0s autopkgtest [13:00:52]: starting date and time: 2024-11-13 13:00:52+0000 0s autopkgtest [13:00:52]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [13:00:52]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yg_x3olv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-7.secgroup --name adt-plucky-s390x-python-biopython-20241113-130052-juju-7f2275-prod-proposed-migration-environment-20-1bef5a9e-06c3-4cdc-b0f0-1ccc1975949b --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 92s autopkgtest [13:02:24]: testbed dpkg architecture: s390x 92s autopkgtest [13:02:24]: testbed apt version: 2.9.8 92s autopkgtest [13:02:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 93s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 93s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 93s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 93s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB] 93s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 93s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [107 kB] 93s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [641 kB] 93s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.4 kB] 93s Fetched 1934 kB in 1s (2390 kB/s) 94s Reading package lists... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Calculating upgrade... 96s The following NEW packages will be installed: 96s python3.13-gdbm 96s The following packages will be upgraded: 96s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 96s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 252 kB of archives. 96s After this operation, 98.3 kB of additional disk space will be used. 96s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 96s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 96s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 96s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 96s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 97s Fetched 252 kB in 0s (518 kB/s) 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 55510 files and directories currently installed.) 97s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 97s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 97s Setting up python3-minimal (3.12.7-1) ... 97s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 55510 files and directories currently installed.) 97s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 97s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 97s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 97s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 97s Selecting previously unselected package python3.13-gdbm. 97s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ... 97s Unpacking python3.13-gdbm (3.13.0-2) ... 97s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ... 97s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 97s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 97s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 97s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 97s Setting up python3.13-gdbm (3.13.0-2) ... 97s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 97s Setting up python3 (3.12.7-1) ... 97s Setting up python3-gdbm:s390x (3.12.7-1) ... 97s Processing triggers for man-db (2.12.1-3) ... 98s Processing triggers for libc-bin (2.40-1ubuntu3) ... 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 98s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 99s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 99s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 99s Reading package lists... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s Calculating upgrade... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s autopkgtest [13:02:34]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 103s autopkgtest [13:02:35]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 106s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (dsc) [3543 B] 106s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (tar) [14.6 MB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (diff) [42.8 kB] 106s gpgv: Signature made Wed Oct 30 21:23:04 2024 UTC 106s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 106s gpgv: issuer "emollier@debian.org" 106s gpgv: Can't check signature: No public key 106s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.84+dfsg-4.dsc: no acceptable signature found 107s autopkgtest [13:02:39]: testing package python-biopython version 1.84+dfsg-4 107s autopkgtest [13:02:39]: build not needed 112s autopkgtest [13:02:44]: test dependencies: preparing testbed 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Starting pkgProblemResolver with broken count: 0 114s Starting 2 pkgProblemResolver with broken count: 0 114s Done 114s The following additional packages will be installed: 114s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 114s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 114s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 114s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 114s liblapack3 liblcms2-2 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 114s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 114s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 114s python3-all python3-biopython python3-biopython-sql python3-cairo 114s python3-freetype python3-numpy python3-pil python3-reportlab 114s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 114s x11-common xfonts-encodings xfonts-utils xml-core 114s Suggested packages: 114s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 114s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 114s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 114s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 114s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 114s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 114s rl-renderpm python3.13-venv python3.13-doc binfmt-support sgml-base-doc 114s debhelper 114s Recommended packages: 114s javascript-common ncbi-blast+ python3-olefile fonts-dejavu-extra 115s The following NEW packages will be installed: 115s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 115s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 115s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 115s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc 115s libjs-underscore liblapack3 liblcms2-2 libopenjp2-7 libpixman-1-0 115s libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 115s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 115s python-biopython-doc python3-all python3-biopython python3-biopython-sql 115s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 115s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 115s x11-common xfonts-encodings xfonts-utils xml-core 115s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 52.8 MB/52.8 MB of archives. 115s After this operation, 146 MB of additional disk space will be used. 115s Get:1 /tmp/autopkgtest.Ou6kQf/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [744 B] 115s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.0-2 [877 kB] 116s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.0-2 [2172 kB] 116s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x sgml-base all 1.31 [11.4 kB] 116s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 116s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 116s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 116s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 116s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 116s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 116s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 116s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB] 116s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 116s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB] 116s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 116s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 116s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 116s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 116s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 116s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.22-1 [46.1 kB] 116s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 116s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 14.2.0-8ubuntu1 [151 kB] 116s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 116s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.0.1-1 [536 kB] 116s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 116s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu2 [150 kB] 116s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 116s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 116s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 116s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 7.4.7-4 [158 kB] 116s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 116s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 116s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.0-2 [2086 kB] 116s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.1-1build1 [16.2 kB] 116s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.4.0-0.1 [16.2 kB] 116s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 116s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.4.0-0.1 [204 kB] 116s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 116s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.4.0-0.1 [12.2 kB] 116s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.4.0-0.1 [25.3 kB] 116s Get:42 http://ftpmaster.internal/ubuntu plucky/universe s390x python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 116s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.0-2 [719 kB] 116s Get:44 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all s390x 3.12.7-1 [890 B] 116s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 116s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.0-2ubuntu1 [208 kB] 116s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 10.4.0-1ubuntu1 [492 kB] 116s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x python3-cairo s390x 1.26.1-2 [119 kB] 116s Get:49 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 116s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 116s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-reportlab all 4.2.5-1 [1107 kB] 117s Get:52 http://ftpmaster.internal/ubuntu plucky/main s390x xml-core all 0.19 [20.3 kB] 117s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 117s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython s390x 1.84+dfsg-4 [1721 kB] 117s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 117s Fetched 52.8 MB in 2s (25.7 MB/s) 117s Selecting previously unselected package libpython3.13-minimal:s390x. 117s (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 ... 55517 files and directories currently installed.) 117s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_s390x.deb ... 117s Unpacking libpython3.13-minimal:s390x (3.13.0-2) ... 117s Selecting previously unselected package python3.13-minimal. 117s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_s390x.deb ... 117s Unpacking python3.13-minimal (3.13.0-2) ... 117s Selecting previously unselected package sgml-base. 117s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 117s Unpacking sgml-base (1.31) ... 117s Selecting previously unselected package fonts-dejavu-mono. 117s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 117s Unpacking fonts-dejavu-mono (2.37-8) ... 117s Selecting previously unselected package fonts-dejavu-core. 117s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 117s Unpacking fonts-dejavu-core (2.37-8) ... 117s Selecting previously unselected package libfontenc1:s390x. 117s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 117s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 117s Selecting previously unselected package libfreetype6:s390x. 117s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 117s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 117s Selecting previously unselected package x11-common. 117s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu3_all.deb ... 117s Unpacking x11-common (1:7.7+23ubuntu3) ... 117s Selecting previously unselected package xfonts-encodings. 117s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 117s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 117s Selecting previously unselected package xfonts-utils. 117s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_s390x.deb ... 117s Unpacking xfonts-utils (1:7.7+7) ... 117s Selecting previously unselected package fonts-urw-base35. 117s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 117s Unpacking fonts-urw-base35 (20200910-8) ... 117s Selecting previously unselected package fontconfig-config. 117s Preparing to unpack .../11-fontconfig-config_2.15.0-1.1ubuntu2_s390x.deb ... 117s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 117s Selecting previously unselected package libblas3:s390x. 117s Preparing to unpack .../12-libblas3_3.12.0-3build2_s390x.deb ... 117s Unpacking libblas3:s390x (3.12.0-3build2) ... 117s Selecting previously unselected package libfontconfig1:s390x. 117s Preparing to unpack .../13-libfontconfig1_2.15.0-1.1ubuntu2_s390x.deb ... 117s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 117s Selecting previously unselected package libpixman-1-0:s390x. 117s Preparing to unpack .../14-libpixman-1-0_0.44.0-3_s390x.deb ... 117s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 117s Selecting previously unselected package libxcb-render0:s390x. 117s Preparing to unpack .../15-libxcb-render0_1.17.0-2_s390x.deb ... 117s Unpacking libxcb-render0:s390x (1.17.0-2) ... 117s Selecting previously unselected package libxcb-shm0:s390x. 117s Preparing to unpack .../16-libxcb-shm0_1.17.0-2_s390x.deb ... 117s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 117s Selecting previously unselected package libxrender1:s390x. 117s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 117s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 117s Selecting previously unselected package libcairo2:s390x. 117s Preparing to unpack .../18-libcairo2_1.18.2-2_s390x.deb ... 117s Unpacking libcairo2:s390x (1.18.2-2) ... 117s Selecting previously unselected package libdeflate0:s390x. 117s Preparing to unpack .../19-libdeflate0_1.22-1_s390x.deb ... 117s Unpacking libdeflate0:s390x (1.22-1) ... 117s Selecting previously unselected package libgfortran5:s390x. 117s Preparing to unpack .../20-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 117s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package libgomp1:s390x. 117s Preparing to unpack .../21-libgomp1_14.2.0-8ubuntu1_s390x.deb ... 117s Unpacking libgomp1:s390x (14.2.0-8ubuntu1) ... 117s Selecting previously unselected package libgraphite2-3:s390x. 117s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 117s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 117s Selecting previously unselected package libharfbuzz0b:s390x. 117s Preparing to unpack .../23-libharfbuzz0b_10.0.1-1_s390x.deb ... 117s Unpacking libharfbuzz0b:s390x (10.0.1-1) ... 117s Selecting previously unselected package libimagequant0:s390x. 118s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_s390x.deb ... 118s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 118s Selecting previously unselected package libjpeg-turbo8:s390x. 118s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu2_s390x.deb ... 118s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 118s Selecting previously unselected package libjpeg8:s390x. 118s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_s390x.deb ... 118s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 118s Selecting previously unselected package libjs-jquery. 118s Preparing to unpack .../27-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 118s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 118s Selecting previously unselected package libjs-underscore. 118s Preparing to unpack .../28-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 118s Unpacking libjs-underscore 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python3-all (3.12.7-1) ... 121s Setting up python3-freetype (2.5.1-1) ... 121s Setting up xfonts-utils (1:7.7+7) ... 121s Setting up libraqm0:s390x (0.10.1-1build1) ... 121s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 125s Setting up libjs-sphinxdoc (7.4.7-4) ... 125s Setting up python-biopython-doc (1.84+dfsg-4) ... 125s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 125s Setting up xml-core (0.19) ... 125s Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 125s Setting up fonts-urw-base35 (20200910-8) ... 125s Setting up libcairo2:s390x (1.18.2-2) ... 125s Setting up python3-pil:s390x (10.4.0-1ubuntu1) ... 126s Setting up python3-cairo (1.26.1-2) ... 126s Setting up python3-rlpycairo (0.3.0-3) ... 126s Setting up python3-reportlab (4.2.5-1) ... 128s Processing triggers for libc-bin (2.40-1ubuntu3) ... 128s Processing triggers for systemd (256.5-2ubuntu4) ... 128s Processing triggers for man-db (2.12.1-3) ... 128s Processing triggers for sgml-base (1.31) ... 128s Setting up w3c-sgml-lib (1.3-3) ... 150s Setting up python3-biopython (1.84+dfsg-4) ... 152s Setting up python3-biopython-sql (1.84+dfsg-4) ... 152s Setting up autopkgtest-satdep (0) ... 155s (Reading database ... 61657 files and directories currently installed.) 155s Removing autopkgtest-satdep (0) ... 156s autopkgtest [13:03:28]: test dependencies: sh debian/tests/run-unit-test 156s autopkgtest [13:03:28]: test dependencies: [----------------------- 156s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 156s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 156s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 156s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 156s mkdir: created directory 'Bio' 156s mkdir: created directory 'Bio/Align' 156s mkdir: created directory 'Bio/Align/substitution_matrices' 156s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 156s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 156s Remove test test_Tutorial.py which is bound to fail 157s test_Ace ... ok 157s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 157s 157s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 157s 157s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 157s 157s test_Align_a2m ... loading tests failed: 157s Failed to import test module: test_Align_a2m 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 157s from . import multiarray 157s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 157s from . import overrides 157s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 157s from numpy.core._multiarray_umath import ( 157s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 157s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 157s 157s During handling of the above exception, another exception occurred: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 157s from numpy.__config__ import show as show_config 157s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 157s from numpy.core._multiarray_umath import ( 157s ...<3 lines>... 157s ) 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 157s raise ImportError(msg) 157s ImportError: 157s 157s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 157s 157s Importing the numpy C-extensions failed. This error can happen for 157s many reasons, often due to issues with your setup or how NumPy was 157s installed. 157s 157s We have compiled some common reasons and troubleshooting tips at: 157s 157s https://numpy.org/devdocs/user/troubleshooting-importerror.html 157s 157s Please note and check the following: 157s 157s * The Python version is: Python3.13 from "/usr/bin/python3.13" 157s * The NumPy version is: "1.26.4" 157s 157s and make sure that they are the versions you expect. 157s Please carefully study the documentation linked above for further help. 157s 157s Original error was: No module named 'numpy.core._multiarray_umath' 157s 157s 157s The above exception was the direct cause of the following exception: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 157s module = __import__(module_name) 157s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 157s import numpy as np 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 157s raise ImportError(msg) from e 157s ImportError: Error importing numpy: you should not try to import numpy from 157s its source directory; please exit the numpy source tree, and relaunch 157s your python interpreter from there. 157s 157s test_Align_bed ... loading tests failed: 157s Failed to import test module: test_Align_bed 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 157s from . import multiarray 157s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 157s from . import overrides 157s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 157s from numpy.core._multiarray_umath import ( 157s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 157s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 157s 157s During handling of the above exception, another exception occurred: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 157s from numpy.__config__ import show as show_config 157s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 157s from numpy.core._multiarray_umath import ( 157s ...<3 lines>... 157s ) 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 157s raise ImportError(msg) 157s ImportError: 157s 157s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 157s 157s Importing the numpy C-extensions failed. This error can happen for 157s many reasons, often due to issues with your setup or how NumPy was 157s installed. 157s 157s We have compiled some common reasons and troubleshooting tips at: 157s 157s https://numpy.org/devdocs/user/troubleshooting-importerror.html 157s 157s Please note and check the following: 157s 157s * The Python version is: Python3.13 from "/usr/bin/python3.13" 157s * The NumPy version is: "1.26.4" 157s 157s and make sure that they are the versions you expect. 157s Please carefully study the documentation linked above for further help. 157s 157s Original error was: No module named 'numpy.core._multiarray_umath' 157s 157s 157s The above exception was the direct cause of the following exception: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 157s module = __import__(module_name) 157s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 157s import numpy as np 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 157s raise ImportError(msg) from e 157s ImportError: Error importing numpy: you should not try to import numpy from 157s its source directory; please exit the numpy source tree, and relaunch 157s your python interpreter from there. 157s 157s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_Align_bigmaf ... loading tests failed: 157s Failed to import test module: test_Align_bigmaf 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 157s from . import multiarray 157s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 157s from . import overrides 157s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 157s from numpy.core._multiarray_umath import ( 157s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 157s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 157s 157s During handling of the above exception, another exception occurred: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 157s from numpy.__config__ import show as show_config 157s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 157s from numpy.core._multiarray_umath import ( 157s ...<3 lines>... 157s ) 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 157s raise ImportError(msg) 157s ImportError: 157s 157s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 157s 157s Importing the numpy C-extensions failed. This error can happen for 157s many reasons, often due to issues with your setup or how NumPy was 157s installed. 157s 157s We have compiled some common reasons and troubleshooting tips at: 157s 157s https://numpy.org/devdocs/user/troubleshooting-importerror.html 157s 157s Please note and check the following: 157s 157s * The Python version is: Python3.13 from "/usr/bin/python3.13" 157s * The NumPy version is: "1.26.4" 157s 157s and make sure that they are the versions you expect. 157s Please carefully study the documentation linked above for further help. 157s 157s Original error was: No module named 'numpy.core._multiarray_umath' 157s 157s 157s The above exception was the direct cause of the following exception: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 157s module = __import__(module_name) 157s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 157s import numpy as np 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 157s raise ImportError(msg) from e 157s ImportError: Error importing numpy: you should not try to import numpy from 157s its source directory; please exit the numpy source tree, and relaunch 157s your python interpreter from there. 157s 157s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_Align_clustal ... loading tests failed: 157s Failed to import test module: test_Align_clustal 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 157s from . import multiarray 157s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 157s from . import overrides 157s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 157s from numpy.core._multiarray_umath import ( 157s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 157s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 157s 157s During handling of the above exception, another exception occurred: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 157s from numpy.__config__ import show as show_config 157s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 157s from numpy.core._multiarray_umath import ( 157s ...<3 lines>... 