0s autopkgtest [11:31:08]: starting date and time: 2024-11-13 11:31:08+0000 0s autopkgtest [11:31:08]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [11:31:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fvacjj5j/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-8.secgroup --name adt-plucky-amd64-python-biopython-20241113-113108-juju-7f2275-prod-proposed-migration-environment-2-65eea040-112e-4356-97b0-bc05381b34aa --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -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/ 57s autopkgtest [11:32:05]: testbed dpkg architecture: amd64 57s autopkgtest [11:32:05]: testbed apt version: 2.9.8 57s autopkgtest [11:32:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 57s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 57s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 57s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 57s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 57s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 57s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 57s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 57s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 57s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 57s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 57s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 57s Fetched 2175 kB in 0s (6721 kB/s) 58s Reading package lists... 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 60s The following NEW packages will be installed: 60s python3.13-gdbm 60s The following packages will be upgraded: 60s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 60s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 253 kB of archives. 60s After this operation, 147 kB of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 60s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 60s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 60s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 60s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 60s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 60s Fetched 253 kB in 0s (5283 kB/s) 60s (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 ... 75541 files and directories currently installed.) 60s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 60s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 60s Setting up python3-minimal (3.12.7-1) ... 61s (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 ... 75541 files and directories currently installed.) 61s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 61s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 61s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 61s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 61s Selecting previously unselected package python3.13-gdbm. 61s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 61s Unpacking python3.13-gdbm (3.13.0-2) ... 61s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 61s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 61s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 61s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 61s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 61s Setting up python3.13-gdbm (3.13.0-2) ... 61s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 61s Setting up python3 (3.12.7-1) ... 61s Setting up python3-gdbm:amd64 (3.12.7-1) ... 61s Processing triggers for man-db (2.12.1-3) ... 62s Processing triggers for libc-bin (2.40-1ubuntu3) ... 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 63s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 64s Reading package lists... 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 65s Calculating upgrade... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s autopkgtest [11:32:14]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 67s autopkgtest [11:32:15]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 68s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (dsc) [3543 B] 68s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (tar) [14.6 MB] 68s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (diff) [42.8 kB] 68s gpgv: Signature made Wed Oct 30 21:23:04 2024 UTC 68s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 68s gpgv: issuer "emollier@debian.org" 68s gpgv: Can't check signature: No public key 68s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.84+dfsg-4.dsc: no acceptable signature found 69s autopkgtest [11:32:17]: testing package python-biopython version 1.84+dfsg-4 69s autopkgtest [11:32:17]: build not needed 70s autopkgtest [11:32:18]: test dependencies: preparing testbed 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Starting pkgProblemResolver with broken count: 0 71s Starting 2 pkgProblemResolver with broken count: 0 71s Done 72s The following additional packages will be installed: 72s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 72s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 72s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 72s libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblcms2-2 72s liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 72s libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 72s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 72s python3-all python3-biopython python3-biopython-sql python3-cairo 72s python3-freetype python3-numpy python3-pil python3-reportlab 72s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 72s x11-common xfonts-encodings xfonts-utils xml-core 72s Suggested packages: 72s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 72s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 72s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 72s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 72s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 72s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 72s rl-renderpm python3.13-venv python3.13-doc binfmt-support sgml-base-doc 72s debhelper 72s Recommended packages: 72s javascript-common ncbi-blast+ python3-olefile fonts-dejavu-extra 72s The following NEW packages will be installed: 72s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 72s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 72s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 72s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 72s liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 72s libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 72s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 72s python-biopython-doc python3-all python3-biopython python3-biopython-sql 72s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 72s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 72s x11-common xfonts-encodings xfonts-utils xml-core 72s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 53.1 MB/53.1 MB of archives. 72s After this operation, 150 MB of additional disk space will be used. 72s Get:1 /tmp/autopkgtest.YFyfMk/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [744 B] 72s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 72s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 72s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 72s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 72s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 72s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 72s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 72s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 72s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 72s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 72s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 72s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 72s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 72s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 72s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 72s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 72s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 72s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 72s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 72s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 72s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 72s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 72s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 72s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 72s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 72s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 72s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 72s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 72s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 72s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 72s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 72s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 72s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 72s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 72s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 72s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 72s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 72s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 72s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 72s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 72s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 73s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 73s Get:44 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 73s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 73s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 73s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 73s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 73s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 73s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 73s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 73s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 73s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 73s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 73s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 73s Fetched 53.1 MB in 1s (68.6 MB/s) 73s Selecting previously unselected package libpython3.13-minimal:amd64. 73s (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 ... 75548 files and directories currently installed.) 73s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 73s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 73s Selecting previously unselected package python3.13-minimal. 73s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 73s Unpacking python3.13-minimal (3.13.0-2) ... 73s Selecting previously unselected package sgml-base. 73s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 73s Unpacking sgml-base (1.31) ... 73s Selecting previously unselected package fonts-dejavu-mono. 73s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 73s Unpacking fonts-dejavu-mono (2.37-8) ... 73s Selecting previously unselected package fonts-dejavu-core. 73s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 73s Unpacking fonts-dejavu-core (2.37-8) ... 73s Selecting previously unselected package libfontenc1:amd64. 73s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 73s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 73s Selecting previously unselected package x11-common. 73s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ... 73s Unpacking x11-common (1:7.7+23ubuntu3) ... 73s Selecting previously unselected package xfonts-encodings. 73s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 73s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 73s Selecting previously unselected package xfonts-utils. 73s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_amd64.deb ... 73s Unpacking xfonts-utils (1:7.7+7) ... 73s Selecting previously unselected package fonts-urw-base35. 73s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ... 74s Unpacking fonts-urw-base35 (20200910-8) ... 74s Selecting previously unselected package fontconfig-config. 74s Preparing to unpack .../10-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 74s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 74s Selecting previously unselected package libblas3:amd64. 74s Preparing to unpack .../11-libblas3_3.12.0-3build2_amd64.deb ... 74s Unpacking libblas3:amd64 (3.12.0-3build2) ... 74s Selecting previously unselected package libfontconfig1:amd64. 74s Preparing to unpack .../12-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 74s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 74s Selecting previously unselected package libpixman-1-0:amd64. 74s Preparing to unpack .../13-libpixman-1-0_0.44.0-3_amd64.deb ... 74s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 74s Selecting previously unselected package libxcb-render0:amd64. 74s Preparing to unpack .../14-libxcb-render0_1.17.0-2_amd64.deb ... 74s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 74s Selecting previously unselected package libxcb-shm0:amd64. 74s Preparing to unpack .../15-libxcb-shm0_1.17.0-2_amd64.deb ... 74s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 74s Selecting previously unselected package libxrender1:amd64. 74s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 74s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 74s Selecting previously unselected package libcairo2:amd64. 74s Preparing to unpack .../17-libcairo2_1.18.2-2_amd64.deb ... 74s Unpacking libcairo2:amd64 (1.18.2-2) ... 74s Selecting previously unselected package libdeflate0:amd64. 74s Preparing to unpack .../18-libdeflate0_1.22-1_amd64.deb ... 74s Unpacking libdeflate0:amd64 (1.22-1) ... 74s Selecting previously unselected package libgfortran5:amd64. 74s Preparing to unpack .../19-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 74s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 74s Selecting previously unselected package libgomp1:amd64. 74s Preparing to unpack .../20-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 74s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 74s Selecting previously unselected package libgraphite2-3:amd64. 74s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 74s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 74s Selecting previously unselected package libharfbuzz0b:amd64. 74s Preparing to unpack .../22-libharfbuzz0b_10.0.1-1_amd64.deb ... 74s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 74s Selecting previously unselected package libimagequant0:amd64. 74s Preparing to unpack .../23-libimagequant0_2.18.0-1build1_amd64.deb ... 74s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 74s Selecting previously unselected package 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81687 files and directories currently installed.) 119s Removing autopkgtest-satdep (0) ... 120s autopkgtest [11:33:08]: test dependencies: sh debian/tests/run-unit-test 120s autopkgtest [11:33:08]: test dependencies: [----------------------- 120s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 120s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 120s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 120s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 122s mkdir: created directory 'Bio' 122s mkdir: created directory 'Bio/Align' 122s mkdir: created directory 'Bio/Align/substitution_matrices' 122s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 122s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 122s Remove test test_Tutorial.py which is bound to fail 122s test_Ace ... ok 122s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 122s 122s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 122s 122s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 122s 122s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 122s 122s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 122s 122s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 122s 122s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 122s 122s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 122s 122s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 122s 122s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 122s 122s test_Align_a2m ... loading tests failed: 122s Failed to import test module: test_Align_a2m 122s Traceback (most recent call last): 122s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 122s from . import multiarray 122s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 122s from . import overrides 122s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 122s from numpy.core._multiarray_umath import ( 122s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 122s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 122s 122s During handling of the above exception, another exception occurred: 122s 122s Traceback (most recent call last): 122s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 122s from numpy.__config__ import show as show_config 122s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 122s from numpy.core._multiarray_umath import ( 122s ...<3 lines>... 122s ) 122s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 122s raise ImportError(msg) 122s ImportError: 122s 122s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 122s 122s Importing the numpy C-extensions failed. This error can happen for 122s many reasons, often due to issues with your setup or how NumPy was 122s installed. 122s 122s We have compiled some common reasons and troubleshooting tips at: 122s 122s https://numpy.org/devdocs/user/troubleshooting-importerror.html 122s 122s Please note and check the following: 122s 122s * The Python version is: Python3.13 from "/usr/bin/python3.13" 122s * The NumPy version is: "1.26.4" 122s 122s and make sure that they are the versions you expect. 122s Please carefully study the documentation linked above for further help. 122s 122s Original error was: No module named 'numpy.core._multiarray_umath' 122s 122s 122s The above exception was the direct cause of the following exception: 122s 122s Traceback (most recent call last): 122s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 122s module = __import__(module_name) 122s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 122s import numpy as np 122s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 122s raise ImportError(msg) from e 122s ImportError: Error importing numpy: you should not try to import numpy from 122s its source directory; please exit the numpy source tree, and relaunch 122s your python interpreter from there. 122s 122s test_Align_bed ... loading tests failed: 122s Failed to import test module: test_Align_bed 122s Traceback (most recent call last): 122s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 122s from . import multiarray 122s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 122s from . import overrides 122s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 122s from numpy.core._multiarray_umath import ( 122s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 122s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 122s 122s During handling of the above exception, another exception occurred: 122s 122s Traceback (most recent call last): 122s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 122s from numpy.__config__ import show as show_config 122s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 122s from numpy.core._multiarray_umath import ( 122s ...<3 lines>... 122s ) 122s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 122s raise ImportError(msg) 122s ImportError: 122s 122s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 122s 122s Importing the numpy C-extensions failed. This error can happen for 122s many reasons, often due to issues with your setup or how NumPy was 122s installed. 122s 122s We have compiled some common reasons and troubleshooting tips at: 122s 122s https://numpy.org/devdocs/user/troubleshooting-importerror.html 122s 122s Please note and check the following: 122s 122s * The Python version is: Python3.13 from "/usr/bin/python3.13" 122s * The NumPy version is: "1.26.4" 122s 122s and make sure that they are the versions you expect. 122s Please carefully study the documentation linked above for further help. 122s 122s Original error was: No module named 'numpy.core._multiarray_umath' 122s 122s 122s The above exception was the direct cause of the following exception: 122s 122s Traceback (most recent call last): 122s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 122s module = __import__(module_name) 122s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 122s import numpy as np 122s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 122s raise ImportError(msg) from e 122s ImportError: Error importing numpy: you should not try to import numpy from 122s its source directory; please exit the numpy source tree, and relaunch 122s your python interpreter from there. 122s 123s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_bigmaf ... loading tests failed: 123s Failed to import test module: test_Align_bigmaf 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 123s from . import multiarray 123s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 123s from . import overrides 123s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 123s from numpy.core._multiarray_umath import ( 123s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 123s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 123s 123s During handling of the above exception, another exception occurred: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 123s from numpy.__config__ import show as show_config 123s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 123s from numpy.core._multiarray_umath import ( 123s ...<3 lines>... 123s ) 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 123s raise ImportError(msg) 123s ImportError: 123s 123s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 123s 123s Importing the numpy C-extensions failed. This error can happen for 123s many reasons, often due to issues with your setup or how NumPy was 123s installed. 123s 123s We have compiled some common reasons and troubleshooting tips at: 123s 123s https://numpy.org/devdocs/user/troubleshooting-importerror.html 123s 123s Please note and check the following: 123s 123s * The Python version is: Python3.13 from "/usr/bin/python3.13" 123s * The NumPy version is: "1.26.4" 123s 123s and make sure that they are the versions you expect. 