0s autopkgtest [21:23:29]: starting date and time: 2024-11-13 21:23:29+0000 0s autopkgtest [21:23:29]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [21:23:29]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7akb3jjv/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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' -- lxd -r lxd-armhf-10.145.243.51 lxd-armhf-10.145.243.51:autopkgtest/ubuntu/plucky/armhf 54s autopkgtest [21:24:23]: testbed dpkg architecture: armhf 56s autopkgtest [21:24:25]: testbed apt version: 2.9.8 56s autopkgtest [21:24:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 65s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 65s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [970 kB] 65s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [104 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [662 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 65s Fetched 1951 kB in 1s (2025 kB/s) 65s Reading package lists... 83s tee: /proc/self/fd/2: Permission denied 105s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 105s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 105s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 105s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 107s Reading package lists... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s Calculating upgrade... 108s The following NEW packages will be installed: 108s python3.13-gdbm 108s The following packages will be upgraded: 108s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 108s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 108s python3-newt whiptail 108s 11 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 1207 kB of archives. 108s After this operation, 124 kB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 108s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 108s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 108s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 108s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 108s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 108s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 108s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 108s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 109s Fetched 1207 kB in 1s (2155 kB/s) 109s (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 ... 59559 files and directories currently installed.) 109s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 109s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Setting up python3-minimal (3.12.7-1) ... 109s (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 ... 59559 files and directories currently installed.) 109s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 109s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 109s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 109s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 109s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 109s (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 ... 59559 files and directories currently installed.) 109s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_armhf.deb ... 110s Unpacking python3-newt:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 110s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_armhf.deb ... 110s Unpacking libnewt0.52:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 110s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_armhf.deb ... 110s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 110s Selecting previously unselected package python3.13-gdbm. 110s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 110s Unpacking python3.13-gdbm (3.13.0-2) ... 110s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 110s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 110s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 110s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 110s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 110s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 110s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 110s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 110s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 110s Setting up libutempter0:armhf (1.2.1-4) ... 110s Setting up whiptail (0.52.24-2ubuntu4) ... 110s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 110s Setting up python3.13-gdbm (3.13.0-2) ... 110s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 110s Setting up python3 (3.12.7-1) ... 110s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 110s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 110s Setting up python3-gdbm:armhf (3.12.7-1) ... 110s Processing triggers for man-db (2.12.1-3) ... 111s Processing triggers for libc-bin (2.40-1ubuntu3) ... 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [21:25:23]: rebooting testbed after setup commands that affected boot 184s autopkgtest [21:26:33]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 212s autopkgtest [21:27:01]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 231s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (dsc) [3543 B] 231s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (tar) [14.6 MB] 231s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.84+dfsg-4 (diff) [42.8 kB] 231s gpgv: Signature made Wed Oct 30 21:23:04 2024 UTC 231s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 231s gpgv: issuer "emollier@debian.org" 231s gpgv: Can't check signature: No public key 231s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.84+dfsg-4.dsc: no acceptable signature found 232s autopkgtest [21:27:21]: testing package python-biopython version 1.84+dfsg-4 234s autopkgtest [21:27:23]: build not needed 239s autopkgtest [21:27:28]: test dependencies: preparing testbed 250s Reading package lists... 250s Building dependency tree... 250s Reading state information... 251s Starting pkgProblemResolver with broken count: 0 251s Starting 2 pkgProblemResolver with broken count: 0 251s Done 251s The following additional packages will be installed: 251s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 251s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libfreetype6 251s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 251s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore 251s liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 251s libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 251s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 251s python-biopython-doc python3-all python3-biopython python3-biopython-sql 251s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 251s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 251s x11-common xfonts-encodings xfonts-utils xml-core 251s Suggested packages: 251s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 251s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 251s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 251s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 251s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 251s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 251s rl-renderpm python3.13-venv python3.13-doc binfmt-support sgml-base-doc 251s debhelper 251s Recommended packages: 251s javascript-common ncbi-blast+ python3-olefile fonts-dejavu-extra 251s The following NEW packages will be installed: 251s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 251s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 251s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 251s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc 251s libjs-underscore liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 251s libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6 251s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 251s python-biopython-doc python3-all python3-biopython python3-biopython-sql 251s python3-cairo python3-freetype python3-numpy python3-pil python3-reportlab 251s python3-rlpycairo python3.13 python3.13-minimal sgml-base w3c-sgml-lib 251s x11-common xfonts-encodings xfonts-utils xml-core 253s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 253s Need to get 50.0 MB/50.0 MB of archives. 253s After this operation, 129 MB of additional disk space will be used. 253s Get:1 /tmp/autopkgtest.5lDf21/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [740 B] 253s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 253s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 253s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 253s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 253s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 253s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 253s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 253s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 253s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 253s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 253s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 253s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 253s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 253s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 253s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 253s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 253s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 253s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 253s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 253s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 253s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 253s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 253s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 253s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 253s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 253s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 253s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 253s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 253s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 253s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 253s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 253s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 253s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 253s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 253s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 253s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 253s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 253s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 253s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 253s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 253s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 253s Get:43 http://ftpmaster.internal/ubuntu plucky/universe armhf python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 253s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 253s Get:45 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 253s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 253s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 253s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 253s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 253s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 253s Get:51 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 253s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 253s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 253s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 253s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 254s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 254s Fetched 50.0 MB in 2s (24.4 MB/s) 254s Selecting previously unselected package libpython3.13-minimal:armhf. 254s (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 ... 59567 files and directories currently installed.) 254s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_armhf.deb ... 254s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 254s Selecting previously unselected package python3.13-minimal. 254s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_armhf.deb ... 254s Unpacking python3.13-minimal (3.13.0-2) ... 254s Selecting previously unselected package sgml-base. 254s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 254s Unpacking sgml-base (1.31) ... 254s Selecting previously unselected package fonts-dejavu-mono. 254s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 254s Unpacking fonts-dejavu-mono (2.37-8) ... 254s Selecting previously unselected package fonts-dejavu-core. 254s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 254s Unpacking fonts-dejavu-core (2.37-8) ... 254s Selecting previously unselected package libfontenc1:armhf. 254s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 254s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 254s Selecting previously unselected package libfreetype6:armhf. 254s Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 254s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 254s Selecting previously unselected package x11-common. 254s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu3_all.deb ... 254s Unpacking x11-common (1:7.7+23ubuntu3) ... 254s Selecting previously unselected package xfonts-encodings. 