157s ) 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 157s raise ImportError(msg) 157s ImportError: 157s 157s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 157s 157s Importing the numpy C-extensions failed. This error can happen for 157s many reasons, often due to issues with your setup or how NumPy was 157s installed. 157s 157s We have compiled some common reasons and troubleshooting tips at: 157s 157s https://numpy.org/devdocs/user/troubleshooting-importerror.html 157s 157s Please note and check the following: 157s 157s * The Python version is: Python3.13 from "/usr/bin/python3.13" 157s * The NumPy version is: "1.26.4" 157s 157s and make sure that they are the versions you expect. 157s Please carefully study the documentation linked above for further help. 157s 157s Original error was: No module named 'numpy.core._multiarray_umath' 157s 157s 157s The above exception was the direct cause of the following exception: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 157s module = __import__(module_name) 157s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 157s import numpy as np 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 157s raise ImportError(msg) from e 157s ImportError: Error importing numpy: you should not try to import numpy from 157s its source directory; please exit the numpy source tree, and relaunch 157s your python interpreter from there. 157s 157s test_Align_codonalign ... loading tests failed: 157s Failed to import test module: test_Align_codonalign 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 157s from . import multiarray 157s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 157s from . import overrides 157s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 157s from numpy.core._multiarray_umath import ( 157s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 157s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 157s 157s During handling of the above exception, another exception occurred: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 157s from numpy.__config__ import show as show_config 157s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 157s from numpy.core._multiarray_umath import ( 157s ...<3 lines>... 157s ) 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 157s raise ImportError(msg) 157s ImportError: 157s 157s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 157s 157s Importing the numpy C-extensions failed. This error can happen for 157s many reasons, often due to issues with your setup or how NumPy was 157s installed. 157s 157s We have compiled some common reasons and troubleshooting tips at: 157s 157s https://numpy.org/devdocs/user/troubleshooting-importerror.html 157s 157s Please note and check the following: 157s 157s * The Python version is: Python3.13 from "/usr/bin/python3.13" 157s * The NumPy version is: "1.26.4" 157s 157s and make sure that they are the versions you expect. 157s Please carefully study the documentation linked above for further help. 157s 157s Original error was: No module named 'numpy.core._multiarray_umath' 157s 157s 157s The above exception was the direct cause of the following exception: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 157s module = __import__(module_name) 157s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 157s import numpy as np 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 157s raise ImportError(msg) from e 157s ImportError: Error importing numpy: you should not try to import numpy from 157s its source directory; please exit the numpy source tree, and relaunch 157s your python interpreter from there. 157s 157s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 157s 157s test_Align_fasta ... loading tests failed: 157s Failed to import test module: test_Align_fasta 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 157s from . import multiarray 157s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 157s from . import overrides 157s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 157s from numpy.core._multiarray_umath import ( 157s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 157s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 157s 157s During handling of the above exception, another exception occurred: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 157s from numpy.__config__ import show as show_config 157s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 157s from numpy.core._multiarray_umath import ( 157s ...<3 lines>... 157s ) 157s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 157s raise ImportError(msg) 157s ImportError: 157s 157s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 157s 157s Importing the numpy C-extensions failed. This error can happen for 157s many reasons, often due to issues with your setup or how NumPy was 157s installed. 157s 157s We have compiled some common reasons and troubleshooting tips at: 157s 157s https://numpy.org/devdocs/user/troubleshooting-importerror.html 157s 157s Please note and check the following: 157s 157s * The Python version is: Python3.13 from "/usr/bin/python3.13" 157s * The NumPy version is: "1.26.4" 157s 157s and make sure that they are the versions you expect. 157s Please carefully study the documentation linked above for further help. 157s 157s Original error was: No module named 'numpy.core._multiarray_umath' 157s 157s 157s The above exception was the direct cause of the following exception: 157s 157s Traceback (most recent call last): 157s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 157s module = __import__(module_name) 157s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 157s import numpy as np 157s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 157s raise ImportError(msg) from e 157s ImportError: Error importing numpy: you should not try to import numpy from 157s its source directory; please exit the numpy source tree, and relaunch 157s your python interpreter from there. 157s 158s test_Align_hhr ... loading tests failed: 158s Failed to import test module: test_Align_hhr 158s Traceback (most recent call last): 158s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 158s from . import multiarray 158s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 158s from . import overrides 158s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 158s from numpy.core._multiarray_umath import ( 158s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 158s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 158s 158s During handling of the above exception, another exception occurred: 158s 158s Traceback (most recent call last): 158s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 158s from numpy.__config__ import show as show_config 158s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 158s from numpy.core._multiarray_umath import ( 158s ...<3 lines>... 158s ) 158s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 158s raise ImportError(msg) 158s ImportError: 158s 158s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 158s 158s Importing the numpy C-extensions failed. This error can happen for 158s many reasons, often due to issues with your setup or how NumPy was 158s installed. 158s 158s We have compiled some common reasons and troubleshooting tips at: 158s 158s https://numpy.org/devdocs/user/troubleshooting-importerror.html 158s 158s Please note and check the following: 158s 158s * The Python version is: Python3.13 from "/usr/bin/python3.13" 158s * The NumPy version is: "1.26.4" 158s 158s and make sure that they are the versions you expect. 158s Please carefully study the documentation linked above for further help. 158s 158s Original error was: No module named 'numpy.core._multiarray_umath' 158s 158s 158s The above exception was the direct cause of the following exception: 158s 158s Traceback (most recent call last): 158s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 158s module = __import__(module_name) 158s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 158s import numpy as np 158s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 158s raise ImportError(msg) from e 158s ImportError: Error importing numpy: you should not try to import numpy from 158s its source directory; please exit the numpy source tree, and relaunch 158s your python interpreter from there. 158s 158s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_Application ... ok 158s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 158s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 158s 159s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 159s 159s test_Blast_Record ... loading tests failed: 159s Failed to import test module: test_Blast_Record 159s Traceback (most recent call last): 159s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 159s from . import multiarray 159s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 159s from . import overrides 159s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 159s from numpy.core._multiarray_umath import ( 159s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 159s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 159s 159s During handling of the above exception, another exception occurred: 159s 159s Traceback (most recent call last): 159s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 159s from numpy.__config__ import show as show_config 159s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 159s from numpy.core._multiarray_umath import ( 159s ...<3 lines>... 159s ) 159s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 159s raise ImportError(msg) 159s ImportError: 159s 159s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 159s 159s Importing the numpy C-extensions failed. This error can happen for 159s many reasons, often due to issues with your setup or how NumPy was 159s installed. 159s 159s We have compiled some common reasons and troubleshooting tips at: 159s 159s https://numpy.org/devdocs/user/troubleshooting-importerror.html 159s 159s Please note and check the following: 159s 159s * The Python version is: Python3.13 from "/usr/bin/python3.13" 159s * The NumPy version is: "1.26.4" 159s 159s and make sure that they are the versions you expect. 159s Please carefully study the documentation linked above for further help. 159s 159s Original error was: No module named 'numpy.core._multiarray_umath' 159s 159s 159s The above exception was the direct cause of the following exception: 159s 159s Traceback (most recent call last): 159s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 159s module = __import__(module_name) 159s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 159s from Bio.Blast.NCBIXML import HSP 159s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 159s import numpy as np 159s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 159s raise ImportError(msg) from e 159s ImportError: Error importing numpy: you should not try to import numpy from 159s its source directory; please exit the numpy source tree, and relaunch 159s your python interpreter from there. 159s 159s test_Blast_parser ... loading tests failed: 159s Failed to import test module: test_Blast_parser 159s Traceback (most recent call last): 159s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 159s from . import multiarray 159s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 159s from . import overrides 159s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 159s from numpy.core._multiarray_umath import ( 159s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 159s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 159s 159s During handling of the above exception, another exception occurred: 159s 159s Traceback (most recent call last): 159s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 159s from numpy.__config__ import show as show_config 159s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 159s from numpy.core._multiarray_umath import ( 159s ...<3 lines>... 159s ) 159s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 159s raise ImportError(msg) 159s ImportError: 159s 159s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 159s 159s Importing the numpy C-extensions failed. This error can happen for 159s many reasons, often due to issues with your setup or how NumPy was 159s installed. 159s 159s We have compiled some common reasons and troubleshooting tips at: 159s 159s https://numpy.org/devdocs/user/troubleshooting-importerror.html 159s 159s Please note and check the following: 159s 159s * The Python version is: Python3.13 from "/usr/bin/python3.13" 159s * The NumPy version is: "1.26.4" 159s 159s and make sure that they are the versions you expect. 159s Please carefully study the documentation linked above for further help. 159s 159s Original error was: No module named 'numpy.core._multiarray_umath' 159s 159s 159s The above exception was the direct cause of the following exception: 159s 159s Traceback (most recent call last): 159s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 159s module = __import__(module_name) 159s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 159s import numpy as np 159s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 159s raise ImportError(msg) from e 159s ImportError: Error importing numpy: you should not try to import numpy from 159s its source directory; please exit the numpy source tree, and relaunch 159s your python interpreter from there. 159s 159s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 159s 159s test_Chi2 ... /usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2131: BiopythonWarning: Import of C module failed (cannot import name 'cnexus' from 'Bio.Nexus' (/usr/lib/python3/dist-packages/Bio/Nexus/__init__.py)). Falling back to slow Python implementation 159s warnings.warn( 159s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 159s 159s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 159s 159s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 159s 159s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 159s 159s test_CodonTable ... ok 159s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 159s 159s test_Compass ... ok 159s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 159s 159s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 159s 159s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 159s 159s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 159s 159s test_EmbossPrimer ... ok 163s test_Entrez ... ok 163s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 163s 163s test_Entrez_parser ... ok 163s test_Enzyme ... ok 163s test_ExPASy ... skipping. internet not available 163s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 163s 163s test_File ... ok 164s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 164s 164s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 164s 164s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 164s 164s test_GraphicsDistribution ... loading tests failed: 164s Failed to import test module: test_GraphicsDistribution 164s Traceback (most recent call last): 164s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 164s module = __import__(module_name) 164s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 164s from Bio.Graphics.Distribution import BarChartDistribution 164s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 164s from reportlab.graphics.charts.barcharts import BarChartProperties 164s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 164s from reportlab.lib import colors 164s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 164s from reportlab.lib.rl_accel import fp_str 164s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 164s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 164s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 164s from PIL import Image 164s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 164s from . import _imaging as core 164s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 164s 164s test_GraphicsGeneral ... loading tests failed: 164s Failed to import test module: test_GraphicsGeneral 164s Traceback (most recent call last): 164s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 164s module = __import__(module_name) 164s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 164s from Bio.Graphics.Comparative import ComparativeScatterPlot 164s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 164s from reportlab.graphics.charts.lineplots import LinePlot 164s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 164s from reportlab.lib import colors 164s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 164s from reportlab.lib.rl_accel import fp_str 164s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 164s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 164s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 164s from PIL import Image 164s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 164s from . import _imaging as core 164s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 164s 164s test_HMMCasino ... ok 164s test_HMMGeneral ... ok 164s test_KEGG ... ok 164s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 164s 164s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 164s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 164s test_KGML_nographics ... ok 165s test_KeyWList ... ok 165s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 165s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 165s 165s test_Medline ... ok 165s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_NCBIXML ... loading tests failed: 165s Failed to import test module: test_NCBIXML 165s Traceback (most recent call last): 165s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 165s from . import multiarray 165s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 165s from . import overrides 165s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 165s from numpy.core._multiarray_umath import ( 165s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 165s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 165s 165s During handling of the above exception, another exception occurred: 165s 165s Traceback (most recent call last): 165s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 165s from numpy.__config__ import show as show_config 165s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 165s from numpy.core._multiarray_umath import ( 165s ...<3 lines>... 165s ) 165s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 165s raise ImportError(msg) 165s ImportError: 165s 165s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 165s 165s Importing the numpy C-extensions failed. This error can happen for 165s many reasons, often due to issues with your setup or how NumPy was 165s installed. 165s 165s We have compiled some common reasons and troubleshooting tips at: 165s 165s https://numpy.org/devdocs/user/troubleshooting-importerror.html 165s 165s Please note and check the following: 165s 165s * The Python version is: Python3.13 from "/usr/bin/python3.13" 165s * The NumPy version is: "1.26.4" 165s 165s and make sure that they are the versions you expect. 165s Please carefully study the documentation linked above for further help. 165s 165s Original error was: No module named 'numpy.core._multiarray_umath' 165s 165s 165s The above exception was the direct cause of the following exception: 165s 165s Traceback (most recent call last): 165s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 165s module = __import__(module_name) 165s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 165s from Bio.Blast import NCBIXML 165s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 165s import numpy as np 165s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 165s raise ImportError(msg) from e 165s ImportError: Error importing numpy: you should not try to import numpy from 165s its source directory; please exit the numpy source tree, and relaunch 165s your python interpreter from there. 165s 165s test_NCBI_BLAST_tools ... loading tests failed: 165s Failed to import test module: test_NCBI_BLAST_tools 165s Traceback (most recent call last): 165s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 165s from . import multiarray 165s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 165s from . import overrides 165s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 165s from numpy.core._multiarray_umath import ( 165s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 165s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 165s 165s During handling of the above exception, another exception occurred: 165s 165s Traceback (most recent call last): 165s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 165s from numpy.__config__ import show as show_config 165s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 165s from numpy.core._multiarray_umath import ( 165s ...<3 lines>... 165s ) 165s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 165s raise ImportError(msg) 165s ImportError: 165s 165s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 165s 165s Importing the numpy C-extensions failed. This error can happen for 165s many reasons, often due to issues with your setup or how NumPy was 165s installed. 165s 165s We have compiled some common reasons and troubleshooting tips at: 165s 165s https://numpy.org/devdocs/user/troubleshooting-importerror.html 165s 165s Please note and check the following: 165s 165s * The Python version is: Python3.13 from "/usr/bin/python3.13" 165s * The NumPy version is: "1.26.4" 165s 165s and make sure that they are the versions you expect. 165s Please carefully study the documentation linked above for further help. 165s 165s Original error was: No module named 'numpy.core._multiarray_umath' 165s 165s 165s The above exception was the direct cause of the following exception: 165s 165s Traceback (most recent call last): 165s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 165s module = __import__(module_name) 165s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 165s from Bio.Blast import Applications 165s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 165s import numpy as np 165s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 165s raise ImportError(msg) from e 165s ImportError: Error importing numpy: you should not try to import numpy from 165s its source directory; please exit the numpy source tree, and relaunch 165s your python interpreter from there. 165s 165s test_NCBI_qblast ... loading tests failed: 165s Failed to import test module: test_NCBI_qblast 165s Traceback (most recent call last): 165s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 165s from . import multiarray 165s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 165s from . import overrides 165s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 165s from numpy.core._multiarray_umath import ( 165s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 165s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 165s 165s During handling of the above exception, another exception occurred: 165s 165s Traceback (most recent call last): 165s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 165s from numpy.__config__ import show as show_config 165s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 165s from numpy.core._multiarray_umath import ( 165s ...<3 lines>... 165s ) 165s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 165s raise ImportError(msg) 165s ImportError: 165s 165s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 165s 165s Importing the numpy C-extensions failed. This error can happen for 165s many reasons, often due to issues with your setup or how NumPy was 165s installed. 165s 165s We have compiled some common reasons and troubleshooting tips at: 165s 165s https://numpy.org/devdocs/user/troubleshooting-importerror.html 165s 165s Please note and check the following: 165s 165s * The Python version is: Python3.13 from "/usr/bin/python3.13" 165s * The NumPy version is: "1.26.4" 165s 165s and make sure that they are the versions you expect. 165s Please carefully study the documentation linked above for further help. 165s 165s Original error was: No module named 'numpy.core._multiarray_umath' 165s 165s 165s The above exception was the direct cause of the following exception: 165s 165s Traceback (most recent call last): 165s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 165s module = __import__(module_name) 165s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 165s from Bio.Blast import NCBIWWW 165s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 165s import numpy as np 165s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 165s raise ImportError(msg) from e 165s ImportError: Error importing numpy: you should not try to import numpy from 165s its source directory; please exit the numpy source tree, and relaunch 165s your python interpreter from there. 165s 165s test_NMR ... ok 165s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 165s 165s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 165s 165s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_Disordered ... loading tests failed: 165s Failed to import test module: test_PDB_Disordered 165s Traceback (most recent call last): 165s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 165s from . import multiarray 165s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 165s from . import overrides 165s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 165s from numpy.core._multiarray_umath import ( 165s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 165s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 165s 165s During handling of the above exception, another exception occurred: 165s 165s Traceback (most recent call last): 165s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 165s from numpy.__config__ import show as show_config 165s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 165s from numpy.core._multiarray_umath import ( 165s ...<3 lines>... 165s ) 165s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 165s raise ImportError(msg) 165s ImportError: 165s 165s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 165s 165s Importing the numpy C-extensions failed. This error can happen for 165s many reasons, often due to issues with your setup or how NumPy was 165s installed. 