123s Please carefully study the documentation linked above for further help. 123s 123s Original error was: No module named 'numpy.core._multiarray_umath' 123s 123s 123s The above exception was the direct cause of the following exception: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 123s module = __import__(module_name) 123s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 123s import numpy as np 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 123s raise ImportError(msg) from e 123s ImportError: Error importing numpy: you should not try to import numpy from 123s its source directory; please exit the numpy source tree, and relaunch 123s your python interpreter from there. 123s 123s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_clustal ... loading tests failed: 123s Failed to import test module: test_Align_clustal 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 123s from . import multiarray 123s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 123s from . import overrides 123s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 123s from numpy.core._multiarray_umath import ( 123s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 123s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 123s 123s During handling of the above exception, another exception occurred: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 123s from numpy.__config__ import show as show_config 123s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 123s from numpy.core._multiarray_umath import ( 123s ...<3 lines>... 123s ) 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 123s raise ImportError(msg) 123s ImportError: 123s 123s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 123s 123s Importing the numpy C-extensions failed. This error can happen for 123s many reasons, often due to issues with your setup or how NumPy was 123s installed. 123s 123s We have compiled some common reasons and troubleshooting tips at: 123s 123s https://numpy.org/devdocs/user/troubleshooting-importerror.html 123s 123s Please note and check the following: 123s 123s * The Python version is: Python3.13 from "/usr/bin/python3.13" 123s * The NumPy version is: "1.26.4" 123s 123s and make sure that they are the versions you expect. 123s Please carefully study the documentation linked above for further help. 123s 123s Original error was: No module named 'numpy.core._multiarray_umath' 123s 123s 123s The above exception was the direct cause of the following exception: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 123s module = __import__(module_name) 123s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 123s import numpy as np 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 123s raise ImportError(msg) from e 123s ImportError: Error importing numpy: you should not try to import numpy from 123s its source directory; please exit the numpy source tree, and relaunch 123s your python interpreter from there. 123s 123s test_Align_codonalign ... loading tests failed: 123s Failed to import test module: test_Align_codonalign 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 123s from . import multiarray 123s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 123s from . import overrides 123s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 123s from numpy.core._multiarray_umath import ( 123s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 123s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 123s 123s During handling of the above exception, another exception occurred: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 123s from numpy.__config__ import show as show_config 123s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 123s from numpy.core._multiarray_umath import ( 123s ...<3 lines>... 123s ) 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 123s raise ImportError(msg) 123s ImportError: 123s 123s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 123s 123s Importing the numpy C-extensions failed. This error can happen for 123s many reasons, often due to issues with your setup or how NumPy was 123s installed. 123s 123s We have compiled some common reasons and troubleshooting tips at: 123s 123s https://numpy.org/devdocs/user/troubleshooting-importerror.html 123s 123s Please note and check the following: 123s 123s * The Python version is: Python3.13 from "/usr/bin/python3.13" 123s * The NumPy version is: "1.26.4" 123s 123s and make sure that they are the versions you expect. 123s Please carefully study the documentation linked above for further help. 123s 123s Original error was: No module named 'numpy.core._multiarray_umath' 123s 123s 123s The above exception was the direct cause of the following exception: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 123s module = __import__(module_name) 123s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 123s import numpy as np 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 123s raise ImportError(msg) from e 123s ImportError: Error importing numpy: you should not try to import numpy from 123s its source directory; please exit the numpy source tree, and relaunch 123s your python interpreter from there. 123s 123s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_fasta ... loading tests failed: 123s Failed to import test module: test_Align_fasta 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 123s from . import multiarray 123s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 123s from . import overrides 123s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 123s from numpy.core._multiarray_umath import ( 123s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 123s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 123s 123s During handling of the above exception, another exception occurred: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 123s from numpy.__config__ import show as show_config 123s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 123s from numpy.core._multiarray_umath import ( 123s ...<3 lines>... 123s ) 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 123s raise ImportError(msg) 123s ImportError: 123s 123s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 123s 123s Importing the numpy C-extensions failed. This error can happen for 123s many reasons, often due to issues with your setup or how NumPy was 123s installed. 123s 123s We have compiled some common reasons and troubleshooting tips at: 123s 123s https://numpy.org/devdocs/user/troubleshooting-importerror.html 123s 123s Please note and check the following: 123s 123s * The Python version is: Python3.13 from "/usr/bin/python3.13" 123s * The NumPy version is: "1.26.4" 123s 123s and make sure that they are the versions you expect. 123s Please carefully study the documentation linked above for further help. 123s 123s Original error was: No module named 'numpy.core._multiarray_umath' 123s 123s 123s The above exception was the direct cause of the following exception: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 123s module = __import__(module_name) 123s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 123s import numpy as np 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 123s raise ImportError(msg) from e 123s ImportError: Error importing numpy: you should not try to import numpy from 123s its source directory; please exit the numpy source tree, and relaunch 123s your python interpreter from there. 123s 123s test_Align_hhr ... loading tests failed: 123s Failed to import test module: test_Align_hhr 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 123s from . import multiarray 123s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 123s from . import overrides 123s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 123s from numpy.core._multiarray_umath import ( 123s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 123s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 123s 123s During handling of the above exception, another exception occurred: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 123s from numpy.__config__ import show as show_config 123s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 123s from numpy.core._multiarray_umath import ( 123s ...<3 lines>... 123s ) 123s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 123s raise ImportError(msg) 123s ImportError: 123s 123s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 123s 123s Importing the numpy C-extensions failed. This error can happen for 123s many reasons, often due to issues with your setup or how NumPy was 123s installed. 123s 123s We have compiled some common reasons and troubleshooting tips at: 123s 123s https://numpy.org/devdocs/user/troubleshooting-importerror.html 123s 123s Please note and check the following: 123s 123s * The Python version is: Python3.13 from "/usr/bin/python3.13" 123s * The NumPy version is: "1.26.4" 123s 123s and make sure that they are the versions you expect. 123s Please carefully study the documentation linked above for further help. 123s 123s Original error was: No module named 'numpy.core._multiarray_umath' 123s 123s 123s The above exception was the direct cause of the following exception: 123s 123s Traceback (most recent call last): 123s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 123s module = __import__(module_name) 123s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 123s import numpy as np 123s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 123s raise ImportError(msg) from e 123s ImportError: Error importing numpy: you should not try to import numpy from 123s its source directory; please exit the numpy source tree, and relaunch 123s your python interpreter from there. 123s 123s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 123s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 123s 124s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_Application ... ok 124s test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython 124s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_Blast_Record ... loading tests failed: 124s Failed to import test module: test_Blast_Record 124s Traceback (most recent call last): 124s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 124s from . import multiarray 124s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 124s from . import overrides 124s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 124s from numpy.core._multiarray_umath import ( 124s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 124s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 124s 124s During handling of the above exception, another exception occurred: 124s 124s Traceback (most recent call last): 124s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 124s from numpy.__config__ import show as show_config 124s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 124s from numpy.core._multiarray_umath import ( 124s ...<3 lines>... 124s ) 124s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 124s raise ImportError(msg) 124s ImportError: 124s 124s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 124s 124s Importing the numpy C-extensions failed. This error can happen for 124s many reasons, often due to issues with your setup or how NumPy was 124s installed. 124s 124s We have compiled some common reasons and troubleshooting tips at: 124s 124s https://numpy.org/devdocs/user/troubleshooting-importerror.html 124s 124s Please note and check the following: 124s 124s * The Python version is: Python3.13 from "/usr/bin/python3.13" 124s * The NumPy version is: "1.26.4" 124s 124s and make sure that they are the versions you expect. 124s Please carefully study the documentation linked above for further help. 124s 124s Original error was: No module named 'numpy.core._multiarray_umath' 124s 124s 124s The above exception was the direct cause of the following exception: 124s 124s Traceback (most recent call last): 124s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 124s module = __import__(module_name) 124s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 124s from Bio.Blast.NCBIXML import HSP 124s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 124s import numpy as np 124s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 124s raise ImportError(msg) from e 124s ImportError: Error importing numpy: you should not try to import numpy from 124s its source directory; please exit the numpy source tree, and relaunch 124s your python interpreter from there. 124s 124s test_Blast_parser ... loading tests failed: 124s Failed to import test module: test_Blast_parser 124s Traceback (most recent call last): 124s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 124s from . import multiarray 124s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 124s from . import overrides 124s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 124s from numpy.core._multiarray_umath import ( 124s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 124s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 124s 124s During handling of the above exception, another exception occurred: 124s 124s Traceback (most recent call last): 124s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 124s from numpy.__config__ import show as show_config 124s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 124s from numpy.core._multiarray_umath import ( 124s ...<3 lines>... 124s ) 124s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 124s raise ImportError(msg) 124s ImportError: 124s 124s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 124s 124s Importing the numpy C-extensions failed. This error can happen for 124s many reasons, often due to issues with your setup or how NumPy was 124s installed. 124s 124s We have compiled some common reasons and troubleshooting tips at: 124s 124s https://numpy.org/devdocs/user/troubleshooting-importerror.html 124s 124s Please note and check the following: 124s 124s * The Python version is: Python3.13 from "/usr/bin/python3.13" 124s * The NumPy version is: "1.26.4" 124s 124s and make sure that they are the versions you expect. 124s Please carefully study the documentation linked above for further help. 124s 124s Original error was: No module named 'numpy.core._multiarray_umath' 124s 124s 124s The above exception was the direct cause of the following exception: 124s 124s Traceback (most recent call last): 124s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 124s module = __import__(module_name) 124s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 124s import numpy as np 124s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 124s raise ImportError(msg) from e 124s ImportError: Error importing numpy: you should not try to import numpy from 124s its source directory; please exit the numpy source tree, and relaunch 124s your python interpreter from there. 124s 124s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s 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 124s warnings.warn( 124s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 124s 124s test_CodonTable ... ok 124s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 124s 124s test_Compass ... ok 124s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 124s 124s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 124s 124s test_EmbossPrimer ... ok 128s test_Entrez ... ok 128s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 128s 129s test_Entrez_parser ... ok 129s test_Enzyme ... ok 129s test_ExPASy ... skipping. internet not available 129s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 129s 129s test_File ... ok 129s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 129s 129s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 129s 129s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 129s 129s test_GraphicsDistribution ... loading tests failed: 129s Failed to import test module: test_GraphicsDistribution 129s Traceback (most recent call last): 129s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 129s module = __import__(module_name) 129s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 129s from Bio.Graphics.Distribution import BarChartDistribution 129s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 129s from reportlab.graphics.charts.barcharts import BarChartProperties 129s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 129s from reportlab.lib import colors 129s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 129s from reportlab.lib.rl_accel import fp_str 129s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 129s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 129s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 129s from PIL import Image 129s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 129s from . import _imaging as core 129s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 129s 129s test_GraphicsGeneral ... loading tests failed: 129s Failed to import test module: test_GraphicsGeneral 129s Traceback (most recent call last): 129s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 129s module = __import__(module_name) 129s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 129s from Bio.Graphics.Comparative import ComparativeScatterPlot 129s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 129s from reportlab.graphics.charts.lineplots import LinePlot 129s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 129s from reportlab.lib import colors 129s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 129s from reportlab.lib.rl_accel import fp_str 129s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 129s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 129s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 129s from PIL import Image 129s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 129s from . import _imaging as core 129s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 129s 129s test_HMMCasino ... ok 129s test_HMMGeneral ... ok 129s test_KEGG ... ok 129s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 129s 129s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 129s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 130s test_KGML_nographics ... ok 130s test_KeyWList ... ok 130s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 130s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 130s 130s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 130s 130s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 130s 130s test_Medline ... ok 130s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 130s 130s test_NCBIXML ... loading tests failed: 130s Failed to import test module: test_NCBIXML 130s Traceback (most recent call last): 130s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 130s from . import multiarray 130s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 130s from . import overrides 130s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 130s from numpy.core._multiarray_umath import ( 130s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 130s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 130s 130s During handling of the above exception, another exception occurred: 130s 130s Traceback (most recent call last): 130s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 130s from numpy.__config__ import show as show_config 130s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 130s from numpy.core._multiarray_umath import ( 130s ...<3 lines>... 130s ) 130s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 130s raise ImportError(msg) 130s ImportError: 130s 130s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 130s 130s Importing the numpy C-extensions failed. This error can happen for 130s many reasons, often due to issues with your setup or how NumPy was 130s installed. 130s 130s We have compiled some common reasons and troubleshooting tips at: 130s 130s https://numpy.org/devdocs/user/troubleshooting-importerror.html 130s 130s Please note and check the following: 130s 130s * The Python version is: Python3.13 from "/usr/bin/python3.13" 130s * The NumPy version is: "1.26.4" 130s 130s and make sure that they are the versions you expect. 130s Please carefully study the documentation linked above for further help. 130s 130s Original error was: No module named 'numpy.core._multiarray_umath' 130s 130s 130s The above exception was the direct cause of the following exception: 130s 130s Traceback (most recent call last): 130s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 130s module = __import__(module_name) 130s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 130s from Bio.Blast import NCBIXML 130s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 130s import numpy as np 130s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 130s raise ImportError(msg) from e 130s ImportError: Error importing numpy: you should not try to import numpy from 130s its source directory; please exit the numpy source tree, and relaunch 130s your python interpreter from there. 130s 130s test_NCBI_BLAST_tools ... loading tests failed: 130s Failed to import test module: test_NCBI_BLAST_tools 130s Traceback (most recent call last): 130s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 130s from . import multiarray 130s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 130s from . import overrides 130s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 130s from numpy.core._multiarray_umath import ( 130s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 130s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 130s 130s During handling of the above exception, another exception occurred: 130s 130s Traceback (most recent call last): 130s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 130s from numpy.__config__ import show as show_config 130s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 130s from numpy.core._multiarray_umath import ( 130s ...<3 lines>... 130s ) 130s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 130s raise ImportError(msg) 130s ImportError: 130s 130s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 130s 130s Importing the numpy C-extensions failed. This error can happen for 130s many reasons, often due to issues with your setup or how NumPy was 130s installed. 130s 130s We have compiled some common reasons and troubleshooting tips at: 130s 130s https://numpy.org/devdocs/user/troubleshooting-importerror.html 130s 130s Please note and check the following: 130s 130s * The Python version is: Python3.13 from "/usr/bin/python3.13" 130s * The NumPy version is: "1.26.4" 130s 130s and make sure that they are the versions you expect. 