255s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 255s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 255s Selecting previously unselected package xfonts-utils. 255s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_armhf.deb ... 255s Unpacking xfonts-utils (1:7.7+7) ... 255s Selecting previously unselected package fonts-urw-base35. 255s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 255s Unpacking fonts-urw-base35 (20200910-8) ... 255s Selecting previously unselected package fontconfig-config. 255s Preparing to unpack .../11-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 255s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 255s Selecting previously unselected package libblas3:armhf. 255s Preparing to unpack .../12-libblas3_3.12.0-3build2_armhf.deb ... 255s Unpacking libblas3:armhf (3.12.0-3build2) ... 255s Selecting previously unselected package libfontconfig1:armhf. 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.../18-libcairo2_1.18.2-2_armhf.deb ... 255s Unpacking libcairo2:armhf (1.18.2-2) ... 255s Selecting previously unselected package libdeflate0:armhf. 255s Preparing to unpack .../19-libdeflate0_1.22-1_armhf.deb ... 255s Unpacking libdeflate0:armhf (1.22-1) ... 255s Selecting previously unselected package libgfortran5:armhf. 255s Preparing to unpack .../20-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 255s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 255s Selecting previously unselected package libgomp1:armhf. 255s Preparing to unpack .../21-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 255s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 255s Selecting previously unselected package libgraphite2-3:armhf. 255s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 255s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 255s Selecting previously unselected package libharfbuzz0b:armhf. 255s Preparing to unpack .../23-libharfbuzz0b_10.0.1-1_armhf.deb ... 255s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 255s Selecting previously unselected package libimagequant0:armhf. 256s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_armhf.deb ... 256s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 256s Selecting previously unselected package libjpeg-turbo8:armhf. 256s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 256s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 256s Selecting previously unselected package libjpeg8:armhf. 256s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_armhf.deb ... 256s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 256s Selecting previously unselected package libjs-jquery. 256s Preparing to unpack .../27-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 256s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 256s Selecting previously unselected package libjs-underscore. 256s Preparing to unpack .../28-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 256s Unpacking libjs-underscore 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package libraqm0:armhf. 256s Preparing to unpack .../34-libraqm0_0.10.1-1build1_armhf.deb ... 256s Unpacking libraqm0:armhf (0.10.1-1build1) ... 256s Selecting previously unselected package libsharpyuv0:armhf. 256s Preparing to unpack .../35-libsharpyuv0_1.4.0-0.1_armhf.deb ... 256s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 256s Selecting previously unselected package libjbig0:armhf. 256s Preparing to unpack .../36-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 256s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 256s Selecting previously unselected package libwebp7:armhf. 256s Preparing to unpack .../37-libwebp7_1.4.0-0.1_armhf.deb ... 256s Unpacking libwebp7:armhf (1.4.0-0.1) ... 256s Selecting previously unselected package libtiff6:armhf. 256s Preparing to unpack .../38-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 256s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 256s Selecting previously unselected package libwebpdemux2:armhf. 256s Preparing to unpack .../39-libwebpdemux2_1.4.0-0.1_armhf.deb ... 256s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 256s Selecting previously unselected package libwebpmux3:armhf. 256s Preparing to unpack .../40-libwebpmux3_1.4.0-0.1_armhf.deb ... 256s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 256s Selecting previously unselected package python-biopython-doc. 256s Preparing to unpack .../41-python-biopython-doc_1.84+dfsg-4_all.deb ... 256s Unpacking python-biopython-doc (1.84+dfsg-4) ... 257s Selecting previously unselected package python3.13. 257s Preparing to unpack .../42-python3.13_3.13.0-2_armhf.deb ... 257s Unpacking python3.13 (3.13.0-2) ... 257s Selecting previously unselected package python3-all. 257s Preparing to unpack .../43-python3-all_3.12.7-1_armhf.deb ... 257s Unpacking python3-all (3.12.7-1) ... 257s Selecting previously unselected package python3-numpy. 257s Preparing to unpack .../44-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 257s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 257s Selecting previously unselected package libopenjp2-7:armhf. 257s Preparing to unpack .../45-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 257s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 257s Selecting previously unselected package python3-pil:armhf. 257s Preparing to unpack .../46-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 257s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 257s Selecting previously unselected package python3-cairo. 257s Preparing to unpack .../47-python3-cairo_1.26.1-2_armhf.deb ... 257s Unpacking python3-cairo (1.26.1-2) ... 257s Selecting previously unselected package python3-freetype. 257s Preparing to unpack .../48-python3-freetype_2.5.1-1_all.deb ... 257s Unpacking python3-freetype (2.5.1-1) ... 257s Selecting previously unselected package python3-rlpycairo. 257s Preparing to unpack .../49-python3-rlpycairo_0.3.0-3_all.deb ... 257s Unpacking python3-rlpycairo (0.3.0-3) ... 257s Selecting previously unselected package python3-reportlab. 257s 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libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 258s Setting up liblcms2-2:armhf (2.16-2) ... 258s Setting up libpixman-1-0:armhf (0.44.0-3) ... 258s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 258s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 258s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 258s Setting up libxcb-render0:armhf (1.17.0-2) ... 258s Setting up x11-common (1:7.7+23ubuntu3) ... 258s Setting up libdeflate0:armhf (1.22-1) ... 258s Setting up libxcb-shm0:armhf (1.17.0-2) ... 258s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 258s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 258s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 258s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 258s Setting up libblas3:armhf (3.12.0-3build2) ... 258s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 258s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 258s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 258s Setting up libimagequant0:armhf (2.18.0-1build1) ... 258s Setting up fonts-dejavu-mono (2.37-8) ... 258s Setting up fonts-dejavu-core (2.37-8) ... 258s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 258s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 258s Setting up libwebp7:armhf (1.4.0-0.1) ... 258s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 258s Setting up python3.13-minimal (3.13.0-2) ... 259s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 259s Setting up sgml-base (1.31) ... 260s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 260s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 260s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 260s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 260s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 260s Setting up liblapack3:armhf (3.12.0-3build2) ... 260s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 260s Setting up python3.13 (3.13.0-2) ... 261s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 262s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 262s Setting up python3-all (3.12.7-1) ... 262s Setting up python3-freetype (2.5.1-1) ... 262s Setting up xfonts-utils (1:7.7+7) ... 262s Setting up libraqm0:armhf (0.10.1-1build1) ... 262s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 266s Setting up libjs-sphinxdoc (7.4.7-4) ... 266s Setting up python-biopython-doc (1.84+dfsg-4) ... 266s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 266s Setting up xml-core (0.19) ... 266s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 266s Setting up fonts-urw-base35 (20200910-8) ... 266s Setting up libcairo2:armhf (1.18.2-2) ... 266s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 267s Setting up python3-cairo (1.26.1-2) ... 267s Setting up python3-rlpycairo (0.3.0-3) ... 267s Setting up python3-reportlab (4.2.5-1) ... 269s Processing triggers for libc-bin (2.40-1ubuntu3) ... 269s Processing triggers for systemd (256.5-2ubuntu4) ... 269s Processing triggers for man-db (2.12.1-3) ... 270s Processing triggers for sgml-base (1.31) ... 270s Setting up w3c-sgml-lib (1.3-3) ... 299s Setting up python3-biopython (1.84+dfsg-4) ... 302s Setting up python3-biopython-sql (1.84+dfsg-4) ... 302s Setting up autopkgtest-satdep (0) ... 323s (Reading database ... 65713 files and directories currently installed.) 323s Removing autopkgtest-satdep (0) ... 329s autopkgtest [21:28:58]: test dependencies: sh debian/tests/run-unit-test 329s autopkgtest [21:28:58]: test dependencies: [----------------------- 331s cp: cannot stat '/usr/share/libcifpp/mmcif_pdbx.dic': No such file or directory 331s cp: cannot stat '/usr/share/libcifpp/mmcif_ma.dic': No such file or directory 331s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 331s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 333s mkdir: created directory 'Bio' 333s mkdir: created directory 'Bio/Align' 333s mkdir: created directory 'Bio/Align/substitution_matrices' 333s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 333s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 333s Remove test test_Tutorial.py which is bound to fail 334s test_Ace ... ok 334s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 334s 334s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 334s 334s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 334s 334s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 334s 334s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 334s 334s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 334s 334s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 334s 334s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 334s 334s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 334s 334s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 334s 334s test_Align_a2m ... loading tests failed: 334s Failed to import test module: test_Align_a2m 334s Traceback (most recent call last): 334s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 334s from . import multiarray 334s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 334s from . import overrides 334s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 334s from numpy.core._multiarray_umath import ( 334s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 334s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 334s 334s During handling of the above exception, another exception occurred: 334s 334s Traceback (most recent call last): 334s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 334s from numpy.__config__ import show as show_config 334s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 334s from numpy.core._multiarray_umath import ( 334s ...<3 lines>... 334s ) 334s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 334s raise ImportError(msg) 334s ImportError: 334s 334s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 334s 334s Importing the numpy C-extensions failed. This error can happen for 334s many reasons, often due to issues with your setup or how NumPy was 334s installed. 334s 334s We have compiled some common reasons and troubleshooting tips at: 334s 334s https://numpy.org/devdocs/user/troubleshooting-importerror.html 334s 334s Please note and check the following: 334s 334s * The Python version is: Python3.13 from "/usr/bin/python3.13" 334s * The NumPy version is: "1.26.4" 334s 334s and make sure that they are the versions you expect. 334s Please carefully study the documentation linked above for further help. 334s 334s Original error was: No module named 'numpy.core._multiarray_umath' 334s 334s 334s The above exception was the direct cause of the following exception: 334s 334s Traceback (most recent call last): 334s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 334s module = __import__(module_name) 334s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 334s import numpy as np 334s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 334s raise ImportError(msg) from e 334s ImportError: Error importing numpy: you should not try to import numpy from 334s its source directory; please exit the numpy source tree, and relaunch 334s your python interpreter from there. 