165s 165s We have compiled some common reasons and troubleshooting tips at: 165s 165s https://numpy.org/devdocs/user/troubleshooting-importerror.html 165s 165s Please note and check the following: 165s 165s * The Python version is: Python3.13 from "/usr/bin/python3.13" 165s * The NumPy version is: "1.26.4" 165s 165s and make sure that they are the versions you expect. 165s Please carefully study the documentation linked above for further help. 165s 165s Original error was: No module named 'numpy.core._multiarray_umath' 165s 165s 165s The above exception was the direct cause of the following exception: 165s 165s Traceback (most recent call last): 165s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 165s module = __import__(module_name) 165s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 165s import numpy as np 165s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 165s raise ImportError(msg) from e 165s ImportError: Error importing numpy: you should not try to import numpy from 165s its source directory; please exit the numpy source tree, and relaunch 165s your python interpreter from there. 165s 165s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 165s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 165s 165s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 165s 165s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 165s 165s test_Pathway ... ok 165s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 165s 165s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_PopGen_GenePop_nodepend ... ok 165s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 165s 165s test_ProtParam ... ok 166s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 166s 166s test_Restriction ... ok 166s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 166s 166s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 166s 166s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 166s 166s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 166s 166s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 166s 166s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 166s 166s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 166s 166s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 166s 166s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 166s 166s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 166s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 166s 166s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 166s 167s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 167s 167s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 167s 167s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 167s 167s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 167s 167s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 167s 167s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 167s 167s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 167s 167s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 167s 167s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 167s 167s test_UniGene ... ok 167s test_UniProt ... skipping. internet not available 167s test_UniProt_GOA ... ok 167s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 167s 167s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 167s 167s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 169s test_bgzf ... ok 169s test_cellosaurus ... ok 169s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 169s 169s test_geo ... ok 170s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 170s 170s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 170s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 170s 170s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 170s 170s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 170s 170s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 170s 170s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 170s 170s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 170s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 170s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 170s 170s test_prodoc ... ok 170s test_prosite ... ok 170s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 170s 170s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 170s test_seq ... ok 170s test_translate ... ok 170s ---------------------------------------------------------------------- 170s Ran 216 tests in 13.411 seconds 170s 170s FAILED (failures = 15) 170s Skipping any tests requiring internet access 170s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 170s Operating system: posix linux 170s test_Ace ... ok 170s test_Affy ... ok 173s test_AlignIO ... ok 173s test_AlignIO_ClustalIO ... ok 173s test_AlignIO_EmbossIO ... ok 173s test_AlignIO_FastaIO ... ok 173s test_AlignIO_MauveIO ... ok 173s test_AlignIO_PhylipIO ... ok 173s test_AlignIO_convert ... ok 173s test_AlignInfo ... ok 173s test_Align_Alignment ... ok 173s test_Align_a2m ... ok 173s test_Align_bed ... ok 173s test_Align_bigbed ... ok 174s test_Align_bigmaf ... ok 174s test_Align_bigpsl ... ok 174s test_Align_chain ... ok 174s test_Align_clustal ... ok 178s test_Align_codonalign ... ok 178s test_Align_emboss ... ok 178s test_Align_exonerate ... ok 178s test_Align_fasta ... ok 178s test_Align_hhr ... ok 179s test_Align_maf ... ok 179s test_Align_mauve ... ok 179s test_Align_msf ... ok 179s test_Align_nexus ... ok 179s test_Align_phylip ... ok 179s test_Align_psl ... ok 180s test_Align_sam ... ok 181s test_Align_stockholm ... ok 181s test_Align_tabular ... ok 181s test_Application ... ok 181s test_BioSQL_MySQLdb_online ... skipping. internet not available 181s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 181s test_BioSQL_mysql_connector_online ... skipping. internet not available 181s test_BioSQL_psycopg2_online ... skipping. internet not available 184s test_BioSQL_sqlite3 ... ok 184s test_BioSQL_sqlite3_online ... skipping. internet not available 184s test_Blast_Record ... ok 185s test_Blast_parser ... ok 185s test_CAPS ... ok 185s test_Chi2 ... ok 185s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 185s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 185s test_Cluster ... ok 185s test_CodonTable ... ok 185s test_ColorSpiral ... ok 185s test_Compass ... ok 186s test_Consensus ... ok 186s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 186s test_EMBL_unittest ... ok 186s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 186s test_EmbossPrimer ... ok 190s test_Entrez ... ok 190s test_Entrez_online ... skipping. internet not available 191s test_Entrez_parser ... ok 191s test_Enzyme ... ok 191s test_ExPASy ... skipping. internet not available 191s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 191s test_File ... ok 191s test_GenBank ... ok 192s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 194s ok 194s test_GraphicsChromosome ... ok 194s test_GraphicsDistribution ... ok 195s test_GraphicsGeneral ... ok 195s test_HMMCasino ... ok 195s test_HMMGeneral ... ok 195s test_KEGG ... ok 195s test_KEGG_online ... skipping. internet not available 200s test_KGML_graphics ... ok 200s test_KGML_graphics_online ... skipping. internet not available 201s test_KGML_nographics ... ok 201s test_KeyWList ... ok 201s test_LogisticRegression ... ok 202s test_MafIO_index ... ok 202s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 202s test_MarkovModel ... ok 202s test_Medline ... ok 202s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 202s test_NCBIXML ... ok 202s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 202s test_NCBI_qblast ... ok 202s test_NMR ... ok 202s test_NaiveBayes ... ok 202s test_Nexus ... ok 203s test_PAML_baseml ... ok 203s test_PAML_codeml ... ok 203s test_PAML_yn00 ... ok 207s test_PDB_CEAligner ... ok 207s test_PDB_DSSP ... ok 207s test_PDB_Dice ... ok 207s test_PDB_Disordered ... ok 207s test_PDB_Exposure ... ok 207s test_PDB_FragmentMapper ... ok 209s test_PDB_KDTree ... ok 209s test_PDB_MMCIF2Dict ... ok 209s test_PDB_MMCIFIO ... ok 210s test_PDB_MMCIFParser ... ok 210s test_PDB_NACCESS ... ok 210s test_PDB_PDBIO ... ok 210s test_PDB_PDBList ... skipping. internet not available 219s test_PDB_PDBMLParser ... ok 219s test_PDB_PDBParser ... ok 219s 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 219s test_PDB_Polypeptide ... ok 219s test_PDB_QCPSuperimposer ... ok 222s test_PDB_SASA ... ok 223s test_PDB_SMCRA ... ok 223s test_PDB_Selection ... ok 223s test_PDB_StructureAlignment ... ok 223s test_PDB_Superimposer ... ok 223s test_PDB_alphafold_db ... skipping. internet not available 223s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 223s 223s test_PDB_parse_pdb_header ... ok 223s test_PDB_vectors ... ok 223s test_PQR ... ok 223s test_Pathway ... ok 223s test_Phd ... ok 224s test_Phylo ... ok 224s test_PhyloXML ... ok 224s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 224s test_Phylo_NeXML ... ok 224s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 224s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 224s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 224s test_PopGen_GenePop_nodepend ... ok 224s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 224s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 225s test_ProtParam ... ok 225s test_RCSBFormats ... ok 225s test_Restriction ... ok 225s test_SCOP_Astral ... ok 225s test_SCOP_Cla ... ok 225s test_SCOP_Des ... ok 225s test_SCOP_Dom ... ok 225s test_SCOP_Hie ... ok 225s test_SCOP_Raf ... ok 225s test_SCOP_Residues ... ok 225s test_SCOP_Scop ... ok 225s test_SVDSuperimposer ... ok 225s test_SearchIO_blast_tab ... ok 225s test_SearchIO_blast_tab_index ... ok 225s test_SearchIO_blast_xml ... ok 227s test_SearchIO_blast_xml_index ... ok 227s test_SearchIO_blat_psl ... ok 227s test_SearchIO_blat_psl_index ... ok 227s test_SearchIO_exonerate ... ok 227s test_SearchIO_exonerate_text_index ... ok 227s test_SearchIO_exonerate_vulgar_index ... ok 227s test_SearchIO_fasta_m10 ... ok 227s test_SearchIO_fasta_m10_index ... ok 227s test_SearchIO_hhsuite2_text ... ok 227s test_SearchIO_hmmer2_text ... ok 228s test_SearchIO_hmmer2_text_index ... ok 228s test_SearchIO_hmmer3_domtab ... ok 228s test_SearchIO_hmmer3_domtab_index ... ok 228s test_SearchIO_hmmer3_tab ... ok 228s test_SearchIO_hmmer3_tab_index ... ok 228s test_SearchIO_hmmer3_text ... ok 228s test_SearchIO_hmmer3_text_index ... ok 228s test_SearchIO_interproscan_xml ... ok 228s test_SearchIO_model ... ok 228s test_SearchIO_write ... ok 228s test_SeqFeature ... ok 242s test_SeqIO ... ok 242s test_SeqIO_AbiIO ... ok 242s test_SeqIO_FastaIO ... ok 242s test_SeqIO_Gck ... ok 242s test_SeqIO_Gfa ... ok 242s test_SeqIO_Insdc ... ok 243s test_SeqIO_NibIO ... ok 244s test_SeqIO_PdbIO ... ok 244s test_SeqIO_QualityIO ... ok 245s test_SeqIO_SeqXML ... ok 245s test_SeqIO_SnapGene ... ok 245s test_SeqIO_TwoBitIO ... ok 245s test_SeqIO_Xdna ... ok 246s test_SeqIO_features ... ok 258s test_SeqIO_index ... ok 259s test_SeqIO_online ... skipping. internet not available 259s test_SeqIO_write ... ok 259s test_SeqRecord ... ok 259s test_SeqUtils ... ok 260s test_Seq_objs ... ok 260s test_SffIO ... ok 260s test_SwissProt ... ok 260s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 260s test_TogoWS ... skipping. internet not available 261s test_TreeConstruction ... ok 261s test_UniGene ... ok 261s test_UniProt ... skipping. internet not available 261s test_UniProt_GOA ... ok 261s test_UniProt_Parser ... ok 261s test_align ... ok 262s test_align_substitution_matrices ... ok 263s test_bgzf ... ok 263s test_cellosaurus ... ok 267s test_codonalign ... ok 268s test_geo ... ok 268s test_kNN ... ok 268s test_motifs ... ok 268s test_motifs_online ... skipping. internet not available 268s 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. 268s warnings.warn( 268s ok 268s test_pairwise2_no_C ... ok 269s test_pairwise_aligner ... ok 269s test_pairwise_alignment_map ... ok 276s test_phenotype ... ok 277s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 277s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 277s test_prodoc ... ok 277s test_prosite ... ok 277s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 277s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 277s test_seq ... ok 277s test_translate ... ok 277s Skipping any tests requiring internet access 277s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 277s Operating system: posix linux 277s ---------------------------------------------------------------------- 277s Ran 216 tests in 106.702 seconds 277s 278s autopkgtest [13:05:30]: test dependencies: -----------------------] 279s dependencies PASS 279s autopkgtest [13:05:31]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 279s autopkgtest [13:05:31]: test full_suite: preparing testbed 390s autopkgtest [13:07:22]: testbed dpkg architecture: s390x 390s autopkgtest [13:07:22]: testbed apt version: 2.9.8 390s autopkgtest [13:07:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 391s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 391s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 391s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 391s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 391s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB] 391s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [107 kB] 391s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [641 kB] 391s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.4 kB] 392s Fetched 1934 kB in 1s (2357 kB/s) 392s Reading package lists... 393s Reading package lists... 394s Building dependency tree... 394s Reading state information... 394s Calculating upgrade... 394s The following NEW packages will be installed: 394s python3.13-gdbm 394s The following packages will be upgraded: 394s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 394s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 394s Need to get 252 kB of archives. 394s After this operation, 98.3 kB of additional disk space will be used. 394s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 394s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 394s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 394s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 394s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 394s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 395s Fetched 252 kB in 0s (536 kB/s) 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 55510 files and directories currently installed.) 395s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 395s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 395s Setting up python3-minimal (3.12.7-1) ... 395s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 55510 files and directories currently installed.) 395s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 395s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 395s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 395s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 395s Selecting previously unselected package python3.13-gdbm. 395s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ... 395s Unpacking python3.13-gdbm (3.13.0-2) ... 395s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ... 395s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 395s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 395s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 395s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 395s Setting up python3.13-gdbm (3.13.0-2) ... 395s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 395s Setting up python3 (3.12.7-1) ... 395s Setting up python3-gdbm:s390x (3.12.7-1) ... 395s Processing triggers for man-db (2.12.1-3) ... 396s Processing triggers for libc-bin (2.40-1ubuntu3) ... 396s Reading package lists... 396s Building dependency tree... 396s Reading state information... 396s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 396s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 396s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 396s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 397s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 397s Reading package lists... 397s Reading package lists... 397s Building dependency tree... 397s Reading state information... 397s Calculating upgrade... 398s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 398s Reading package lists... 398s Building dependency tree... 398s Reading state information... 398s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 402s Reading package lists... 402s Building dependency tree... 402s Reading state information... 402s Starting pkgProblemResolver with broken count: 0 402s Starting 2 pkgProblemResolver with broken count: 0 402s Done 402s The following additional packages will be installed: 402s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 402s cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit 402s dh-autoreconf dh-python dh-strip-nondeterminism dialign docutils-common dssp 402s dwz fasttree flex fontconfig-config fonts-dejavu-core fonts-dejavu-mono 402s fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ 402s g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 402s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gettext ghostscript hevea 402s hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 402s intltool-debian libaom3 libapache-pom-java libarchive-zip-perl 402s libargtable2-0 libasan8 libavahi-client3 libavahi-common-data 402s libavahi-common3 libblas3 libcairo2 libcc1-0 libcifpp-data libcifpp7 402s libcommons-logging-java libcommons-parent-java libcups2t64 libde265-0 402s libdebhelper-perl libdeflate0 libexpat1-dev libfftw3-double3 402s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 402s libfreetype6 libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libgs-common 402s libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 402s libheif-plugin-libde265 libheif1 libice6 libidn12 libijs-0.35 libimagequant0 402s libisl23 libitm1 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery 402s libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 402s liblapack3 liblbfgsb0 liblcms2-2 liblqr-1-0 libltdl7 402s libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmbedcrypto7t64 402s libmbedtls14t64 libmbedx509-1t64 libmpc3 libmpfi0 libmysqlclient21 402s libnetpbm11t64 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java 402s libpixman-1-0 libpotrace0 libptexenc1 libpython3-all-dev libpython3-dev 402s libpython3.12-dev libpython3.13 libpython3.13-dev libpython3.13-minimal 402s libpython3.13-stdlib libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 402s libstdc++-14-dev libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 402s libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 402s libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 402s libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft mysql-common 402s ncbi-blast+ ncbi-data netpbm phylip po-debconf poppler-data prank 402s preview-latex-style probcons python-biopython-doc python-matplotlib-data 402s python3-alabaster python3-all python3-all-dev python3-appdirs 402s python3-biopython python3-biopython-sql python3-brotli python3-cairo 402s python3-contourpy python3-cycler python3-dateutil python3-decorator 402s python3-defusedxml python3-dev python3-docutils python3-fonttools 402s python3-freetype python3-fs python3-imagesize python3-isodate 402s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 402s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 402s python3-numpy python3-numpydoc python3-packaging python3-pil 402s python3-pil.imagetk python3-rdflib python3-reportlab python3-rlpycairo 402s python3-roman python3-scipy python3-six python3-snowballstemmer 402s python3-sphinx python3-sphinx-rtd-theme python3-sphinxcontrib.jquery 402s python3-sympy python3-tabulate python3-tk python3-tz python3-ufolib2 402s python3.12-dev python3.12-tk python3.13 python3.13-dev python3.13-minimal 402s python3.13-tk sgml-base sphinx-common sphinx-rtd-theme-common t-coffee 402s t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended 402s texlive-latex-base texlive-latex-extra texlive-latex-recommended 402s texlive-pictures tk8.6-blt2.5 unicode-data w3c-sgml-lib wise wise-data 402s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 402s Suggested packages: 402s autoconf-archive gnu-standards autoconf-doc blt-demo samtools cpp-doc 402s gcc-14-locales cpp-14-doc dh-make flit python3-build python3-installer 402s python3-wheel bison flex-doc fonts-freefont-otf | fonts-freefont-ttf 402s fonts-texgyre gcc-14-doc gcc-multilib manpages-dev gdb gcc-doc 402s gdb-s390x-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev hevea-doc 402s imagemagick-6-doc autotrace cups-bsd | lpr | lprng enscript ffmpeg gimp 402s gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance 402s sane-utils transfig libraw-bin libavalon-framework-java 402s libexcalibur-logkit-java liblog4j1.2-java cups-common libfftw3-bin 402s libfftw3-dev libheif-plugin-x265 libheif-plugin-ffmpegdec 402s libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec 402s libheif-plugin-j2kenc libheif-plugin-kvazaar libheif-plugin-rav1e 402s libheif-plugin-svtenc libjs-jquery-ui-docs liblcms2-utils 402s libmagickcore-6.q16-7-extra libmpfi-doc libstdc++-14-doc tcl8.6 tk8.6 402s libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc phylip-doc 402s libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho 402s fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai 402s fonts-arphic-uming fonts-nanum probcons-extra clustalw emboss muscle3 phyml 402s python3-psycopg2 raxml python-cycler-doc docutils-doc fonts-linuxlibertine 402s | ttf-linux-libertine texlive-lang-french python-lxml-doc cm-super-minimal 402s dvipng fonts-staypuft gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 402s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 402s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 402s python-mpmath-doc python3-gmpy2 default-mysql-server | virtual-mysql-server 402s python3-gdal python3-pydot python3-pygraphviz gfortran python-numpy-doc 402s python3-pytest python-pil-doc python-rdflib-doc pdf-viewer 402s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 402s python-scipy-doc python3-stemmer dvisvgm fonts-freefont-otf latexmk 402s libjs-mathjax sphinx-doc tex-gyre texlive-fonts-extra texlive-plain-generic 402s python-sympy-doc tix python3-tk-dbg python3.13-venv python3.13-doc 402s binfmt-support sgml-base-doc boxshade seaview t-coffee-examples perl-tk xpdf 402s | pdf-viewer xzdec hintview texlive-fonts-recommended-doc 402s texlive-latex-base-doc wp2latex icc-profiles libfile-which-perl 402s texlive-latex-extra-doc texlive-science texlive-latex-recommended-doc 402s texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex 402s wise-doc 402s Recommended packages: 402s libfl-dev libmagickcore-6.q16-7-extra libarchive-cpio-perl 402s fonts-droid-fallback libheif-plugin-aomenc javascript-common libjson-xs-perl 402s libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 402s python3-cssselect python3-html5lib python3-olefile python3-sparqlwrapper 402s fonts-dejavu-extra isympy-common amap-align clustalw dialign-tx fsa kalign 402s libsoap-lite-perl libxml-simple-perl muscle mustang poa proda tm-align 402s lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl 402s texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl 402s libx11-protocol-perl x11-utils x11-xserver-utils 402s The following NEW packages will be installed: 402s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 402s build-essential bwa clustalo cpp cpp-14 cpp-14-s390x-linux-gnu 402s cpp-s390x-linux-gnu debhelper debugedit dh-autoreconf dh-python 402s dh-strip-nondeterminism dialign docutils-common dssp dwz fasttree flex 402s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 402s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 402s g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 gcc-14-s390x-linux-gnu 402s gcc-s390x-linux-gnu gettext ghostscript hevea hicolor-icon-theme imagemagick 402s imagemagick-6-common imagemagick-6.q16 intltool-debian libaom3 402s libapache-pom-java libarchive-zip-perl libargtable2-0 libasan8 402s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libcairo2 402s libcc1-0 libcifpp-data libcifpp7 libcommons-logging-java 402s libcommons-parent-java libcups2t64 libde265-0 libdebhelper-perl libdeflate0 402s libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl 402s libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev 402s libgfortran5 libgomp1 libgraphite2-3 libgs-common libgs10 libgs10-common 402s libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 402s libidn12 libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 402s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 402s libjs-underscore libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 402s liblqr-1-0 libltdl7 libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 402s libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libmpc3 libmpfi0 402s libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils libpaper1 402s libpdfbox-java libpixman-1-0 libpotrace0 libptexenc1 libpython3-all-dev 403s libpython3-dev libpython3.12-dev libpython3.13 libpython3.13-dev 403s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 403s libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 403s libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libubsan1 libwebp7 403s libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 403s libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 403s mafft mysql-common ncbi-blast+ ncbi-data netpbm phylip po-debconf 403s poppler-data prank preview-latex-style probcons python-biopython-doc 403s python-matplotlib-data python3-alabaster python3-all python3-all-dev 403s python3-appdirs python3-biopython python3-biopython-sql python3-brotli 403s python3-cairo python3-contourpy python3-cycler python3-dateutil 403s python3-decorator python3-defusedxml python3-dev python3-docutils 403s python3-fonttools python3-freetype python3-fs python3-imagesize 403s python3-isodate python3-kiwisolver python3-lxml python3-lz4 403s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 403s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 403s python3-packaging python3-pil python3-pil.imagetk python3-rdflib 403s python3-reportlab python3-rlpycairo python3-roman python3-scipy python3-six 403s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 403s python3-sphinxcontrib.jquery python3-sympy python3-tabulate python3-tk 403s python3-tz python3-ufolib2 python3.12-dev python3.12-tk python3.13 403s python3.13-dev python3.13-minimal python3.13-tk sgml-base sphinx-common 403s sphinx-rtd-theme-common t-coffee t1utils tex-common texlive-base 403s texlive-binaries texlive-fonts-recommended texlive-latex-base 403s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 403s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 403s xfonts-encodings xfonts-utils xml-core zlib1g-dev 403s 0 upgraded, 251 newly installed, 0 to remove and 0 not upgraded. 