130s Please carefully study the documentation linked above for further help. 130s 130s Original error was: No module named 'numpy.core._multiarray_umath' 130s 130s 130s The above exception was the direct cause of the following exception: 130s 130s Traceback (most recent call last): 130s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 130s module = __import__(module_name) 130s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 130s from Bio.Blast import Applications 130s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 130s import numpy as np 130s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 130s raise ImportError(msg) from e 130s ImportError: Error importing numpy: you should not try to import numpy from 130s its source directory; please exit the numpy source tree, and relaunch 130s your python interpreter from there. 130s 130s test_NCBI_qblast ... loading tests failed: 130s Failed to import test module: test_NCBI_qblast 130s Traceback (most recent call last): 130s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 130s from . import multiarray 130s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 130s from . import overrides 130s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 130s from numpy.core._multiarray_umath import ( 130s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 130s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 130s 130s During handling of the above exception, another exception occurred: 130s 130s Traceback (most recent call last): 130s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 130s from numpy.__config__ import show as show_config 130s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 130s from numpy.core._multiarray_umath import ( 130s ...<3 lines>... 130s ) 130s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 130s raise ImportError(msg) 130s ImportError: 130s 130s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 130s 130s Importing the numpy C-extensions failed. This error can happen for 130s many reasons, often due to issues with your setup or how NumPy was 130s installed. 130s 130s We have compiled some common reasons and troubleshooting tips at: 130s 130s https://numpy.org/devdocs/user/troubleshooting-importerror.html 130s 130s Please note and check the following: 130s 130s * The Python version is: Python3.13 from "/usr/bin/python3.13" 130s * The NumPy version is: "1.26.4" 130s 130s and make sure that they are the versions you expect. 130s Please carefully study the documentation linked above for further help. 130s 130s Original error was: No module named 'numpy.core._multiarray_umath' 130s 130s 130s The above exception was the direct cause of the following exception: 130s 130s Traceback (most recent call last): 130s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 130s module = __import__(module_name) 130s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 130s from Bio.Blast import NCBIWWW 130s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 130s import numpy as np 130s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 130s raise ImportError(msg) from e 130s ImportError: Error importing numpy: you should not try to import numpy from 130s its source directory; please exit the numpy source tree, and relaunch 130s your python interpreter from there. 130s 130s test_NMR ... ok 130s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 130s 130s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 130s 130s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 130s 130s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 130s 131s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_Disordered ... loading tests failed: 131s Failed to import test module: test_PDB_Disordered 131s Traceback (most recent call last): 131s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 131s from . import multiarray 131s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 131s from . import overrides 131s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 131s from numpy.core._multiarray_umath import ( 131s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 131s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 131s 131s During handling of the above exception, another exception occurred: 131s 131s Traceback (most recent call last): 131s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 131s from numpy.__config__ import show as show_config 131s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 131s from numpy.core._multiarray_umath import ( 131s ...<3 lines>... 131s ) 131s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 131s raise ImportError(msg) 131s ImportError: 131s 131s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 131s 131s Importing the numpy C-extensions failed. This error can happen for 131s many reasons, often due to issues with your setup or how NumPy was 131s installed. 131s 131s We have compiled some common reasons and troubleshooting tips at: 131s 131s https://numpy.org/devdocs/user/troubleshooting-importerror.html 131s 131s Please note and check the following: 131s 131s * The Python version is: Python3.13 from "/usr/bin/python3.13" 131s * The NumPy version is: "1.26.4" 131s 131s and make sure that they are the versions you expect. 131s Please carefully study the documentation linked above for further help. 131s 131s Original error was: No module named 'numpy.core._multiarray_umath' 131s 131s 131s The above exception was the direct cause of the following exception: 131s 131s Traceback (most recent call last): 131s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 131s module = __import__(module_name) 131s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 131s import numpy as np 131s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 131s raise ImportError(msg) from e 131s ImportError: Error importing numpy: you should not try to import numpy from 131s its source directory; please exit the numpy source tree, and relaunch 131s your python interpreter from there. 131s 131s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 131s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 131s 131s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_binary_cif ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 131s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 131s 131s test_Pathway ... ok 131s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 131s 131s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_PopGen_GenePop_nodepend ... ok 131s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 131s 131s test_ProtParam ... ok 131s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 131s 132s test_Restriction ... ok 132s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 132s 132s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 132s 132s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 132s 132s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 132s 132s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 132s 132s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 132s 132s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 132s 132s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 132s 132s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 132s 132s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 132s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 132s 133s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 133s 133s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 133s 133s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 133s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 133s 134s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 134s 134s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 134s 134s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 134s 134s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 134s 134s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 134s 134s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 134s 134s test_UniGene ... ok 134s test_UniProt ... skipping. internet not available 134s test_UniProt_GOA ... ok 134s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 134s 134s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 134s 134s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 136s test_bgzf ... ok 136s test_cellosaurus ... ok 136s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 136s 136s test_geo ... ok 136s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 136s 137s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 137s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 137s 137s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 137s 137s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 137s 137s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 137s 137s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 137s 137s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 137s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 137s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 137s 137s test_prodoc ... ok 137s test_prosite ... ok 137s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 137s 137s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 137s test_seq ... ok 137s test_translate ... ok 137s Skipping any tests requiring internet access 137s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 137s Operating system: posix linux 137s ---------------------------------------------------------------------- 137s Ran 218 tests in 14.883 seconds 137s 137s FAILED (failures = 15) 137s test_Ace ... ok 137s test_Affy ... ok 140s test_AlignIO ... ok 140s test_AlignIO_ClustalIO ... ok 140s test_AlignIO_EmbossIO ... ok 140s test_AlignIO_FastaIO ... ok 140s test_AlignIO_MauveIO ... ok 140s test_AlignIO_PhylipIO ... ok 140s test_AlignIO_convert ... ok 140s test_AlignInfo ... ok 141s test_Align_Alignment ... ok 141s test_Align_a2m ... ok 141s test_Align_bed ... ok 141s test_Align_bigbed ... ok 142s test_Align_bigmaf ... ok 142s test_Align_bigpsl ... ok 142s test_Align_chain ... ok 142s test_Align_clustal ... ok 145s test_Align_codonalign ... ok 145s test_Align_emboss ... ok 146s test_Align_exonerate ... ok 146s test_Align_fasta ... ok 146s test_Align_hhr ... ok 147s test_Align_maf ... ok 147s test_Align_mauve ... ok 147s test_Align_msf ... ok 147s test_Align_nexus ... ok 147s test_Align_phylip ... ok 147s test_Align_psl ... ok 147s test_Align_sam ... ok 149s test_Align_stockholm ... ok 150s test_Align_tabular ... ok 150s test_Application ... ok 150s test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython 150s test_BioSQL_MySQLdb_online ... skipping. internet not available 150s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 150s test_BioSQL_mysql_connector_online ... skipping. internet not available 150s test_BioSQL_psycopg2_online ... skipping. internet not available 154s test_BioSQL_sqlite3 ... ok 154s test_BioSQL_sqlite3_online ... skipping. internet not available 154s test_Blast_Record ... ok 155s test_Blast_parser ... ok 155s test_CAPS ... ok 155s test_Chi2 ... ok 155s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 155s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 155s test_Cluster ... ok 155s test_CodonTable ... ok 155s test_ColorSpiral ... ok 155s test_Compass ... ok 157s test_Consensus ... ok 157s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 157s test_EMBL_unittest ... ok 157s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 157s test_EmbossPrimer ... ok 161s test_Entrez ... ok 161s test_Entrez_online ... skipping. internet not available 161s test_Entrez_parser ... ok 161s test_Enzyme ... ok 161s test_ExPASy ... skipping. internet not available 161s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 161s test_File ... ok 162s test_GenBank ... ok 164s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 166s ok 167s test_GraphicsChromosome ... ok 167s test_GraphicsDistribution ... ok 168s test_GraphicsGeneral ... ok 168s test_HMMCasino ... ok 168s test_HMMGeneral ... ok 168s test_KEGG ... ok 168s test_KEGG_online ... skipping. internet not available 173s test_KGML_graphics ... ok 173s test_KGML_graphics_online ... skipping. internet not available 174s test_KGML_nographics ... ok 174s test_KeyWList ... ok 174s test_LogisticRegression ... ok 175s test_MafIO_index ... ok 175s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 175s test_MarkovModel ... ok 175s test_Medline ... ok 175s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 176s test_NCBIXML ... ok 176s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 176s test_NCBI_qblast ... ok 176s test_NMR ... ok 176s test_NaiveBayes ... ok 176s test_Nexus ... ok 176s test_PAML_baseml ... ok 177s test_PAML_codeml ... ok 177s test_PAML_yn00 ... ok 180s test_PDB_CEAligner ... ok 180s test_PDB_DSSP ... ok 180s test_PDB_Dice ... ok 180s test_PDB_Disordered ... ok 180s test_PDB_Exposure ... ok 180s test_PDB_FragmentMapper ... ok 182s test_PDB_KDTree ... ok 182s test_PDB_MMCIF2Dict ... ok 182s test_PDB_MMCIFIO ... ok 183s test_PDB_MMCIFParser ... ok 183s test_PDB_NACCESS ... ok 184s test_PDB_PDBIO ... ok 184s test_PDB_PDBList ... skipping. internet not available 190s test_PDB_PDBMLParser ... ok 191s test_PDB_PDBParser ... ok 191s 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 191s test_PDB_Polypeptide ... ok 191s test_PDB_QCPSuperimposer ... ok 194s test_PDB_SASA ... ok 195s test_PDB_SMCRA ... ok 195s test_PDB_Selection ... ok 195s test_PDB_StructureAlignment ... ok 195s test_PDB_Superimposer ... ok 195s test_PDB_alphafold_db ... skipping. internet not available 195s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 195s 195s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 195s 195s test_PDB_parse_pdb_header ... ok 195s test_PDB_vectors ... ok 195s test_PQR ... ok 195s test_Pathway ... ok 195s test_Phd ... ok 196s test_Phylo ... ok 196s test_PhyloXML ... ok 196s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 196s test_Phylo_NeXML ... ok 196s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 196s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 196s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 197s test_PopGen_GenePop_nodepend ... ok 197s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 197s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 197s test_ProtParam ... ok 197s test_RCSBFormats ... ok 197s test_Restriction ... ok 197s test_SCOP_Astral ... ok 197s test_SCOP_Cla ... ok 197s test_SCOP_Des ... ok 197s test_SCOP_Dom ... ok 197s test_SCOP_Hie ... ok 197s test_SCOP_Raf ... ok 198s test_SCOP_Residues ... ok 198s test_SCOP_Scop ... ok 198s test_SVDSuperimposer ... ok 198s test_SearchIO_blast_tab ... ok 198s test_SearchIO_blast_tab_index ... ok 198s test_SearchIO_blast_xml ... ok 199s test_SearchIO_blast_xml_index ... ok 199s test_SearchIO_blat_psl ... ok 199s test_SearchIO_blat_psl_index ... ok 199s test_SearchIO_exonerate ... ok 199s test_SearchIO_exonerate_text_index ... ok 199s test_SearchIO_exonerate_vulgar_index ... ok 200s test_SearchIO_fasta_m10 ... ok 200s test_SearchIO_fasta_m10_index ... ok 200s test_SearchIO_hhsuite2_text ... ok 200s test_SearchIO_hmmer2_text ... ok 200s test_SearchIO_hmmer2_text_index ... ok 200s test_SearchIO_hmmer3_domtab ... ok 200s test_SearchIO_hmmer3_domtab_index ... ok 200s test_SearchIO_hmmer3_tab ... ok 200s test_SearchIO_hmmer3_tab_index ... ok 200s test_SearchIO_hmmer3_text ... ok 201s test_SearchIO_hmmer3_text_index ... ok 201s test_SearchIO_interproscan_xml ... ok 201s test_SearchIO_model ... ok 201s test_SearchIO_write ... ok 201s test_SeqFeature ... ok 218s test_SeqIO ... ok 218s test_SeqIO_AbiIO ... ok 218s test_SeqIO_FastaIO ... ok 218s test_SeqIO_Gck ... ok 218s test_SeqIO_Gfa ... ok 218s test_SeqIO_Insdc ... ok 218s test_SeqIO_NibIO ... ok 220s test_SeqIO_PdbIO ... ok 221s test_SeqIO_QualityIO ... ok 221s test_SeqIO_SeqXML ... ok 221s test_SeqIO_SnapGene ... ok 222s test_SeqIO_TwoBitIO ... ok 222s test_SeqIO_Xdna ... ok 222s test_SeqIO_features ... ok 237s test_SeqIO_index ... ok 237s test_SeqIO_online ... skipping. internet not available 237s test_SeqIO_write ... ok 237s test_SeqRecord ... ok 237s test_SeqUtils ... ok 238s test_Seq_objs ... ok 238s test_SffIO ... ok 239s test_SwissProt ... ok 239s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 239s test_TogoWS ... skipping. internet not available 239s test_TreeConstruction ... ok 239s test_UniGene ... ok 239s test_UniProt ... skipping. internet not available 239s test_UniProt_GOA ... ok 239s test_UniProt_Parser ... ok 240s test_align ... ok 240s test_align_substitution_matrices ... ok 242s test_bgzf ... ok 242s test_cellosaurus ... ok 246s test_codonalign ... ok 246s test_geo ... ok 247s test_kNN ... ok 247s test_motifs ... ok 247s test_motifs_online ... skipping. internet not available 247s 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. 247s warnings.warn( 247s ok 247s test_pairwise2_no_C ... ok 247s test_pairwise_aligner ... ok 248s test_pairwise_alignment_map ... ok 255s test_phenotype ... ok 255s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 255s 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. 255s test_prodoc ... ok 255s test_prosite ... ok 255s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 255s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 256s test_seq ... ok 256s test_translate ... ok 256s Skipping any tests requiring internet access 256s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 256s Operating system: posix linux 256s ---------------------------------------------------------------------- 256s Ran 218 tests in 118.236 seconds 256s 256s autopkgtest [11:35:24]: test dependencies: -----------------------] 256s autopkgtest [11:35:24]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 256s dependencies PASS 257s autopkgtest [11:35:25]: test full_suite: preparing testbed 327s autopkgtest [11:36:35]: testbed dpkg architecture: amd64 327s autopkgtest [11:36:35]: testbed apt version: 2.9.8 327s autopkgtest [11:36:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 328s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 328s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 328s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 328s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 328s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 328s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 328s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 328s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 328s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 328s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 328s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 328s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 328s Fetched 2175 kB in 0s (4749 kB/s) 328s Reading package lists... 330s Reading package lists... 330s Building dependency tree... 330s Reading state information... 330s Calculating upgrade... 331s The following NEW packages will be installed: 331s python3.13-gdbm 331s The following packages will be upgraded: 331s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 331s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 331s Need to get 253 kB of archives. 331s After this operation, 147 kB of additional disk space will be used. 331s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 331s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 331s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 331s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 331s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 331s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 331s Fetched 253 kB in 0s (3298 kB/s) 331s (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 ... 75541 files and directories currently installed.) 331s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 331s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 331s Setting up python3-minimal (3.12.7-1) ... 331s (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 ... 75541 files and directories currently installed.) 331s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 332s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 332s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 332s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 332s Selecting previously unselected package python3.13-gdbm. 332s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 332s Unpacking python3.13-gdbm (3.13.0-2) ... 332s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 332s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 332s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 332s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 332s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 332s Setting up python3.13-gdbm (3.13.0-2) ... 332s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 332s Setting up python3 (3.12.7-1) ... 332s Setting up python3-gdbm:amd64 (3.12.7-1) ... 332s Processing triggers for man-db (2.12.1-3) ... 333s Processing triggers for libc-bin (2.40-1ubuntu3) ... 333s Reading package lists... 333s Building dependency tree... 333s Reading state information... 334s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 334s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 334s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 334s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 334s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 335s Reading package lists... 335s Reading package lists... 335s Building dependency tree... 335s Reading state information... 336s Calculating upgrade... 336s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 336s Reading package lists... 337s Building dependency tree... 337s Reading state information... 337s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 338s Reading package lists... 339s Building dependency tree... 339s Reading state information... 