334s 334s test_Align_bed ... loading tests failed: 334s Failed to import test module: test_Align_bed 334s Traceback (most recent call last): 334s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 334s from . import multiarray 334s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 334s from . import overrides 334s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 334s from numpy.core._multiarray_umath import ( 334s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 334s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 334s 334s During handling of the above exception, another exception occurred: 334s 334s Traceback (most recent call last): 334s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 334s from numpy.__config__ import show as show_config 334s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 334s from numpy.core._multiarray_umath import ( 334s ...<3 lines>... 334s ) 334s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 334s raise ImportError(msg) 334s ImportError: 334s 334s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 334s 334s Importing the numpy C-extensions failed. This error can happen for 334s many reasons, often due to issues with your setup or how NumPy was 334s installed. 334s 334s We have compiled some common reasons and troubleshooting tips at: 334s 334s https://numpy.org/devdocs/user/troubleshooting-importerror.html 334s 334s Please note and check the following: 334s 334s * The Python version is: Python3.13 from "/usr/bin/python3.13" 334s * The NumPy version is: "1.26.4" 334s 334s and make sure that they are the versions you expect. 334s Please carefully study the documentation linked above for further help. 334s 334s Original error was: No module named 'numpy.core._multiarray_umath' 334s 334s 334s The above exception was the direct cause of the following exception: 334s 334s Traceback (most recent call last): 334s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 334s module = __import__(module_name) 334s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 334s import numpy as np 334s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 334s raise ImportError(msg) from e 334s ImportError: Error importing numpy: you should not try to import numpy from 334s its source directory; please exit the numpy source tree, and relaunch 334s your python interpreter from there. 334s 334s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 334s 335s test_Align_bigmaf ... loading tests failed: 335s Failed to import test module: test_Align_bigmaf 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 335s from . import multiarray 335s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 335s from . import overrides 335s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 335s from numpy.core._multiarray_umath import ( 335s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 335s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 335s 335s During handling of the above exception, another exception occurred: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 335s from numpy.__config__ import show as show_config 335s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 335s from numpy.core._multiarray_umath import ( 335s ...<3 lines>... 335s ) 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 335s raise ImportError(msg) 335s ImportError: 335s 335s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 335s 335s Importing the numpy C-extensions failed. This error can happen for 335s many reasons, often due to issues with your setup or how NumPy was 335s installed. 335s 335s We have compiled some common reasons and troubleshooting tips at: 335s 335s https://numpy.org/devdocs/user/troubleshooting-importerror.html 335s 335s Please note and check the following: 335s 335s * The Python version is: Python3.13 from "/usr/bin/python3.13" 335s * The NumPy version is: "1.26.4" 335s 335s and make sure that they are the versions you expect. 335s Please carefully study the documentation linked above for further help. 335s 335s Original error was: No module named 'numpy.core._multiarray_umath' 335s 335s 335s The above exception was the direct cause of the following exception: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 335s module = __import__(module_name) 335s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 335s import numpy as np 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 335s raise ImportError(msg) from e 335s ImportError: Error importing numpy: you should not try to import numpy from 335s its source directory; please exit the numpy source tree, and relaunch 335s your python interpreter from there. 335s 335s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_clustal ... loading tests failed: 335s Failed to import test module: test_Align_clustal 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 335s from . import multiarray 335s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 335s from . import overrides 335s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 335s from numpy.core._multiarray_umath import ( 335s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 335s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 335s 335s During handling of the above exception, another exception occurred: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 335s from numpy.__config__ import show as show_config 335s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 335s from numpy.core._multiarray_umath import ( 335s ...<3 lines>... 335s ) 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 335s raise ImportError(msg) 335s ImportError: 335s 335s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 335s 335s Importing the numpy C-extensions failed. This error can happen for 335s many reasons, often due to issues with your setup or how NumPy was 335s installed. 335s 335s We have compiled some common reasons and troubleshooting tips at: 335s 335s https://numpy.org/devdocs/user/troubleshooting-importerror.html 335s 335s Please note and check the following: 335s 335s * The Python version is: Python3.13 from "/usr/bin/python3.13" 335s * The NumPy version is: "1.26.4" 335s 335s and make sure that they are the versions you expect. 335s Please carefully study the documentation linked above for further help. 335s 335s Original error was: No module named 'numpy.core._multiarray_umath' 335s 335s 335s The above exception was the direct cause of the following exception: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 335s module = __import__(module_name) 335s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 335s import numpy as np 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 335s raise ImportError(msg) from e 335s ImportError: Error importing numpy: you should not try to import numpy from 335s its source directory; please exit the numpy source tree, and relaunch 335s your python interpreter from there. 335s 335s test_Align_codonalign ... loading tests failed: 335s Failed to import test module: test_Align_codonalign 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 335s from . import multiarray 335s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 335s from . import overrides 335s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 335s from numpy.core._multiarray_umath import ( 335s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 335s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 335s 335s During handling of the above exception, another exception occurred: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 335s from numpy.__config__ import show as show_config 335s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 335s from numpy.core._multiarray_umath import ( 335s ...<3 lines>... 335s ) 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 335s raise ImportError(msg) 335s ImportError: 335s 335s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 335s 335s Importing the numpy C-extensions failed. This error can happen for 335s many reasons, often due to issues with your setup or how NumPy was 335s installed. 335s 335s We have compiled some common reasons and troubleshooting tips at: 335s 335s https://numpy.org/devdocs/user/troubleshooting-importerror.html 335s 335s Please note and check the following: 335s 335s * The Python version is: Python3.13 from "/usr/bin/python3.13" 335s * The NumPy version is: "1.26.4" 335s 335s and make sure that they are the versions you expect. 335s Please carefully study the documentation linked above for further help. 335s 335s Original error was: No module named 'numpy.core._multiarray_umath' 335s 335s 335s The above exception was the direct cause of the following exception: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 335s module = __import__(module_name) 335s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 335s import numpy as np 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 335s raise ImportError(msg) from e 335s ImportError: Error importing numpy: you should not try to import numpy from 335s its source directory; please exit the numpy source tree, and relaunch 335s your python interpreter from there. 335s 335s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_fasta ... loading tests failed: 335s Failed to import test module: test_Align_fasta 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 335s from . import multiarray 335s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 335s from . import overrides 335s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 335s from numpy.core._multiarray_umath import ( 335s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 335s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 335s 335s During handling of the above exception, another exception occurred: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 335s from numpy.__config__ import show as show_config 335s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 335s from numpy.core._multiarray_umath import ( 335s ...<3 lines>... 335s ) 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 335s raise ImportError(msg) 335s ImportError: 335s 335s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 335s 335s Importing the numpy C-extensions failed. This error can happen for 335s many reasons, often due to issues with your setup or how NumPy was 335s installed. 335s 335s We have compiled some common reasons and troubleshooting tips at: 335s 335s https://numpy.org/devdocs/user/troubleshooting-importerror.html 335s 335s Please note and check the following: 335s 335s * The Python version is: Python3.13 from "/usr/bin/python3.13" 335s * The NumPy version is: "1.26.4" 335s 335s and make sure that they are the versions you expect. 335s Please carefully study the documentation linked above for further help. 335s 335s Original error was: No module named 'numpy.core._multiarray_umath' 335s 335s 335s The above exception was the direct cause of the following exception: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 335s module = __import__(module_name) 335s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 335s import numpy as np 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 335s raise ImportError(msg) from e 335s ImportError: Error importing numpy: you should not try to import numpy from 335s its source directory; please exit the numpy source tree, and relaunch 335s your python interpreter from there. 335s 335s test_Align_hhr ... loading tests failed: 335s Failed to import test module: test_Align_hhr 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 335s from . import multiarray 335s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 335s from . import overrides 335s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 335s from numpy.core._multiarray_umath import ( 335s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 335s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 335s 335s During handling of the above exception, another exception occurred: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 335s from numpy.__config__ import show as show_config 335s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 335s from numpy.core._multiarray_umath import ( 335s ...<3 lines>... 335s ) 335s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 335s raise ImportError(msg) 335s ImportError: 335s 335s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 335s 335s Importing the numpy C-extensions failed. This error can happen for 335s many reasons, often due to issues with your setup or how NumPy was 335s installed. 335s 335s We have compiled some common reasons and troubleshooting tips at: 335s 335s https://numpy.org/devdocs/user/troubleshooting-importerror.html 335s 335s Please note and check the following: 335s 335s * The Python version is: Python3.13 from "/usr/bin/python3.13" 335s * The NumPy version is: "1.26.4" 335s 335s and make sure that they are the versions you expect. 335s Please carefully study the documentation linked above for further help. 335s 335s Original error was: No module named 'numpy.core._multiarray_umath' 335s 335s 335s The above exception was the direct cause of the following exception: 335s 335s Traceback (most recent call last): 335s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 335s module = __import__(module_name) 335s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 335s import numpy as np 335s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 335s raise ImportError(msg) from e 335s ImportError: Error importing numpy: you should not try to import numpy from 335s its source directory; please exit the numpy source tree, and relaunch 335s your python interpreter from there. 