403s Need to get 333 MB/333 MB of archives. 403s After this operation, 1233 MB of additional disk space will be used. 403s Get:1 /tmp/autopkgtest.Ou6kQf/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [992 B] 403s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x m4 s390x 1.4.19-4build1 [256 kB] 403s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x flex s390x 2.6.4-8.2build1 [311 kB] 403s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-lato all 2.015-1 [2781 kB] 403s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 14.2.0-8ubuntu1 [151 kB] 403s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libfftw3-double3 s390x 3.3.10-1ubuntu4 [511 kB] 403s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 403s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 403s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 403s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 403s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 403s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 403s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 403s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 404s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB] 404s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB] 404s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.4.0-0.1 [16.2 kB] 404s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libaom3 s390x 3.11.0~rc1-1 [1492 kB] 404s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libheif-plugin-aomdec s390x 1.18.1-2 [11.1 kB] 404s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libde265-0 s390x 1.0.15-1build4 [175 kB] 404s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libheif-plugin-libde265 s390x 1.18.1-2 [8800 B] 404s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libheif1 s390x 1.18.1-2 [312 kB] 404s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 404s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu2 [150 kB] 404s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 404s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 404s Get:27 http://ftpmaster.internal/ubuntu plucky/universe s390x liblqr-1-0 s390x 0.4.2-2.1build2 [32.6 kB] 404s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libltdl7 s390x 2.4.7-7build1 [41.8 kB] 404s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.0-2ubuntu1 [208 kB] 404s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libraw23t64 s390x 0.21.3-1 [415 kB] 404s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.22-1 [46.1 kB] 404s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.4.0-0.1 [204 kB] 404s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 404s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.4.0-0.1 [12.2 kB] 404s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.4.0-0.1 [25.3 kB] 404s Get:36 http://ftpmaster.internal/ubuntu plucky/universe s390x imagemagick-6-common all 8:6.9.13.12+dfsg1-1build1 [69.6 kB] 404s Get:37 http://ftpmaster.internal/ubuntu plucky/universe s390x libmagickcore-6.q16-7t64 s390x 8:6.9.13.12+dfsg1-1build1 [1909 kB] 404s Get:38 http://ftpmaster.internal/ubuntu plucky/universe s390x libmagickwand-6.q16-7t64 s390x 8:6.9.13.12+dfsg1-1build1 [344 kB] 404s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x poppler-data all 0.4.12-1 [2060 kB] 404s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.0-2 [877 kB] 404s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.0-2 [2172 kB] 404s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x sgml-base all 1.31 [11.4 kB] 404s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x autoconf all 2.72-3 [382 kB] 404s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x autotools-dev all 20220109.1 [44.9 kB] 404s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x automake all 1:1.16.5-1.3ubuntu1 [558 kB] 404s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x autopoint all 0.22.5-2 [616 kB] 404s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.15+dfsg-2 [1034 kB] 404s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 404s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 404s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 404s Get:51 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.15-1 [828 kB] 404s Get:52 http://ftpmaster.internal/ubuntu plucky/main s390x tk8.6-blt2.5 s390x 2.5.3+dfsg-7build1 [662 kB] 404s Get:53 http://ftpmaster.internal/ubuntu plucky/main s390x blt s390x 2.5.3+dfsg-7build1 [4840 B] 404s Get:54 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB] 404s Get:55 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 404s Get:56 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-8ubuntu1 [9570 kB] 405s Get:57 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-8ubuntu1 [1026 B] 405s Get:58 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.1.0-2ubuntu1 [5452 B] 405s Get:59 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.1.0-2ubuntu1 [22.4 kB] 405s Get:60 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 14.2.0-8ubuntu1 [50.6 kB] 405s Get:61 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 14.2.0-8ubuntu1 [30.9 kB] 405s Get:62 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 14.2.0-8ubuntu1 [2963 kB] 405s Get:63 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 14.2.0-8ubuntu1 [1184 kB] 405s Get:64 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-8ubuntu1 [1037 kB] 405s Get:65 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-8ubuntu1 [18.7 MB] 405s Get:66 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-8ubuntu1 [518 kB] 405s Get:67 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.1.0-2ubuntu1 [1204 B] 405s Get:68 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.1.0-2ubuntu1 [4996 B] 405s Get:69 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-8ubuntu1 [2608 kB] 406s Get:70 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-8ubuntu1 [11.0 MB] 406s Get:71 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-8ubuntu1 [19.9 kB] 406s Get:72 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.1.0-2ubuntu1 [956 B] 406s Get:73 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.1.0-2ubuntu1 [1076 B] 406s Get:74 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 406s Get:75 http://ftpmaster.internal/ubuntu plucky/universe s390x bwa s390x 0.7.18-1 [249 kB] 406s Get:76 http://ftpmaster.internal/ubuntu plucky/universe s390x libargtable2-0 s390x 13-2 [15.5 kB] 406s Get:77 http://ftpmaster.internal/ubuntu plucky/universe s390x clustalo s390x 1.2.4-8build1 [218 kB] 406s Get:78 http://ftpmaster.internal/ubuntu plucky/main s390x libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 406s Get:79 http://ftpmaster.internal/ubuntu plucky/main s390x libtool all 2.4.7-7build1 [166 kB] 406s Get:80 http://ftpmaster.internal/ubuntu plucky/main s390x dh-autoreconf all 20 [16.1 kB] 406s Get:81 http://ftpmaster.internal/ubuntu plucky/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 406s Get:82 http://ftpmaster.internal/ubuntu plucky/main s390x libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 406s Get:83 http://ftpmaster.internal/ubuntu plucky/main s390x dh-strip-nondeterminism all 1.14.0-1 [5058 B] 406s Get:84 http://ftpmaster.internal/ubuntu plucky/main s390x debugedit s390x 1:5.1-1 [49.9 kB] 406s Get:85 http://ftpmaster.internal/ubuntu plucky/main s390x dwz s390x 0.15-1build6 [122 kB] 406s Get:86 http://ftpmaster.internal/ubuntu plucky/main s390x gettext s390x 0.22.5-2 [996 kB] 406s Get:87 http://ftpmaster.internal/ubuntu plucky/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] 406s Get:88 http://ftpmaster.internal/ubuntu plucky/main s390x po-debconf all 1.0.21+nmu1 [233 kB] 406s Get:89 http://ftpmaster.internal/ubuntu plucky/main s390x debhelper all 13.20ubuntu1 [893 kB] 406s Get:90 http://ftpmaster.internal/ubuntu plucky/universe s390x dh-python all 6.20241024 [112 kB] 406s Get:91 http://ftpmaster.internal/ubuntu plucky/universe s390x dialign s390x 2.2.1-13 [155 kB] 406s Get:92 http://ftpmaster.internal/ubuntu plucky/main s390x xml-core all 0.19 [20.3 kB] 406s Get:93 http://ftpmaster.internal/ubuntu plucky/main s390x docutils-common all 0.21.2+dfsg-2 [131 kB] 406s Get:94 http://ftpmaster.internal/ubuntu plucky/universe s390x libcifpp-data all 7.0.7-3 [480 kB] 406s Get:95 http://ftpmaster.internal/ubuntu plucky/universe s390x libcifpp7 s390x 7.0.7-3 [1100 kB] 406s Get:96 http://ftpmaster.internal/ubuntu plucky/universe s390x dssp s390x 4.4.10-1 [784 kB] 406s Get:97 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 406s Get:98 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-lmodern all 2.005-1 [4799 kB] 406s Get:99 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-lyx all 2.4.2.1-1 [171 kB] 406s Get:100 http://ftpmaster.internal/ubuntu plucky/main s390x libgs-common all 10.03.1~dfsg1-0ubuntu2 [175 kB] 406s Get:101 http://ftpmaster.internal/ubuntu plucky/main s390x libgs10-common all 10.03.1~dfsg1-0ubuntu2 [488 kB] 406s Get:102 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-common-data s390x 0.8-13ubuntu6 [29.7 kB] 407s Get:103 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-common3 s390x 0.8-13ubuntu6 [24.1 kB] 407s Get:104 http://ftpmaster.internal/ubuntu plucky/main s390x libavahi-client3 s390x 0.8-13ubuntu6 [27.2 kB] 407s Get:105 http://ftpmaster.internal/ubuntu plucky/main s390x libcups2t64 s390x 2.4.10-1ubuntu2 [281 kB] 407s Get:106 http://ftpmaster.internal/ubuntu plucky/main s390x libidn12 s390x 1.42-2 [58.5 kB] 407s Get:107 http://ftpmaster.internal/ubuntu plucky/main s390x libijs-0.35 s390x 0.35-15.1build1 [15.5 kB] 407s Get:108 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig2dec0 s390x 0.20-1build3 [69.3 kB] 407s Get:109 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper1 s390x 1.1.29build1 [13.4 kB] 407s Get:110 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 407s Get:111 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 407s Get:112 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 407s Get:113 http://ftpmaster.internal/ubuntu plucky/main s390x libgs10 s390x 10.03.1~dfsg1-0ubuntu2 [3917 kB] 407s Get:114 http://ftpmaster.internal/ubuntu plucky/main s390x ghostscript s390x 10.03.1~dfsg1-0ubuntu2 [43.5 kB] 407s Get:115 http://ftpmaster.internal/ubuntu plucky/universe s390x libnetpbm11t64 s390x 2:11.08.01-1 [124 kB] 407s Get:116 http://ftpmaster.internal/ubuntu plucky/universe s390x netpbm s390x 2:11.08.01-1 [2202 kB] 407s Get:117 http://ftpmaster.internal/ubuntu plucky/universe s390x tex-common all 6.18 [32.8 kB] 407s Get:118 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 1.1.29build1 [8442 B] 407s Get:119 http://ftpmaster.internal/ubuntu plucky/main s390x libkpathsea6 s390x 2024.20240313.70630+ds-5 [66.7 kB] 407s Get:120 http://ftpmaster.internal/ubuntu plucky/main s390x libptexenc1 s390x 2024.20240313.70630+ds-5 [43.4 kB] 407s Get:121 http://ftpmaster.internal/ubuntu plucky/main s390x libsynctex2 s390x 2024.20240313.70630+ds-5 [64.6 kB] 407s Get:122 http://ftpmaster.internal/ubuntu plucky/main s390x libtexlua53-5 s390x 2024.20240313.70630+ds-5 [131 kB] 407s Get:123 http://ftpmaster.internal/ubuntu plucky/main s390x t1utils s390x 1.41-4build3 [65.6 kB] 407s Get:124 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 407s Get:125 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 407s Get:126 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 407s Get:127 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 407s Get:128 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 407s Get:129 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.0.1-1 [536 kB] 407s Get:130 http://ftpmaster.internal/ubuntu plucky/universe s390x libmpfi0 s390x 1.5.4+ds-4 [34.1 kB] 407s Get:131 http://ftpmaster.internal/ubuntu plucky/universe s390x libpotrace0 s390x 1.16-2build1 [18.7 kB] 407s Get:132 http://ftpmaster.internal/ubuntu plucky/universe s390x libteckit0 s390x 2.5.12+ds1-1 [433 kB] 407s Get:133 http://ftpmaster.internal/ubuntu plucky/main s390x libxmu6 s390x 2:1.1.3-3build2 [53.0 kB] 407s Get:134 http://ftpmaster.internal/ubuntu plucky/main s390x libxpm4 s390x 1:3.5.17-1build2 [41.2 kB] 407s Get:135 http://ftpmaster.internal/ubuntu plucky/main s390x libxaw7 s390x 2:1.0.16-1 [201 kB] 407s Get:136 http://ftpmaster.internal/ubuntu plucky/main s390x libxi6 s390x 2:1.8.2-1 [35.4 kB] 408s Get:137 http://ftpmaster.internal/ubuntu plucky/universe s390x libzzip-0-13t64 s390x 0.13.72+dfsg.1-1.2build1 [28.6 kB] 408s Get:138 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-binaries s390x 2024.20240313.70630+ds-5 [9172 kB] 408s Get:139 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 408s Get:140 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-base all 2024.20241102-1 [22.5 MB] 409s Get:141 http://ftpmaster.internal/ubuntu plucky/main s390x hicolor-icon-theme all 0.18-1 [13.5 kB] 409s Get:142 http://ftpmaster.internal/ubuntu plucky/universe s390x imagemagick-6.q16 s390x 8:6.9.13.12+dfsg1-1build1 [254 kB] 409s Get:143 http://ftpmaster.internal/ubuntu plucky/universe s390x imagemagick s390x 8:6.9.13.12+dfsg1-1build1 [14.2 kB] 409s Get:144 http://ftpmaster.internal/ubuntu plucky/universe s390x hevea s390x 2.36-2 [2045 kB] 409s Get:145 http://ftpmaster.internal/ubuntu plucky/universe s390x libapache-pom-java all 33-2 [5874 B] 409s Get:146 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 409s Get:147 http://ftpmaster.internal/ubuntu plucky/universe s390x libcommons-parent-java all 56-1 [10.7 kB] 409s Get:148 http://ftpmaster.internal/ubuntu plucky/universe s390x libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 409s Get:149 http://ftpmaster.internal/ubuntu plucky/main s390x libexpat1-dev s390x 2.6.2-2 [146 kB] 409s Get:150 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 409s Get:151 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 409s Get:152 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 409s Get:153 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 409s Get:154 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 409s Get:155 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 7.4.7-4 [158 kB] 409s Get:156 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-perl all 4.10000-1 [81.9 kB] 409s Get:157 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 409s Get:158 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 409s Get:159 http://ftpmaster.internal/ubuntu plucky/universe s390x libmbedcrypto7t64 s390x 2.28.8-1 [219 kB] 409s Get:160 http://ftpmaster.internal/ubuntu plucky/universe s390x libmbedx509-1t64 s390x 2.28.8-1 [46.2 kB] 409s Get:161 http://ftpmaster.internal/ubuntu plucky/universe s390x libmbedtls14t64 s390x 2.28.8-1 [84.7 kB] 409s Get:162 http://ftpmaster.internal/ubuntu plucky/main s390x mysql-common all 5.8+1.1.1 [6800 B] 409s Get:163 http://ftpmaster.internal/ubuntu plucky/main s390x libmysqlclient21 s390x 8.0.40-1 [1294 kB] 409s Get:164 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 409s Get:165 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.12-dev s390x 3.12.7-3 [5838 kB] 410s Get:166 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-dev s390x 3.12.7-1 [10.3 kB] 410s Get:167 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.0-2 [2086 kB] 410s Get:168 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13 s390x 3.13.0-2 [2477 kB] 410s Get:169 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-dev s390x 3.13.0-2 [5586 kB] 410s Get:170 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-all-dev s390x 3.12.7-1 [918 B] 410s Get:171 http://ftpmaster.internal/ubuntu plucky/universe s390x libqhull-r8.0 s390x 2020.2-6build1 [199 kB] 410s Get:172 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.1-1build1 [16.2 kB] 410s Get:173 http://ftpmaster.internal/ubuntu plucky/main s390x libxslt1.1 s390x 1.1.39-0exp1ubuntu1 [169 kB] 410s Get:174 http://ftpmaster.internal/ubuntu plucky/universe s390x mafft s390x 7.505-1 [766 kB] 410s Get:175 http://ftpmaster.internal/ubuntu plucky/universe s390x ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 410s Get:176 http://ftpmaster.internal/ubuntu plucky/universe s390x ncbi-blast+ s390x 2.16.0+ds-6 [15.2 MB] 411s Get:177 http://ftpmaster.internal/ubuntu plucky/universe s390x phylip s390x 1:3.697+dfsg-4build1 [1051 kB] 411s Get:178 http://ftpmaster.internal/ubuntu plucky/universe s390x prank s390x 0.0.170427+dfsg-3 [357 kB] 411s Get:179 http://ftpmaster.internal/ubuntu plucky/universe s390x preview-latex-style all 13.2-1 [347 kB] 411s Get:180 http://ftpmaster.internal/ubuntu plucky/universe s390x probcons s390x 1.12-14 [109 kB] 411s Get:181 http://ftpmaster.internal/ubuntu plucky/universe s390x python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 412s Get:182 http://ftpmaster.internal/ubuntu plucky/universe s390x python-matplotlib-data all 3.8.3-3 [2928 kB] 412s Get:183 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.0-2 [719 kB] 412s Get:184 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all s390x 3.12.7-1 [890 B] 412s Get:185 http://ftpmaster.internal/ubuntu plucky/main s390x python3.12-dev s390x 3.12.7-3 [505 kB] 412s Get:186 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-dev s390x 3.12.7-1 [26.7 kB] 412s Get:187 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-dev s390x 3.13.0-2 [507 kB] 412s Get:188 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all-dev s390x 3.12.7-1 [914 B] 412s Get:189 http://ftpmaster.internal/ubuntu plucky/main s390x python3-appdirs all 1.4.4-4 [10.9 kB] 412s Get:190 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 412s Get:191 http://ftpmaster.internal/ubuntu plucky/main s390x python3.12-tk s390x 3.12.7-3 [117 kB] 412s Get:192 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-tk s390x 3.13.0-2 [107 kB] 412s Get:193 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-tk s390x 3.12.7-1 [9750 B] 412s Get:194 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pil.imagetk s390x 10.4.0-1ubuntu1 [9314 B] 412s Get:195 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 10.4.0-1ubuntu1 [492 kB] 412s Get:196 http://ftpmaster.internal/ubuntu plucky/main s390x python3-cairo s390x 1.26.1-2 [119 kB] 412s Get:197 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 412s Get:198 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 412s Get:199 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-reportlab all 4.2.5-1 [1107 kB] 412s Get:200 http://ftpmaster.internal/ubuntu plucky/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 412s Get:201 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython s390x 1.84+dfsg-4 [1721 kB] 412s Get:202 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 412s Get:203 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-brotli s390x 1.1.0-2build2 [376 kB] 413s Get:204 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-contourpy s390x 1.3.0-2 [195 kB] 413s Get:205 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-cycler all 0.12.1-1 [9716 B] 413s Get:206 http://ftpmaster.internal/ubuntu plucky/main s390x python3-six all 1.16.0-7 [13.1 kB] 413s Get:207 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-2 [80.3 kB] 413s Get:208 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 413s Get:209 http://ftpmaster.internal/ubuntu plucky/main s390x python3-defusedxml all 0.7.1-2 [42.0 kB] 413s Get:210 http://ftpmaster.internal/ubuntu plucky/main s390x python3-roman all 4.2-1 [10.0 kB] 413s Get:211 http://ftpmaster.internal/ubuntu plucky/main s390x python3-docutils all 0.21.2+dfsg-2 [409 kB] 413s Get:212 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5 [17.5 MB] 414s Get:213 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 414s Get:214 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mpmath all 1.3.0-1 [425 kB] 414s Get:215 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-sympy all 1.13.3-1 [4228 kB] 414s Get:216 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2024.1-2 [31.4 kB] 414s Get:217 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fs all 2.4.16-4 [91.3 kB] 414s Get:218 http://ftpmaster.internal/ubuntu plucky/main s390x python3-lxml s390x 5.3.0-1 [1314 kB] 414s Get:219 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-lz4 s390x 4.0.2+dfsg-1build4 [26.4 kB] 414s Get:220 http://ftpmaster.internal/ubuntu plucky/universe s390x unicode-data all 15.1.0-1 [8878 kB] 414s Get:221 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-fonttools s390x 4.46.0-1build2 [1453 kB] 414s Get:222 http://ftpmaster.internal/ubuntu plucky/main s390x python3-imagesize all 1.4.1-1 [6844 B] 414s Get:223 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-isodate all 0.6.1-3 [24.3 kB] 414s Get:224 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-kiwisolver s390x 1.4.7-2 [54.9 kB] 414s Get:225 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.1-1 [41.4 kB] 414s Get:226 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-matplotlib s390x 3.8.3-3 [4554 kB] 415s Get:227 http://ftpmaster.internal/ubuntu plucky/main s390x python3-msgpack s390x 1.0.3-3build2 [85.0 kB] 415s Get:228 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mmtf all 1.1.3-1 [16.2 kB] 415s Get:229 http://ftpmaster.internal/ubuntu plucky/main s390x python3-mysqldb s390x 1.4.6-2build3 [47.5 kB] 415s Get:230 http://ftpmaster.internal/ubuntu plucky/main s390x python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 415s Get:231 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-common all 7.4.7-4 [775 kB] 415s Get:232 http://ftpmaster.internal/ubuntu plucky/main s390x python3-alabaster all 0.7.16-0.1 [18.5 kB] 415s Get:233 http://ftpmaster.internal/ubuntu plucky/main s390x python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 415s Get:234 http://ftpmaster.internal/ubuntu plucky/main s390x python3-sphinx all 7.4.7-4 [593 kB] 415s Get:235 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tabulate all 0.9.0-1 [45.3 kB] 415s Get:236 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-numpydoc all 1.6.0-2 [50.5 kB] 415s Get:237 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rdflib all 7.0.0-1 [405 kB] 415s Get:238 http://ftpmaster.internal/ubuntu plucky/main s390x sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 415s Get:239 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 415s Get:240 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 415s Get:241 http://ftpmaster.internal/ubuntu plucky/universe s390x t-coffee s390x 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [945 kB] 415s Get:242 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-fonts-recommended all 2024.20241102-1 [4974 kB] 416s Get:243 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-latex-base all 2024.20241102-1 [1260 kB] 416s Get:244 http://ftpmaster.internal/ubuntu plucky/universe s390x libfontbox-java all 1:1.8.16-5 [208 kB] 416s Get:245 http://ftpmaster.internal/ubuntu plucky/universe s390x libpdfbox-java all 1:1.8.16-5 [5521 kB] 416s Get:246 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-latex-recommended all 2024.20241102-1 [8739 kB] 416s Get:247 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-pictures all 2024.20241102-1 [17.0 MB] 417s Get:248 http://ftpmaster.internal/ubuntu plucky/universe s390x texlive-latex-extra all 2024.20241102-1 [24.2 MB] 418s Get:249 http://ftpmaster.internal/ubuntu plucky/universe s390x wise-data all 2.4.1-25 [83.0 kB] 418s Get:250 http://ftpmaster.internal/ubuntu plucky/universe s390x wise s390x 2.4.1-25 [935 kB] 418s Get:251 http://ftpmaster.internal/ubuntu plucky/universe s390x fasttree s390x 2.1.11-2 [190 kB] 419s Preconfiguring packages ... 419s Fetched 333 MB in 16s (21.1 MB/s) 419s Selecting previously unselected package m4. 419s (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 ... 55517 files and directories currently installed.) 419s Preparing to unpack .../000-m4_1.4.19-4build1_s390x.deb ... 419s Unpacking m4 (1.4.19-4build1) ... 419s Selecting previously unselected package flex. 419s Preparing to unpack .../001-flex_2.6.4-8.2build1_s390x.deb ... 419s Unpacking flex (2.6.4-8.2build1) ... 419s Selecting previously unselected package fonts-lato. 419s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 419s Unpacking fonts-lato (2.015-1) ... 419s Selecting previously unselected package libgomp1:s390x. 419s Preparing to unpack .../003-libgomp1_14.2.0-8ubuntu1_s390x.deb ... 419s Unpacking libgomp1:s390x (14.2.0-8ubuntu1) ... 419s Selecting previously unselected package libfftw3-double3:s390x. 419s Preparing to unpack .../004-libfftw3-double3_3.3.10-1ubuntu4_s390x.deb ... 419s Unpacking libfftw3-double3:s390x (3.3.10-1ubuntu4) ... 419s Selecting previously unselected package libfreetype6:s390x. 419s Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 419s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 419s Selecting previously unselected package fonts-dejavu-mono. 419s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 419s Unpacking fonts-dejavu-mono (2.37-8) ... 