339s Starting pkgProblemResolver with broken count: 0 339s Starting 2 pkgProblemResolver with broken count: 0 339s Done 339s The following additional packages will be installed: 339s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 339s clustalw cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper 339s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 339s docutils-common dssp dwz emboss emboss-data emboss-lib fasttree flex 339s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 339s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 339s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 339s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext ghostscript hevea 339s hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 339s intltool-debian libamd-comgr2 libamdhip64-5 libaom3 libapache-pom-java 339s libarchive-zip-perl libargtable2-0 libasan8 libavahi-client3 339s libavahi-common-data libavahi-common3 libblas3 libcairo2 libcc1-0 339s libcifpp-data libcifpp7 libcommons-logging-java libcommons-parent-java 339s libcups2t64 libde265-0 libdebhelper-perl libdeflate0 libdrm-amdgpu1 339s libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfftw3-double3 339s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 339s libgcc-14-dev libgd3 libgfortran5 libgomp1 libgraphite2-3 libgs-common 339s libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 339s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhsakmt1 339s libhts3t64 libhtscodecs2 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 339s libibumad3 libice6 libidn12 libijs-0.35 libimagequant0 libisl23 libitm1 339s libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 339s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 339s liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblqr-1-0 liblsan0 libltdl7 339s libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmbedcrypto7t64 339s libmbedtls14t64 libmbedx509-1t64 libmpc3 libmpfi0 libmunge2 libmysqlclient21 339s libnetpbm11t64 libopenjp2-7 libopenmpi3t64 libpaper-utils libpaper1 339s libpciaccess0 libpdfbox-java libpixman-1-0 libpmix2t64 libpotrace0 libpq5 339s libpsm-infinipath1 libpsm2-2 libptexenc1 libpython3-all-dev libpython3-dev 339s libpython3.12-dev libpython3.13 libpython3.13-dev libpython3.13-minimal 339s libpython3.13-stdlib libqhull-r8.0 libquadmath0 libraqm0 libraw23t64 339s librdmacm1t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 339s libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 339s libucx0 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 339s libxcb-shm0 libxft2 libxi6 libxmu6 libxnvctrl0 libxpm4 libxrender1 339s libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft muscle3 mysql-common 339s ncbi-blast+ ncbi-data netpbm ocl-icd-libopencl1 openmpi-bin openmpi-common 339s phylip phyml po-debconf poppler-data prank preview-latex-style probcons 339s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 339s python3-all-dev python3-appdirs python3-biopython python3-biopython-sql 339s python3-brotli python3-cairo python3-contourpy python3-cycler 339s python3-dateutil python3-decorator python3-defusedxml python3-dev 339s python3-docutils python3-fonttools python3-freetype python3-fs 339s python3-imagesize python3-isodate python3-kiwisolver python3-lxml 339s python3-lz4 python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 339s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 339s python3-packaging python3-pil python3-pil.imagetk python3-psycopg2 339s python3-rdflib python3-reportlab python3-rlpycairo python3-roman 339s python3-scipy python3-six python3-snowballstemmer python3-sphinx 339s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 339s python3-tabulate python3-tk python3-tz python3-ufolib2 python3.12-dev 339s python3.12-tk python3.13 python3.13-dev python3.13-minimal python3.13-tk 339s raxml samtools sgml-base sphinx-common sphinx-rtd-theme-common t-coffee 339s t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended 339s texlive-latex-base texlive-latex-extra texlive-latex-recommended 339s texlive-pictures tk8.6-blt2.5 unicode-data w3c-sgml-lib wise wise-data 339s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 339s Suggested packages: 339s autoconf-archive gnu-standards autoconf-doc blt-demo clustalx seaview 339s cpp-doc gcc-14-locales cpp-14-doc dh-make flit python3-build 339s python3-installer python3-wheel emboss-doc emboss-test embassy bison 339s flex-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre g++-multilib 339s g++-14-multilib gcc-14-doc gcc-multilib manpages-dev gdb gcc-doc 339s gcc-14-multilib gdb-x86-64-linux-gnu gettext-doc libasprintf-dev 339s libgettextpo-dev hevea-doc imagemagick-6-doc autotrace cups-bsd | lpr 339s | lprng enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin 339s mplayer povray radiance sane-utils transfig libraw-bin 339s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 339s cups-common libfftw3-bin libfftw3-dev libgd-tools libheif-plugin-x265 339s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 339s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar 339s libheif-plugin-rav1e libheif-plugin-svtenc libhwloc-contrib-plugins 339s libjs-jquery-ui-docs liblcms2-utils libmagickcore-6.q16-7-extra libmpfi-doc 339s libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler 339s gcj-jdk m4-doc opencl-icd gfortran | fortran-compiler phylip-doc 339s libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho 339s fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai 339s fonts-arphic-uming fonts-nanum probcons-extra python-cycler-doc docutils-doc 339s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 339s python-lxml-doc cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 339s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 339s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 339s texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server 339s | virtual-mysql-server python3-gdal python3-pydot python3-pygraphviz 339s gfortran python-numpy-doc python3-pytest python-pil-doc python-psycopg2-doc 339s python-rdflib-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc 339s rl-accel rl-renderpm python-scipy-doc python3-stemmer dvisvgm 339s fonts-freefont-otf latexmk libjs-mathjax sphinx-doc tex-gyre 339s texlive-fonts-extra texlive-plain-generic python-sympy-doc tix 339s python3-tk-dbg python3.13-venv python3.13-doc binfmt-support cwltool 339s sgml-base-doc boxshade t-coffee-examples perl-tk xpdf | pdf-viewer xzdec 339s texlive-binaries-sse2 hintview texlive-fonts-recommended-doc 339s texlive-latex-base-doc wp2latex icc-profiles libfile-which-perl 339s texlive-latex-extra-doc texlive-science texlive-latex-recommended-doc 339s texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex 339s wise-doc 339s Recommended packages: 339s primer3 libfl-dev libmagickcore-6.q16-7-extra libarchive-cpio-perl 339s fonts-droid-fallback libheif-plugin-aomenc javascript-common libjson-xs-perl 339s libltdl-dev blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 339s python3-cssselect python3-html5lib python3-olefile python3-sparqlwrapper 339s fonts-dejavu-extra isympy-common amap-align dialign-tx fsa kalign 339s libsoap-lite-perl libxml-simple-perl muscle mustang poa proda tm-align 339s lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl 339s texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl 339s libx11-protocol-perl x11-utils x11-xserver-utils 339s The following NEW packages will be installed: 339s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 339s build-essential bwa clustalo clustalw cpp cpp-14 cpp-14-x86-64-linux-gnu 339s cpp-x86-64-linux-gnu debhelper debugedit dh-autoreconf dh-python 339s dh-strip-nondeterminism dialign docutils-common dssp dwz emboss emboss-data 339s emboss-lib fasttree flex fontconfig-config fonts-dejavu-core 339s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 339s fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 339s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext ghostscript 339s hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 339s intltool-debian libamd-comgr2 libamdhip64-5 libaom3 libapache-pom-java 339s libarchive-zip-perl libargtable2-0 libasan8 libavahi-client3 339s libavahi-common-data libavahi-common3 libblas3 libcairo2 libcc1-0 339s libcifpp-data libcifpp7 libcommons-logging-java libcommons-parent-java 339s libcups2t64 libde265-0 libdebhelper-perl libdeflate0 libdrm-amdgpu1 339s libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfftw3-double3 339s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 339s libgcc-14-dev libgd3 libgfortran5 libgomp1 libgraphite2-3 libgs-common 339s libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 339s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhsakmt1 339s libhts3t64 libhtscodecs2 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 339s libibumad3 libice6 libidn12 libijs-0.35 libimagequant0 libisl23 libitm1 339s libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 339s libjs-sphinxdoc libjs-underscore libjson-perl libkpathsea6 liblapack3 339s liblbfgsb0 liblcms2-2 liblerc4 libllvm17t64 liblqr-1-0 liblsan0 libltdl7 339s libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmbedcrypto7t64 339s libmbedtls14t64 libmbedx509-1t64 libmpc3 libmpfi0 libmunge2 libmysqlclient21 339s libnetpbm11t64 libopenjp2-7 libopenmpi3t64 libpaper-utils libpaper1 339s libpciaccess0 libpdfbox-java libpixman-1-0 libpmix2t64 libpotrace0 libpq5 339s libpsm-infinipath1 libpsm2-2 libptexenc1 libpython3-all-dev libpython3-dev 339s libpython3.12-dev libpython3.13 libpython3.13-dev libpython3.13-minimal 339s libpython3.13-stdlib libqhull-r8.0 libquadmath0 libraqm0 libraw23t64 339s librdmacm1t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 339s libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 339s libucx0 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 339s libxcb-shm0 libxft2 libxi6 libxmu6 libxnvctrl0 libxpm4 libxrender1 339s libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft muscle3 mysql-common 339s ncbi-blast+ ncbi-data netpbm ocl-icd-libopencl1 openmpi-bin openmpi-common 339s phylip phyml po-debconf poppler-data prank preview-latex-style probcons 339s python-biopython-doc python-matplotlib-data python3-alabaster python3-all 339s python3-all-dev python3-appdirs python3-biopython python3-biopython-sql 339s python3-brotli python3-cairo python3-contourpy python3-cycler 339s python3-dateutil python3-decorator python3-defusedxml python3-dev 339s python3-docutils python3-fonttools python3-freetype python3-fs 339s python3-imagesize python3-isodate python3-kiwisolver python3-lxml 339s python3-lz4 python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 339s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 339s python3-packaging python3-pil python3-pil.imagetk python3-psycopg2 339s python3-rdflib python3-reportlab python3-rlpycairo python3-roman 339s python3-scipy python3-six python3-snowballstemmer python3-sphinx 339s python3-sphinx-rtd-theme python3-sphinxcontrib.jquery python3-sympy 339s python3-tabulate python3-tk python3-tz python3-ufolib2 python3.12-dev 339s python3.12-tk python3.13 python3.13-dev python3.13-minimal python3.13-tk 339s raxml samtools sgml-base sphinx-common sphinx-rtd-theme-common t-coffee 339s t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended 339s texlive-latex-base texlive-latex-extra texlive-latex-recommended 339s texlive-pictures tk8.6-blt2.5 unicode-data w3c-sgml-lib wise wise-data 339s x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g-dev 340s 0 upgraded, 293 newly installed, 0 to remove and 0 not upgraded. 340s Need to get 478 MB/478 MB of archives. 340s After this operation, 2061 MB of additional disk space will be used. 340s Get:1 /tmp/autopkgtest.YFyfMk/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [1028 B] 340s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 340s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 flex amd64 2.6.4-8.2build1 [301 kB] 340s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 340s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 340s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu4 [839 kB] 340s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 340s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 340s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 340s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 340s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 340s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 340s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 340s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 340s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 340s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 340s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libaom3 amd64 3.11.0~rc1-1 [2762 kB] 340s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-aomdec amd64 1.18.1-2 [11.1 kB] 340s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libde265-0 amd64 1.0.15-1build4 [168 kB] 340s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-libde265 amd64 1.18.1-2 [8758 B] 340s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif1 amd64 1.18.1-2 [293 kB] 340s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 340s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 340s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 340s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 340s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblqr-1-0 amd64 0.4.2-2.1build2 [28.5 kB] 340s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.4.7-7build1 [40.3 kB] 340s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 340s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libraw23t64 amd64 0.21.3-1 [433 kB] 340s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 340s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 340s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 340s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 340s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 340s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 340s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick-6-common all 8:6.9.13.12+dfsg1-1build1 [69.6 kB] 340s Get:37 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmagickcore-6.q16-7t64 amd64 8:6.9.13.12+dfsg1-1build1 [1851 kB] 340s Get:38 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmagickwand-6.q16-7t64 amd64 8:6.9.13.12+dfsg1-1build1 [316 kB] 340s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-data all 0.4.12-1 [2060 kB] 340s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 340s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 340s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 340s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 340s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 340s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 340s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 340s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 340s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 340s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 340s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 340s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 340s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 340s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 340s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 340s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 340s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 340s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 340s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 340s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 340s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 340s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 340s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 340s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 340s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 340s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 340s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 340s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 340s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 340s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 340s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 340s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 340s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 340s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 341s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 341s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 341s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 341s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 341s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 341s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 bwa amd64 0.7.18-1 [204 kB] 341s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 libargtable2-0 amd64 13-2 [14.6 kB] 341s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 clustalo amd64 1.2.4-8build1 [202 kB] 341s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 clustalw amd64 2.1+lgpl-7 [275 kB] 341s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 341s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 341s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 341s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 341s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 341s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 341s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 341s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 341s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 341s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 341s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 341s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 341s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB] 341s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 dialign amd64 2.2.1-13 [154 kB] 341s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 341s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 341s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcifpp-data all 7.0.7-3 [480 kB] 341s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcifpp7 amd64 7.0.7-3 [1141 kB] 341s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 dssp amd64 4.4.10-1 [786 kB] 341s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 341s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 341s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 341s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 341s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB] 341s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libgd3 amd64 2.3.3-12ubuntu3 [127 kB] 341s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1build3 [432 kB] 341s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 mysql-common all 5.8+1.1.1 [6800 B] 341s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libmysqlclient21 amd64 8.0.40-1 [1250 kB] 342s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libpq5 amd64 17.0-1 [249 kB] 342s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss-lib amd64 6.6.0+dfsg-12ubuntu2 [2976 kB] 342s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss-data all 6.6.0+dfsg-12ubuntu2 [61.0 MB] 344s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss amd64 6.6.0+dfsg-12ubuntu2 [980 kB] 344s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 344s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lmodern all 2.005-1 [4799 kB] 344s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 344s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs-common all 10.03.1~dfsg1-0ubuntu2 [175 kB] 344s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs10-common all 10.03.1~dfsg1-0ubuntu2 [488 kB] 344s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-13ubuntu6 [29.7 kB] 344s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-13ubuntu6 [23.3 kB] 344s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-13ubuntu6 [26.8 kB] 344s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.10-1ubuntu2 [271 kB] 344s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libidn12 amd64 1.42-2 [55.9 kB] 344s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libijs-0.35 amd64 0.35-15.1build1 [15.3 kB] 344s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig2dec0 amd64 0.20-1build3 [65.0 kB] 344s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB] 344s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 344s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 344s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 344s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs10 amd64 10.03.1~dfsg1-0ubuntu2 [3672 kB] 344s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 ghostscript amd64 10.03.1~dfsg1-0ubuntu2 [43.5 kB] 344s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetpbm11t64 amd64 2:11.08.01-1 [125 kB] 344s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 netpbm amd64 2:11.08.01-1 [2282 kB] 344s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 tex-common all 6.18 [32.8 kB] 344s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B] 344s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5 [66.8 kB] 344s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5 [43.7 kB] 344s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5 [62.3 kB] 344s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5 [145 kB] 344s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 t1utils amd64 1.41-4build3 [61.3 kB] 344s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 344s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 344s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 344s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 344s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] 344s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpotrace0 amd64 1.16-2build1 [17.7 kB] 344s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 libteckit0 amd64 2.5.12+ds1-1 [411 kB] 344s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB] 344s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 libxaw7 amd64 2:1.0.16-1 [207 kB] 344s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 344s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2build1 [28.1 kB] 344s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-binaries amd64 2024.20240313.70630+ds-5 [9801 kB] 344s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 344s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-base all 2024.20241102-1 [22.5 MB] 345s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-1 [13.5 kB] 345s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick-6.q16 amd64 8:6.9.13.12+dfsg1-1build1 [254 kB] 345s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick amd64 8:6.9.13.12+dfsg1-1build1 [14.2 kB] 345s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 hevea amd64 2.36-2 [2023 kB] 345s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-18 [26.0 MB] 345s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 345s Get:162 