeqIO_FastaIO ... ok 3596s test_SeqIO_Gck ... ok 3596s test_SeqIO_Gfa ... ok 3599s test_SeqIO_Insdc ... ok 3600s test_SeqIO_NibIO ... ok 3611s test_SeqIO_PdbIO ... ok 3615s test_SeqIO_QualityIO ... ok 3617s test_SeqIO_SeqXML ... ok 3618s test_SeqIO_SffIO ... ok 3621s test_SeqIO_SnapGene ... ok 3626s test_SeqIO_TwoBitIO ... ok 3630s test_SeqIO_UniprotIO ... ok 3631s test_SeqIO_Xdna ... ok 3637s test_SeqIO_features ... ok 3702s test_SeqIO_index ... ok 3703s test_SeqIO_online ... skipping. internet not available 3703s test_SeqIO_write ... ok 3705s test_SeqRecord ... ok 3706s test_SeqUtils ... ok 3714s test_Seq_objs ... ok 3717s test_SwissProt ... ok 3717s test_TogoWS ... skipping. internet not available 3718s test_TreeConstruction ... ERROR 3719s test_UniGene ... ok 3721s test_UniProt ... skipping. internet not available 3722s test_UniProt_GOA ... ok 3724s test_align ... ok 3727s test_align_substitution_matrices ... ok 3739s test_bgzf ... ok 3740s test_cellosaurus ... ok 3765s test_codonalign ... FAIL 3767s test_geo ... ok 3770s test_motifs ... ok 3772s test_motifs_online ... skipping. internet not available 3774s 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. 3774s warnings.warn( 3774s ok 3775s test_pairwise2_no_C ... ok 3780s test_pairwise_aligner ... ok 3783s test_pairwise_alignment_map ... ok 3825s test_phenotype ... ok 3828s test_phenotype_fit ... ok 3829s test_prodoc ... ok 3830s test_prosite ... ok 3833s test_seq ... ok 3834s test_translate ... ok 3836s ====================================================================== 3836s ERROR: test_dn_ds (test_Align_codonalign.Test_dn_ds.test_dn_ds) 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 8313, in test_dn_ds 3836s dn, ds = calculate_dn_ds_matrix(alignment) 3836s ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/Bio/Align/analysis.py", line 1012, in calculate_dn_ds_matrix 3836s from Bio.Phylo.TreeConstruction import DistanceMatrix 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s 3836s ====================================================================== 3836s ERROR: test_Chi2 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_Chi2.py", line 10, in 3836s from Bio.Phylo.PAML import chi2 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_Consensus 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_Consensus.py", line 15, in 3836s from Bio import Phylo 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_PAML_baseml 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_PAML_baseml.py", line 12, in 3836s from Bio.Phylo.PAML import baseml 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_PAML_codeml 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_PAML_codeml.py", line 13, in 3836s from Bio.Phylo.PAML import codeml 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_PAML_yn00 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_PAML_yn00.py", line 13, in 3836s from Bio.Phylo.PAML import yn00 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_Phylo 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_Phylo.py", line 13, in 3836s from Bio import Phylo 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_PhyloXML 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_PhyloXML.py", line 17, in 3836s from Bio.Phylo import PhyloXML as PX 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_Phylo_CDAO 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_Phylo_CDAO.py", line 13, in 3836s import Bio.Phylo as bp 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_Phylo_NeXML 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_Phylo_NeXML.py", line 14, in 3836s from Bio import Phylo 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_Phylo_igraph 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_Phylo_igraph.py", line 13, in 3836s from Bio import Phylo 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_Phylo_matplotlib 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_Phylo_matplotlib.py", line 13, in 3836s from Bio import Phylo 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_Phylo_networkx 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_Phylo_networkx.py", line 12, in 3836s from Bio import Phylo 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_TreeConstruction 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/run_tests.py", line 245, in runTest 3836s suite = loader.loadTestsFromName(name) 3836s File "/usr/lib/python3.14/unittest/loader.py", line 137, in loadTestsFromName 3836s module = __import__(module_name) 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_TreeConstruction.py", line 16, in 3836s from Bio import Phylo 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s ====================================================================== 3836s ERROR: test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) 3836s ---------------------------------------------------------------------- 3836s Traceback (most recent call last): 3836s File "/tmp/autopkgtest.Fc1qB0/autopkgtest_tmp/Tests/test_codonalign.py", line 381, in test_dn_ds_matrix 3836s dn, ds = self.aln.get_dn_ds_matrix() 3836s ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 3836s File "/usr/lib/python3/dist-packages/Bio/codonalign/codonalignment.py", line 159, in get_dn_ds_matrix 3836s from Bio.Phylo.TreeConstruction import DistanceMatrix as DM 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py", line 14, in 3836s from Bio.Phylo._io import convert 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/_io.py", line 29, in 3836s from Bio.Phylo import CDAOIO 3836s File "/usr/lib/python3/dist-packages/Bio/Phylo/CDAOIO.py", line 37, in 3836s import rdflib 3836s File "/usr/lib/python3/dist-packages/rdflib/__init__.py", line 168, in 3836s from rdflib.graph import ConjunctiveGraph, Dataset, Graph 3836s File "/usr/lib/python3/dist-packages/rdflib/graph.py", line 292, in 3836s from rdflib.resource import Resource 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 296, in 3836s class Resource: 3836s ...<164 lines>... 3836s return "Resource(%s,%s)" % (self._graph, self._identifier) 3836s File "/usr/lib/python3/dist-packages/rdflib/resource.py", line 379, in Resource 3836s def value(self, p=RDF.value, o=None, default=None, any=True): 3836s ^^^^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 285, in __getattr__ 3836s return cls.__getitem__(name) 3836s ~~~~~~~~~~~~~~~^^^^^^ 3836s File "/usr/lib/python3/dist-packages/rdflib/namespace/__init__.py", line 268, in __getitem__ 3836s raise AttributeError(f"term '{name}' not in namespace '{cls._NS}'") 3836s AttributeError: term 'value' not in namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' 3836s 3836s ---------------------------------------------------------------------- 3836s Ran 199 tests in 717.017 seconds 3836s 3836s FAILED (failures = 15) 3836s Skipping any tests requiring internet access 3836s Python version: 3.14.2 (main, Dec 6 2025, 13:20:08) [GCC 15.2.0] 3836s Operating system: posix linux 3839s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/protein_lib.fa' mode='rt' encoding='UTF-8'> 3839s :0: ResourceWarning: unclosed file <_io.TextIOWrapper name='Fasta/nucleotide_lib.fa' mode='rt' encoding='UTF-8'> 3841s autopkgtest [18:04:37]: test full_suite: -----------------------] 3842s full_suite FAIL non-zero exit status 1 3842s autopkgtest [18:04:38]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 3842s autopkgtest [18:04:38]: @@@@@@@@@@@@@@@@@@@@ summary 3842s dependencies PASS 3842s full_suite FAIL non-zero exit status 1