419s Selecting previously unselected package fonts-dejavu-core. 419s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 419s Unpacking fonts-dejavu-core (2.37-8) ... 419s Selecting previously unselected package libfontenc1:s390x. 419s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 419s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 419s Selecting previously unselected package x11-common. 419s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu3_all.deb ... 419s Unpacking x11-common (1:7.7+23ubuntu3) ... 419s Selecting previously unselected package xfonts-encodings. 419s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 419s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 419s Selecting previously unselected package xfonts-utils. 419s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_s390x.deb ... 419s Unpacking xfonts-utils (1:7.7+7) ... 419s Selecting previously unselected package fonts-urw-base35. 419s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 419s Unpacking fonts-urw-base35 (20200910-8) ... 420s Selecting previously unselected package fontconfig-config. 420s Preparing to unpack .../013-fontconfig-config_2.15.0-1.1ubuntu2_s390x.deb ... 420s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 420s Selecting previously unselected package libfontconfig1:s390x. 420s Preparing to unpack .../014-libfontconfig1_2.15.0-1.1ubuntu2_s390x.deb ... 420s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 420s Selecting previously unselected package libsharpyuv0:s390x. 420s Preparing to unpack .../015-libsharpyuv0_1.4.0-0.1_s390x.deb ... 420s Unpacking libsharpyuv0:s390x (1.4.0-0.1) ... 420s Selecting previously unselected package libaom3:s390x. 420s Preparing to unpack .../016-libaom3_3.11.0~rc1-1_s390x.deb ... 420s Unpacking libaom3:s390x (3.11.0~rc1-1) ... 420s Selecting previously unselected package libheif-plugin-aomdec:s390x. 420s Preparing to unpack .../017-libheif-plugin-aomdec_1.18.1-2_s390x.deb ... 420s Unpacking libheif-plugin-aomdec:s390x (1.18.1-2) ... 420s Selecting previously unselected package libde265-0:s390x. 420s Preparing to unpack .../018-libde265-0_1.0.15-1build4_s390x.deb ... 420s Unpacking libde265-0:s390x (1.0.15-1build4) ... 420s Selecting previously unselected package libheif-plugin-libde265:s390x. 420s Preparing to unpack .../019-libheif-plugin-libde265_1.18.1-2_s390x.deb ... 420s Unpacking libheif-plugin-libde265:s390x (1.18.1-2) ... 420s Selecting previously unselected package libheif1:s390x. 420s Preparing to unpack .../020-libheif1_1.18.1-2_s390x.deb ... 420s Unpacking libheif1:s390x (1.18.1-2) ... 420s Selecting previously unselected package libjbig0:s390x. 420s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 420s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 420s Selecting previously unselected package libjpeg-turbo8:s390x. 420s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-2ubuntu2_s390x.deb ... 420s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 420s Selecting previously unselected package libjpeg8:s390x. 420s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_s390x.deb ... 420s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 420s Selecting previously unselected package liblcms2-2:s390x. 420s Preparing to unpack .../024-liblcms2-2_2.16-2_s390x.deb ... 420s Unpacking liblcms2-2:s390x (2.16-2) ... 420s Selecting previously unselected package liblqr-1-0:s390x. 420s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_s390x.deb ... 420s Unpacking liblqr-1-0:s390x (0.4.2-2.1build2) ... 420s Selecting previously unselected package libltdl7:s390x. 420s Preparing to unpack .../026-libltdl7_2.4.7-7build1_s390x.deb ... 420s Unpacking libltdl7:s390x (2.4.7-7build1) ... 420s Selecting previously unselected package libopenjp2-7:s390x. 420s Preparing to unpack .../027-libopenjp2-7_2.5.0-2ubuntu1_s390x.deb ... 420s Unpacking libopenjp2-7:s390x (2.5.0-2ubuntu1) ... 420s Selecting previously unselected package libraw23t64:s390x. 420s Preparing to unpack .../028-libraw23t64_0.21.3-1_s390x.deb ... 420s Unpacking libraw23t64:s390x (0.21.3-1) ... 420s Selecting previously unselected package libdeflate0:s390x. 420s Preparing to unpack .../029-libdeflate0_1.22-1_s390x.deb ... 420s Unpacking libdeflate0:s390x (1.22-1) ... 420s Selecting previously unselected package libwebp7:s390x. 420s Preparing to unpack .../030-libwebp7_1.4.0-0.1_s390x.deb ... 420s Unpacking libwebp7:s390x (1.4.0-0.1) ... 420s Selecting previously unselected package libtiff6:s390x. 420s Preparing to unpack .../031-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 420s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 420s Selecting previously unselected package libwebpdemux2:s390x. 420s Preparing to unpack .../032-libwebpdemux2_1.4.0-0.1_s390x.deb ... 420s Unpacking libwebpdemux2:s390x (1.4.0-0.1) ... 420s Selecting previously unselected package libwebpmux3:s390x. 420s Preparing to unpack .../033-libwebpmux3_1.4.0-0.1_s390x.deb ... 420s Unpacking libwebpmux3:s390x (1.4.0-0.1) ... 420s Selecting previously unselected package imagemagick-6-common. 420s Preparing to unpack .../034-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1build1_all.deb ... 420s Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 420s Selecting previously unselected package libmagickcore-6.q16-7t64:s390x. 420s Preparing to unpack .../035-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_s390x.deb ... 420s Unpacking libmagickcore-6.q16-7t64:s390x (8:6.9.13.12+dfsg1-1build1) ... 420s Selecting previously unselected package libmagickwand-6.q16-7t64:s390x. 420s Preparing to unpack .../036-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_s390x.deb ... 420s Unpacking libmagickwand-6.q16-7t64:s390x (8:6.9.13.12+dfsg1-1build1) ... 420s Selecting previously unselected package poppler-data. 420s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 420s Unpacking poppler-data (0.4.12-1) ... 420s Selecting previously unselected package libpython3.13-minimal:s390x. 420s Preparing to unpack .../038-libpython3.13-minimal_3.13.0-2_s390x.deb ... 420s Unpacking libpython3.13-minimal:s390x (3.13.0-2) ... 420s Selecting previously unselected package python3.13-minimal. 420s Preparing to unpack .../039-python3.13-minimal_3.13.0-2_s390x.deb ... 420s Unpacking python3.13-minimal (3.13.0-2) ... 420s Selecting previously unselected package sgml-base. 420s Preparing to unpack .../040-sgml-base_1.31_all.deb ... 420s Unpacking sgml-base (1.31) ... 420s Selecting previously unselected package autoconf. 420s Preparing to unpack .../041-autoconf_2.72-3_all.deb ... 420s Unpacking autoconf (2.72-3) ... 420s Selecting previously unselected package autotools-dev. 420s Preparing to unpack .../042-autotools-dev_20220109.1_all.deb ... 420s Unpacking autotools-dev (20220109.1) ... 420s Selecting previously unselected package automake. 420s Preparing to unpack .../043-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 420s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 420s Selecting previously unselected package autopoint. 420s Preparing to unpack .../044-autopoint_0.22.5-2_all.deb ... 420s Unpacking autopoint (0.22.5-2) ... 420s Selecting previously unselected package libtcl8.6:s390x. 420s Preparing to unpack .../045-libtcl8.6_8.6.15+dfsg-2_s390x.deb ... 420s Unpacking libtcl8.6:s390x (8.6.15+dfsg-2) ... 420s Selecting previously unselected package libxrender1:s390x. 420s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 420s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 420s Selecting previously unselected package libxft2:s390x. 420s Preparing to unpack .../047-libxft2_2.3.6-1build1_s390x.deb ... 420s Unpacking libxft2:s390x (2.3.6-1build1) ... 420s Selecting previously unselected package libxss1:s390x. 420s Preparing to unpack .../048-libxss1_1%3a1.2.3-1build3_s390x.deb ... 420s Unpacking libxss1:s390x (1:1.2.3-1build3) ... 420s Selecting previously unselected package libtk8.6:s390x. 420s Preparing to unpack .../049-libtk8.6_8.6.15-1_s390x.deb ... 420s Unpacking libtk8.6:s390x (8.6.15-1) ... 420s Selecting previously unselected package tk8.6-blt2.5. 420s Preparing to unpack .../050-tk8.6-blt2.5_2.5.3+dfsg-7build1_s390x.deb ... 420s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 420s Selecting previously unselected package blt. 420s Preparing to unpack .../051-blt_2.5.3+dfsg-7build1_s390x.deb ... 420s Unpacking blt (2.5.3+dfsg-7build1) ... 420s Selecting previously unselected package libisl23:s390x. 420s Preparing to unpack .../052-libisl23_0.27-1_s390x.deb ... 420s Unpacking libisl23:s390x (0.27-1) ... 420s Selecting previously unselected package libmpc3:s390x. 420s Preparing to unpack .../053-libmpc3_1.3.1-1build2_s390x.deb ... 420s Unpacking libmpc3:s390x (1.3.1-1build2) ... 420s Selecting previously unselected package cpp-14-s390x-linux-gnu. 420s Preparing to unpack .../054-cpp-14-s390x-linux-gnu_14.2.0-8ubuntu1_s390x.deb ... 420s Unpacking cpp-14-s390x-linux-gnu (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package cpp-14. 421s Preparing to unpack .../055-cpp-14_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package cpp-s390x-linux-gnu. 421s Preparing to unpack .../056-cpp-s390x-linux-gnu_4%3a14.1.0-2ubuntu1_s390x.deb ... 421s Unpacking cpp-s390x-linux-gnu (4:14.1.0-2ubuntu1) ... 421s Selecting previously unselected package cpp. 421s Preparing to unpack .../057-cpp_4%3a14.1.0-2ubuntu1_s390x.deb ... 421s Unpacking cpp (4:14.1.0-2ubuntu1) ... 421s Selecting previously unselected package libcc1-0:s390x. 421s Preparing to unpack .../058-libcc1-0_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking libcc1-0:s390x (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package libitm1:s390x. 421s Preparing to unpack .../059-libitm1_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking libitm1:s390x (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package libasan8:s390x. 421s Preparing to unpack .../060-libasan8_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking libasan8:s390x (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package libubsan1:s390x. 421s Preparing to unpack .../061-libubsan1_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking libubsan1:s390x (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package libgcc-14-dev:s390x. 421s Preparing to unpack .../062-libgcc-14-dev_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking libgcc-14-dev:s390x (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package gcc-14-s390x-linux-gnu. 421s Preparing to unpack .../063-gcc-14-s390x-linux-gnu_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking gcc-14-s390x-linux-gnu (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package gcc-14. 421s Preparing to unpack .../064-gcc-14_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package gcc-s390x-linux-gnu. 421s Preparing to unpack .../065-gcc-s390x-linux-gnu_4%3a14.1.0-2ubuntu1_s390x.deb ... 421s Unpacking gcc-s390x-linux-gnu (4:14.1.0-2ubuntu1) ... 421s Selecting previously unselected package gcc. 421s Preparing to unpack .../066-gcc_4%3a14.1.0-2ubuntu1_s390x.deb ... 421s Unpacking gcc (4:14.1.0-2ubuntu1) ... 421s Selecting previously unselected package libstdc++-14-dev:s390x. 421s Preparing to unpack .../067-libstdc++-14-dev_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking libstdc++-14-dev:s390x (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package g++-14-s390x-linux-gnu. 421s Preparing to unpack .../068-g++-14-s390x-linux-gnu_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking g++-14-s390x-linux-gnu (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package g++-14. 421s Preparing to unpack .../069-g++-14_14.2.0-8ubuntu1_s390x.deb ... 421s Unpacking g++-14 (14.2.0-8ubuntu1) ... 421s Selecting previously unselected package g++-s390x-linux-gnu. 421s Preparing to unpack .../070-g++-s390x-linux-gnu_4%3a14.1.0-2ubuntu1_s390x.deb ... 421s Unpacking g++-s390x-linux-gnu (4:14.1.0-2ubuntu1) ... 421s Selecting previously unselected package g++. 421s Preparing to unpack .../071-g++_4%3a14.1.0-2ubuntu1_s390x.deb ... 421s Unpacking g++ (4:14.1.0-2ubuntu1) ... 421s Selecting previously unselected package build-essential. 421s Preparing to unpack .../072-build-essential_12.10ubuntu1_s390x.deb ... 421s Unpacking build-essential (12.10ubuntu1) ... 421s Selecting previously unselected package bwa. 421s Preparing to unpack .../073-bwa_0.7.18-1_s390x.deb ... 421s Unpacking bwa (0.7.18-1) ... 421s Selecting previously unselected package libargtable2-0. 421s Preparing to unpack .../074-libargtable2-0_13-2_s390x.deb ... 421s Unpacking libargtable2-0 (13-2) ... 421s Selecting previously unselected package clustalo. 421s Preparing to unpack .../075-clustalo_1.2.4-8build1_s390x.deb ... 421s Unpacking clustalo (1.2.4-8build1) ... 421s Selecting previously unselected package libdebhelper-perl. 421s Preparing to unpack .../076-libdebhelper-perl_13.20ubuntu1_all.deb ... 421s Unpacking libdebhelper-perl (13.20ubuntu1) ... 421s Selecting previously unselected package libtool. 421s Preparing to unpack .../077-libtool_2.4.7-7build1_all.deb ... 421s Unpacking libtool (2.4.7-7build1) ... 421s Selecting previously unselected package dh-autoreconf. 421s Preparing to unpack .../078-dh-autoreconf_20_all.deb ... 421s Unpacking dh-autoreconf (20) ... 421s Selecting previously unselected package libarchive-zip-perl. 421s Preparing to unpack .../079-libarchive-zip-perl_1.68-1_all.deb ... 421s Unpacking libarchive-zip-perl (1.68-1) ... 421s Selecting previously unselected package libfile-stripnondeterminism-perl. 421s Preparing to unpack .../080-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 421s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 422s Selecting previously unselected package dh-strip-nondeterminism. 422s Preparing to unpack .../081-dh-strip-nondeterminism_1.14.0-1_all.deb ... 422s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 422s Selecting previously unselected package debugedit. 422s Preparing to unpack .../082-debugedit_1%3a5.1-1_s390x.deb ... 422s Unpacking debugedit (1:5.1-1) ... 422s Selecting previously unselected package dwz. 422s Preparing to unpack .../083-dwz_0.15-1build6_s390x.deb ... 422s Unpacking dwz (0.15-1build6) ... 422s Selecting previously unselected package gettext. 422s Preparing to unpack .../084-gettext_0.22.5-2_s390x.deb ... 422s Unpacking gettext (0.22.5-2) ... 422s Selecting previously unselected package intltool-debian. 422s Preparing to unpack .../085-intltool-debian_0.35.0+20060710.6_all.deb ... 422s Unpacking intltool-debian (0.35.0+20060710.6) ... 422s Selecting previously unselected package po-debconf. 422s Preparing to unpack .../086-po-debconf_1.0.21+nmu1_all.deb ... 422s Unpacking po-debconf (1.0.21+nmu1) ... 422s Selecting previously unselected package debhelper. 422s Preparing to unpack .../087-debhelper_13.20ubuntu1_all.deb ... 422s Unpacking debhelper (13.20ubuntu1) ... 422s Selecting previously unselected package dh-python. 422s Preparing to unpack .../088-dh-python_6.20241024_all.deb ... 422s Unpacking dh-python (6.20241024) ... 422s Selecting previously unselected package dialign. 422s Preparing to unpack .../089-dialign_2.2.1-13_s390x.deb ... 422s Unpacking dialign (2.2.1-13) ... 422s Selecting previously unselected package xml-core. 422s Preparing to unpack .../090-xml-core_0.19_all.deb ... 422s Unpacking xml-core (0.19) ... 422s Selecting previously unselected package docutils-common. 422s Preparing to unpack .../091-docutils-common_0.21.2+dfsg-2_all.deb ... 422s Unpacking docutils-common (0.21.2+dfsg-2) ... 422s Selecting previously unselected package libcifpp-data. 422s Preparing to unpack .../092-libcifpp-data_7.0.7-3_all.deb ... 422s Unpacking libcifpp-data (7.0.7-3) ... 422s Selecting previously unselected package libcifpp7:s390x. 422s Preparing to unpack .../093-libcifpp7_7.0.7-3_s390x.deb ... 422s Unpacking libcifpp7:s390x (7.0.7-3) ... 422s Selecting previously unselected package dssp. 422s Preparing to unpack .../094-dssp_4.4.10-1_s390x.deb ... 422s Unpacking dssp (4.4.10-1) ... 422s Selecting previously unselected package fonts-font-awesome. 422s Preparing to unpack .../095-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 422s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 422s Selecting previously unselected package fonts-lmodern. 422s Preparing to unpack .../096-fonts-lmodern_2.005-1_all.deb ... 422s Unpacking fonts-lmodern (2.005-1) ... 422s Selecting previously unselected package fonts-lyx. 422s Preparing to unpack .../097-fonts-lyx_2.4.2.1-1_all.deb ... 422s Unpacking fonts-lyx (2.4.2.1-1) ... 422s Selecting previously unselected package libgs-common. 422s Preparing to unpack .../098-libgs-common_10.03.1~dfsg1-0ubuntu2_all.deb ... 422s Unpacking libgs-common (10.03.1~dfsg1-0ubuntu2) ... 422s Selecting previously unselected package libgs10-common. 422s Preparing to unpack .../099-libgs10-common_10.03.1~dfsg1-0ubuntu2_all.deb ... 422s Unpacking libgs10-common (10.03.1~dfsg1-0ubuntu2) ... 422s Selecting previously unselected package libavahi-common-data:s390x. 422s Preparing to unpack .../100-libavahi-common-data_0.8-13ubuntu6_s390x.deb ... 422s Unpacking libavahi-common-data:s390x (0.8-13ubuntu6) ... 422s Selecting previously unselected package libavahi-common3:s390x. 422s Preparing to unpack .../101-libavahi-common3_0.8-13ubuntu6_s390x.deb ... 422s Unpacking libavahi-common3:s390x (0.8-13ubuntu6) ... 422s Selecting previously unselected package libavahi-client3:s390x. 422s Preparing to unpack .../102-libavahi-client3_0.8-13ubuntu6_s390x.deb ... 422s Unpacking libavahi-client3:s390x (0.8-13ubuntu6) ... 422s Selecting previously unselected package libcups2t64:s390x. 422s Preparing to unpack .../103-libcups2t64_2.4.10-1ubuntu2_s390x.deb ... 422s Unpacking libcups2t64:s390x (2.4.10-1ubuntu2) ... 422s Selecting previously unselected package libidn12:s390x. 422s Preparing to unpack .../104-libidn12_1.42-2_s390x.deb ... 422s Unpacking libidn12:s390x (1.42-2) ... 422s Selecting previously unselected package libijs-0.35:s390x. 422s Preparing to unpack .../105-libijs-0.35_0.35-15.1build1_s390x.deb ... 422s Unpacking libijs-0.35:s390x (0.35-15.1build1) ... 422s Selecting previously unselected package libjbig2dec0:s390x. 422s Preparing to unpack .../106-libjbig2dec0_0.20-1build3_s390x.deb ... 422s Unpacking libjbig2dec0:s390x (0.20-1build3) ... 422s Selecting previously unselected package libpaper1:s390x. 422s Preparing to unpack .../107-libpaper1_1.1.29build1_s390x.deb ... 422s Unpacking libpaper1:s390x (1.1.29build1) ... 422s Selecting previously unselected package libice6:s390x. 422s Preparing to unpack .../108-libice6_2%3a1.1.1-1_s390x.deb ... 422s Unpacking libice6:s390x (2:1.1.1-1) ... 422s Selecting previously unselected package libsm6:s390x. 422s Preparing to unpack .../109-libsm6_2%3a1.2.4-1_s390x.deb ... 422s Unpacking libsm6:s390x (2:1.2.4-1) ... 422s Selecting previously unselected package libxt6t64:s390x. 422s Preparing to unpack .../110-libxt6t64_1%3a1.2.1-1.2build1_s390x.deb ... 422s Unpacking libxt6t64:s390x (1:1.2.1-1.2build1) ... 422s Selecting previously unselected package libgs10:s390x. 422s Preparing to unpack .../111-libgs10_10.03.1~dfsg1-0ubuntu2_s390x.deb ... 422s Unpacking libgs10:s390x (10.03.1~dfsg1-0ubuntu2) ... 422s Selecting previously unselected package ghostscript. 422s Preparing to unpack .../112-ghostscript_10.03.1~dfsg1-0ubuntu2_s390x.deb ... 422s Unpacking ghostscript (10.03.1~dfsg1-0ubuntu2) ... 422s Selecting previously unselected package libnetpbm11t64:s390x. 422s Preparing to unpack .../113-libnetpbm11t64_2%3a11.08.01-1_s390x.deb ... 422s Unpacking libnetpbm11t64:s390x (2:11.08.01-1) ... 422s Selecting previously unselected package netpbm. 422s Preparing to unpack .../114-netpbm_2%3a11.08.01-1_s390x.deb ... 422s Unpacking netpbm (2:11.08.01-1) ... 422s Selecting previously unselected package tex-common. 422s Preparing to unpack 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libcairo2:s390x (1.18.2-2) ... 422s Selecting previously unselected package libgraphite2-3:s390x. 422s Preparing to unpack .../126-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 422s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 422s Selecting previously unselected package libharfbuzz0b:s390x. 422s Preparing to unpack .../127-libharfbuzz0b_10.0.1-1_s390x.deb ... 422s Unpacking libharfbuzz0b:s390x (10.0.1-1) ... 422s Selecting previously unselected package libmpfi0:s390x. 422s Preparing to unpack .../128-libmpfi0_1.5.4+ds-4_s390x.deb ... 422s Unpacking libmpfi0:s390x (1.5.4+ds-4) ... 422s Selecting previously unselected package libpotrace0:s390x. 422s Preparing to unpack .../129-libpotrace0_1.16-2build1_s390x.deb ... 422s Unpacking libpotrace0:s390x (1.16-2build1) ... 422s Selecting previously unselected package libteckit0:s390x. 422s Preparing to unpack .../130-libteckit0_2.5.12+ds1-1_s390x.deb ... 422s Unpacking libteckit0:s390x (2.5.12+ds1-1) ... 423s Selecting previously unselected package libxmu6:s390x. 423s Preparing to unpack .../131-libxmu6_2%3a1.1.3-3build2_s390x.deb ... 423s Unpacking libxmu6:s390x (2:1.1.3-3build2) ... 423s Selecting previously unselected package libxpm4:s390x. 423s Preparing to unpack .../132-libxpm4_1%3a3.5.17-1build2_s390x.deb ... 423s Unpacking libxpm4:s390x (1:3.5.17-1build2) ... 423s Selecting previously unselected package libxaw7:s390x. 423s Preparing to unpack .../133-libxaw7_2%3a1.0.16-1_s390x.deb ... 423s Unpacking libxaw7:s390x (2:1.0.16-1) ... 423s Selecting previously unselected package libxi6:s390x. 423s Preparing to unpack .../134-libxi6_2%3a1.8.2-1_s390x.deb ... 423s Unpacking libxi6:s390x (2:1.8.2-1) ... 423s Selecting previously unselected package libzzip-0-13t64:s390x. 423s Preparing to unpack .../135-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_s390x.deb ... 423s Unpacking libzzip-0-13t64:s390x (0.13.72+dfsg.1-1.2build1) ... 423s Selecting previously unselected package texlive-binaries. 423s Preparing to unpack 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.../141-imagemagick_8%3a6.9.13.12+dfsg1-1build1_s390x.deb ... 424s Unpacking imagemagick (8:6.9.13.12+dfsg1-1build1) ... 424s Selecting previously unselected package hevea. 424s Preparing to unpack .../142-hevea_2.36-2_s390x.deb ... 424s Unpacking hevea (2.36-2) ... 424s Selecting previously unselected package libapache-pom-java. 424s Preparing to unpack .../143-libapache-pom-java_33-2_all.deb ... 424s Unpacking libapache-pom-java (33-2) ... 424s Selecting previously unselected package libblas3:s390x. 424s Preparing to unpack .../144-libblas3_3.12.0-3build2_s390x.deb ... 424s Unpacking libblas3:s390x (3.12.0-3build2) ... 424s Selecting previously unselected package libcommons-parent-java. 424s Preparing to unpack .../145-libcommons-parent-java_56-1_all.deb ... 424s Unpacking libcommons-parent-java (56-1) ... 424s Selecting previously unselected package libcommons-logging-java. 424s Preparing to unpack .../146-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 424s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 424s Selecting previously unselected package libexpat1-dev:s390x. 424s Preparing to unpack .../147-libexpat1-dev_2.6.2-2_s390x.deb ... 424s Unpacking libexpat1-dev:s390x (2.6.2-2) ... 424s Selecting previously unselected package libgfortran5:s390x. 424s Preparing to unpack .../148-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 424s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 424s Selecting previously unselected package libimagequant0:s390x. 424s Preparing to unpack .../149-libimagequant0_2.18.0-1build1_s390x.deb ... 424s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 424s Selecting previously unselected package libjs-jquery. 424s Preparing to unpack .../150-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 424s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 424s Selecting previously unselected package libjs-jquery-ui. 424s Preparing to unpack .../151-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 424s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 424s Selecting previously unselected package libjs-underscore. 424s Preparing to unpack .../152-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 424s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 424s Selecting previously unselected package libjs-sphinxdoc. 424s Preparing to unpack .../153-libjs-sphinxdoc_7.4.7-4_all.deb ... 424s Unpacking libjs-sphinxdoc (7.4.7-4) ... 424s Selecting previously unselected package libjson-perl. 424s Preparing to unpack .../154-libjson-perl_4.10000-1_all.deb ... 424s Unpacking libjson-perl (4.10000-1) ... 424s Selecting previously unselected package liblapack3:s390x. 424s Preparing to unpack .../155-liblapack3_3.12.0-3build2_s390x.deb ... 424s Unpacking liblapack3:s390x (3.12.0-3build2) ... 424s Selecting previously unselected package liblbfgsb0:s390x. 424s Preparing to unpack .../156-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 424s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 424s Selecting previously unselected package libmbedcrypto7t64:s390x. 424s Preparing to unpack .../157-libmbedcrypto7t64_2.28.8-1_s390x.deb ... 424s Unpacking libmbedcrypto7t64:s390x (2.28.8-1) ... 424s Selecting previously unselected package libmbedx509-1t64:s390x. 424s Preparing to unpack .../158-libmbedx509-1t64_2.28.8-1_s390x.deb ... 424s Unpacking libmbedx509-1t64:s390x (2.28.8-1) ... 424s Selecting previously unselected package libmbedtls14t64:s390x. 424s Preparing to unpack .../159-libmbedtls14t64_2.28.8-1_s390x.deb ... 424s Unpacking libmbedtls14t64:s390x (2.28.8-1) ... 424s Selecting previously unselected package mysql-common. 424s Preparing to unpack .../160-mysql-common_5.8+1.1.1_all.deb ... 424s Unpacking mysql-common (5.8+1.1.1) ... 424s Selecting previously unselected package libmysqlclient21:s390x. 424s Preparing to unpack .../161-libmysqlclient21_8.0.40-1_s390x.deb ... 