335s 335s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 335s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 335s 336s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_Application ... ok 336s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_Blast_Record ... loading tests failed: 336s Failed to import test module: test_Blast_Record 336s Traceback (most recent call last): 336s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 336s from . import multiarray 336s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 336s from . import overrides 336s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 336s from numpy.core._multiarray_umath import ( 336s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 336s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 336s 336s During handling of the above exception, another exception occurred: 336s 336s Traceback (most recent call last): 336s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 336s from numpy.__config__ import show as show_config 336s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 336s from numpy.core._multiarray_umath import ( 336s ...<3 lines>... 336s ) 336s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 336s raise ImportError(msg) 336s ImportError: 336s 336s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 336s 336s Importing the numpy C-extensions failed. This error can happen for 336s many reasons, often due to issues with your setup or how NumPy was 336s installed. 336s 336s We have compiled some common reasons and troubleshooting tips at: 336s 336s https://numpy.org/devdocs/user/troubleshooting-importerror.html 336s 336s Please note and check the following: 336s 336s * The Python version is: Python3.13 from "/usr/bin/python3.13" 336s * The NumPy version is: "1.26.4" 336s 336s and make sure that they are the versions you expect. 336s Please carefully study the documentation linked above for further help. 336s 336s Original error was: No module named 'numpy.core._multiarray_umath' 336s 336s 336s The above exception was the direct cause of the following exception: 336s 336s Traceback (most recent call last): 336s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 336s module = __import__(module_name) 336s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 336s from Bio.Blast.NCBIXML import HSP 336s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 336s import numpy as np 336s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 336s raise ImportError(msg) from e 336s ImportError: Error importing numpy: you should not try to import numpy from 336s its source directory; please exit the numpy source tree, and relaunch 336s your python interpreter from there. 336s 336s test_Blast_parser ... loading tests failed: 336s Failed to import test module: test_Blast_parser 336s Traceback (most recent call last): 336s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 336s from . import multiarray 336s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 336s from . import overrides 336s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 336s from numpy.core._multiarray_umath import ( 336s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 336s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 336s 336s During handling of the above exception, another exception occurred: 336s 336s Traceback (most recent call last): 336s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 336s from numpy.__config__ import show as show_config 336s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 336s from numpy.core._multiarray_umath import ( 336s ...<3 lines>... 336s ) 336s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 336s raise ImportError(msg) 336s ImportError: 336s 336s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 336s 336s Importing the numpy C-extensions failed. This error can happen for 336s many reasons, often due to issues with your setup or how NumPy was 336s installed. 336s 336s We have compiled some common reasons and troubleshooting tips at: 336s 336s https://numpy.org/devdocs/user/troubleshooting-importerror.html 336s 336s Please note and check the following: 336s 336s * The Python version is: Python3.13 from "/usr/bin/python3.13" 336s * The NumPy version is: "1.26.4" 336s 336s and make sure that they are the versions you expect. 336s Please carefully study the documentation linked above for further help. 336s 336s Original error was: No module named 'numpy.core._multiarray_umath' 336s 336s 336s The above exception was the direct cause of the following exception: 336s 336s Traceback (most recent call last): 336s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 336s module = __import__(module_name) 336s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 336s import numpy as np 336s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 336s raise ImportError(msg) from e 336s ImportError: Error importing numpy: you should not try to import numpy from 336s its source directory; please exit the numpy source tree, and relaunch 336s your python interpreter from there. 336s 336s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s 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 336s warnings.warn( 336s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 336s 336s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 336s 336s test_CodonTable ... ok 336s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 336s 336s test_Compass ... ok 337s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 337s 337s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 337s 337s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 337s 337s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 337s 337s test_EmbossPrimer ... ok 341s test_Entrez ... ok 341s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 341s 341s test_Entrez_parser ... ok 341s test_Enzyme ... ok 341s test_ExPASy ... skipping. internet not available 342s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 342s 342s test_File ... ok 342s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 342s 342s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 342s 342s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 342s 342s test_GraphicsDistribution ... loading tests failed: 342s Failed to import test module: test_GraphicsDistribution 342s Traceback (most recent call last): 342s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 342s module = __import__(module_name) 342s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 342s from Bio.Graphics.Distribution import BarChartDistribution 342s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 342s from reportlab.graphics.charts.barcharts import BarChartProperties 342s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 342s from reportlab.lib import colors 342s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 342s from reportlab.lib.rl_accel import fp_str 342s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 342s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 342s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 342s from PIL import Image 342s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 342s from . import _imaging as core 342s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 342s 342s test_GraphicsGeneral ... loading tests failed: 342s Failed to import test module: test_GraphicsGeneral 342s Traceback (most recent call last): 342s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 342s module = __import__(module_name) 342s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 342s from Bio.Graphics.Comparative import ComparativeScatterPlot 342s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 342s from reportlab.graphics.charts.lineplots import LinePlot 342s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 342s from reportlab.lib import colors 342s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 342s from reportlab.lib.rl_accel import fp_str 342s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 342s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 342s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 342s from PIL import Image 342s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 342s from . import _imaging as core 342s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 342s 342s test_HMMCasino ... ok 342s test_HMMGeneral ... ok 342s test_KEGG ... ok 342s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 342s 342s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 342s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 343s test_KGML_nographics ... ok 343s test_KeyWList ... ok 343s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 343s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 343s 343s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 343s 343s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 343s 343s test_Medline ... ok 343s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 343s 343s test_NCBIXML ... loading tests failed: 343s Failed to import test module: test_NCBIXML 343s Traceback (most recent call last): 343s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 343s from . import multiarray 343s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 343s from . import overrides 343s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 343s from numpy.core._multiarray_umath import ( 343s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 343s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 343s 343s During handling of the above exception, another exception occurred: 343s 343s Traceback (most recent call last): 343s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 343s from numpy.__config__ import show as show_config 343s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 343s from numpy.core._multiarray_umath import ( 343s ...<3 lines>... 343s ) 343s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 343s raise ImportError(msg) 343s ImportError: 343s 343s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 343s 343s Importing the numpy C-extensions failed. This error can happen for 343s many reasons, often due to issues with your setup or how NumPy was 343s installed. 343s 343s We have compiled some common reasons and troubleshooting tips at: 343s 343s https://numpy.org/devdocs/user/troubleshooting-importerror.html 343s 343s Please note and check the following: 343s 343s * The Python version is: Python3.13 from "/usr/bin/python3.13" 343s * The NumPy version is: "1.26.4" 343s 343s and make sure that they are the versions you expect. 343s Please carefully study the documentation linked above for further help. 343s 343s Original error was: No module named 'numpy.core._multiarray_umath' 343s 343s 343s The above exception was the direct cause of the following exception: 343s 343s Traceback (most recent call last): 343s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 343s module = __import__(module_name) 343s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 343s from Bio.Blast import NCBIXML 343s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 343s import numpy as np 343s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 343s raise ImportError(msg) from e 343s ImportError: Error importing numpy: you should not try to import numpy from 343s its source directory; please exit the numpy source tree, and relaunch 343s your python interpreter from there. 343s 343s test_NCBI_BLAST_tools ... loading tests failed: 343s Failed to import test module: test_NCBI_BLAST_tools 343s Traceback (most recent call last): 343s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 343s from . import multiarray 343s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 343s from . import overrides 343s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 343s from numpy.core._multiarray_umath import ( 343s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 343s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 343s 343s During handling of the above exception, another exception occurred: 343s 343s Traceback (most recent call last): 343s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 343s from numpy.__config__ import show as show_config 343s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 343s from numpy.core._multiarray_umath import ( 343s ...<3 lines>... 343s ) 343s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 343s raise ImportError(msg) 343s ImportError: 343s 343s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 343s 343s Importing the numpy C-extensions failed. This error can happen for 343s many reasons, often due to issues with your setup or how NumPy was 343s installed. 343s 343s We have compiled some common reasons and troubleshooting tips at: 343s 343s https://numpy.org/devdocs/user/troubleshooting-importerror.html 343s 343s Please note and check the following: 343s 343s * The Python version is: Python3.13 from "/usr/bin/python3.13" 343s * The NumPy version is: "1.26.4" 343s 343s and make sure that they are the versions you expect. 