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [21.7 kB] 345s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 345s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 345s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 345s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B] 345s Get:167 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 345s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 345s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 345s Get:170 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 345s Get:171 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.2-2 [140 kB] 345s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 345s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 345s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 52.0-2ubuntu1 [70.8 kB] 345s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3ubuntu1 [658 kB] 345s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 345s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 345s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 345s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.11.2-1 [193 kB] 345s Get:180 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 345s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 345s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 345s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 345s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 345s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 345s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 345s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto7t64 amd64 2.28.8-1 [209 kB] 345s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-1t64 amd64 2.28.8-1 [46.6 kB] 345s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls14t64 amd64 2.28.8-1 [82.2 kB] 345s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.15-4build1 [14.7 kB] 345s Get:191 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 345s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 345s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 345s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.11.2-1 [16.0 kB] 345s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.3-2 [697 kB] 345s Get:196 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 52.0-2ubuntu1 [29.0 kB] 345s Get:197 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 52.0-2ubuntu1 [42.6 kB] 345s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.17.0+ds-3build1 [1162 kB] 345s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi3t64 amd64 4.1.6-13.3ubuntu2 [2575 kB] 345s Get:200 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 345s Get:201 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.7-3 [5699 kB] 345s Get:202 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-dev amd64 3.12.7-1 [10.3 kB] 345s Get:203 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 345s Get:204 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.0-2 [2321 kB] 345s Get:205 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-dev amd64 3.13.0-2 [5488 kB] 346s Get:206 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-all-dev amd64 3.12.7-1 [916 B] 346s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 346s Get:208 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 346s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 mafft amd64 7.505-1 [795 kB] 346s Get:210 http://ftpmaster.internal/ubuntu plucky/universe amd64 muscle3 amd64 3.8.1551-3 [198 kB] 346s Get:211 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 346s Get:212 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] 346s Get:213 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-common all 4.1.6-13.3ubuntu2 [170 kB] 346s Get:214 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-bin amd64 4.1.6-13.3ubuntu2 [114 kB] 346s Get:215 http://ftpmaster.internal/ubuntu plucky/universe amd64 phylip amd64 1:3.697+dfsg-4build1 [874 kB] 346s Get:216 http://ftpmaster.internal/ubuntu plucky/universe amd64 phyml amd64 3:3.3.20220408-3build3 [965 kB] 346s Get:217 http://ftpmaster.internal/ubuntu plucky/universe amd64 prank amd64 0.0.170427+dfsg-3 [396 kB] 346s Get:218 http://ftpmaster.internal/ubuntu plucky/universe amd64 preview-latex-style all 13.2-1 [347 kB] 346s Get:219 http://ftpmaster.internal/ubuntu plucky/universe amd64 probcons amd64 1.12-14 [125 kB] 346s Get:220 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 347s Get:221 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 347s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 347s Get:223 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 347s Get:224 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] 347s Get:225 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-dev amd64 3.12.7-1 [26.7 kB] 347s Get:226 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-dev amd64 3.13.0-2 [507 kB] 347s Get:227 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all-dev amd64 3.12.7-1 [914 B] 347s Get:228 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 347s Get:229 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 347s Get:230 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 347s Get:231 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 347s Get:232 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 347s Get:233 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 347s Get:234 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 347s Get:235 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 347s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 347s Get:237 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 347s Get:238 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 347s Get:239 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 347s Get:240 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 347s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 347s Get:242 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 347s Get:243 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 347s Get:244 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 347s Get:245 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 347s Get:246 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 347s Get:247 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 347s Get:248 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-defusedxml all 0.7.1-2 [42.0 kB] 347s Get:249 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-roman all 4.2-1 [10.0 kB] 347s Get:250 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 347s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 347s Get:252 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 347s Get:253 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 347s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 347s Get:255 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 347s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 347s Get:257 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 347s Get:258 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 347s Get:259 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 347s Get:260 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 347s Get:261 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-imagesize all 1.4.1-1 [6844 B] 347s Get:262 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-isodate all 0.6.1-3 [24.3 kB] 347s Get:263 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 347s Get:264 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 347s Get:265 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 347s Get:266 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-msgpack amd64 1.0.3-3build2 [80.1 kB] 347s Get:267 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mmtf all 1.1.3-1 [16.2 kB] 347s Get:268 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-mysqldb amd64 1.4.6-2build3 [47.3 kB] 347s Get:269 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 347s Get:270 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-common all 7.4.7-4 [775 kB] 347s Get:271 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 347s Get:272 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 347s Get:273 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sphinx all 7.4.7-4 [593 kB] 347s Get:274 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tabulate all 0.9.0-1 [45.3 kB] 347s Get:275 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numpydoc all 1.6.0-2 [50.5 kB] 347s Get:276 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psycopg2 amd64 2.9.9-2 [132 kB] 347s Get:277 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rdflib all 7.0.0-1 [405 kB] 347s Get:278 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 347s Get:279 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 347s Get:280 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 347s Get:281 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB] 347s Get:282 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 347s Get:283 http://ftpmaster.internal/ubuntu plucky/universe amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [929 kB] 347s Get:284 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-fonts-recommended all 2024.20241102-1 [4974 kB] 347s Get:285 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-base all 2024.20241102-1 [1260 kB] 347s Get:286 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfontbox-java all 1:1.8.16-5 [208 kB] 347s Get:287 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 347s Get:288 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-recommended all 2024.20241102-1 [8739 kB] 348s Get:289 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-pictures all 2024.20241102-1 [17.0 MB] 348s Get:290 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-extra all 2024.20241102-1 [24.2 MB] 348s Get:291 http://ftpmaster.internal/ubuntu plucky/universe amd64 wise-data all 2.4.1-25 [83.0 kB] 348s Get:292 http://ftpmaster.internal/ubuntu plucky/universe amd64 wise amd64 2.4.1-25 [843 kB] 348s Get:293 http://ftpmaster.internal/ubuntu plucky/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 349s Preconfiguring packages ... 349s Fetched 478 MB in 9s (55.6 MB/s) 349s Selecting previously unselected package m4. 349s (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 ... 75548 files and directories currently installed.) 349s Preparing to unpack .../000-m4_1.4.19-4build1_amd64.deb ... 349s Unpacking m4 (1.4.19-4build1) ... 349s Selecting previously unselected package flex. 349s Preparing to unpack .../001-flex_2.6.4-8.2build1_amd64.deb ... 349s Unpacking flex (2.6.4-8.2build1) ... 349s Selecting previously unselected package fonts-lato. 349s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 349s Unpacking fonts-lato (2.015-1) ... 349s Selecting previously unselected package libgomp1:amd64. 349s Preparing to unpack .../003-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 349s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 349s Selecting previously unselected package libfftw3-double3:amd64. 349s Preparing to unpack .../004-libfftw3-double3_3.3.10-1ubuntu4_amd64.deb ... 349s Unpacking libfftw3-double3:amd64 (3.3.10-1ubuntu4) ... 349s Selecting previously unselected package fonts-dejavu-mono. 349s Preparing to unpack .../005-fonts-dejavu-mono_2.37-8_all.deb ... 349s Unpacking fonts-dejavu-mono (2.37-8) ... 349s Selecting previously unselected package fonts-dejavu-core. 349s Preparing to unpack .../006-fonts-dejavu-core_2.37-8_all.deb ... 349s Unpacking fonts-dejavu-core (2.37-8) ... 349s Selecting previously unselected package libfontenc1:amd64. 349s Preparing to unpack .../007-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 349s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 349s Selecting previously unselected package x11-common. 349s Preparing to unpack .../008-x11-common_1%3a7.7+23ubuntu3_all.deb ... 349s Unpacking x11-common (1:7.7+23ubuntu3) ... 349s Selecting previously unselected package xfonts-encodings. 349s Preparing to unpack .../009-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 349s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 349s Selecting previously unselected package xfonts-utils. 349s Preparing to unpack .../010-xfonts-utils_1%3a7.7+7_amd64.deb ... 349s Unpacking xfonts-utils (1:7.7+7) ... 349s Selecting previously unselected package fonts-urw-base35. 349s Preparing to unpack .../011-fonts-urw-base35_20200910-8_all.deb ... 349s Unpacking fonts-urw-base35 (20200910-8) ... 350s Selecting previously unselected package fontconfig-config. 350s Preparing to unpack .../012-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 350s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 350s Selecting previously unselected package libfontconfig1:amd64. 350s Preparing to unpack .../013-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 350s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 350s Selecting previously unselected package libsharpyuv0:amd64. 350s Preparing to unpack .../014-libsharpyuv0_1.4.0-0.1_amd64.deb ... 350s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 350s Selecting previously unselected package libaom3:amd64. 350s Preparing to unpack .../015-libaom3_3.11.0~rc1-1_amd64.deb ... 350s Unpacking libaom3:amd64 (3.11.0~rc1-1) ... 350s Selecting previously unselected package libheif-plugin-aomdec:amd64. 350s Preparing to unpack .../016-libheif-plugin-aomdec_1.18.1-2_amd64.deb ... 350s Unpacking libheif-plugin-aomdec:amd64 (1.18.1-2) ... 350s Selecting previously unselected package libde265-0:amd64. 350s Preparing to unpack .../017-libde265-0_1.0.15-1build4_amd64.deb ... 350s Unpacking libde265-0:amd64 (1.0.15-1build4) ... 350s Selecting previously unselected package libheif-plugin-libde265:amd64. 350s Preparing to unpack .../018-libheif-plugin-libde265_1.18.1-2_amd64.deb ... 350s Unpacking libheif-plugin-libde265:amd64 (1.18.1-2) ... 350s Selecting previously unselected package libheif1:amd64. 350s Preparing to unpack .../019-libheif1_1.18.1-2_amd64.deb ... 350s Unpacking libheif1:amd64 (1.18.1-2) ... 350s Selecting previously unselected package libjbig0:amd64. 350s Preparing to unpack .../020-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 350s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 350s Selecting previously unselected package libjpeg-turbo8:amd64. 350s Preparing to unpack .../021-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 350s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 350s Selecting previously unselected package libjpeg8:amd64. 350s Preparing to unpack .../022-libjpeg8_8c-2ubuntu11_amd64.deb ... 350s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 350s Selecting previously unselected package liblcms2-2:amd64. 350s Preparing to unpack .../023-liblcms2-2_2.16-2_amd64.deb ... 350s Unpacking liblcms2-2:amd64 (2.16-2) ... 350s Selecting previously unselected package liblqr-1-0:amd64. 350s Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1build2_amd64.deb ... 350s Unpacking liblqr-1-0:amd64 (0.4.2-2.1build2) ... 350s Selecting previously unselected package libltdl7:amd64. 350s Preparing to unpack .../025-libltdl7_2.4.7-7build1_amd64.deb ... 350s Unpacking libltdl7:amd64 (2.4.7-7build1) ... 350s Selecting previously unselected package libopenjp2-7:amd64. 350s Preparing to unpack .../026-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 350s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 350s Selecting previously unselected package libraw23t64:amd64. 350s Preparing to unpack .../027-libraw23t64_0.21.3-1_amd64.deb ... 350s Unpacking libraw23t64:amd64 (0.21.3-1) ... 350s Selecting previously unselected package libdeflate0:amd64. 350s Preparing to unpack .../028-libdeflate0_1.22-1_amd64.deb ... 350s Unpacking libdeflate0:amd64 (1.22-1) ... 350s Selecting previously unselected package liblerc4:amd64. 350s Preparing to unpack .../029-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 350s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 350s Selecting previously unselected package libwebp7:amd64. 350s Preparing to unpack .../030-libwebp7_1.4.0-0.1_amd64.deb ... 350s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 350s Selecting previously unselected package libtiff6:amd64. 350s Preparing to unpack .../031-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 350s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 350s Selecting previously unselected package libwebpdemux2:amd64. 350s Preparing to unpack .../032-libwebpdemux2_1.4.0-0.1_amd64.deb ... 350s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 350s Selecting previously unselected package libwebpmux3:amd64. 350s Preparing to unpack .../033-libwebpmux3_1.4.0-0.1_amd64.deb ... 350s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 350s Selecting previously unselected package imagemagick-6-common. 350s Preparing to unpack .../034-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1build1_all.deb ... 350s Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 350s Selecting previously unselected package libmagickcore-6.q16-7t64:amd64. 350s Preparing to unpack .../035-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 350s Unpacking libmagickcore-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 351s Selecting previously unselected package libmagickwand-6.q16-7t64:amd64. 351s Preparing to unpack .../036-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 351s Unpacking libmagickwand-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 351s Selecting previously unselected package poppler-data. 351s Preparing to unpack .../037-poppler-data_0.4.12-1_all.deb ... 351s Unpacking poppler-data (0.4.12-1) ... 351s Selecting previously unselected package libpython3.13-minimal:amd64. 351s Preparing to unpack .../038-libpython3.13-minimal_3.13.0-2_amd64.deb ... 351s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 351s Selecting previously unselected package python3.13-minimal. 351s Preparing to unpack .../039-python3.13-minimal_3.13.0-2_amd64.deb ... 351s Unpacking python3.13-minimal (3.13.0-2) ... 351s Selecting previously unselected package sgml-base. 351s Preparing to unpack .../040-sgml-base_1.31_all.deb ... 351s Unpacking sgml-base (1.31) ... 351s Selecting previously unselected package autoconf. 351s Preparing to unpack .../041-autoconf_2.72-3_all.deb ... 351s Unpacking autoconf (2.72-3) ... 351s Selecting previously unselected package autotools-dev. 351s Preparing to unpack .../042-autotools-dev_20220109.1_all.deb ... 351s Unpacking autotools-dev (20220109.1) ... 351s Selecting previously unselected package automake. 351s Preparing to unpack .../043-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 351s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 351s Selecting previously unselected package autopoint. 351s Preparing to unpack .../044-autopoint_0.22.5-2_all.deb ... 351s Unpacking autopoint (0.22.5-2) ... 351s Selecting previously unselected package libtcl8.6:amd64. 351s Preparing to unpack .../045-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 351s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 351s Selecting previously unselected package libxrender1:amd64. 351s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 351s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 351s Selecting previously unselected package libxft2:amd64. 351s Preparing to unpack .../047-libxft2_2.3.6-1build1_amd64.deb ... 351s Unpacking libxft2:amd64 (2.3.6-1build1) ... 351s Selecting previously unselected package libxss1:amd64. 351s Preparing to unpack .../048-libxss1_1%3a1.2.3-1build3_amd64.deb ... 351s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 351s Selecting previously unselected package libtk8.6:amd64. 351s Preparing to unpack .../049-libtk8.6_8.6.15-1_amd64.deb ... 351s Unpacking libtk8.6:amd64 (8.6.15-1) ... 351s Selecting previously unselected package tk8.6-blt2.5. 351s Preparing to unpack .../050-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 351s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 351s Selecting previously unselected package blt. 351s Preparing to unpack .../051-blt_2.5.3+dfsg-7build1_amd64.deb ... 351s Unpacking blt (2.5.3+dfsg-7build1) ... 351s Selecting previously unselected package libisl23:amd64. 351s Preparing to unpack .../052-libisl23_0.27-1_amd64.deb ... 351s Unpacking libisl23:amd64 (0.27-1) ... 351s Selecting previously unselected package libmpc3:amd64. 351s Preparing to unpack .../053-libmpc3_1.3.1-1build2_amd64.deb ... 351s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 351s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 351s Preparing to unpack .../054-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 351s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package cpp-14. 352s Preparing to unpack .../055-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package cpp-x86-64-linux-gnu. 352s Preparing to unpack .../056-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 352s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 352s Selecting previously unselected package cpp. 352s Preparing to unpack .../057-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 352s Unpacking cpp (4:14.1.0-2ubuntu1) ... 352s Selecting previously unselected package libcc1-0:amd64. 352s Preparing to unpack .../058-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package libitm1:amd64. 352s Preparing to unpack .../059-libitm1_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package libasan8:amd64. 352s Preparing to unpack .../060-libasan8_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package liblsan0:amd64. 352s Preparing to unpack .../061-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package libtsan2:amd64. 352s Preparing to unpack .../062-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package libubsan1:amd64. 352s Preparing to unpack .../063-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package libhwasan0:amd64. 352s Preparing to unpack .../064-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package libquadmath0:amd64. 352s Preparing to unpack .../065-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package libgcc-14-dev:amd64. 352s Preparing to unpack .../066-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 352s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 352s Preparing to unpack .../067-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 352s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 353s Selecting previously unselected package gcc-14. 