424s Unpacking libmysqlclient21:s390x (8.0.40-1) ... 424s Selecting previously unselected package zlib1g-dev:s390x. 424s Preparing to unpack .../162-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 424s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 424s Selecting previously unselected package libpython3.12-dev:s390x. 424s Preparing to unpack .../163-libpython3.12-dev_3.12.7-3_s390x.deb ... 424s Unpacking libpython3.12-dev:s390x (3.12.7-3) ... 425s Selecting previously unselected package libpython3-dev:s390x. 425s Preparing to unpack .../164-libpython3-dev_3.12.7-1_s390x.deb ... 425s Unpacking libpython3-dev:s390x (3.12.7-1) ... 425s Selecting previously unselected package libpython3.13-stdlib:s390x. 425s Preparing to unpack .../165-libpython3.13-stdlib_3.13.0-2_s390x.deb ... 425s Unpacking libpython3.13-stdlib:s390x (3.13.0-2) ... 425s Selecting previously unselected package libpython3.13:s390x. 425s Preparing to unpack .../166-libpython3.13_3.13.0-2_s390x.deb ... 425s Unpacking libpython3.13:s390x (3.13.0-2) ... 425s Selecting previously unselected package libpython3.13-dev:s390x. 425s Preparing to unpack .../167-libpython3.13-dev_3.13.0-2_s390x.deb ... 425s Unpacking libpython3.13-dev:s390x (3.13.0-2) ... 425s Selecting previously unselected package libpython3-all-dev:s390x. 425s Preparing to unpack .../168-libpython3-all-dev_3.12.7-1_s390x.deb ... 425s Unpacking libpython3-all-dev:s390x (3.12.7-1) ... 425s Selecting previously unselected package libqhull-r8.0:s390x. 425s Preparing to unpack .../169-libqhull-r8.0_2020.2-6build1_s390x.deb ... 425s Unpacking libqhull-r8.0:s390x (2020.2-6build1) ... 425s Selecting previously unselected package libraqm0:s390x. 425s Preparing to unpack .../170-libraqm0_0.10.1-1build1_s390x.deb ... 425s Unpacking libraqm0:s390x (0.10.1-1build1) ... 425s Selecting previously unselected package libxslt1.1:s390x. 425s Preparing to unpack .../171-libxslt1.1_1.1.39-0exp1ubuntu1_s390x.deb ... 425s Unpacking libxslt1.1:s390x (1.1.39-0exp1ubuntu1) ... 425s Selecting previously unselected package mafft. 425s Preparing to unpack .../172-mafft_7.505-1_s390x.deb ... 425s Unpacking mafft (7.505-1) ... 425s Selecting previously unselected package ncbi-data. 425s Preparing to unpack .../173-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 425s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 425s Selecting previously unselected package ncbi-blast+. 425s Preparing to unpack .../174-ncbi-blast+_2.16.0+ds-6_s390x.deb ... 425s Unpacking ncbi-blast+ (2.16.0+ds-6) ... 425s Selecting previously unselected package phylip. 425s Preparing to unpack .../175-phylip_1%3a3.697+dfsg-4build1_s390x.deb ... 425s Unpacking phylip (1:3.697+dfsg-4build1) ... 425s Selecting previously unselected package prank. 425s Preparing to unpack .../176-prank_0.0.170427+dfsg-3_s390x.deb ... 425s Unpacking prank (0.0.170427+dfsg-3) ... 425s Selecting previously unselected package preview-latex-style. 425s Preparing to unpack .../177-preview-latex-style_13.2-1_all.deb ... 425s Unpacking preview-latex-style (13.2-1) ... 425s Selecting previously unselected package probcons. 425s Preparing to unpack .../178-probcons_1.12-14_s390x.deb ... 425s Unpacking probcons (1.12-14) ... 425s Selecting previously unselected package python-biopython-doc. 425s Preparing to unpack .../179-python-biopython-doc_1.84+dfsg-4_all.deb ... 425s Unpacking python-biopython-doc (1.84+dfsg-4) ... 426s Selecting previously unselected package python-matplotlib-data. 426s Preparing to unpack .../180-python-matplotlib-data_3.8.3-3_all.deb ... 426s Unpacking python-matplotlib-data (3.8.3-3) ... 426s Selecting previously unselected package python3.13. 426s Preparing to unpack .../181-python3.13_3.13.0-2_s390x.deb ... 426s Unpacking python3.13 (3.13.0-2) ... 426s Selecting previously unselected package python3-all. 426s Preparing to unpack .../182-python3-all_3.12.7-1_s390x.deb ... 426s Unpacking python3-all (3.12.7-1) ... 426s Selecting previously unselected package python3.12-dev. 426s Preparing to unpack .../183-python3.12-dev_3.12.7-3_s390x.deb ... 426s Unpacking python3.12-dev (3.12.7-3) ... 426s Selecting previously unselected package python3-dev. 426s Preparing to unpack .../184-python3-dev_3.12.7-1_s390x.deb ... 426s Unpacking python3-dev (3.12.7-1) ... 426s Selecting previously unselected package python3.13-dev. 426s Preparing to unpack .../185-python3.13-dev_3.13.0-2_s390x.deb ... 426s Unpacking python3.13-dev (3.13.0-2) ... 426s Selecting previously unselected package python3-all-dev. 426s Preparing to unpack .../186-python3-all-dev_3.12.7-1_s390x.deb ... 426s Unpacking python3-all-dev (3.12.7-1) ... 426s Selecting previously unselected package python3-appdirs. 426s Preparing to unpack .../187-python3-appdirs_1.4.4-4_all.deb ... 426s Unpacking python3-appdirs (1.4.4-4) ... 426s Selecting previously unselected package python3-numpy. 426s Preparing to unpack .../188-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ... 426s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 426s Selecting previously unselected package python3.12-tk. 426s Preparing to unpack .../189-python3.12-tk_3.12.7-3_s390x.deb ... 426s Unpacking python3.12-tk (3.12.7-3) ... 426s Selecting previously unselected package python3.13-tk. 426s Preparing to unpack .../190-python3.13-tk_3.13.0-2_s390x.deb ... 426s Unpacking python3.13-tk (3.13.0-2) ... 426s Selecting previously unselected package python3-tk:s390x. 426s Preparing to unpack .../191-python3-tk_3.12.7-1_s390x.deb ... 426s Unpacking python3-tk:s390x (3.12.7-1) ... 426s Selecting previously unselected package python3-pil.imagetk:s390x. 426s Preparing to unpack .../192-python3-pil.imagetk_10.4.0-1ubuntu1_s390x.deb ... 426s Unpacking python3-pil.imagetk:s390x (10.4.0-1ubuntu1) ... 426s Selecting previously unselected package python3-pil:s390x. 426s Preparing to unpack .../193-python3-pil_10.4.0-1ubuntu1_s390x.deb ... 426s Unpacking python3-pil:s390x (10.4.0-1ubuntu1) ... 426s Selecting previously unselected package python3-cairo. 426s Preparing to unpack .../194-python3-cairo_1.26.1-2_s390x.deb ... 426s Unpacking python3-cairo (1.26.1-2) ... 426s Selecting previously unselected package python3-freetype. 426s Preparing to unpack .../195-python3-freetype_2.5.1-1_all.deb ... 426s Unpacking python3-freetype (2.5.1-1) ... 426s Selecting previously unselected package python3-rlpycairo. 426s Preparing to unpack .../196-python3-rlpycairo_0.3.0-3_all.deb ... 426s Unpacking python3-rlpycairo (0.3.0-3) ... 426s Selecting previously unselected package python3-reportlab. 426s Preparing to unpack .../197-python3-reportlab_4.2.5-1_all.deb ... 426s Unpacking python3-reportlab (4.2.5-1) ... 426s Selecting previously unselected package w3c-sgml-lib. 426s Preparing to unpack .../198-w3c-sgml-lib_1.3-3_all.deb ... 426s Unpacking w3c-sgml-lib (1.3-3) ... 426s Selecting previously unselected package python3-biopython. 426s Preparing to unpack .../199-python3-biopython_1.84+dfsg-4_s390x.deb ... 426s Unpacking python3-biopython (1.84+dfsg-4) ... 426s Selecting previously unselected package python3-biopython-sql. 426s Preparing to unpack .../200-python3-biopython-sql_1.84+dfsg-4_all.deb ... 426s Unpacking python3-biopython-sql (1.84+dfsg-4) ... 426s Selecting previously unselected package python3-brotli. 426s Preparing to unpack .../201-python3-brotli_1.1.0-2build2_s390x.deb ... 426s Unpacking python3-brotli (1.1.0-2build2) ... 426s Selecting previously unselected package python3-contourpy. 426s Preparing to unpack .../202-python3-contourpy_1.3.0-2_s390x.deb ... 426s Unpacking python3-contourpy (1.3.0-2) ... 426s Selecting previously unselected package python3-cycler. 426s Preparing to unpack .../203-python3-cycler_0.12.1-1_all.deb ... 426s Unpacking python3-cycler (0.12.1-1) ... 426s Selecting previously unselected package python3-six. 426s Preparing to unpack .../204-python3-six_1.16.0-7_all.deb ... 426s Unpacking python3-six (1.16.0-7) ... 426s Selecting previously unselected package python3-dateutil. 426s Preparing to unpack .../205-python3-dateutil_2.9.0-2_all.deb ... 426s Unpacking python3-dateutil (2.9.0-2) ... 426s Selecting previously unselected package python3-decorator. 426s Preparing to unpack .../206-python3-decorator_5.1.1-5_all.deb ... 426s Unpacking python3-decorator (5.1.1-5) ... 426s Selecting previously unselected package python3-defusedxml. 426s Preparing to unpack .../207-python3-defusedxml_0.7.1-2_all.deb ... 426s Unpacking python3-defusedxml (0.7.1-2) ... 426s Selecting previously unselected package python3-roman. 426s Preparing to unpack .../208-python3-roman_4.2-1_all.deb ... 426s Unpacking python3-roman (4.2-1) ... 426s Selecting previously unselected package python3-docutils. 426s Preparing to unpack .../209-python3-docutils_0.21.2+dfsg-2_all.deb ... 426s Unpacking python3-docutils (0.21.2+dfsg-2) ... 426s Selecting previously unselected package python3-scipy. 426s Preparing to unpack .../210-python3-scipy_1.13.1-5_s390x.deb ... 426s Unpacking python3-scipy (1.13.1-5) ... 427s Selecting previously unselected package python3-ufolib2. 427s Preparing to unpack .../211-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 427s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 427s Selecting previously unselected package python3-mpmath. 427s Preparing to unpack .../212-python3-mpmath_1.3.0-1_all.deb ... 427s Unpacking python3-mpmath (1.3.0-1) ... 427s Selecting previously unselected package python3-sympy. 427s Preparing to unpack .../213-python3-sympy_1.13.3-1_all.deb ... 427s Unpacking python3-sympy (1.13.3-1) ... 427s Selecting previously unselected package python3-tz. 427s Preparing to unpack .../214-python3-tz_2024.1-2_all.deb ... 427s Unpacking python3-tz (2024.1-2) ... 427s Selecting previously unselected package python3-fs. 427s Preparing to unpack .../215-python3-fs_2.4.16-4_all.deb ... 427s Unpacking python3-fs (2.4.16-4) ... 427s Selecting previously unselected package python3-lxml:s390x. 427s Preparing to unpack .../216-python3-lxml_5.3.0-1_s390x.deb ... 427s Unpacking python3-lxml:s390x (5.3.0-1) ... 427s Selecting previously unselected package python3-lz4. 427s Preparing to unpack .../217-python3-lz4_4.0.2+dfsg-1build4_s390x.deb ... 427s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 427s Selecting previously unselected package unicode-data. 427s Preparing to unpack .../218-unicode-data_15.1.0-1_all.deb ... 427s Unpacking unicode-data (15.1.0-1) ... 427s Selecting previously unselected package python3-fonttools. 427s Preparing to unpack .../219-python3-fonttools_4.46.0-1build2_s390x.deb ... 427s Unpacking python3-fonttools (4.46.0-1build2) ... 427s Selecting previously unselected package python3-imagesize. 427s Preparing to unpack .../220-python3-imagesize_1.4.1-1_all.deb ... 427s Unpacking python3-imagesize (1.4.1-1) ... 427s Selecting previously unselected package python3-isodate. 427s Preparing to unpack .../221-python3-isodate_0.6.1-3_all.deb ... 427s Unpacking python3-isodate (0.6.1-3) ... 427s Selecting previously unselected package python3-kiwisolver. 427s Preparing to unpack .../222-python3-kiwisolver_1.4.7-2_s390x.deb ... 427s Unpacking python3-kiwisolver (1.4.7-2) ... 427s Selecting previously unselected package python3-packaging. 427s Preparing to unpack .../223-python3-packaging_24.1-1_all.deb ... 427s Unpacking python3-packaging (24.1-1) ... 427s Selecting previously unselected package python3-matplotlib. 427s Preparing to unpack .../224-python3-matplotlib_3.8.3-3_s390x.deb ... 427s Unpacking python3-matplotlib (3.8.3-3) ... 427s Selecting previously unselected package python3-msgpack. 427s Preparing to unpack .../225-python3-msgpack_1.0.3-3build2_s390x.deb ... 427s Unpacking python3-msgpack (1.0.3-3build2) ... 427s Selecting previously unselected package python3-mmtf. 427s Preparing to unpack .../226-python3-mmtf_1.1.3-1_all.deb ... 427s Unpacking python3-mmtf (1.1.3-1) ... 427s Selecting previously unselected package python3-mysqldb. 427s Preparing to unpack .../227-python3-mysqldb_1.4.6-2build3_s390x.deb ... 427s Unpacking python3-mysqldb (1.4.6-2build3) ... 427s Selecting previously unselected package python3-networkx. 427s Preparing to unpack .../228-python3-networkx_3.2.1-4ubuntu1_all.deb ... 427s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 428s Selecting previously unselected package sphinx-common. 428s Preparing to unpack .../229-sphinx-common_7.4.7-4_all.deb ... 428s Unpacking sphinx-common (7.4.7-4) ... 428s Selecting previously unselected package python3-alabaster. 428s Preparing to unpack .../230-python3-alabaster_0.7.16-0.1_all.deb ... 428s Unpacking python3-alabaster (0.7.16-0.1) ... 428s Selecting previously unselected package python3-snowballstemmer. 428s Preparing to unpack .../231-python3-snowballstemmer_2.2.0-4build1_all.deb ... 428s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 428s Selecting previously unselected package python3-sphinx. 428s Preparing to unpack .../232-python3-sphinx_7.4.7-4_all.deb ... 428s Unpacking python3-sphinx (7.4.7-4) ... 428s Selecting previously unselected package python3-tabulate. 428s Preparing to unpack .../233-python3-tabulate_0.9.0-1_all.deb ... 428s Unpacking python3-tabulate (0.9.0-1) ... 428s Selecting previously unselected package python3-numpydoc. 428s Preparing to unpack .../234-python3-numpydoc_1.6.0-2_all.deb ... 428s Unpacking python3-numpydoc (1.6.0-2) ... 428s Selecting previously unselected package python3-rdflib. 428s Preparing to unpack .../235-python3-rdflib_7.0.0-1_all.deb ... 428s Unpacking python3-rdflib (7.0.0-1) ... 428s Selecting previously unselected package sphinx-rtd-theme-common. 428s Preparing to unpack .../236-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 428s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 428s Selecting previously unselected package python3-sphinxcontrib.jquery. 428s Preparing to unpack .../237-python3-sphinxcontrib.jquery_4.1-5_all.deb ... 428s Unpacking python3-sphinxcontrib.jquery (4.1-5) ... 428s Selecting previously unselected package python3-sphinx-rtd-theme. 428s Preparing to unpack .../238-python3-sphinx-rtd-theme_3.0.1+dfsg-1_all.deb ... 428s Unpacking python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 428s Selecting previously unselected package t-coffee. 428s Preparing to unpack .../239-t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_s390x.deb ... 428s Unpacking t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 428s Selecting previously unselected package texlive-fonts-recommended. 428s Preparing to unpack .../240-texlive-fonts-recommended_2024.20241102-1_all.deb ... 428s Unpacking texlive-fonts-recommended (2024.20241102-1) ... 428s Selecting previously unselected package texlive-latex-base. 428s Preparing to unpack .../241-texlive-latex-base_2024.20241102-1_all.deb ... 428s Unpacking texlive-latex-base (2024.20241102-1) ... 429s Selecting previously unselected package libfontbox-java. 429s Preparing to unpack .../242-libfontbox-java_1%3a1.8.16-5_all.deb ... 429s Unpacking libfontbox-java (1:1.8.16-5) ... 429s Selecting previously unselected package libpdfbox-java. 429s Preparing to unpack .../243-libpdfbox-java_1%3a1.8.16-5_all.deb ... 429s Unpacking libpdfbox-java (1:1.8.16-5) ... 429s Selecting previously unselected package texlive-latex-recommended. 429s Preparing to unpack .../244-texlive-latex-recommended_2024.20241102-1_all.deb ... 429s Unpacking texlive-latex-recommended (2024.20241102-1) ... 429s Selecting previously unselected package texlive-pictures. 429s Preparing to unpack .../245-texlive-pictures_2024.20241102-1_all.deb ... 429s Unpacking texlive-pictures (2024.20241102-1) ... 430s Selecting previously unselected package texlive-latex-extra. 430s Preparing to unpack .../246-texlive-latex-extra_2024.20241102-1_all.deb ... 430s Unpacking texlive-latex-extra (2024.20241102-1) ... 431s Selecting previously unselected package wise-data. 431s Preparing to unpack .../247-wise-data_2.4.1-25_all.deb ... 431s Unpacking wise-data (2.4.1-25) ... 431s Selecting previously unselected package wise. 431s Preparing to unpack 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(my.cnf) in auto mode 432s Setting up libmysqlclient21:s390x (8.0.40-1) ... 432s Setting up imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 432s Setting up fonts-lato (2.015-1) ... 432s Setting up libxpm4:s390x (1:3.5.17-1build2) ... 432s Setting up hicolor-icon-theme (0.18-1) ... 432s Setting up libxi6:s390x (2:1.8.2-1) ... 432s Setting up probcons (1.12-14) ... 432s Setting up libmbedcrypto7t64:s390x (2.28.8-1) ... 432s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 432s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 432s Setting up libxcb-render0:s390x (1.17.0-2) ... 432s Setting up python3-defusedxml (0.7.1-2) ... 432s Setting up mafft (7.505-1) ... 432s Setting up libarchive-zip-perl (1.68-1) ... 432s Setting up bwa (0.7.18-1) ... 432s Setting up python3-alabaster (0.7.16-0.1) ... 432s Setting up fonts-lyx (2.4.2.1-1) ... 432s Setting up libijs-0.35:s390x (0.35-15.1build1) ... 432s Setting up libdebhelper-perl (13.20ubuntu1) ... 432s Setting up libgs-common 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libpython3.13-minimal:s390x (3.13.0-2) ... 436s Setting up tex-common (6.18) ... 436s update-language: texlive-base not installed and configured, doing nothing! 436s Setting up python3-isodate (0.6.1-3) ... 436s Setting up python3-roman (4.2-1) ... 436s Setting up python3-decorator (5.1.1-5) ... 436s Setting up libfontenc1:s390x (1:1.1.8-1build1) ... 436s Setting up autotools-dev (20220109.1) ... 436s Setting up libblas3:s390x (3.12.0-3build2) ... 436s 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 436s Setting up python3-packaging (24.1-1) ... 437s Setting up libexpat1-dev:s390x (2.6.2-2) ... 437s Setting up libzzip-0-13t64:s390x (0.13.72+dfsg.1-1.2build1) ... 437s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 437s Setting up libjbig2dec0:s390x (0.20-1build3) ... 437s Setting up python3-snowballstemmer (2.2.0-4build1) ... 437s Setting up libteckit0:s390x (2.5.12+ds1-1) ... 437s Setting up python3-brotli (1.1.0-2build2) ... 437s Setting up libapache-pom-java (33-2) ... 437s Setting up libavahi-common-data:s390x (0.8-13ubuntu6) ... 437s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 437s Setting up t1utils (1.41-4build3) ... 437s Setting up python3-cycler (0.12.1-1) ... 437s Setting up libtexlua53-5:s390x (2024.20240313.70630+ds-5) ... 437s Setting up libimagequant0:s390x (2.18.0-1build1) ... 437s Setting up fonts-dejavu-mono (2.37-8) ... 437s Setting up python3-kiwisolver (1.4.7-2) ... 437s Setting up libmpc3:s390x (1.3.1-1build2) ... 437s Setting up libidn12:s390x (1.42-2) ... 437s Setting up libtcl8.6:s390x (8.6.15+dfsg-2) ... 437s Setting up autopoint (0.22.5-2) ... 437s Setting up libmpfi0:s390x (1.5.4+ds-4) ... 437s Setting up fonts-dejavu-core (2.37-8) ... 437s Setting up wise-data (2.4.1-25) ... 437s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... 437s Setting up libltdl7:s390x (2.4.7-7build1) ... 437s Setting up libfftw3-double3:s390x (3.3.10-1ubuntu4) ... 437s Setting up libcifpp-data (7.0.7-3) ... 438s Setting up libkpathsea6:s390x (2024.20240313.70630+ds-5) ... 438s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 438s Setting up autoconf (2.72-3) ... 438s Setting up libwebp7:s390x (1.4.0-0.1) ... 438s Setting up libubsan1:s390x (14.2.0-8ubuntu1) ... 438s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 438s Setting up dwz (0.15-1build6) ... 438s Setting up liblqr-1-0:s390x (0.4.2-2.1build2) ... 438s Setting up python3-rdflib (7.0.0-1) ... 438s Setting up libasan8:s390x (14.2.0-8ubuntu1) ... 438s Setting up libjson-perl (4.10000-1) ... 438s Setting up libxslt1.1:s390x (1.1.39-0exp1ubuntu1) ... 438s Setting up debugedit (1:5.1-1) ... 438s Setting up fonts-lmodern (2.005-1) ... 438s Setting up libopenjp2-7:s390x (2.5.0-2ubuntu1) ... 438s Setting up python3.13-minimal (3.13.0-2) ... 439s Setting up libharfbuzz0b:s390x (10.0.1-1) ... 439s Setting up python3-dateutil (2.9.0-2) ... 439s Setting up fasttree (2.1.11-2) ... 439s Setting up sgml-base (1.31) ... 439s Setting up python3-msgpack (1.0.3-3build2) ... 439s Setting up libxss1:s390x (1:1.2.3-1build3) ... 439s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 439s Setting up python3-mpmath (1.3.0-1) ... 440s Setting up libisl23:s390x (0.27-1) ... 440s Setting up libde265-0:s390x (1.0.15-1build4) ... 440s Setting up python-matplotlib-data (3.8.3-3) ... 440s Setting up libwebpmux3:s390x (1.4.0-0.1) ... 440s Setting up python3-appdirs (1.4.4-4) ... 440s Setting up dialign (2.2.1-13) ... 440s Setting up libpython3.13-stdlib:s390x (3.13.0-2) ... 440s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 440s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 440s Setting up xdg-utils (1.2.1-0ubuntu1) ... 440s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 440s Setting up libcc1-0:s390x (14.2.0-8ubuntu1) ... 441s Setting up libitm1:s390x (14.2.0-8ubuntu1) ... 441s Setting up libsynctex2:s390x (2024.20240313.70630+ds-5) ... 441s Setting up prank (0.0.170427+dfsg-3) ... 441s Setting up libargtable2-0 (13-2) ... 441s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 441s Setting up python3-imagesize (1.4.1-1) ... 441s Setting up libpotrace0:s390x (1.16-2build1) ... 441s Setting up libpython3.13:s390x (3.13.0-2) ... 441s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 441s Setting up automake (1:1.16.5-1.3ubuntu1) ... 441s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 441s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 441s Setting up python3-sympy (1.13.3-1) ... 454s Setting up libice6:s390x (2:1.1.1-1) ... 454s Setting up flex (2.6.4-8.2build1) ... 454s Setting up liblapack3:s390x (3.12.0-3build2) ... 454s 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 454s Setting up gettext (0.22.5-2) ... 454s Setting up libmbedx509-1t64:s390x (2.28.8-1) ... 454s Setting up libpdfbox-java (1:1.8.16-5) ... 454s Setting up python3.13 (3.13.0-2) ... 455s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 455s Setting up wise (2.4.1-25) ... 455s Setting up preview-latex-style (13.2-1) ... 455s Setting up libwebpdemux2:s390x (1.4.0-0.1) ... 455s Setting up libcommons-parent-java (56-1) ... 455s Setting up libavahi-common3:s390x (0.8-13ubuntu6) ... 455s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 455s Setting up python3-all (3.12.7-1) ... 455s Setting up libcifpp7:s390x (7.0.7-3) ... 455s Setting up libpython3.12-dev:s390x (3.12.7-3) ... 455s Setting up clustalo (1.2.4-8build1) ... 455s Setting up dssp (4.4.10-1) ... 455s Setting up python3-freetype (2.5.1-1) ... 455s Setting up xfonts-utils (1:7.7+7) ... 455s Setting up intltool-debian (0.35.0+20060710.6) ... 455s Setting up python3-fs (2.4.16-4) ... 455s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 455s Setting up libptexenc1:s390x (2024.20240313.70630+ds-5) ... 456s Setting up libraqm0:s390x (0.10.1-1build1) ... 456s Setting up libpython3.13-dev:s390x (3.13.0-2) ... 456s Setting up python3.12-dev (3.12.7-3) ... 456s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 459s Setting up libjs-sphinxdoc (7.4.7-4) ... 459s Setting up cpp-14-s390x-linux-gnu (14.2.0-8ubuntu1) ... 459s Setting up libraw23t64:s390x (0.21.3-1) ... 459s Setting up cpp-14 (14.2.0-8ubuntu1) ... 459s Setting up dh-strip-nondeterminism (1.14.0-1) ... 459s Setting up libmbedtls14t64:s390x (2.28.8-1) ... 459s Setting up python3-lxml:s390x (5.3.0-1) ... 460s Setting up python-biopython-doc (1.84+dfsg-4) ... 460s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 460s Setting up xml-core (0.19) ... 460s Setting up python3-contourpy (1.3.0-2) ... 460s Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 460s Setting up libgcc-14-dev:s390x 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(10.4.0-1ubuntu1) ... 469s Setting up python3-rlpycairo (0.3.0-3) ... 469s Setting up python3-reportlab (4.2.5-1) ... 471s Setting up texlive-binaries (2024.20240313.70630+ds-5) ... 471s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 471s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 471s Setting up g++-14 (14.2.0-8ubuntu1) ... 471s Setting up texlive-base (2024.20241102-1) ... 471s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 471s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 472s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 472s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 472s Setting up libgs10:s390x (10.03.1~dfsg1-0ubuntu2) ... 472s Setting up libtool (2.4.7-7build1) ... 472s Setting up ghostscript (10.03.1~dfsg1-0ubuntu2) ... 472s Setting up gcc (4:14.1.0-2ubuntu1) ... 472s Setting up dh-autoreconf (20) ... 472s Setting up texlive-latex-base (2024.20241102-1) ... 472s Setting up texlive-latex-recommended (2024.20241102-1) ... 472s Setting up texlive-pictures (2024.20241102-1) ... 472s Setting up g++ (4:14.1.0-2ubuntu1) ... 472s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 472s Setting up texlive-fonts-recommended (2024.20241102-1) ... 472s Setting up build-essential (12.10ubuntu1) ... 472s Setting up debhelper (13.20ubuntu1) ... 472s Setting up texlive-latex-extra (2024.20241102-1) ... 472s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 472s Setting up libheif-plugin-aomdec:s390x (1.18.1-2) ... 472s Setting up libheif-plugin-libde265:s390x (1.18.1-2) ... 472s Setting up libheif1:s390x (1.18.1-2) ... 472s Setting up libmagickcore-6.q16-7t64:s390x (8:6.9.13.12+dfsg1-1build1) ... 472s Setting up python3-fonttools (4.46.0-1build2) ... 474s Setting up libmagickwand-6.q16-7t64:s390x (8:6.9.13.12+dfsg1-1build1) ... 