343s Please carefully study the documentation linked above for further help. 343s 343s Original error was: No module named 'numpy.core._multiarray_umath' 343s 343s 343s The above exception was the direct cause of the following exception: 343s 343s Traceback (most recent call last): 343s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 343s module = __import__(module_name) 343s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 343s from Bio.Blast import Applications 343s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 343s import numpy as np 343s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 343s raise ImportError(msg) from e 343s ImportError: Error importing numpy: you should not try to import numpy from 343s its source directory; please exit the numpy source tree, and relaunch 343s your python interpreter from there. 343s 343s test_NCBI_qblast ... loading tests failed: 343s Failed to import test module: test_NCBI_qblast 343s Traceback (most recent call last): 343s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 343s from . import multiarray 343s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 343s from . import overrides 343s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 343s from numpy.core._multiarray_umath import ( 343s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 343s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 343s 343s During handling of the above exception, another exception occurred: 343s 343s Traceback (most recent call last): 343s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 343s from numpy.__config__ import show as show_config 343s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 343s from numpy.core._multiarray_umath import ( 343s ...<3 lines>... 343s ) 343s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 343s raise ImportError(msg) 343s ImportError: 343s 343s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 343s 343s Importing the numpy C-extensions failed. This error can happen for 343s many reasons, often due to issues with your setup or how NumPy was 343s installed. 343s 343s We have compiled some common reasons and troubleshooting tips at: 343s 343s https://numpy.org/devdocs/user/troubleshooting-importerror.html 343s 343s Please note and check the following: 343s 343s * The Python version is: Python3.13 from "/usr/bin/python3.13" 343s * The NumPy version is: "1.26.4" 343s 343s and make sure that they are the versions you expect. 343s Please carefully study the documentation linked above for further help. 343s 343s Original error was: No module named 'numpy.core._multiarray_umath' 343s 343s 343s The above exception was the direct cause of the following exception: 343s 343s Traceback (most recent call last): 343s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 343s module = __import__(module_name) 343s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 343s from Bio.Blast import NCBIWWW 343s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 343s import numpy as np 343s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 343s raise ImportError(msg) from e 343s ImportError: Error importing numpy: you should not try to import numpy from 343s its source directory; please exit the numpy source tree, and relaunch 343s your python interpreter from there. 343s 343s test_NMR ... ok 343s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 343s 343s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 343s 343s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 343s 343s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 343s 343s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 343s 343s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 343s 343s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 343s 343s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 343s 344s test_PDB_Disordered ... loading tests failed: 344s Failed to import test module: test_PDB_Disordered 344s Traceback (most recent call last): 344s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 344s from . import multiarray 344s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 344s from . import overrides 344s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 344s from numpy.core._multiarray_umath import ( 344s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 344s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 344s 344s During handling of the above exception, another exception occurred: 344s 344s Traceback (most recent call last): 344s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 344s from numpy.__config__ import show as show_config 344s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 344s from numpy.core._multiarray_umath import ( 344s ...<3 lines>... 344s ) 344s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 344s raise ImportError(msg) 344s ImportError: 344s 344s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 344s 344s Importing the numpy C-extensions failed. This error can happen for 344s many reasons, often due to issues with your setup or how NumPy was 344s installed. 344s 344s We have compiled some common reasons and troubleshooting tips at: 344s 344s https://numpy.org/devdocs/user/troubleshooting-importerror.html 344s 344s Please note and check the following: 344s 344s * The Python version is: Python3.13 from "/usr/bin/python3.13" 344s * The NumPy version is: "1.26.4" 344s 344s and make sure that they are the versions you expect. 344s Please carefully study the documentation linked above for further help. 344s 344s Original error was: No module named 'numpy.core._multiarray_umath' 344s 344s 344s The above exception was the direct cause of the following exception: 344s 344s Traceback (most recent call last): 344s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 344s module = __import__(module_name) 344s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 344s import numpy as np 344s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 344s raise ImportError(msg) from e 344s ImportError: Error importing numpy: you should not try to import numpy from 344s its source directory; please exit the numpy source tree, and relaunch 344s your python interpreter from there. 344s 344s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 344s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 344s 344s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 344s 344s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_binary_cif ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 344s 344s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 344s 344s test_Pathway ... ok 344s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 344s 344s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 344s 344s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 344s 344s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 344s 345s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 345s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 345s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 345s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 345s test_PopGen_GenePop_nodepend ... ok 345s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 345s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 345s test_ProtParam ... ok 345s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 345s 345s test_Restriction ... ok 345s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 345s 345s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 345s 345s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 345s 345s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 345s 345s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 345s 345s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 345s 345s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 345s 345s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 345s 345s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 345s 345s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 345s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 345s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 345s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 345s 346s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 346s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 346s 346s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 346s 347s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 347s 347s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 347s 347s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 347s 347s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 347s 347s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 347s 347s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 347s 347s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 347s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 347s 348s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 348s 348s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 348s 348s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 348s 348s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 348s 348s test_UniGene ... ok 348s test_UniProt ... skipping. internet not available 348s test_UniProt_GOA ... ok 348s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 348s 348s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 348s 348s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 350s test_bgzf ... ok 350s test_cellosaurus ... ok 350s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 350s 350s test_geo ... ok 351s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 351s 351s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 351s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 351s 351s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 351s 351s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 351s 351s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 351s 351s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 351s 351s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 351s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 351s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 351s 351s test_prodoc ... ok 351s test_prosite ... ok 351s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 351s 351s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 351s test_seq ... ok 351s test_translate ... ok 351s Skipping any tests requiring internet access 351s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 351s Operating system: posix linux 351s ---------------------------------------------------------------------- 351s Ran 217 tests in 17.369 seconds 351s 351s FAILED (failures = 15) 352s test_Ace ... ok 352s test_Affy ... ok 355s test_AlignIO ... ok 355s test_AlignIO_ClustalIO ... ok 355s test_AlignIO_EmbossIO ... ok 355s test_AlignIO_FastaIO ... ok 355s test_AlignIO_MauveIO ... ok 355s test_AlignIO_PhylipIO ... ok 355s test_AlignIO_convert ... ok 355s test_AlignInfo ... ok 355s test_Align_Alignment ... ok 355s test_Align_a2m ... ok 356s test_Align_bed ... ok 356s test_Align_bigbed ... ok 356s test_Align_bigmaf ... ok 357s test_Align_bigpsl ... ok 357s test_Align_chain ... ok 357s test_Align_clustal ... ok 360s test_Align_codonalign ... ok 360s test_Align_emboss ... ok 361s test_Align_exonerate ... ok 361s test_Align_fasta ... ok 361s test_Align_hhr ... ok 362s test_Align_maf ... ok 362s test_Align_mauve ... ok 362s test_Align_msf ... ok 362s test_Align_nexus ... ok 362s test_Align_phylip ... ok 362s test_Align_psl ... ok 363s test_Align_sam ... ok 365s test_Align_stockholm ... ok 365s test_Align_tabular ... ok 365s test_Application ... ok 365s test_BioSQL_MySQLdb_online ... skipping. internet not available 365s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 365s test_BioSQL_mysql_connector_online ... skipping. internet not available 365s test_BioSQL_psycopg2_online ... skipping. internet not available 370s test_BioSQL_sqlite3 ... ok 370s test_BioSQL_sqlite3_online ... skipping. internet not available 370s test_Blast_Record ... ok 371s test_Blast_parser ... ok 371s test_CAPS ... ok 371s test_Chi2 ... ok 371s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 371s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 371s test_Cluster ... ok 371s test_CodonTable ... ok 371s test_ColorSpiral ... ok 371s test_Compass ... ok 373s test_Consensus ... ok 373s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 373s test_EMBL_unittest ... ok 373s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 373s test_EmbossPrimer ... ok 377s test_Entrez ... ok 377s test_Entrez_online ... skipping. internet not available 377s test_Entrez_parser ... ok 378s test_Enzyme ... ok 378s test_ExPASy ... skipping. internet not available 378s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 378s test_File ... ok 378s test_GenBank ... ok 380s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 382s ok 382s test_GraphicsChromosome ... ok 382s test_GraphicsDistribution ... ok 383s test_GraphicsGeneral ... ok 383s test_HMMCasino ... ok 384s test_HMMGeneral ... ok 384s test_KEGG ... ok 384s test_KEGG_online ... skipping. internet not available 389s