353s Preparing to unpack .../068-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 353s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 353s Selecting previously unselected package gcc-x86-64-linux-gnu. 353s Preparing to unpack .../069-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 353s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 353s Selecting previously unselected package gcc. 353s Preparing to unpack .../070-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 353s Unpacking gcc (4:14.1.0-2ubuntu1) ... 353s Selecting previously unselected package 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libxpm4:amd64 (1:3.5.17-1build2) ... 354s Selecting previously unselected package libgd3:amd64. 354s Preparing to unpack .../105-libgd3_2.3.3-12ubuntu3_amd64.deb ... 354s Unpacking libgd3:amd64 (2.3.3-12ubuntu3) ... 354s Selecting previously unselected package libhpdf-2.3.0:amd64. 354s Preparing to unpack .../106-libhpdf-2.3.0_2.3.0+dfsg-1build3_amd64.deb ... 354s Unpacking libhpdf-2.3.0:amd64 (2.3.0+dfsg-1build3) ... 354s Selecting previously unselected package mysql-common. 354s Preparing to unpack .../107-mysql-common_5.8+1.1.1_all.deb ... 354s Unpacking mysql-common (5.8+1.1.1) ... 354s Selecting previously unselected package libmysqlclient21:amd64. 354s Preparing to unpack .../108-libmysqlclient21_8.0.40-1_amd64.deb ... 354s Unpacking libmysqlclient21:amd64 (8.0.40-1) ... 354s Selecting previously unselected package libpq5:amd64. 354s Preparing to unpack .../109-libpq5_17.0-1_amd64.deb ... 354s Unpacking libpq5:amd64 (17.0-1) ... 355s Selecting previously unselected package emboss-lib. 355s Preparing to unpack .../110-emboss-lib_6.6.0+dfsg-12ubuntu2_amd64.deb ... 355s Unpacking emboss-lib (6.6.0+dfsg-12ubuntu2) ... 355s Selecting previously unselected package emboss-data. 355s Preparing to unpack .../111-emboss-data_6.6.0+dfsg-12ubuntu2_all.deb ... 355s Unpacking emboss-data (6.6.0+dfsg-12ubuntu2) ... 358s Selecting previously unselected package emboss. 358s Preparing to unpack .../112-emboss_6.6.0+dfsg-12ubuntu2_amd64.deb ... 358s Unpacking emboss (6.6.0+dfsg-12ubuntu2) ... 358s Selecting previously unselected package fonts-font-awesome. 358s Preparing to unpack .../113-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 358s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 358s Selecting previously unselected package fonts-lmodern. 358s Preparing to unpack .../114-fonts-lmodern_2.005-1_all.deb ... 358s Unpacking fonts-lmodern (2.005-1) ... 358s Selecting previously unselected package fonts-lyx. 358s Preparing to unpack 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unselected package libnetpbm11t64:amd64. 359s Preparing to unpack .../131-libnetpbm11t64_2%3a11.08.01-1_amd64.deb ... 359s Unpacking libnetpbm11t64:amd64 (2:11.08.01-1) ... 359s Selecting previously unselected package netpbm. 359s Preparing to unpack .../132-netpbm_2%3a11.08.01-1_amd64.deb ... 359s Unpacking netpbm (2:11.08.01-1) ... 359s Selecting previously unselected package tex-common. 359s Preparing to unpack .../133-tex-common_6.18_all.deb ... 359s Unpacking tex-common (6.18) ... 359s Selecting previously unselected package libpaper-utils. 359s Preparing to unpack .../134-libpaper-utils_1.1.29build1_amd64.deb ... 359s Unpacking libpaper-utils (1.1.29build1) ... 359s Selecting previously unselected package libkpathsea6:amd64. 359s Preparing to unpack .../135-libkpathsea6_2024.20240313.70630+ds-5_amd64.deb ... 359s Unpacking libkpathsea6:amd64 (2024.20240313.70630+ds-5) ... 359s Selecting previously unselected package libptexenc1:amd64. 359s Preparing to unpack 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.../141-libxcb-render0_1.17.0-2_amd64.deb ... 359s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 359s Selecting previously unselected package libxcb-shm0:amd64. 359s Preparing to unpack .../142-libxcb-shm0_1.17.0-2_amd64.deb ... 359s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 359s Selecting previously unselected package libcairo2:amd64. 359s Preparing to unpack .../143-libcairo2_1.18.2-2_amd64.deb ... 359s Unpacking libcairo2:amd64 (1.18.2-2) ... 359s Selecting previously unselected package libmpfi0:amd64. 359s Preparing to unpack .../144-libmpfi0_1.5.4+ds-4_amd64.deb ... 359s Unpacking libmpfi0:amd64 (1.5.4+ds-4) ... 359s Selecting previously unselected package libpotrace0:amd64. 359s Preparing to unpack .../145-libpotrace0_1.16-2build1_amd64.deb ... 359s Unpacking libpotrace0:amd64 (1.16-2build1) ... 359s Selecting previously unselected package libteckit0:amd64. 359s Preparing to unpack .../146-libteckit0_2.5.12+ds1-1_amd64.deb ... 359s Unpacking libteckit0:amd64 (2.5.12+ds1-1) ... 359s Selecting previously unselected package libxmu6:amd64. 359s Preparing to unpack .../147-libxmu6_2%3a1.1.3-3build2_amd64.deb ... 359s Unpacking libxmu6:amd64 (2:1.1.3-3build2) ... 359s Selecting previously unselected package libxaw7:amd64. 359s Preparing to unpack .../148-libxaw7_2%3a1.0.16-1_amd64.deb ... 359s Unpacking libxaw7:amd64 (2:1.0.16-1) ... 359s Selecting previously unselected package libxi6:amd64. 359s Preparing to unpack .../149-libxi6_2%3a1.8.2-1_amd64.deb ... 359s Unpacking libxi6:amd64 (2:1.8.2-1) ... 359s Selecting previously unselected package libzzip-0-13t64:amd64. 359s Preparing to unpack .../150-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_amd64.deb ... 359s Unpacking libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2build1) ... 359s Selecting previously unselected package texlive-binaries. 359s Preparing to unpack .../151-texlive-binaries_2024.20240313.70630+ds-5_amd64.deb ... 359s Unpacking texlive-binaries (2024.20240313.70630+ds-5) ... 360s Selecting previously unselected package xdg-utils. 360s Preparing to unpack .../152-xdg-utils_1.2.1-0ubuntu1_all.deb ... 360s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 360s Selecting previously unselected package texlive-base. 360s Preparing to unpack .../153-texlive-base_2024.20241102-1_all.deb ... 360s Unpacking texlive-base (2024.20241102-1) ... 360s Selecting previously unselected package hicolor-icon-theme. 360s Preparing to unpack .../154-hicolor-icon-theme_0.18-1_all.deb ... 360s Unpacking hicolor-icon-theme (0.18-1) ... 361s Selecting previously unselected package imagemagick-6.q16. 361s Preparing to unpack .../155-imagemagick-6.q16_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 361s Unpacking imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 361s Selecting previously unselected package imagemagick. 361s Preparing to unpack .../156-imagemagick_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 361s Unpacking imagemagick (8:6.9.13.12+dfsg1-1build1) ... 361s Selecting previously unselected package hevea. 361s Preparing to unpack .../157-hevea_2.36-2_amd64.deb ... 361s Unpacking hevea (2.36-2) ... 361s Selecting previously unselected package libllvm17t64:amd64. 361s Preparing to unpack .../158-libllvm17t64_1%3a17.0.6-18_amd64.deb ... 361s Unpacking libllvm17t64:amd64 (1:17.0.6-18) ... 361s Selecting previously unselected package libamd-comgr2:amd64. 361s Preparing to unpack .../159-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 361s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 362s Selecting previously unselected package libdrm-amdgpu1:amd64. 362s Preparing to unpack .../160-libdrm-amdgpu1_2.4.123-1_amd64.deb ... 362s Unpacking libdrm-amdgpu1:amd64 (2.4.123-1) ... 362s Selecting previously unselected package libhsakmt1:amd64. 362s Preparing to unpack .../161-libhsakmt1_5.7.0-1build1_amd64.deb ... 362s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 362s Selecting previously unselected package libhsa-runtime64-1. 362s Preparing to unpack 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libhwloc15:amd64 (2.11.2-1) ... 363s Selecting previously unselected package libjs-jquery. 363s Preparing to unpack .../178-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 363s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 363s Selecting previously unselected package libjs-jquery-ui. 363s Preparing to unpack .../179-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 363s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 363s Selecting previously unselected package libjs-underscore. 363s Preparing to unpack .../180-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 363s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 363s Selecting previously unselected package libjs-sphinxdoc. 363s Preparing to unpack .../181-libjs-sphinxdoc_7.4.7-4_all.deb ... 363s Unpacking libjs-sphinxdoc (7.4.7-4) ... 363s Selecting previously unselected package libjson-perl. 363s Preparing to unpack .../182-libjson-perl_4.10000-1_all.deb ... 363s Unpacking libjson-perl (4.10000-1) ... 363s Selecting previously unselected package liblapack3:amd64. 363s Preparing to unpack .../183-liblapack3_3.12.0-3build2_amd64.deb ... 363s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 363s Selecting previously unselected package liblbfgsb0:amd64. 363s Preparing to unpack .../184-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 363s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 363s Selecting previously unselected package libmbedcrypto7t64:amd64. 363s Preparing to unpack .../185-libmbedcrypto7t64_2.28.8-1_amd64.deb ... 363s Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ... 363s Selecting previously unselected package libmbedx509-1t64:amd64. 363s Preparing to unpack .../186-libmbedx509-1t64_2.28.8-1_amd64.deb ... 363s Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ... 363s Selecting previously unselected package libmbedtls14t64:amd64. 363s Preparing to unpack .../187-libmbedtls14t64_2.28.8-1_amd64.deb ... 363s Unpacking libmbedtls14t64:amd64 (2.28.8-1) ... 363s Selecting previously unselected package libmunge2:amd64. 363s Preparing to unpack .../188-libmunge2_0.5.15-4build1_amd64.deb ... 363s Unpacking libmunge2:amd64 (0.5.15-4build1) ... 363s Selecting previously unselected package libpciaccess0:amd64. 363s Preparing to unpack .../189-libpciaccess0_0.17-3build1_amd64.deb ... 363s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 363s Selecting previously unselected package libxnvctrl0:amd64. 363s Preparing to unpack .../190-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 363s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 363s Selecting previously unselected package ocl-icd-libopencl1:amd64. 363s Preparing to unpack .../191-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 363s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 363s Selecting previously unselected package libhwloc-plugins:amd64. 363s Preparing to unpack .../192-libhwloc-plugins_2.11.2-1_amd64.deb ... 363s Unpacking libhwloc-plugins:amd64 (2.11.2-1) ... 363s Selecting previously unselected package 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phyml. 365s Preparing to unpack .../214-phyml_3%3a3.3.20220408-3build3_amd64.deb ... 365s Unpacking phyml (3:3.3.20220408-3build3) ... 365s Selecting previously unselected package prank. 365s Preparing to unpack .../215-prank_0.0.170427+dfsg-3_amd64.deb ... 365s Unpacking prank (0.0.170427+dfsg-3) ... 365s Selecting previously unselected package preview-latex-style. 365s Preparing to unpack .../216-preview-latex-style_13.2-1_all.deb ... 365s Unpacking preview-latex-style (13.2-1) ... 365s Selecting previously unselected package probcons. 365s Preparing to unpack .../217-probcons_1.12-14_amd64.deb ... 365s Unpacking probcons (1.12-14) ... 365s Selecting previously unselected package python-biopython-doc. 365s Preparing to unpack .../218-python-biopython-doc_1.84+dfsg-4_all.deb ... 365s Unpacking python-biopython-doc (1.84+dfsg-4) ... 365s Selecting previously unselected package python-matplotlib-data. 365s Preparing to unpack .../219-python-matplotlib-data_3.8.3-3_all.deb ... 365s 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Selecting previously unselected package python3-pil.imagetk:amd64. 366s Preparing to unpack .../231-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 366s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 366s Selecting previously unselected package python3-pil:amd64. 366s Preparing to unpack .../232-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 366s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 366s Selecting previously unselected package python3-cairo. 366s Preparing to unpack .../233-python3-cairo_1.26.1-2_amd64.deb ... 366s Unpacking python3-cairo (1.26.1-2) ... 366s Selecting previously unselected package python3-freetype. 366s Preparing to unpack .../234-python3-freetype_2.5.1-1_all.deb ... 366s Unpacking python3-freetype (2.5.1-1) ... 366s Selecting previously unselected package python3-rlpycairo. 366s Preparing to unpack .../235-python3-rlpycairo_0.3.0-3_all.deb ... 366s Unpacking python3-rlpycairo (0.3.0-3) ... 366s Selecting previously unselected package 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previously unselected package python3-roman. 367s Preparing to unpack .../247-python3-roman_4.2-1_all.deb ... 367s Unpacking python3-roman (4.2-1) ... 367s Selecting previously unselected package python3-docutils. 367s Preparing to unpack .../248-python3-docutils_0.21.2+dfsg-2_all.deb ... 367s Unpacking python3-docutils (0.21.2+dfsg-2) ... 367s Selecting previously unselected package python3-scipy. 367s Preparing to unpack .../249-python3-scipy_1.13.1-5_amd64.deb ... 367s Unpacking python3-scipy (1.13.1-5) ... 367s Selecting previously unselected package python3-ufolib2. 367s Preparing to unpack .../250-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 367s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 367s Selecting previously unselected package python3-mpmath. 367s Preparing to unpack .../251-python3-mpmath_1.3.0-1_all.deb ... 367s Unpacking python3-mpmath (1.3.0-1) ... 368s Selecting previously unselected package python3-sympy. 368s Preparing to unpack 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python3-fonttools. 368s Preparing to unpack .../258-python3-fonttools_4.46.0-1build2_amd64.deb ... 368s Unpacking python3-fonttools (4.46.0-1build2) ... 368s Selecting previously unselected package python3-imagesize. 368s Preparing to unpack .../259-python3-imagesize_1.4.1-1_all.deb ... 368s Unpacking python3-imagesize (1.4.1-1) ... 368s Selecting previously unselected package python3-isodate. 368s Preparing to unpack .../260-python3-isodate_0.6.1-3_all.deb ... 368s Unpacking python3-isodate (0.6.1-3) ... 368s Selecting previously unselected package python3-kiwisolver. 368s Preparing to unpack .../261-python3-kiwisolver_1.4.7-2_amd64.deb ... 368s Unpacking python3-kiwisolver (1.4.7-2) ... 368s Selecting previously unselected package python3-packaging. 368s Preparing to unpack .../262-python3-packaging_24.1-1_all.deb ... 368s Unpacking python3-packaging (24.1-1) ... 368s Selecting previously unselected package python3-matplotlib. 368s Preparing to unpack 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408s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 408s Setting up python3-rlpycairo (0.3.0-3) ... 409s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 409s Setting up python3-reportlab (4.2.5-1) ... 410s Setting up texlive-binaries (2024.20240313.70630+ds-5) ... 410s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 410s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 410s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 410s Setting up g++-14 (14.2.0-8ubuntu1) ... 410s Setting up texlive-base (2024.20241102-1) ... 411s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 411s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 411s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 411s tl-paper: setting paper size for pdftex to a4: 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provide /usr/bin/montage-im6 (montage-im6) in auto mode 414s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 414s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode 414s Setting up emboss-lib (6.6.0+dfsg-12ubuntu2) ... 414s Setting up python3-matplotlib (3.8.3-3) ... 416s Setting up emboss (6.6.0+dfsg-12ubuntu2) ... 416s Setting up hevea (2.36-2) ... 416s Setting up imagemagick (8:6.9.13.12+dfsg1-1build1) ... 416s Processing triggers for install-info (7.1.1-1) ... 417s Processing triggers for libc-bin (2.40-1ubuntu3) ... 417s Processing triggers for systemd (256.5-2ubuntu4) ... 417s Processing triggers for man-db (2.12.1-3) ... 418s Processing triggers for shared-mime-info (2.4-5) ... 419s Processing triggers for sgml-base (1.31) ... 419s Setting up w3c-sgml-lib (1.3-3) ... 445s Setting up docutils-common (0.21.2+dfsg-2) ... 445s Setting up python3-biopython (1.84+dfsg-4) ... 447s Setting up python3-biopython-sql (1.84+dfsg-4) ... 447s Processing triggers for sgml-base (1.31) ... 447s Setting up python3-docutils (0.21.2+dfsg-2) ... 448s Setting up python3-sphinx (7.4.7-4) ... 449s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 450s Setting up python3-numpydoc (1.6.0-2) ... 450s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 450s Setting up autopkgtest-satdep (0) ... 450s Processing triggers for tex-common (6.18) ... 450s Running updmap-sys. This may take some time... done. 450s Running mktexlsr /var/lib/texmf ... done. 451s Building format(s) --all. 501s This may take some time... done. 508s (Reading database ... 124381 files and directories currently installed.) 508s Removing autopkgtest-satdep (0) ... 519s autopkgtest [11:39:47]: test full_suite: sh debian/tests/run-unit-test 519s autopkgtest [11:39:47]: test full_suite: [----------------------- 519s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 519s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 521s mkdir: created directory 'Bio' 521s mkdir: created directory 'Bio/Align' 521s mkdir: created directory 'Bio/Align/substitution_matrices' 521s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 521s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 521s Remove test test_Tutorial.py which is bound to fail 521s test_Ace ... ok 521s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 521s 521s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 521s 521s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 521s 521s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 521s 521s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 521s 521s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 521s 521s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 521s 521s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 521s 521s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 521s 521s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 521s 521s test_Align_a2m ... loading tests failed: 521s Failed to import test module: test_Align_a2m 521s Traceback (most recent call last): 521s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 521s from . import multiarray 521s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 521s from . import overrides 521s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 521s from numpy.core._multiarray_umath import ( 521s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 521s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 521s 521s During handling of the above exception, another exception occurred: 521s 521s Traceback (most recent call last): 521s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 521s from numpy.__config__ import show as show_config 521s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 521s from numpy.core._multiarray_umath import ( 521s ...<3 lines>... 521s ) 521s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 521s raise ImportError(msg) 521s ImportError: 521s 521s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 521s 521s Importing the numpy C-extensions failed. This error can happen for 521s many reasons, often due to issues with your setup or how NumPy was 521s installed. 521s 521s We have compiled some common reasons and troubleshooting tips at: 521s 521s https://numpy.org/devdocs/user/troubleshooting-importerror.html 521s 521s Please note and check the following: 521s 521s * The Python version is: Python3.13 from "/usr/bin/python3.13" 521s * The NumPy version is: "1.26.4" 521s 521s and make sure that they are the versions you expect. 521s Please carefully study the documentation linked above for further help. 521s 521s Original error was: No module named 'numpy.core._multiarray_umath' 521s 521s 521s The above exception was the direct cause of the following exception: 521s 521s Traceback (most recent call last): 521s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 521s module = __import__(module_name) 521s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 521s import numpy as np 521s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 521s raise ImportError(msg) from e 521s ImportError: Error importing numpy: you should not try to import numpy from 521s its source directory; please exit the numpy source tree, and relaunch 521s your python interpreter from there. 521s 521s test_Align_bed ... loading tests failed: 521s Failed to import test module: test_Align_bed 521s Traceback (most recent call last): 521s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 521s from . import multiarray 521s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 521s from . import overrides 521s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 521s from numpy.core._multiarray_umath import ( 521s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 521s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 521s 521s During handling of the above exception, another exception occurred: 521s 521s Traceback (most recent call last): 521s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 521s from numpy.__config__ import show as show_config 521s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 521s from numpy.core._multiarray_umath import ( 521s ...<3 lines>... 521s ) 521s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 521s raise ImportError(msg) 521s ImportError: 521s 521s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 521s 521s Importing the numpy C-extensions failed. This error can happen for 521s many reasons, often due to issues with your setup or how NumPy was 521s installed. 