474s Setting up imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 474s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode 474s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode 474s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode 474s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode 474s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode 474s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode 474s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode 474s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode 474s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode 474s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode 474s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode 474s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode 474s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode 474s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode 474s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode 474s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode 474s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode 474s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode 474s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode 474s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode 474s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 474s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode 474s Setting up python3-matplotlib (3.8.3-3) ... 478s Setting up hevea (2.36-2) ... 478s Setting up imagemagick (8:6.9.13.12+dfsg1-1build1) ... 478s Processing triggers for install-info (7.1.1-1) ... 478s Processing triggers for libc-bin (2.40-1ubuntu3) ... 478s Processing triggers for systemd (256.5-2ubuntu4) ... 478s Processing triggers for man-db (2.12.1-3) ... 479s Processing triggers for sgml-base (1.31) ... 479s Setting up docutils-common (0.21.2+dfsg-2) ... 479s Setting up w3c-sgml-lib (1.3-3) ... 501s Setting up python3-biopython (1.84+dfsg-4) ... 503s Setting up python3-biopython-sql (1.84+dfsg-4) ... 503s Processing triggers for sgml-base (1.31) ... 503s Setting up python3-docutils (0.21.2+dfsg-2) ... 504s Setting up python3-sphinx (7.4.7-4) ... 505s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 505s Setting up python3-numpydoc (1.6.0-2) ... 506s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 506s Setting up autopkgtest-satdep (0) ... 506s Processing triggers for tex-common (6.18) ... 506s Running updmap-sys. This may take some time... done. 506s Running mktexlsr /var/lib/texmf ... done. 506s Building format(s) --all. 579s This may take some time... done. 584s (Reading database ... 101368 files and directories currently installed.) 584s Removing autopkgtest-satdep (0) ... 596s autopkgtest [13:10:48]: test full_suite: sh debian/tests/run-unit-test 596s autopkgtest [13:10:48]: test full_suite: [----------------------- 597s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 597s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 597s mkdir: created directory 'Bio' 597s mkdir: created directory 'Bio/Align' 597s mkdir: created directory 'Bio/Align/substitution_matrices' 597s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 597s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 597s Remove test test_Tutorial.py which is bound to fail 598s test_Ace ... ok 598s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 598s 598s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 598s 598s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 598s 598s test_Align_a2m ... loading tests failed: 598s Failed to import test module: test_Align_a2m 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 598s from . import multiarray 598s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 598s from . import overrides 598s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 598s from numpy.core._multiarray_umath import ( 598s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 598s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 598s 598s During handling of the above exception, another exception occurred: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 598s from numpy.__config__ import show as show_config 598s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 598s from numpy.core._multiarray_umath import ( 598s ...<3 lines>... 598s ) 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 598s raise ImportError(msg) 598s ImportError: 598s 598s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 598s 598s Importing the numpy C-extensions failed. This error can happen for 598s many reasons, often due to issues with your setup or how NumPy was 598s installed. 598s 598s We have compiled some common reasons and troubleshooting tips at: 598s 598s https://numpy.org/devdocs/user/troubleshooting-importerror.html 598s 598s Please note and check the following: 598s 598s * The Python version is: Python3.13 from "/usr/bin/python3.13" 598s * The NumPy version is: "1.26.4" 598s 598s and make sure that they are the versions you expect. 598s Please carefully study the documentation linked above for further help. 598s 598s Original error was: No module named 'numpy.core._multiarray_umath' 598s 598s 598s The above exception was the direct cause of the following exception: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 598s module = __import__(module_name) 598s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 598s import numpy as np 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 598s raise ImportError(msg) from e 598s ImportError: Error importing numpy: you should not try to import numpy from 598s its source directory; please exit the numpy source tree, and relaunch 598s your python interpreter from there. 598s 598s test_Align_bed ... loading tests failed: 598s Failed to import test module: test_Align_bed 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 598s from . import multiarray 598s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 598s from . import overrides 598s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 598s from numpy.core._multiarray_umath import ( 598s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 598s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 598s 598s During handling of the above exception, another exception occurred: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 598s from numpy.__config__ import show as show_config 598s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 598s from numpy.core._multiarray_umath import ( 598s ...<3 lines>... 598s ) 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 598s raise ImportError(msg) 598s ImportError: 598s 598s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 598s 598s Importing the numpy C-extensions failed. This error can happen for 598s many reasons, often due to issues with your setup or how NumPy was 598s installed. 598s 598s We have compiled some common reasons and troubleshooting tips at: 598s 598s https://numpy.org/devdocs/user/troubleshooting-importerror.html 598s 598s Please note and check the following: 598s 598s * The Python version is: Python3.13 from "/usr/bin/python3.13" 598s * The NumPy version is: "1.26.4" 598s 598s and make sure that they are the versions you expect. 598s Please carefully study the documentation linked above for further help. 598s 598s Original error was: No module named 'numpy.core._multiarray_umath' 598s 598s 598s The above exception was the direct cause of the following exception: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 598s module = __import__(module_name) 598s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 598s import numpy as np 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 598s raise ImportError(msg) from e 598s ImportError: Error importing numpy: you should not try to import numpy from 598s its source directory; please exit the numpy source tree, and relaunch 598s your python interpreter from there. 598s 598s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_Align_bigmaf ... loading tests failed: 598s Failed to import test module: test_Align_bigmaf 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 598s from . import multiarray 598s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 598s from . import overrides 598s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 598s from numpy.core._multiarray_umath import ( 598s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 598s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 598s 598s During handling of the above exception, another exception occurred: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 598s from numpy.__config__ import show as show_config 598s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 598s from numpy.core._multiarray_umath import ( 598s ...<3 lines>... 598s ) 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 598s raise ImportError(msg) 598s ImportError: 598s 598s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 598s 598s Importing the numpy C-extensions failed. This error can happen for 598s many reasons, often due to issues with your setup or how NumPy was 598s installed. 598s 598s We have compiled some common reasons and troubleshooting tips at: 598s 598s https://numpy.org/devdocs/user/troubleshooting-importerror.html 598s 598s Please note and check the following: 598s 598s * The Python version is: Python3.13 from "/usr/bin/python3.13" 598s * The NumPy version is: "1.26.4" 598s 598s and make sure that they are the versions you expect. 598s Please carefully study the documentation linked above for further help. 598s 598s Original error was: No module named 'numpy.core._multiarray_umath' 598s 598s 598s The above exception was the direct cause of the following exception: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 598s module = __import__(module_name) 598s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 598s import numpy as np 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 598s raise ImportError(msg) from e 598s ImportError: Error importing numpy: you should not try to import numpy from 598s its source directory; please exit the numpy source tree, and relaunch 598s your python interpreter from there. 598s 598s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_Align_clustal ... loading tests failed: 598s Failed to import test module: test_Align_clustal 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 598s from . import multiarray 598s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 598s from . import overrides 598s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 598s from numpy.core._multiarray_umath import ( 598s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 598s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 598s 598s During handling of the above exception, another exception occurred: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 598s from numpy.__config__ import show as show_config 598s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 598s from numpy.core._multiarray_umath import ( 598s ...<3 lines>... 598s ) 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 598s raise ImportError(msg) 598s ImportError: 598s 598s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 598s 598s Importing the numpy C-extensions failed. This error can happen for 598s many reasons, often due to issues with your setup or how NumPy was 598s installed. 598s 598s We have compiled some common reasons and troubleshooting tips at: 598s 598s https://numpy.org/devdocs/user/troubleshooting-importerror.html 598s 598s Please note and check the following: 598s 598s * The Python version is: Python3.13 from "/usr/bin/python3.13" 598s * The NumPy version is: "1.26.4" 598s 598s and make sure that they are the versions you expect. 598s Please carefully study the documentation linked above for further help. 598s 598s Original error was: No module named 'numpy.core._multiarray_umath' 598s 598s 598s The above exception was the direct cause of the following exception: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 598s module = __import__(module_name) 598s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 598s import numpy as np 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 598s raise ImportError(msg) from e 598s ImportError: Error importing numpy: you should not try to import numpy from 598s its source directory; please exit the numpy source tree, and relaunch 598s your python interpreter from there. 598s 598s test_Align_codonalign ... loading tests failed: 598s Failed to import test module: test_Align_codonalign 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 598s from . import multiarray 598s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 598s from . import overrides 598s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 598s from numpy.core._multiarray_umath import ( 598s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 598s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 598s 598s During handling of the above exception, another exception occurred: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 598s from numpy.__config__ import show as show_config 598s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 598s from numpy.core._multiarray_umath import ( 598s ...<3 lines>... 598s ) 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 598s raise ImportError(msg) 598s ImportError: 598s 598s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 598s 598s Importing the numpy C-extensions failed. This error can happen for 598s many reasons, often due to issues with your setup or how NumPy was 598s installed. 598s 598s We have compiled some common reasons and troubleshooting tips at: 598s 598s https://numpy.org/devdocs/user/troubleshooting-importerror.html 598s 598s Please note and check the following: 598s 598s * The Python version is: Python3.13 from "/usr/bin/python3.13" 598s * The NumPy version is: "1.26.4" 598s 598s and make sure that they are the versions you expect. 598s Please carefully study the documentation linked above for further help. 598s 598s Original error was: No module named 'numpy.core._multiarray_umath' 598s 598s 598s The above exception was the direct cause of the following exception: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 598s module = __import__(module_name) 598s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 598s import numpy as np 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 598s raise ImportError(msg) from e 598s ImportError: Error importing numpy: you should not try to import numpy from 598s its source directory; please exit the numpy source tree, and relaunch 598s your python interpreter from there. 598s 598s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 598s 598s test_Align_fasta ... loading tests failed: 598s Failed to import test module: test_Align_fasta 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 598s from . import multiarray 598s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 598s from . import overrides 598s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 598s from numpy.core._multiarray_umath import ( 598s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 598s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 598s 598s During handling of the above exception, another exception occurred: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 598s from numpy.__config__ import show as show_config 598s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 598s from numpy.core._multiarray_umath import ( 598s ...<3 lines>... 598s ) 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 598s raise ImportError(msg) 598s ImportError: 598s 598s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 598s 598s Importing the numpy C-extensions failed. This error can happen for 598s many reasons, often due to issues with your setup or how NumPy was 598s installed. 598s 598s We have compiled some common reasons and troubleshooting tips at: 598s 598s https://numpy.org/devdocs/user/troubleshooting-importerror.html 598s 598s Please note and check the following: 598s 598s * The Python version is: Python3.13 from "/usr/bin/python3.13" 598s * The NumPy version is: "1.26.4" 598s 598s and make sure that they are the versions you expect. 598s Please carefully study the documentation linked above for further help. 598s 598s Original error was: No module named 'numpy.core._multiarray_umath' 598s 598s 598s The above exception was the direct cause of the following exception: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 598s module = __import__(module_name) 598s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 598s import numpy as np 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 598s raise ImportError(msg) from e 598s ImportError: Error importing numpy: you should not try to import numpy from 598s its source directory; please exit the numpy source tree, and relaunch 598s your python interpreter from there. 598s 598s test_Align_hhr ... loading tests failed: 598s Failed to import test module: test_Align_hhr 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 598s from . import multiarray 598s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 598s from . import overrides 598s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 598s from numpy.core._multiarray_umath import ( 598s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 598s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 598s 598s During handling of the above exception, another exception occurred: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 598s from numpy.__config__ import show as show_config 598s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 598s from numpy.core._multiarray_umath import ( 598s ...<3 lines>... 598s ) 598s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 598s raise ImportError(msg) 598s ImportError: 598s 598s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 598s 598s Importing the numpy C-extensions failed. This error can happen for 598s many reasons, often due to issues with your setup or how NumPy was 598s installed. 598s 598s We have compiled some common reasons and troubleshooting tips at: 598s 598s https://numpy.org/devdocs/user/troubleshooting-importerror.html 598s 598s Please note and check the following: 598s 598s * The Python version is: Python3.13 from "/usr/bin/python3.13" 598s * The NumPy version is: "1.26.4" 598s 598s and make sure that they are the versions you expect. 598s Please carefully study the documentation linked above for further help. 598s 598s Original error was: No module named 'numpy.core._multiarray_umath' 598s 598s 598s The above exception was the direct cause of the following exception: 598s 598s Traceback (most recent call last): 598s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 598s module = __import__(module_name) 598s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 598s import numpy as np 598s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 598s raise ImportError(msg) from e 598s ImportError: Error importing numpy: you should not try to import numpy from 598s its source directory; please exit the numpy source tree, and relaunch 598s your python interpreter from there. 598s 599s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Application ... ok 599s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 599s 599s test_Blast_Record ... loading tests failed: 599s Failed to import test module: test_Blast_Record 599s Traceback (most recent call last): 599s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 599s from . import multiarray 599s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 599s from . import overrides 599s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 599s from numpy.core._multiarray_umath import ( 599s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 599s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 599s 599s During handling of the above exception, another exception occurred: 599s 599s Traceback (most recent call last): 599s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 599s from numpy.__config__ import show as show_config 599s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 599s from numpy.core._multiarray_umath import ( 599s ...<3 lines>... 599s ) 599s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 599s raise ImportError(msg) 599s ImportError: 599s 599s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 599s 599s Importing the numpy C-extensions failed. This error can happen for 599s many reasons, often due to issues with your setup or how NumPy was 599s installed. 599s 599s We have compiled some common reasons and troubleshooting tips at: 599s 599s https://numpy.org/devdocs/user/troubleshooting-importerror.html 599s 599s Please note and check the following: 599s 599s * The Python version is: Python3.13 from "/usr/bin/python3.13" 599s * The NumPy version is: "1.26.4" 599s 599s and make sure that they are the versions you expect. 599s Please carefully study the documentation linked above for further help. 599s 599s Original error was: No module named 'numpy.core._multiarray_umath' 599s 599s 599s The above exception was the direct cause of the following exception: 599s 599s Traceback (most recent call last): 599s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 599s module = __import__(module_name) 599s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 599s from Bio.Blast.NCBIXML import HSP 599s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 599s import numpy as np 599s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 599s raise ImportError(msg) from e 599s ImportError: Error importing numpy: you should not try to import numpy from 599s its source directory; please exit the numpy source tree, and relaunch 599s your python interpreter from there. 599s 600s test_Blast_parser ... loading tests failed: 600s Failed to import test module: test_Blast_parser 600s Traceback (most recent call last): 600s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 600s from . import multiarray 600s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 600s from . import overrides 600s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 600s from numpy.core._multiarray_umath import ( 600s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 600s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 600s 600s During handling of the above exception, another exception occurred: 600s 600s Traceback (most recent call last): 600s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 600s from numpy.__config__ import show as show_config 600s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 600s from numpy.core._multiarray_umath import ( 600s ...<3 lines>... 600s ) 600s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 600s raise ImportError(msg) 600s ImportError: 600s 600s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 600s 600s Importing the numpy C-extensions failed. This error can happen for 600s many reasons, often due to issues with your setup or how NumPy was 600s installed. 600s 600s We have compiled some common reasons and troubleshooting tips at: 600s 600s https://numpy.org/devdocs/user/troubleshooting-importerror.html 600s 600s Please note and check the following: 600s 600s * The Python version is: Python3.13 from "/usr/bin/python3.13" 600s * The NumPy version is: "1.26.4" 600s 600s and make sure that they are the versions you expect. 600s Please carefully study the documentation linked above for further help. 600s 600s Original error was: No module named 'numpy.core._multiarray_umath' 600s 600s 600s The above exception was the direct cause of the following exception: 600s 600s Traceback (most recent call last): 600s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 600s module = __import__(module_name) 600s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 600s import numpy as np 600s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 600s raise ImportError(msg) from e 600s ImportError: Error importing numpy: you should not try to import numpy from 600s its source directory; please exit the numpy source tree, and relaunch 600s your python interpreter from there. 