test_KGML_graphics ... ok 389s test_KGML_graphics_online ... skipping. internet not available 390s test_KGML_nographics ... ok 390s test_KeyWList ... ok 390s test_LogisticRegression ... ok 391s test_MafIO_index ... ok 391s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 391s test_MarkovModel ... ok 391s test_Medline ... ok 391s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 392s test_NCBIXML ... ok 392s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 392s test_NCBI_qblast ... ok 392s test_NMR ... ok 392s test_NaiveBayes ... ok 392s test_Nexus ... ok 393s test_PAML_baseml ... ok 393s test_PAML_codeml ... ok 393s test_PAML_yn00 ... ok 396s test_PDB_CEAligner ... ok 397s test_PDB_DSSP ... ok 397s test_PDB_Dice ... ok 397s test_PDB_Disordered ... ok 397s test_PDB_Exposure ... ok 397s test_PDB_FragmentMapper ... ok 399s test_PDB_KDTree ... ok 399s test_PDB_MMCIF2Dict ... ok 399s test_PDB_MMCIFIO ... ok 401s test_PDB_MMCIFParser ... ok 401s test_PDB_NACCESS ... ok 401s test_PDB_PDBIO ... ok 401s test_PDB_PDBList ... skipping. internet not available 408s test_PDB_PDBMLParser ... ok 408s test_PDB_PDBParser ... ok 408s 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 408s test_PDB_Polypeptide ... ok 408s test_PDB_QCPSuperimposer ... ok 412s test_PDB_SASA ... ok 413s test_PDB_SMCRA ... ok 413s test_PDB_Selection ... ok 413s test_PDB_StructureAlignment ... ok 413s test_PDB_Superimposer ... ok 413s test_PDB_alphafold_db ... skipping. internet not available 413s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 413s 413s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 413s 413s test_PDB_parse_pdb_header ... ok 413s test_PDB_vectors ... ok 413s test_PQR ... ok 413s test_Pathway ... ok 414s test_Phd ... ok 414s test_Phylo ... ok 414s test_PhyloXML ... ok 414s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 415s test_Phylo_NeXML ... ok 415s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 415s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 415s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 415s test_PopGen_GenePop_nodepend ... ok 415s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 415s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 415s test_ProtParam ... ok 415s test_RCSBFormats ... ok 416s test_Restriction ... ok 416s test_SCOP_Astral ... ok 416s test_SCOP_Cla ... ok 416s test_SCOP_Des ... ok 416s test_SCOP_Dom ... ok 416s test_SCOP_Hie ... ok 416s test_SCOP_Raf ... ok 416s test_SCOP_Residues ... ok 416s test_SCOP_Scop ... ok 416s test_SVDSuperimposer ... ok 416s test_SearchIO_blast_tab ... ok 416s test_SearchIO_blast_tab_index ... ok 417s test_SearchIO_blast_xml ... ok 418s test_SearchIO_blast_xml_index ... ok 418s test_SearchIO_blat_psl ... ok 418s test_SearchIO_blat_psl_index ... ok 418s test_SearchIO_exonerate ... ok 418s test_SearchIO_exonerate_text_index ... ok 418s test_SearchIO_exonerate_vulgar_index ... ok 418s test_SearchIO_fasta_m10 ... ok 418s test_SearchIO_fasta_m10_index ... ok 419s test_SearchIO_hhsuite2_text ... ok 419s test_SearchIO_hmmer2_text ... ok 419s test_SearchIO_hmmer2_text_index ... ok 419s test_SearchIO_hmmer3_domtab ... ok 419s test_SearchIO_hmmer3_domtab_index ... ok 419s test_SearchIO_hmmer3_tab ... ok 419s test_SearchIO_hmmer3_tab_index ... ok 419s test_SearchIO_hmmer3_text ... ok 419s test_SearchIO_hmmer3_text_index ... ok 420s test_SearchIO_interproscan_xml ... ok 420s test_SearchIO_model ... ok 420s test_SearchIO_write ... ok 420s test_SeqFeature ... ok 437s test_SeqIO ... ok 437s test_SeqIO_AbiIO ... ok 437s test_SeqIO_FastaIO ... ok 437s test_SeqIO_Gck ... ok 437s test_SeqIO_Gfa ... ok 437s test_SeqIO_Insdc ... ok 437s test_SeqIO_NibIO ... ok 440s test_SeqIO_PdbIO ... ok 440s test_SeqIO_QualityIO ... ok 440s test_SeqIO_SeqXML ... ok 440s test_SeqIO_SnapGene ... ok 441s test_SeqIO_TwoBitIO ... ok 441s test_SeqIO_Xdna ... ok 442s test_SeqIO_features ... ok 458s test_SeqIO_index ... ok 458s test_SeqIO_online ... skipping. internet not available 458s test_SeqIO_write ... ok 458s test_SeqRecord ... ok 458s test_SeqUtils ... ok 459s test_Seq_objs ... ok 460s test_SffIO ... ok 460s test_SwissProt ... ok 460s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 460s test_TogoWS ... skipping. internet not available 460s test_TreeConstruction ... ok 460s test_UniGene ... ok 460s test_UniProt ... skipping. internet not available 461s test_UniProt_GOA ... ok 461s test_UniProt_Parser ... ok 461s test_align ... ok 461s test_align_substitution_matrices ... ok 464s test_bgzf ... ok 464s test_cellosaurus ... ok 468s test_codonalign ... ok 468s test_geo ... ok 468s test_kNN ... ok 469s test_motifs ... ok 469s test_motifs_online ... skipping. internet not available 469s 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. 469s warnings.warn( 469s ok 469s test_pairwise2_no_C ... ok 469s test_pairwise_aligner ... ok 469s test_pairwise_alignment_map ... ok 478s test_phenotype ... ok 478s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 478s 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. 478s test_prodoc ... ok 479s test_prosite ... ok 479s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 479s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 479s test_seq ... ok 479s test_translate ... ok 479s Skipping any tests requiring internet access 479s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 479s Operating system: posix linux 479s ---------------------------------------------------------------------- 479s Ran 217 tests in 127.027 seconds 479s 480s autopkgtest [21:31:29]: test dependencies: -----------------------] 484s autopkgtest [21:31:33]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 484s dependencies PASS 488s autopkgtest [21:31:37]: test full_suite: preparing testbed 544s autopkgtest [21:32:33]: testbed dpkg architecture: armhf 546s autopkgtest [21:32:35]: testbed apt version: 2.9.8 546s autopkgtest [21:32:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 554s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 554s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 554s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 554s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 554s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [970 kB] 555s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [104 kB] 555s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [662 kB] 555s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 555s Fetched 1951 kB in 1s (2175 kB/s) 555s Reading package lists... 570s tee: /proc/self/fd/2: Permission denied 594s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 594s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 594s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 594s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 594s Reading package lists... 594s Reading package lists... 594s Building dependency tree... 594s Reading state information... 595s Calculating upgrade... 596s The following NEW packages will be installed: 596s python3.13-gdbm 596s The following packages will be upgraded: 596s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 596s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 596s python3-newt whiptail 597s 11 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 597s Need to get 1207 kB of archives. 597s After this operation, 124 kB of additional disk space will be used. 597s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 597s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 597s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 597s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 597s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 597s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 597s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 597s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 597s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 597s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 597s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 597s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 598s Fetched 1207 kB in 1s (2007 kB/s) 598s (Reading database ... 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(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 ... 59559 files and directories currently installed.) 598s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 598s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 598s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 598s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 598s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 598s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 598s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 598s (Reading database ... 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(0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 598s Selecting previously unselected package python3.13-gdbm. 598s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 598s Unpacking python3.13-gdbm (3.13.0-2) ... 598s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 598s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 598s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 598s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 598s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 598s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 599s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 599s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 599s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 599s Setting up libutempter0:armhf (1.2.1-4) ... 599s Setting up whiptail (0.52.24-2ubuntu4) ... 599s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 599s Setting up python3.13-gdbm (3.13.0-2) ... 599s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 599s Setting up python3 (3.12.7-1) ... 599s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 599s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 599s Setting up python3-gdbm:armhf (3.12.7-1) ... 599s Processing triggers for man-db (2.12.1-3) ... 599s Processing triggers for libc-bin (2.40-1ubuntu3) ... 600s Reading package lists... 600s Building dependency tree... 600s Reading state information... 601s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 603s autopkgtest [21:33:32]: rebooting testbed after setup commands that affected boot 707s Reading package lists... 708s Building dependency tree... 708s Reading state information... 709s Starting pkgProblemResolver with broken count: 0 709s Starting 2 pkgProblemResolver with broken count: 0 709s Done 711s The following additional packages will be installed: 711s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 711s cpp cpp-14 cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf debhelper 711s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign 711s docutils-common dssp dwz fasttree flex fontconfig-config fonts-dejavu-core 711s fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lmodern fonts-lyx 711s fonts-urw-base35 g++ g++-14 g++-14-arm-linux-gnueabihf 711s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 711s gcc-arm-linux-gnueabihf gettext ghostscript hevea hicolor-icon-theme 711s imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libaom3 711s libapache-pom-java libarchive-zip-perl libargtable2-0 libasan8 711s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libc-dev-bin 711s libc6-dev libcairo2 libcc1-0 libcifpp-data libcifpp7 libcommons-logging-java 711s libcommons-parent-java libcrypt-dev libcups2t64 libde265-0 libdebhelper-perl 711s libdeflate0 libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl 711s libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev 711s libgfortran5 libgomp1 libgraphite2-3 libgs-common libgs10 libgs10-common 711s libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 711s libidn12 libijs-0.35 libimagequant0 libisl23 libjbig0 libjbig2dec0 711s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 711s libjs-underscore libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 711s liblerc4 liblqr-1-0 libltdl7 libmagickcore-6.q16-7t64 711s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 711s libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils 711s libpaper1 libpdfbox-java libpixman-1-0 libpotrace0 libptexenc1 711s libpython3-all-dev libpython3-dev libpython3.12-dev libpython3.12t64 711s libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib 711s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 711s libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool 711s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 711s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 711s libxt6t64 libzzip-0-13t64 linux-libc-dev m4 mafft mysql-common ncbi-blast+ 711s ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style 711s probcons python-biopython-doc python-matplotlib-data python3-alabaster 711s python3-all python3-all-dev python3-appdirs python3-biopython 711s python3-biopython-sql python3-brotli python3-cairo python3-contourpy 711s python3-cycler python3-dateutil python3-decorator python3-defusedxml 711s python3-dev python3-docutils python3-fonttools python3-freetype python3-fs 711s python3-imagesize python3-isodate python3-kiwisolver python3-lxml 711s python3-lz4 