521s 521s We have compiled some common reasons and troubleshooting tips at: 521s 521s https://numpy.org/devdocs/user/troubleshooting-importerror.html 521s 521s Please note and check the following: 521s 521s * The Python version is: Python3.13 from "/usr/bin/python3.13" 521s * The NumPy version is: "1.26.4" 521s 521s and make sure that they are the versions you expect. 521s Please carefully study the documentation linked above for further help. 521s 521s Original error was: No module named 'numpy.core._multiarray_umath' 521s 521s 521s The above exception was the direct cause of the following exception: 521s 521s Traceback (most recent call last): 521s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 521s module = __import__(module_name) 521s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 521s import numpy as np 521s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 521s raise ImportError(msg) from e 521s ImportError: Error importing numpy: you should not try to import numpy from 521s its source directory; please exit the numpy source tree, and relaunch 521s your python interpreter from there. 521s 521s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 521s 522s test_Align_bigmaf ... loading tests failed: 522s Failed to import test module: test_Align_bigmaf 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 522s from . import multiarray 522s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 522s from . import overrides 522s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 522s from numpy.core._multiarray_umath import ( 522s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 522s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 522s 522s During handling of the above exception, another exception occurred: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 522s from numpy.__config__ import show as show_config 522s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 522s from numpy.core._multiarray_umath import ( 522s ...<3 lines>... 522s ) 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 522s raise ImportError(msg) 522s ImportError: 522s 522s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 522s 522s Importing the numpy C-extensions failed. This error can happen for 522s many reasons, often due to issues with your setup or how NumPy was 522s installed. 522s 522s We have compiled some common reasons and troubleshooting tips at: 522s 522s https://numpy.org/devdocs/user/troubleshooting-importerror.html 522s 522s Please note and check the following: 522s 522s * The Python version is: Python3.13 from "/usr/bin/python3.13" 522s * The NumPy version is: "1.26.4" 522s 522s and make sure that they are the versions you expect. 522s Please carefully study the documentation linked above for further help. 522s 522s Original error was: No module named 'numpy.core._multiarray_umath' 522s 522s 522s The above exception was the direct cause of the following exception: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 522s module = __import__(module_name) 522s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 522s import numpy as np 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 522s raise ImportError(msg) from e 522s ImportError: Error importing numpy: you should not try to import numpy from 522s its source directory; please exit the numpy source tree, and relaunch 522s your python interpreter from there. 522s 522s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_clustal ... loading tests failed: 522s Failed to import test module: test_Align_clustal 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 522s from . import multiarray 522s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 522s from . import overrides 522s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 522s from numpy.core._multiarray_umath import ( 522s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 522s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 522s 522s During handling of the above exception, another exception occurred: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 522s from numpy.__config__ import show as show_config 522s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 522s from numpy.core._multiarray_umath import ( 522s ...<3 lines>... 522s ) 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 522s raise ImportError(msg) 522s ImportError: 522s 522s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 522s 522s Importing the numpy C-extensions failed. This error can happen for 522s many reasons, often due to issues with your setup or how NumPy was 522s installed. 522s 522s We have compiled some common reasons and troubleshooting tips at: 522s 522s https://numpy.org/devdocs/user/troubleshooting-importerror.html 522s 522s Please note and check the following: 522s 522s * The Python version is: Python3.13 from "/usr/bin/python3.13" 522s * The NumPy version is: "1.26.4" 522s 522s and make sure that they are the versions you expect. 522s Please carefully study the documentation linked above for further help. 522s 522s Original error was: No module named 'numpy.core._multiarray_umath' 522s 522s 522s The above exception was the direct cause of the following exception: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 522s module = __import__(module_name) 522s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 522s import numpy as np 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 522s raise ImportError(msg) from e 522s ImportError: Error importing numpy: you should not try to import numpy from 522s its source directory; please exit the numpy source tree, and relaunch 522s your python interpreter from there. 522s 522s test_Align_codonalign ... loading tests failed: 522s Failed to import test module: test_Align_codonalign 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 522s from . import multiarray 522s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 522s from . import overrides 522s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 522s from numpy.core._multiarray_umath import ( 522s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 522s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 522s 522s During handling of the above exception, another exception occurred: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 522s from numpy.__config__ import show as show_config 522s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 522s from numpy.core._multiarray_umath import ( 522s ...<3 lines>... 522s ) 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 522s raise ImportError(msg) 522s ImportError: 522s 522s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 522s 522s Importing the numpy C-extensions failed. This error can happen for 522s many reasons, often due to issues with your setup or how NumPy was 522s installed. 522s 522s We have compiled some common reasons and troubleshooting tips at: 522s 522s https://numpy.org/devdocs/user/troubleshooting-importerror.html 522s 522s Please note and check the following: 522s 522s * The Python version is: Python3.13 from "/usr/bin/python3.13" 522s * The NumPy version is: "1.26.4" 522s 522s and make sure that they are the versions you expect. 522s Please carefully study the documentation linked above for further help. 522s 522s Original error was: No module named 'numpy.core._multiarray_umath' 522s 522s 522s The above exception was the direct cause of the following exception: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 522s module = __import__(module_name) 522s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 522s import numpy as np 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 522s raise ImportError(msg) from e 522s ImportError: Error importing numpy: you should not try to import numpy from 522s its source directory; please exit the numpy source tree, and relaunch 522s your python interpreter from there. 522s 522s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_fasta ... loading tests failed: 522s Failed to import test module: test_Align_fasta 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 522s from . import multiarray 522s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 522s from . import overrides 522s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 522s from numpy.core._multiarray_umath import ( 522s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 522s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 522s 522s During handling of the above exception, another exception occurred: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 522s from numpy.__config__ import show as show_config 522s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 522s from numpy.core._multiarray_umath import ( 522s ...<3 lines>... 522s ) 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 522s raise ImportError(msg) 522s ImportError: 522s 522s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 522s 522s Importing the numpy C-extensions failed. This error can happen for 522s many reasons, often due to issues with your setup or how NumPy was 522s installed. 522s 522s We have compiled some common reasons and troubleshooting tips at: 522s 522s https://numpy.org/devdocs/user/troubleshooting-importerror.html 522s 522s Please note and check the following: 522s 522s * The Python version is: Python3.13 from "/usr/bin/python3.13" 522s * The NumPy version is: "1.26.4" 522s 522s and make sure that they are the versions you expect. 522s Please carefully study the documentation linked above for further help. 522s 522s Original error was: No module named 'numpy.core._multiarray_umath' 522s 522s 522s The above exception was the direct cause of the following exception: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 522s module = __import__(module_name) 522s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 522s import numpy as np 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 522s raise ImportError(msg) from e 522s ImportError: Error importing numpy: you should not try to import numpy from 522s its source directory; please exit the numpy source tree, and relaunch 522s your python interpreter from there. 522s 522s test_Align_hhr ... loading tests failed: 522s Failed to import test module: test_Align_hhr 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 522s from . import multiarray 522s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 522s from . import overrides 522s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 522s from numpy.core._multiarray_umath import ( 522s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 522s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 522s 522s During handling of the above exception, another exception occurred: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 522s from numpy.__config__ import show as show_config 522s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 522s from numpy.core._multiarray_umath import ( 522s ...<3 lines>... 522s ) 522s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 522s raise ImportError(msg) 522s ImportError: 522s 522s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 522s 522s Importing the numpy C-extensions failed. This error can happen for 522s many reasons, often due to issues with your setup or how NumPy was 522s installed. 522s 522s We have compiled some common reasons and troubleshooting tips at: 522s 522s https://numpy.org/devdocs/user/troubleshooting-importerror.html 522s 522s Please note and check the following: 522s 522s * The Python version is: Python3.13 from "/usr/bin/python3.13" 522s * The NumPy version is: "1.26.4" 522s 522s and make sure that they are the versions you expect. 522s Please carefully study the documentation linked above for further help. 522s 522s Original error was: No module named 'numpy.core._multiarray_umath' 522s 522s 522s The above exception was the direct cause of the following exception: 522s 522s Traceback (most recent call last): 522s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 522s module = __import__(module_name) 522s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 522s import numpy as np 522s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 522s raise ImportError(msg) from e 522s ImportError: Error importing numpy: you should not try to import numpy from 522s its source directory; please exit the numpy source tree, and relaunch 522s your python interpreter from there. 522s 522s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 522s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 522s 523s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_Application ... ok 523s test_BWA_tool ... ok 523s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_Blast_Record ... loading tests failed: 523s Failed to import test module: test_Blast_Record 523s Traceback (most recent call last): 523s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 523s from . import multiarray 523s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 523s from . import overrides 523s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 523s from numpy.core._multiarray_umath import ( 523s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 523s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 523s 523s During handling of the above exception, another exception occurred: 523s 523s Traceback (most recent call last): 523s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 523s from numpy.__config__ import show as show_config 523s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 523s from numpy.core._multiarray_umath import ( 523s ...<3 lines>... 523s ) 523s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 523s raise ImportError(msg) 523s ImportError: 523s 523s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 523s 523s Importing the numpy C-extensions failed. This error can happen for 523s many reasons, often due to issues with your setup or how NumPy was 523s installed. 523s 523s We have compiled some common reasons and troubleshooting tips at: 523s 523s https://numpy.org/devdocs/user/troubleshooting-importerror.html 523s 523s Please note and check the following: 523s 523s * The Python version is: Python3.13 from "/usr/bin/python3.13" 523s * The NumPy version is: "1.26.4" 523s 523s and make sure that they are the versions you expect. 523s Please carefully study the documentation linked above for further help. 523s 523s Original error was: No module named 'numpy.core._multiarray_umath' 523s 523s 523s The above exception was the direct cause of the following exception: 523s 523s Traceback (most recent call last): 523s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 523s module = __import__(module_name) 523s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 523s from Bio.Blast.NCBIXML import HSP 523s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 523s import numpy as np 523s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 523s raise ImportError(msg) from e 523s ImportError: Error importing numpy: you should not try to import numpy from 523s its source directory; please exit the numpy source tree, and relaunch 523s your python interpreter from there. 523s 523s test_Blast_parser ... loading tests failed: 523s Failed to import test module: test_Blast_parser 523s Traceback (most recent call last): 523s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 523s from . import multiarray 523s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 523s from . import overrides 523s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 523s from numpy.core._multiarray_umath import ( 523s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 523s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 523s 523s During handling of the above exception, another exception occurred: 523s 523s Traceback (most recent call last): 523s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 523s from numpy.__config__ import show as show_config 523s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 523s from numpy.core._multiarray_umath import ( 523s ...<3 lines>... 523s ) 523s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 523s raise ImportError(msg) 523s ImportError: 523s 523s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 523s 523s Importing the numpy C-extensions failed. This error can happen for 523s many reasons, often due to issues with your setup or how NumPy was 523s installed. 523s 523s We have compiled some common reasons and troubleshooting tips at: 523s 523s https://numpy.org/devdocs/user/troubleshooting-importerror.html 523s 523s Please note and check the following: 523s 523s * The Python version is: Python3.13 from "/usr/bin/python3.13" 523s * The NumPy version is: "1.26.4" 523s 523s and make sure that they are the versions you expect. 523s Please carefully study the documentation linked above for further help. 523s 523s Original error was: No module named 'numpy.core._multiarray_umath' 523s 523s 523s The above exception was the direct cause of the following exception: 523s 523s Traceback (most recent call last): 523s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 523s module = __import__(module_name) 523s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 523s import numpy as np 523s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 523s raise ImportError(msg) from e 523s ImportError: Error importing numpy: you should not try to import numpy from 523s its source directory; please exit the numpy source tree, and relaunch 523s your python interpreter from there. 523s 523s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s 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 523s warnings.warn( 523s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 523s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 523s 523s test_CodonTable ... ok 523s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 523s 523s test_Compass ... ok 523s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 523s 524s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 524s 524s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 524s 524s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 524s 524s test_EmbossPrimer ... ok 528s test_Entrez ... ok 528s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 528s 528s test_Entrez_parser ... ok 528s test_Enzyme ... ok 528s test_ExPASy ... skipping. internet not available 528s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 528s 528s test_File ... ok 528s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 528s 528s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 528s 528s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 528s 528s test_GraphicsDistribution ... loading tests failed: 528s Failed to import test module: test_GraphicsDistribution 528s Traceback (most recent call last): 528s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 528s module = __import__(module_name) 528s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 528s from Bio.Graphics.Distribution import BarChartDistribution 528s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 528s from reportlab.graphics.charts.barcharts import BarChartProperties 528s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 528s from reportlab.lib import colors 528s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 528s from reportlab.lib.rl_accel import fp_str 528s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 528s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 528s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 528s from PIL import Image 528s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 528s from . import _imaging as core 528s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 528s 528s test_GraphicsGeneral ... loading tests failed: 528s Failed to import test module: test_GraphicsGeneral 528s Traceback (most recent call last): 528s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 528s module = __import__(module_name) 528s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 528s from Bio.Graphics.Comparative import ComparativeScatterPlot 528s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 528s from reportlab.graphics.charts.lineplots import LinePlot 528s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 528s from reportlab.lib import colors 528s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 528s from reportlab.lib.rl_accel import fp_str 528s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 528s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 528s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 528s from PIL import Image 528s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 528s from . import _imaging as core 528s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 528s 528s test_HMMCasino ... ok 528s test_HMMGeneral ... ok 529s test_KEGG ... ok 529s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 529s 529s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 529s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 529s test_KGML_nographics ... ok 529s test_KeyWList ... ok 529s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 529s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 529s 529s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 529s 529s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 529s 529s test_Medline ... ok 529s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 529s 529s test_NCBIXML ... loading tests failed: 529s Failed to import test module: test_NCBIXML 529s Traceback (most recent call last): 529s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 529s from . import multiarray 529s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 529s from . import overrides 529s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 529s from numpy.core._multiarray_umath import ( 529s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 529s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 529s 529s During handling of the above exception, another exception occurred: 529s 529s Traceback (most recent call last): 529s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 529s from numpy.__config__ import show as show_config 529s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 529s from numpy.core._multiarray_umath import ( 529s ...<3 lines>... 529s ) 529s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 529s raise ImportError(msg) 529s ImportError: 529s 529s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 529s 529s Importing the numpy C-extensions failed. This error can happen for 529s many reasons, often due to issues with your setup or how NumPy was 529s installed. 