600s 600s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 600s 600s test_Chi2 ... /usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2131: BiopythonWarning: Import of C module failed (cannot import name 'cnexus' from 'Bio.Nexus' (/usr/lib/python3/dist-packages/Bio/Nexus/__init__.py)). Falling back to slow Python implementation 600s warnings.warn( 600s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 600s 600s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 600s 600s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 600s 600s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 600s 600s test_CodonTable ... ok 600s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 600s 600s test_Compass ... ok 600s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 600s 600s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 600s 600s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 600s 600s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 600s 600s test_EmbossPrimer ... ok 604s test_Entrez ... ok 604s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 604s 605s test_Entrez_parser ... ok 605s test_Enzyme ... ok 605s test_ExPASy ... skipping. internet not available 605s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 605s 605s test_File ... ok 605s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 605s 605s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 605s 605s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 605s 605s test_GraphicsDistribution ... loading tests failed: 605s Failed to import test module: test_GraphicsDistribution 605s Traceback (most recent call last): 605s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 605s module = __import__(module_name) 605s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 605s from Bio.Graphics.Distribution import BarChartDistribution 605s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 605s from reportlab.graphics.charts.barcharts import BarChartProperties 605s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 605s from reportlab.lib import colors 605s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 605s from reportlab.lib.rl_accel import fp_str 605s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 605s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 605s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 605s from PIL import Image 605s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 605s from . import _imaging as core 605s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 605s 605s test_GraphicsGeneral ... loading tests failed: 605s Failed to import test module: test_GraphicsGeneral 605s Traceback (most recent call last): 605s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 605s module = __import__(module_name) 605s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 605s from Bio.Graphics.Comparative import ComparativeScatterPlot 605s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 605s from reportlab.graphics.charts.lineplots import LinePlot 605s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 605s from reportlab.lib import colors 605s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 605s from reportlab.lib.rl_accel import fp_str 605s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 605s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 605s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 605s from PIL import Image 605s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 605s from . import _imaging as core 605s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 605s 605s test_HMMCasino ... ok 605s test_HMMGeneral ... ok 605s test_KEGG ... ok 605s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 605s 605s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 605s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 606s test_KGML_nographics ... ok 606s test_KeyWList ... ok 606s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 606s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 606s 606s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 606s 606s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 606s 606s test_Medline ... ok 606s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 606s 606s test_NCBIXML ... loading tests failed: 606s Failed to import test module: test_NCBIXML 606s Traceback (most recent call last): 606s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 606s from . import multiarray 606s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 606s from . import overrides 606s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 606s from numpy.core._multiarray_umath import ( 606s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 606s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 606s 606s During handling of the above exception, another exception occurred: 606s 606s Traceback (most recent call last): 606s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 606s from numpy.__config__ import show as show_config 606s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 606s from numpy.core._multiarray_umath import ( 606s ...<3 lines>... 606s ) 606s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 606s raise ImportError(msg) 606s ImportError: 606s 606s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 606s 606s Importing the numpy C-extensions failed. This error can happen for 606s many reasons, often due to issues with your setup or how NumPy was 606s installed. 606s 606s We have compiled some common reasons and troubleshooting tips at: 606s 606s https://numpy.org/devdocs/user/troubleshooting-importerror.html 606s 606s Please note and check the following: 606s 606s * The Python version is: Python3.13 from "/usr/bin/python3.13" 606s * The NumPy version is: "1.26.4" 606s 606s and make sure that they are the versions you expect. 606s Please carefully study the documentation linked above for further help. 606s 606s Original error was: No module named 'numpy.core._multiarray_umath' 606s 606s 606s The above exception was the direct cause of the following exception: 606s 606s Traceback (most recent call last): 606s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 606s module = __import__(module_name) 606s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 606s from Bio.Blast import NCBIXML 606s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 606s import numpy as np 606s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 606s raise ImportError(msg) from e 606s ImportError: Error importing numpy: you should not try to import numpy from 606s its source directory; please exit the numpy source tree, and relaunch 606s your python interpreter from there. 606s 606s test_NCBI_BLAST_tools ... loading tests failed: 606s Failed to import test module: test_NCBI_BLAST_tools 606s Traceback (most recent call last): 606s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 606s from . import multiarray 606s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 606s from . import overrides 606s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 606s from numpy.core._multiarray_umath import ( 606s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 606s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 606s 606s During handling of the above exception, another exception occurred: 606s 606s Traceback (most recent call last): 606s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 606s from numpy.__config__ import show as show_config 606s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 606s from numpy.core._multiarray_umath import ( 606s ...<3 lines>... 606s ) 606s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 606s raise ImportError(msg) 606s ImportError: 606s 606s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 606s 606s Importing the numpy C-extensions failed. This error can happen for 606s many reasons, often due to issues with your setup or how NumPy was 606s installed. 606s 606s We have compiled some common reasons and troubleshooting tips at: 606s 606s https://numpy.org/devdocs/user/troubleshooting-importerror.html 606s 606s Please note and check the following: 606s 606s * The Python version is: Python3.13 from "/usr/bin/python3.13" 606s * The NumPy version is: "1.26.4" 606s 606s and make sure that they are the versions you expect. 606s Please carefully study the documentation linked above for further help. 606s 606s Original error was: No module named 'numpy.core._multiarray_umath' 606s 606s 606s The above exception was the direct cause of the following exception: 606s 606s Traceback (most recent call last): 606s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 606s module = __import__(module_name) 606s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 606s from Bio.Blast import Applications 606s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 606s import numpy as np 606s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 606s raise ImportError(msg) from e 606s ImportError: Error importing numpy: you should not try to import numpy from 606s its source directory; please exit the numpy source tree, and relaunch 606s your python interpreter from there. 606s 606s test_NCBI_qblast ... loading tests failed: 606s Failed to import test module: test_NCBI_qblast 606s Traceback (most recent call last): 606s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 606s from . import multiarray 606s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 606s from . import overrides 606s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 606s from numpy.core._multiarray_umath import ( 606s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 606s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 606s 606s During handling of the above exception, another exception occurred: 606s 606s Traceback (most recent call last): 606s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 606s from numpy.__config__ import show as show_config 606s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 606s from numpy.core._multiarray_umath import ( 606s ...<3 lines>... 606s ) 606s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 606s raise ImportError(msg) 606s ImportError: 606s 606s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 606s 606s Importing the numpy C-extensions failed. This error can happen for 606s many reasons, often due to issues with your setup or how NumPy was 606s installed. 606s 606s We have compiled some common reasons and troubleshooting tips at: 606s 606s https://numpy.org/devdocs/user/troubleshooting-importerror.html 606s 606s Please note and check the following: 606s 606s * The Python version is: Python3.13 from "/usr/bin/python3.13" 606s * The NumPy version is: "1.26.4" 606s 606s and make sure that they are the versions you expect. 606s Please carefully study the documentation linked above for further help. 606s 606s Original error was: No module named 'numpy.core._multiarray_umath' 606s 606s 606s The above exception was the direct cause of the following exception: 606s 606s Traceback (most recent call last): 606s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 606s module = __import__(module_name) 606s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 606s from Bio.Blast import NCBIWWW 606s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 606s import numpy as np 606s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 606s raise ImportError(msg) from e 606s ImportError: Error importing numpy: you should not try to import numpy from 606s its source directory; please exit the numpy source tree, and relaunch 606s your python interpreter from there. 606s 606s test_NMR ... ok 606s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 606s 606s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 606s 606s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 606s 606s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 606s 606s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 606s 606s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 606s 606s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 606s 606s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 606s 606s test_PDB_Disordered ... loading tests failed: 606s Failed to import test module: test_PDB_Disordered 606s Traceback (most recent call last): 606s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 606s from . import multiarray 606s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 606s from . import overrides 606s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 606s from numpy.core._multiarray_umath import ( 606s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 606s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 606s 606s During handling of the above exception, another exception occurred: 606s 606s Traceback (most recent call last): 606s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 606s from numpy.__config__ import show as show_config 606s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 606s from numpy.core._multiarray_umath import ( 606s ...<3 lines>... 606s ) 606s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 606s raise ImportError(msg) 606s ImportError: 606s 606s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 606s 606s Importing the numpy C-extensions failed. This error can happen for 606s many reasons, often due to issues with your setup or how NumPy was 606s installed. 606s 606s We have compiled some common reasons and troubleshooting tips at: 606s 606s https://numpy.org/devdocs/user/troubleshooting-importerror.html 606s 606s Please note and check the following: 606s 606s * The Python version is: Python3.13 from "/usr/bin/python3.13" 606s * The NumPy version is: "1.26.4" 606s 606s and make sure that they are the versions you expect. 606s Please carefully study the documentation linked above for further help. 606s 606s Original error was: No module named 'numpy.core._multiarray_umath' 606s 606s 606s The above exception was the direct cause of the following exception: 606s 606s Traceback (most recent call last): 606s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 606s module = __import__(module_name) 606s File "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 606s import numpy as np 606s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 606s raise ImportError(msg) from e 606s ImportError: Error importing numpy: you should not try to import numpy from 606s its source directory; please exit the numpy source tree, and relaunch 606s your python interpreter from there. 606s 606s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 606s 606s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 606s 606s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 606s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 606s 607s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 607s 607s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 607s 607s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 607s 607s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 607s 607s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 607s 607s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 607s 607s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 607s 607s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 607s 607s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 607s 607s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 607s 607s test_Pathway ... ok 607s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 607s 607s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_PopGen_GenePop_nodepend ... ok 607s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 607s 607s test_ProtParam ... ok 607s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 607s 608s test_Restriction ... ok 608s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 608s 608s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 608s 608s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 608s 608s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 608s 608s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 608s 608s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 608s 608s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 608s 608s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 608s 608s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 608s 608s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 608s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 608s 609s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 609s 609s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 609s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 609s 609s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 609s 610s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 610s 610s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 610s 610s test_UniGene ... ok 610s test_UniProt ... skipping. internet not available 610s test_UniProt_GOA ... ok 610s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 610s 610s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 610s 610s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 612s test_bgzf ... ok 612s test_cellosaurus ... ok 612s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 612s 612s test_geo ... ok 612s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 612s 612s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 612s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 612s 612s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 612s 612s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 612s 612s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 612s 612s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 612s 612s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 612s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 612s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 612s 612s test_prodoc ... ok 612s test_prosite ... ok 612s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 612s 612s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 613s test_seq ... ok 613s test_translate ... ok 613s Skipping any tests requiring internet access 613s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 613s Operating system: posix linux 613s ---------------------------------------------------------------------- 613s Ran 216 tests in 14.988 seconds 613s 613s FAILED (failures = 15) 613s test_Ace ... ok 613s test_Affy ... ok 616s test_AlignIO ... ok 616s test_AlignIO_ClustalIO ... ok 616s test_AlignIO_EmbossIO ... ok 616s test_AlignIO_FastaIO ... ok 616s test_AlignIO_MauveIO ... ok 616s test_AlignIO_PhylipIO ... ok 616s test_AlignIO_convert ... ok 616s test_AlignInfo ... ok 616s test_Align_Alignment ... ok 616s test_Align_a2m ... ok 616s test_Align_bed ... ok 616s test_Align_bigbed ... ok 617s test_Align_bigmaf ... ok 617s test_Align_bigpsl ... ok 617s test_Align_chain ... ok 617s test_Align_clustal ... ok 623s test_Align_codonalign ... ok 623s test_Align_emboss ... ok 623s test_Align_exonerate ... ok 623s test_Align_fasta ... ok 624s test_Align_hhr ... ok 624s test_Align_maf ... ok 624s test_Align_mauve ... ok 624s test_Align_msf ... ok 625s test_Align_nexus ... ok 625s test_Align_phylip ... ok 625s test_Align_psl ... ok 625s test_Align_sam ... ok 627s test_Align_stockholm ... ok 627s test_Align_tabular ... ok 627s test_Application ... ok 627s test_BioSQL_MySQLdb_online ... skipping. internet not available 627s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 627s test_BioSQL_mysql_connector_online ... skipping. internet not available 627s test_BioSQL_psycopg2_online ... skipping. internet not available 630s test_BioSQL_sqlite3 ... ok 630s test_BioSQL_sqlite3_online ... skipping. internet not available 630s test_Blast_Record ... ok 631s test_Blast_parser ... ok 631s test_CAPS ... ok 631s test_Chi2 ... ok 633s test_ClustalOmega_tool ... ok 633s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 633s test_Cluster ... ok 633s test_CodonTable ... ok 633s test_ColorSpiral ... ok 633s test_Compass ... ok 634s test_Consensus ... ok 635s test_Dialign_tool ... ok 636s test_EMBL_unittest ... ok 636s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 636s test_EmbossPrimer ... ok 640s test_Entrez ... ok 640s test_Entrez_online ... skipping. internet not available 640s test_Entrez_parser ... ok 640s test_Enzyme ... ok 640s test_ExPASy ... skipping. internet not available 640s test_Fasttree_tool ... ok 640s test_File ... ok 641s test_GenBank ... ok 642s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 644s ok 644s test_GraphicsChromosome ... ok 644s test_GraphicsDistribution ... ok 645s test_GraphicsGeneral ... ok 645s test_HMMCasino ... ok 645s test_HMMGeneral ... ok 645s test_KEGG ... ok 645s test_KEGG_online ... skipping. internet not available 651s test_KGML_graphics ... ok 651s test_KGML_graphics_online ... skipping. internet not available 652s test_KGML_nographics ... ok 652s test_KeyWList ... ok 652s test_LogisticRegression ... ok 653s test_MafIO_index ... ok 654s test_Mafft_tool ... ok 654s test_MarkovModel ... ok 654s test_Medline ... ok 654s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 655s test_NCBIXML ... ok 656s test_NCBI_BLAST_tools ... ok 656s test_NCBI_qblast ... ok 656s test_NMR ... ok 657s test_NaiveBayes ... ok 657s test_Nexus ... ok 657s test_PAML_baseml ... ok 657s test_PAML_codeml ... ok 657s test_PAML_yn00 ... ok 661s test_PDB_CEAligner ... ok 662s test_PDB_DSSP ... /usr/lib/python3/dist-packages/Bio/PDB/DSSP.py:199: UserWarning: 662s Configuration error: 662s 662s The attempt to retrieve compound information for "SO4" failed. 662s 662s This information is searched for in a CCD file called components.cif or 662s components.cif.gz which should be located in one of the following directories: 662s 662s "/usr/share/libcifpp" 662s "/var/cache/libcifpp" 662s "/tmp/autopkgtest.Ou6kQf/autopkgtest_tmp/libcifpp-data" 662s "/usr/share/libcifpp" 662s "/usr/share/libcifpp" 662s 662s (Note that you can add a directory to the search paths by setting the 662s LIBCIFPP_DATA_DIR environmental variable) 662s 662s On Linux an optional cron script might have been installed that automatically updates 662s components.cif and mmCIF dictionary files. This script only works when the file 662s libcifpp.conf contains an uncommented line with the text: 662s 662s update=true 662s 662s If you do not have a working cron script, you can manually update the files 662s in /var/cache/libcifpp using the following commands: 662s 662s curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif 662s curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic 662s curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic 662s 662s The current order of compound factory objects is: 662s 662s CCD components.cif resource 662s CCD components.cif resource 662s Unknown compound: SO4 662s Missing compound information for SO4 662s 662s warnings.warn(err) 663s ok 663s test_PDB_Dice ... ok 663s test_PDB_Disordered ... ok 663s test_PDB_Exposure ... ok 663s test_PDB_FragmentMapper ... ok 665s test_PDB_KDTree ... ok 665s test_PDB_MMCIF2Dict ... ok 665s test_PDB_MMCIFIO ... ok 666s test_PDB_MMCIFParser ... ok 666s test_PDB_NACCESS ... ok 666s test_PDB_PDBIO ... ok 666s test_PDB_PDBList ... skipping. internet not available 676s test_PDB_PDBMLParser ... ok 677s test_PDB_PDBParser ... ok 677s 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 677s test_PDB_Polypeptide ... ok 677s test_PDB_QCPSuperimposer ... ok 681s test_PDB_SASA ... ok 682s test_PDB_SMCRA ... ok 682s test_PDB_Selection ... ok 682s test_PDB_StructureAlignment ... ok 682s test_PDB_Superimposer ... ok 682s test_PDB_alphafold_db ... skipping. internet not available 692s test_PDB_internal_coords ... ok 692s test_PDB_parse_pdb_header ... ok 693s test_PDB_vectors ... ok 693s test_PQR ... ok 693s test_Pathway ... ok 694s test_Phd ... ok 694s test_Phylo ... ok 695s test_PhyloXML ... ok 696s test_Phylo_CDAO ... ok 696s test_Phylo_NeXML ... ok 696s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 700s test_Phylo_matplotlib ... ok 701s test_Phylo_networkx ... ok 702s test_PopGen_GenePop_nodepend ... ok 703s test_Prank_tool ... ok 704s test_Probcons_tool ... ok 705s test_ProtParam ... ok 706s test_RCSBFormats ... ok 707s test_Restriction ... ok 708s test_SCOP_Astral ... ok 708s test_SCOP_Cla ... ok 709s test_SCOP_Des ... ok 710s test_SCOP_Dom ... ok 711s test_SCOP_Hie ... ok 711s test_SCOP_Raf ... ok 712s test_SCOP_Residues ... ok 713s test_SCOP_Scop ... ok 713s test_SVDSuperimposer ... ok 714s test_SearchIO_blast_tab ... ok 715s test_SearchIO_blast_tab_index ... ok 716s test_SearchIO_blast_xml ... ok 718s test_SearchIO_blast_xml_index ... ok 719s test_SearchIO_blat_psl ... ok 720s test_SearchIO_blat_psl_index ... ok 720s test_SearchIO_exonerate ... ok 721s test_SearchIO_exonerate_text_index ... ok 721s test_SearchIO_exonerate_vulgar_index ... ok 722s test_SearchIO_fasta_m10 ... ok 723s test_SearchIO_fasta_m10_index ... ok 723s test_SearchIO_hhsuite2_text ... ok 724s test_SearchIO_hmmer2_text ... ok 725s test_SearchIO_hmmer2_text_index ... ok 726s test_SearchIO_hmmer3_domtab ... ok 726s test_SearchIO_hmmer3_domtab_index ... ok 727s test_SearchIO_hmmer3_tab ... ok 728s test_SearchIO_hmmer3_tab_index ... ok 729s test_SearchIO_hmmer3_text ... ok 729s test_SearchIO_hmmer3_text_index ... ok 730s test_SearchIO_interproscan_xml ... ok 730s test_SearchIO_model ... ok 731s test_SearchIO_write ... ok 732s test_SeqFeature ... ok 748s test_SeqIO ... ok 749s test_SeqIO_AbiIO ... ok 750s test_SeqIO_FastaIO ... ok 751s test_SeqIO_Gck ... ok 751s test_SeqIO_Gfa ... ok 752s test_SeqIO_Insdc ... ok 753s test_SeqIO_NibIO ... ok 755s test_SeqIO_PdbIO ... ok 756s test_SeqIO_QualityIO ... ok 757s test_SeqIO_SeqXML ... ok 758s test_SeqIO_SnapGene ... ok 759s test_SeqIO_TwoBitIO ... ok 760s test_SeqIO_Xdna ... ok 761s test_SeqIO_features ... ok 774s test_SeqIO_index ... ok 774s test_SeqIO_online ... skipping. internet not available 775s test_SeqIO_write ... ok 776s test_SeqRecord ... ok 777s test_SeqUtils ... ok 779s test_Seq_objs ... ok 779s test_SffIO ... ok 780s test_SwissProt ... ok 783s test_TCoffee_tool ... ok 783s test_TogoWS ... skipping. internet not available 784s test_TreeConstruction ... ok 784s test_UniGene ... ok 785s test_UniProt ... skipping. internet not available 786s test_UniProt_GOA ... ok 786s test_UniProt_Parser ... ok 787s test_align ... ok 788s test_align_substitution_matrices ... ok 791s test_bgzf ... ok 792s test_cellosaurus ... ok 797s test_codonalign ... ok 798s test_geo ... ok 799s test_kNN ... ok 800s test_motifs ... ok 800s test_motifs_online ... skipping. internet not available 801s 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. 801s warnings.warn( 801s ok 802s test_pairwise2_no_C ... ok 803s test_pairwise_aligner ... ok 803s test_pairwise_alignment_map ... ok 811s test_phenotype ... ok 811s test_phenotype_fit ... ok 812s test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. 812s test_prodoc ... ok 813s test_prosite ... ok 813s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 814s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 815s test_seq ... ok 815s test_translate ... ok 816s ---------------------------------------------------------------------- 816s Ran 216 tests in 202.787 seconds 816s Skipping any tests requiring internet access 816s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 816s Operating system: posix linux 816s 818s autopkgtest [13:14:30]: test full_suite: -----------------------] 818s autopkgtest [13:14:30]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 818s full_suite PASS 819s autopkgtest [13:14:31]: @@@@@@@@@@@@@@@@@@@@ summary 819s dependencies PASS 819s full_suite PASS 831s nova [W] Using flock in prodstack6-s390x 831s Creating nova instance adt-plucky-s390x-python-biopython-20241113-130052-juju-7f2275-prod-proposed-migration-environment-20-1bef5a9e-06c3-4cdc-b0f0-1ccc1975949b from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)... 831s nova [W] Using flock in prodstack6-s390x 831s Creating nova instance adt-plucky-s390x-python-biopython-20241113-130052-juju-7f2275-prod-proposed-migration-environment-20-1bef5a9e-06c3-4cdc-b0f0-1ccc1975949b from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...