529s 529s We have compiled some common reasons and troubleshooting tips at: 529s 529s https://numpy.org/devdocs/user/troubleshooting-importerror.html 529s 529s Please note and check the following: 529s 529s * The Python version is: Python3.13 from "/usr/bin/python3.13" 529s * The NumPy version is: "1.26.4" 529s 529s and make sure that they are the versions you expect. 529s Please carefully study the documentation linked above for further help. 529s 529s Original error was: No module named 'numpy.core._multiarray_umath' 529s 529s 529s The above exception was the direct cause of the following exception: 529s 529s Traceback (most recent call last): 529s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 529s module = __import__(module_name) 529s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 529s from Bio.Blast import NCBIXML 529s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 529s import numpy as np 529s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 529s raise ImportError(msg) from e 529s ImportError: Error importing numpy: you should not try to import numpy from 529s its source directory; please exit the numpy source tree, and relaunch 529s your python interpreter from there. 529s 530s test_NCBI_BLAST_tools ... loading tests failed: 530s Failed to import test module: test_NCBI_BLAST_tools 530s Traceback (most recent call last): 530s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 530s from . import multiarray 530s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 530s from . import overrides 530s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 530s from numpy.core._multiarray_umath import ( 530s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 530s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 530s 530s During handling of the above exception, another exception occurred: 530s 530s Traceback (most recent call last): 530s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 530s from numpy.__config__ import show as show_config 530s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 530s from numpy.core._multiarray_umath import ( 530s ...<3 lines>... 530s ) 530s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 530s raise ImportError(msg) 530s ImportError: 530s 530s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 530s 530s Importing the numpy C-extensions failed. This error can happen for 530s many reasons, often due to issues with your setup or how NumPy was 530s installed. 530s 530s We have compiled some common reasons and troubleshooting tips at: 530s 530s https://numpy.org/devdocs/user/troubleshooting-importerror.html 530s 530s Please note and check the following: 530s 530s * The Python version is: Python3.13 from "/usr/bin/python3.13" 530s * The NumPy version is: "1.26.4" 530s 530s and make sure that they are the versions you expect. 530s Please carefully study the documentation linked above for further help. 530s 530s Original error was: No module named 'numpy.core._multiarray_umath' 530s 530s 530s The above exception was the direct cause of the following exception: 530s 530s Traceback (most recent call last): 530s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 530s module = __import__(module_name) 530s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 530s from Bio.Blast import Applications 530s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 530s import numpy as np 530s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 530s raise ImportError(msg) from e 530s ImportError: Error importing numpy: you should not try to import numpy from 530s its source directory; please exit the numpy source tree, and relaunch 530s your python interpreter from there. 530s 530s test_NCBI_qblast ... loading tests failed: 530s Failed to import test module: test_NCBI_qblast 530s Traceback (most recent call last): 530s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 530s from . import multiarray 530s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 530s from . import overrides 530s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 530s from numpy.core._multiarray_umath import ( 530s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 530s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 530s 530s During handling of the above exception, another exception occurred: 530s 530s Traceback (most recent call last): 530s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 530s from numpy.__config__ import show as show_config 530s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 530s from numpy.core._multiarray_umath import ( 530s ...<3 lines>... 530s ) 530s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 530s raise ImportError(msg) 530s ImportError: 530s 530s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 530s 530s Importing the numpy C-extensions failed. This error can happen for 530s many reasons, often due to issues with your setup or how NumPy was 530s installed. 530s 530s We have compiled some common reasons and troubleshooting tips at: 530s 530s https://numpy.org/devdocs/user/troubleshooting-importerror.html 530s 530s Please note and check the following: 530s 530s * The Python version is: Python3.13 from "/usr/bin/python3.13" 530s * The NumPy version is: "1.26.4" 530s 530s and make sure that they are the versions you expect. 530s Please carefully study the documentation linked above for further help. 530s 530s Original error was: No module named 'numpy.core._multiarray_umath' 530s 530s 530s The above exception was the direct cause of the following exception: 530s 530s Traceback (most recent call last): 530s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 530s module = __import__(module_name) 530s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 530s from Bio.Blast import NCBIWWW 530s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 530s import numpy as np 530s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 530s raise ImportError(msg) from e 530s ImportError: Error importing numpy: you should not try to import numpy from 530s its source directory; please exit the numpy source tree, and relaunch 530s your python interpreter from there. 530s 530s test_NMR ... ok 530s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 530s 530s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 530s 530s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_Disordered ... loading tests failed: 530s Failed to import test module: test_PDB_Disordered 530s Traceback (most recent call last): 530s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 530s from . import multiarray 530s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 530s from . import overrides 530s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 530s from numpy.core._multiarray_umath import ( 530s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 530s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 530s 530s During handling of the above exception, another exception occurred: 530s 530s Traceback (most recent call last): 530s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 530s from numpy.__config__ import show as show_config 530s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 530s from numpy.core._multiarray_umath import ( 530s ...<3 lines>... 530s ) 530s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 530s raise ImportError(msg) 530s ImportError: 530s 530s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 530s 530s Importing the numpy C-extensions failed. This error can happen for 530s many reasons, often due to issues with your setup or how NumPy was 530s installed. 530s 530s We have compiled some common reasons and troubleshooting tips at: 530s 530s https://numpy.org/devdocs/user/troubleshooting-importerror.html 530s 530s Please note and check the following: 530s 530s * The Python version is: Python3.13 from "/usr/bin/python3.13" 530s * The NumPy version is: "1.26.4" 530s 530s and make sure that they are the versions you expect. 530s Please carefully study the documentation linked above for further help. 530s 530s Original error was: No module named 'numpy.core._multiarray_umath' 530s 530s 530s The above exception was the direct cause of the following exception: 530s 530s Traceback (most recent call last): 530s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 530s module = __import__(module_name) 530s File "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 530s import numpy as np 530s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 530s raise ImportError(msg) from e 530s ImportError: Error importing numpy: you should not try to import numpy from 530s its source directory; please exit the numpy source tree, and relaunch 530s your python interpreter from there. 530s 530s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 530s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 530s 530s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_binary_cif ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 530s 530s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 530s 530s test_Pathway ... ok 530s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 530s 530s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_PopGen_GenePop_nodepend ... ok 530s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 530s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 530s 531s test_ProtParam ... ok 531s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 531s 531s test_Restriction ... ok 531s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 531s 531s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 531s 531s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 531s 531s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 531s 531s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 531s 531s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 531s 531s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 531s 531s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 531s 531s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 531s 531s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 531s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 531s 532s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 532s 532s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 532s 532s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 532s 532s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 532s 532s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 532s 532s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 532s 532s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 532s 532s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 532s 532s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 532s 532s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 532s 532s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 532s 533s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 533s 533s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 533s 533s test_UniGene ... ok 533s test_UniProt ... skipping. internet not available 533s test_UniProt_GOA ... ok 533s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 533s 533s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 533s 533s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 535s test_bgzf ... ok 535s test_cellosaurus ... ok 535s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 535s 535s test_geo ... ok 535s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 535s 535s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 535s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 535s 535s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 535s 535s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 535s 536s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 536s 536s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 536s 536s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 536s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 536s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 536s 536s test_prodoc ... ok 536s test_prosite ... ok 536s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 536s 536s test_samtools_tool ... ok 536s test_seq ... ok 536s test_translate ... ok 536s ---------------------------------------------------------------------- 536s Ran 218 tests in 14.829 seconds 536s 536s FAILED (failures = 15) 536s Skipping any tests requiring internet access 536s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 536s Operating system: posix linux 536s test_Ace ... ok 536s test_Affy ... ok 539s test_AlignIO ... ok 539s test_AlignIO_ClustalIO ... ok 539s test_AlignIO_EmbossIO ... ok 539s test_AlignIO_FastaIO ... ok 539s test_AlignIO_MauveIO ... ok 539s test_AlignIO_PhylipIO ... ok 539s test_AlignIO_convert ... ok 539s test_AlignInfo ... ok 539s test_Align_Alignment ... ok 539s test_Align_a2m ... ok 540s test_Align_bed ... ok 540s test_Align_bigbed ... ok 540s test_Align_bigmaf ... ok 541s test_Align_bigpsl ... ok 541s test_Align_chain ... ok 541s test_Align_clustal ... ok 546s test_Align_codonalign ... ok 546s test_Align_emboss ... ok 546s test_Align_exonerate ... ok 546s test_Align_fasta ... ok 546s test_Align_hhr ... ok 547s test_Align_maf ... ok 547s test_Align_mauve ... ok 547s test_Align_msf ... ok 547s test_Align_nexus ... ok 547s test_Align_phylip ... ok 547s test_Align_psl ... ok 548s test_Align_sam ... ok 549s test_Align_stockholm ... ok 550s test_Align_tabular ... ok 550s test_Application ... ok 550s test_BWA_tool ... ok 550s test_BioSQL_MySQLdb_online ... skipping. internet not available 550s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 550s test_BioSQL_mysql_connector_online ... skipping. internet not available 550s test_BioSQL_psycopg2_online ... skipping. internet not available 555s test_BioSQL_sqlite3 ... ok 555s test_BioSQL_sqlite3_online ... skipping. internet not available 555s test_Blast_Record ... ok 555s test_Blast_parser ... ok 555s test_CAPS ... ok 555s test_Chi2 ... ok 556s test_ClustalOmega_tool ... ok 557s test_Clustalw_tool ... ok 557s test_Cluster ... ok 557s test_CodonTable ... ok 557s test_ColorSpiral ... ok 557s test_Compass ... ok 558s test_Consensus ... ok 560s test_Dialign_tool ... ok 560s test_EMBL_unittest ... ok 566s test_Emboss ... ok 566s test_EmbossPrimer ... ok 570s test_Entrez ... ok 570s test_Entrez_online ... skipping. internet not available 570s test_Entrez_parser ... ok 571s test_Enzyme ... ok 571s test_ExPASy ... skipping. internet not available 571s test_Fasttree_tool ... ok 571s test_File ... ok 571s test_GenBank ... ok 573s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 575s ok 576s test_GraphicsChromosome ... ok 576s test_GraphicsDistribution ... ok 576s test_GraphicsGeneral ... ok 577s test_HMMCasino ... ok 577s test_HMMGeneral ... ok 577s test_KEGG ... ok 577s test_KEGG_online ... skipping. internet not available 582s test_KGML_graphics ... ok 582s test_KGML_graphics_online ... skipping. internet not available 583s test_KGML_nographics ... ok 583s test_KeyWList ... ok 583s test_LogisticRegression ... ok 584s test_MafIO_index ... ok 585s test_Mafft_tool ... ok 586s test_MarkovModel ... ok 586s test_Medline ... ok 586s test_Muscle_tool ... ok 587s test_NCBIXML ... ok 588s test_NCBI_BLAST_tools ... ok 588s test_NCBI_qblast ... ok 588s test_NMR ... ok 588s test_NaiveBayes ... ok 589s test_Nexus ... ok 589s test_PAML_baseml ... ok 589s test_PAML_codeml ... ok 589s test_PAML_yn00 ... ok 592s test_PDB_CEAligner ... ok 593s test_PDB_DSSP ... /usr/lib/python3/dist-packages/Bio/PDB/DSSP.py:199: UserWarning: 593s Configuration error: 593s 593s The attempt to retrieve compound information for "SO4" failed. 593s 593s This information is searched for in a CCD file called components.cif or 593s components.cif.gz which should be located in one of the following directories: 593s 593s "/usr/share/libcifpp" 593s "/var/cache/libcifpp" 593s "/tmp/autopkgtest.YFyfMk/autopkgtest_tmp/libcifpp-data" 593s "/usr/share/libcifpp" 593s "/usr/share/libcifpp" 593s 593s (Note that you can add a directory to the search paths by setting the 593s LIBCIFPP_DATA_DIR environmental variable) 593s 593s On Linux an optional cron script might have been installed that automatically updates 593s components.cif and mmCIF dictionary files. This script only works when the file 593s libcifpp.conf contains an uncommented line with the text: 593s 593s update=true 593s 593s If you do not have a working cron script, you can manually update the files 593s in /var/cache/libcifpp using the following commands: 593s 593s curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif 593s curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic 593s curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic 593s 593s The current order of compound factory objects is: 593s 593s CCD components.cif resource 593s CCD components.cif resource 593s Unknown compound: SO4 593s Missing compound information for SO4 593s 593s warnings.warn(err) 593s ok 593s test_PDB_Dice ... ok 594s test_PDB_Disordered ... ok 594s test_PDB_Exposure ... ok 594s test_PDB_FragmentMapper ... ok 595s test_PDB_KDTree ... ok 596s test_PDB_MMCIF2Dict ... ok 596s test_PDB_MMCIFIO ... ok 597s test_PDB_MMCIFParser ... ok 597s test_PDB_NACCESS ... ok 597s test_PDB_PDBIO ... ok 597s test_PDB_PDBList ... skipping. internet not available 604s test_PDB_PDBMLParser ... ok 604s test_PDB_PDBParser ... ok 604s 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 604s test_PDB_Polypeptide ... ok 604s test_PDB_QCPSuperimposer ... ok 608s test_PDB_SASA ... ok 608s test_PDB_SMCRA ... ok 608s test_PDB_Selection ... ok 608s test_PDB_StructureAlignment ... ok 609s test_PDB_Superimposer ... ok 609s test_PDB_alphafold_db ... skipping. internet not available 612s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 612s warnings.warn( 612s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 612s warnings.warn( 612s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 612s warnings.warn( 612s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 612s warnings.warn( 612s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 612s warnings.warn( 612s ok 621s test_PDB_internal_coords ... ok 621s test_PDB_parse_pdb_header ... ok 621s test_PDB_vectors ... ok 621s test_PQR ... ok 621s test_Pathway ... ok 622s test_Phd ... ok 622s test_Phylo ... ok 622s test_PhyloXML ... ok 623s test_Phylo_CDAO ... ok 623s test_Phylo_NeXML ... ok 623s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 626s test_Phylo_matplotlib ... ok 627s test_Phylo_networkx ... ok 627s test_PopGen_GenePop_nodepend ... ok 629s test_Prank_tool ... ok 629s test_Probcons_tool ... ok 630s test_ProtParam ... ok 630s test_RCSBFormats ... ok 631s test_Restriction ... ok 631s test_SCOP_Astral ... ok 632s test_SCOP_Cla ... ok 632s test_SCOP_Des ... ok 633s test_SCOP_Dom ... ok 633s test_SCOP_Hie ... ok 633s test_SCOP_Raf ... ok 634s test_SCOP_Residues ... ok 634s test_SCOP_Scop ... ok 635s test_SVDSuperimposer ... ok 635s test_SearchIO_blast_tab ... ok 635s test_SearchIO_blast_tab_index ... ok 636s test_SearchIO_blast_xml ... ok 637s test_SearchIO_blast_xml_index ... ok 638s test_SearchIO_blat_psl ... ok 638s test_SearchIO_blat_psl_index ... ok 639s test_SearchIO_exonerate ... ok 639s test_SearchIO_exonerate_text_index ... ok 640s test_SearchIO_exonerate_vulgar_index ... ok 640s test_SearchIO_fasta_m10 ... ok 640s test_SearchIO_fasta_m10_index ... ok 641s test_SearchIO_hhsuite2_text ... ok 641s test_SearchIO_hmmer2_text ... ok 642s test_SearchIO_hmmer2_text_index ... ok 642s test_SearchIO_hmmer3_domtab ... ok 643s test_SearchIO_hmmer3_domtab_index ... ok 643s test_SearchIO_hmmer3_tab ... ok 644s test_SearchIO_hmmer3_tab_index ... ok 644s test_SearchIO_hmmer3_text ... ok 644s test_SearchIO_hmmer3_text_index ... ok 645s test_SearchIO_interproscan_xml ... ok 645s test_SearchIO_model ... ok 646s test_SearchIO_write ... ok 646s test_SeqFeature ... ok 662s test_SeqIO ... ok 663s test_SeqIO_AbiIO ... ok 664s test_SeqIO_FastaIO ... ok 664s test_SeqIO_Gck ... ok 664s test_SeqIO_Gfa ... ok 665s test_SeqIO_Insdc ... ok 665s test_SeqIO_NibIO ... ok 667s test_SeqIO_PdbIO ... ok 668s test_SeqIO_QualityIO ... ok 669s test_SeqIO_SeqXML ... ok 669s test_SeqIO_SnapGene ... ok 670s test_SeqIO_TwoBitIO ... ok 671s test_SeqIO_Xdna ... ok 671s test_SeqIO_features ... ok 686s test_SeqIO_index ... ok 686s test_SeqIO_online ... skipping. internet not available 687s test_SeqIO_write ... ok 687s test_SeqRecord ... ok 688s test_SeqUtils ... ok 689s test_Seq_objs ... ok 690s test_SffIO ... ok 690s test_SwissProt ... ok 693s test_TCoffee_tool ... ok 694s test_TogoWS ... skipping. internet not available 695s test_TreeConstruction ... ok 695s test_UniGene ... ok 696s test_UniProt ... skipping. internet not available 696s test_UniProt_GOA ... ok 696s test_UniProt_Parser ... ok 697s test_align ... ok 698s test_align_substitution_matrices ... ok 700s test_bgzf ... ok 701s test_cellosaurus ... ok 706s test_codonalign ... ok 707s test_geo ... ok 707s test_kNN ... ok 708s test_motifs ... ok 708s test_motifs_online ... skipping. internet not available 709s 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. 709s warnings.warn( 709s ok 709s test_pairwise2_no_C ... ok 710s test_pairwise_aligner ... ok 710s test_pairwise_alignment_map ... ok 718s test_phenotype ... ok 719s test_phenotype_fit ... ok 719s test_phyml_tool ... ok 719s test_prodoc ... ok 720s test_prosite ... ok 720s test_raxml_tool ... ok 721s test_samtools_tool ... ok 721s test_seq ... ok 722s test_translate ... ok 722s Skipping any tests requiring internet access 722s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 722s Operating system: posix linux 722s ---------------------------------------------------------------------- 722s Ran 218 tests in 185.956 seconds 722s 724s autopkgtest [11:43:12]: test full_suite: -----------------------] 725s autopkgtest [11:43:13]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 725s full_suite PASS 726s autopkgtest [11:43:14]: @@@@@@@@@@@@@@@@@@@@ summary 726s dependencies PASS 726s full_suite PASS 744s virt: nova [W] Skipping flock for amd64 744s virt: Creating nova instance adt-plucky-amd64-python-biopython-20241113-113108-juju-7f2275-prod-proposed-migration-environment-2-65eea040-112e-4356-97b0-bc05381b34aa from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)... 744s virt: nova [W] Skipping flock for amd64 744s virt: Creating nova instance adt-plucky-amd64-python-biopython-20241113-113108-juju-7f2275-prod-proposed-migration-environment-2-65eea040-112e-4356-97b0-bc05381b34aa from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...