python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 711s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 711s python3-packaging python3-pil python3-pil.imagetk python3-rdflib 711s python3-reportlab python3-rlpycairo python3-roman python3-scipy python3-six 711s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 711s python3-sphinxcontrib.jquery python3-sympy python3-tabulate python3-tk 711s python3-tz python3-ufolib2 python3.12-dev python3.12-tk python3.13 711s python3.13-dev python3.13-minimal python3.13-tk rpcsvc-proto sgml-base 711s sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 711s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 711s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 711s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 711s xfonts-encodings xfonts-utils xml-core zlib1g-dev 711s Suggested packages: 711s autoconf-archive gnu-standards autoconf-doc blt-demo samtools cpp-doc 711s gcc-14-locales cpp-14-doc dh-make flit python3-build python3-installer 711s python3-wheel bison flex-doc fonts-freefont-otf | fonts-freefont-ttf 711s fonts-texgyre gcc-14-doc gcc-multilib manpages-dev gdb gcc-doc 711s gdb-arm-linux-gnueabihf gettext-doc libasprintf-dev libgettextpo-dev 711s hevea-doc imagemagick-6-doc autotrace cups-bsd | lpr | lprng enscript ffmpeg 711s gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance 711s sane-utils transfig libraw-bin libc-devtools glibc-doc 711s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 711s cups-common libfftw3-bin libfftw3-dev libheif-plugin-x265 711s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 711s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar 711s libheif-plugin-rav1e libheif-plugin-svtenc libjs-jquery-ui-docs 711s liblcms2-utils libmagickcore-6.q16-7-extra libmpfi-doc libstdc++-14-doc 711s tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 711s phylip-doc libmail-box-perl poppler-utils fonts-japanese-mincho 711s | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic 711s fonts-arphic-ukai fonts-arphic-uming fonts-nanum probcons-extra clustalw 711s emboss muscle3 phyml python3-psycopg2 raxml python-cycler-doc docutils-doc 711s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 711s python-lxml-doc cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 711s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 711s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 711s texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server 711s | virtual-mysql-server python3-gdal python3-pydot python3-pygraphviz 711s gfortran python-numpy-doc python3-pytest python-pil-doc python-rdflib-doc 711s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 711s rl-renderpm python-scipy-doc python3-stemmer dvisvgm fonts-freefont-otf 711s latexmk libjs-mathjax sphinx-doc tex-gyre texlive-fonts-extra 711s texlive-plain-generic python-sympy-doc tix python3-tk-dbg python3.13-venv 711s python3.13-doc binfmt-support sgml-base-doc boxshade seaview 711s t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 711s hintview texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex 711s icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science 711s texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex 711s texlive-pictures-doc vprerex wise-doc 711s Recommended packages: 711s libfl-dev libmagickcore-6.q16-7-extra manpages manpages-dev 711s libarchive-cpio-perl fonts-droid-fallback libheif-plugin-aomenc 711s javascript-common libjson-xs-perl libltdl-dev blast2 libwww-perl lynx ruby 711s libmail-sendmail-perl python3-bs4 python3-cssselect python3-html5lib 711s python3-olefile python3-sparqlwrapper fonts-dejavu-extra isympy-common 711s amap-align clustalw dialign-tx fsa kalign libsoap-lite-perl 711s libxml-simple-perl muscle mustang poa proda tm-align lmodern dvisvgm 711s tex-gyre tipa default-jre libspreadsheet-parseexcel-perl 711s texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl 711s libx11-protocol-perl x11-utils x11-xserver-utils 711s The following NEW packages will be installed: 711s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 711s build-essential bwa clustalo cpp cpp-14 cpp-14-arm-linux-gnueabihf 711s cpp-arm-linux-gnueabihf debhelper debugedit dh-autoreconf dh-python 711s dh-strip-nondeterminism dialign docutils-common dssp dwz fasttree flex 711s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 711s fonts-lato fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 711s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 711s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext ghostscript hevea 711s hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 711s intltool-debian libaom3 libapache-pom-java libarchive-zip-perl 711s libargtable2-0 libasan8 libavahi-client3 libavahi-common-data 711s libavahi-common3 libblas3 libc-dev-bin libc6-dev libcairo2 libcc1-0 711s libcifpp-data libcifpp7 libcommons-logging-java libcommons-parent-java 711s libcrypt-dev libcups2t64 libde265-0 libdebhelper-perl libdeflate0 711s libexpat1-dev libfftw3-double3 libfile-stripnondeterminism-perl 711s libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev 711s libgfortran5 libgomp1 libgraphite2-3 libgs-common libgs10 libgs10-common 711s libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 711s libidn12 libijs-0.35 libimagequant0 libisl23 libjbig0 libjbig2dec0 711s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 711s libjs-underscore libjson-perl libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 711s liblerc4 liblqr-1-0 libltdl7 libmagickcore-6.q16-7t64 711s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 711s libmpc3 libmpfi0 libmysqlclient21 libnetpbm11t64 libopenjp2-7 libpaper-utils 711s libpaper1 libpdfbox-java libpixman-1-0 libpotrace0 libptexenc1 711s libpython3-all-dev libpython3-dev libpython3.12-dev libpython3.12t64 711s libpython3.13 libpython3.13-dev libpython3.13-minimal libpython3.13-stdlib 711s libqhull-r8.0 libraqm0 libraw23t64 libsharpyuv0 libsm6 libstdc++-14-dev 711s libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool 711s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 711s libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxslt1.1 libxss1 711s libxt6t64 libzzip-0-13t64 linux-libc-dev m4 mafft mysql-common ncbi-blast+ 711s ncbi-data netpbm phylip po-debconf poppler-data prank preview-latex-style 711s probcons python-biopython-doc python-matplotlib-data python3-alabaster 711s python3-all python3-all-dev python3-appdirs python3-biopython 711s python3-biopython-sql python3-brotli python3-cairo python3-contourpy 711s python3-cycler python3-dateutil python3-decorator python3-defusedxml 711s python3-dev python3-docutils python3-fonttools python3-freetype python3-fs 711s python3-imagesize python3-isodate python3-kiwisolver python3-lxml 711s python3-lz4 python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 711s python3-mysqldb python3-networkx python3-numpy python3-numpydoc 711s python3-packaging python3-pil python3-pil.imagetk python3-rdflib 711s python3-reportlab python3-rlpycairo python3-roman python3-scipy python3-six 711s python3-snowballstemmer python3-sphinx python3-sphinx-rtd-theme 711s python3-sphinxcontrib.jquery python3-sympy python3-tabulate python3-tk 711s python3-tz python3-ufolib2 python3.12-dev python3.12-tk python3.13 711s python3.13-dev python3.13-minimal python3.13-tk rpcsvc-proto sgml-base 711s sphinx-common sphinx-rtd-theme-common t-coffee t1utils tex-common 711s texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base 711s texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.6-blt2.5 711s unicode-data w3c-sgml-lib wise wise-data x11-common xdg-utils 711s xfonts-encodings xfonts-utils xml-core zlib1g-dev 711s 0 upgraded, 257 newly installed, 0 to remove and 0 not upgraded. 711s Need to get 324 MB/324 MB of archives. 711s After this operation, 1149 MB of additional disk space will be used. 711s Get:1 /tmp/autopkgtest.5lDf21/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [996 B] 712s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB] 712s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf flex armhf 2.6.4-8.2build1 [293 kB] 712s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 712s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 712s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libfftw3-double3 armhf 3.3.10-1ubuntu4 [368 kB] 712s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 712s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 712s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 712s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 712s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 712s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 712s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 712s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 713s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 713s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 713s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 713s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libaom3 armhf 3.11.0~rc1-1 [1762 kB] 713s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libheif-plugin-aomdec armhf 1.18.1-2 [10.6 kB] 713s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libde265-0 armhf 1.0.15-1build4 [157 kB] 713s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libheif-plugin-libde265 armhf 1.18.1-2 [11.1 kB] 713s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libheif1 armhf 1.18.1-2 [288 kB] 713s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 713s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 713s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 713s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 713s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf liblqr-1-0 armhf 0.4.2-2.1build2 [23.2 kB] 713s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libltdl7 armhf 2.4.7-7build1 [37.6 kB] 713s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 713s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libraw23t64 armhf 0.21.3-1 [353 kB] 713s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 713s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 713s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 713s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 713s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 713s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 713s Get:37 http://ftpmaster.internal/ubuntu plucky/universe armhf imagemagick-6-common all 8:6.9.13.12+dfsg1-1build1 [69.6 kB] 713s Get:38 http://ftpmaster.internal/ubuntu plucky/universe armhf libmagickcore-6.q16-7t64 armhf 8:6.9.13.12+dfsg1-1build1 [1748 kB] 713s Get:39 http://ftpmaster.internal/ubuntu plucky/universe armhf libmagickwand-6.q16-7t64 armhf 8:6.9.13.12+dfsg1-1build1 [336 kB] 713s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf poppler-data all 0.4.12-1 [2060 kB] 713s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 713s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 713s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 713s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 713s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 713s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] 713s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB] 713s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.15+dfsg-2 [909 kB] 713s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 713s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 713s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 713s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.15-1 [685 kB] 713s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7build1 [525 kB] 713s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf blt armhf 2.5.3+dfsg-7build1 [4840 B] 713s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB] 713s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB] 713s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB] 713s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 713s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB] 713s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 713s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 713s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [9219 kB] 714s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-8ubuntu1 [1032 B] 714s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B] 714s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB] 714s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-8ubuntu1 [43.3 kB] 714s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-8ubuntu1 [2901 kB] 714s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-8ubuntu1 [1150 kB] 714s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-8ubuntu1 [897 kB] 714s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [18.0 MB] 715s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-8ubuntu1 [498 kB] 715s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B] 715s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B] 715s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-8ubuntu1 [2569 kB] 715s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [10.5 MB] 715s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-8ubuntu1 [19.9 kB] 715s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B] 715s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B] 715s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 715s Get:80 http://ftpmaster.internal/ubuntu plucky/universe armhf bwa armhf 0.7.18-1 [198 kB] 715s Get:81 http://ftpmaster.internal/ubuntu plucky/universe armhf libargtable2-0 armhf 13-2 [12.2 kB] 715s Get:82 http://ftpmaster.internal/ubuntu plucky/universe armhf clustalo armhf 1.2.4-8build1 [249 kB] 715s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 715s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-7build1 [166 kB] 715s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 715s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 715s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 715s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B] 715s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB] 715s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 715s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB] 716s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 716s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 716s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB] 716s Get:95 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20241024 [112 kB] 716s Get:96 http://ftpmaster.internal/ubuntu plucky/universe armhf dialign armhf 2.2.1-13 [156 kB] 716s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 716s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 716s Get:99 http://ftpmaster.internal/ubuntu plucky/universe armhf libcifpp-data all 7.0.7-3 [480 kB] 716s Get:100 http://ftpmaster.internal/ubuntu plucky/universe armhf libcifpp7 armhf 7.0.7-3 [959 kB] 716s Get:101 http://ftpmaster.internal/ubuntu plucky/universe armhf dssp armhf 4.4.10-1 [696 kB] 716s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 716s Get:103 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lmodern all 2.005-1 [4799 kB] 717s Get:104 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lyx all 2.4.2.1-1 [171 kB] 717s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libgs-common all 10.03.1~dfsg1-0ubuntu2 [175 kB] 717s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libgs10-common all 10.03.1~dfsg1-0ubuntu2 [488 kB] 717s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libavahi-common-data armhf 0.8-13ubuntu6 [29.7 kB] 717s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libavahi-common3 armhf 0.8-13ubuntu6 [20.2 kB] 717s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libavahi-client3 armhf 0.8-13ubuntu6 [24.2 kB] 717s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libcups2t64 armhf 2.4.10-1ubuntu2 [239 kB] 717s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libidn12 armhf 1.42-2 [55.1 kB] 717s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libijs-0.35 armhf 0.35-15.1build1 [13.5 kB] 717s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig2dec0 armhf 0.20-1build3 [57.6 kB] 717s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper1 armhf 1.1.29build1 [12.6 kB] 717s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 717s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 717s Get:117 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 717s Get:118 http://ftpmaster.internal/ubuntu plucky/main armhf libgs10 armhf 10.03.1~dfsg1-0ubuntu2 [4182 kB] 717s Get:119 http://ftpmaster.internal/ubuntu plucky/main armhf ghostscript armhf 10.03.1~dfsg1-0ubuntu2 [43.4 kB] 717s Get:120 http://ftpmaster.internal/ubuntu plucky/universe armhf libnetpbm11t64 armhf 2:11.08.01-1 [97.5 kB] 717s Get:121 http://ftpmaster.internal/ubuntu plucky/universe armhf netpbm armhf 2:11.08.01-1 [1935 kB] 717s Get:122 http://ftpmaster.internal/ubuntu plucky/universe armhf tex-common all 6.18 [32.8 kB] 717s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 1.1.29build1 [8184 B] 717s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf libkpathsea6 armhf 2024.20240313.70630+ds-5 [58.8 kB] 717s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf libptexenc1 armhf 2024.20240313.70630+ds-5 [37.7 kB] 717s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf libsynctex2 armhf 2024.20240313.70630+ds-5 [48.0 kB] 717s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf libtexlua53-5 armhf 2024.20240313.70630+ds-5 [98.1 kB] 717s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf t1utils armhf 1.41-4build3 [51.8 kB] 717s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 717s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 717s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 717s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 717s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 717s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 717s Get:135 http://ftpmaster.internal/ubuntu plucky/universe armhf libmpfi0 armhf 1.5.4+ds-4 [28.0 kB] 717s Get:136 http://ftpmaster.internal/ubuntu plucky/universe armhf libpotrace0 armhf 1.16-2build1 [15.2 kB] 717s Get:137 http://ftpmaster.internal/ubuntu plucky/universe armhf libteckit0 armhf 2.5.12+ds1-1 [323 kB] 717s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf libxmu6 armhf 2:1.1.3-3build2 [40.4 kB] 717s Get:139 http://ftpmaster.internal/ubuntu plucky/main armhf libxpm4 armhf 1:3.5.17-1build2 [30.1 kB] 717s Get:140 http://ftpmaster.internal/ubuntu plucky/main armhf libxaw7 armhf 2:1.0.16-1 [154 kB] 717s Get:141 http://ftpmaster.internal/ubuntu plucky/main armhf libxi6 armhf 2:1.8.2-1 [26.5 kB] 717s Get:142 http://ftpmaster.internal/ubuntu plucky/universe armhf libzzip-0-13t64 armhf 0.13.72+dfsg.1-1.2build1 [24.4 kB] 717s Get:143 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-binaries armhf 2024.20240313.70630+ds-5 [7093 kB] 717s Get:144 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 717s Get:145 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-base all 2024.20241102-1 [22.5 MB] 718s Get:146 http://ftpmaster.internal/ubuntu plucky/main armhf hicolor-icon-theme all 0.18-1 [13.5 kB] 718s Get:147 http://ftpmaster.internal/ubuntu plucky/universe armhf imagemagick-6.q16 armhf 8:6.9.13.12+dfsg1-1build1 [254 kB] 718s Get:148 http://ftpmaster.internal/ubuntu plucky/universe armhf imagemagick armhf 8:6.9.13.12+dfsg1-1build1 [14.2 kB] 718s Get:149 http://ftpmaster.internal/ubuntu plucky/universe armhf hevea armhf 2.36-2 [1938 kB] 718s Get:150 http://ftpmaster.internal/ubuntu plucky/universe armhf libapache-pom-java all 33-2 [5874 B] 718s Get:151 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 718s Get:152 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-parent-java all 56-1 [10.7 kB] 718s Get:153 http://ftpmaster.internal/ubuntu plucky/universe armhf libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 718s Get:154 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.2-2 [121 kB] 718s Get:155 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 718s Get:156 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 718s Get:157 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 718s Get:158 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 718s Get:159 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 718s Get:160 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 718s Get:161 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-perl all 4.10000-1 [81.9 kB] 718s Get:162 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 718s Get:163 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 718s Get:164 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedcrypto7t64 armhf 2.28.8-1 [182 kB] 718s Get:165 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedx509-1t64 armhf 2.28.8-1 [43.0 kB] 718s Get:166 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedtls14t64 armhf 2.28.8-1 [77.2 kB] 718s Get:167 http://ftpmaster.internal/ubuntu plucky/main armhf mysql-common all 5.8+1.1.1 [6800 B] 718s Get:168 http://ftpmaster.internal/ubuntu plucky/main armhf libmysqlclient21 armhf 8.0.40-1 [1234 kB] 718s Get:169 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.7-3 [2075 kB] 718s Get:170 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 718s Get:171 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.7-3 [4344 kB] 719s Get:172 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-dev armhf 3.12.7-1 [10.3 kB] 719s Get:173 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 719s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13 armhf 3.13.0-2 [2045 kB] 719s Get:175 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-dev armhf 3.13.0-2 [4254 kB] 719s Get:176 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-all-dev armhf 3.12.7-1 [916 B] 719s Get:177 http://ftpmaster.internal/ubuntu plucky/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 719s Get:178 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 719s Get:179 http://ftpmaster.internal/ubuntu plucky/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu1 [150 kB] 719s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf mafft armhf 7.505-1 [928 kB] 719s Get:181 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 719s Get:182 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-blast+ armhf 2.16.0+ds-6 [14.8 MB] 719s Get:183 http://ftpmaster.internal/ubuntu plucky/universe armhf phylip armhf 1:3.697+dfsg-4build1 [876 kB] 719s Get:184 http://ftpmaster.internal/ubuntu plucky/universe armhf prank armhf 0.0.170427+dfsg-3 [340 kB] 719s Get:185 http://ftpmaster.internal/ubuntu plucky/universe armhf preview-latex-style all 13.2-1 [347 kB] 719s Get:186 http://ftpmaster.internal/ubuntu plucky/universe armhf probcons armhf 1.12-14 [120 kB] 719s Get:187 http://ftpmaster.internal/ubuntu plucky/universe armhf python-biopython-doc all 1.84+dfsg-4 [18.1 MB] 720s Get:188 http://ftpmaster.internal/ubuntu plucky/universe armhf python-matplotlib-data all 3.8.3-3 [2928 kB] 720s Get:189 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 720s Get:190 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 720s Get:191 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.7-3 [505 kB] 720s Get:192 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-dev armhf 3.12.7-1 [26.7 kB] 720s Get:193 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-dev armhf 3.13.0-2 [507 kB] 720s Get:194 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all-dev armhf 3.12.7-1 [914 B] 720s Get:195 http://ftpmaster.internal/ubuntu plucky/main armhf python3-appdirs all 1.4.4-4 [10.9 kB] 720s Get:196 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 720s Get:197 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-tk armhf 3.12.7-3 [112 kB] 720s Get:198 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-tk armhf 3.13.0-2 [103 kB] 720s Get:199 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-tk armhf 3.12.7-1 [9752 B] 720s Get:200 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pil.imagetk armhf 10.4.0-1ubuntu1 [8848 B] 720s Get:201 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 720s Get:202 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 720s Get:203 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 720s Get:204 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 720s Get:205 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 721s Get:206 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 721s Get:207 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 721s Get:208 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython-sql all 1.84+dfsg-4 [26.4 kB] 721s Get:209 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-brotli armhf 1.1.0-2build2 [321 kB] 721s Get:210 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-contourpy armhf 1.3.0-2 [192 kB] 721s Get:211 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cycler all 0.12.1-1 [9716 B] 721s Get:212 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 721s Get:213 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-2 [80.3 kB] 721s Get:214 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 721s Get:215 http://ftpmaster.internal/ubuntu plucky/main armhf python3-defusedxml all 0.7.1-2 [42.0 kB] 721s Get:216 http://ftpmaster.internal/ubuntu plucky/main armhf python3-roman all 4.2-1 [10.0 kB] 721s Get:217 http://ftpmaster.internal/ubuntu plucky/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 721s Get:218 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB] 721s Get:219 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 721s Get:220 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 721s Get:221 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sympy all 1.13.3-1 [4228 kB] 722s Get:222 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 722s Get:223 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fs all 2.4.16-4 [91.3 kB] 722s Get:224 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lxml armhf 5.3.0-1 [1234 kB] 722s Get:225 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-lz4 armhf 4.0.2+dfsg-1build4 [24.8 kB] 722s Get:226 http://ftpmaster.internal/ubuntu plucky/universe armhf unicode-data all 15.1.0-1 [8878 kB] 722s Get:227 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fonttools armhf 4.46.0-1build2 [1402 kB] 722s Get:228 http://ftpmaster.internal/ubuntu plucky/main armhf python3-imagesize all 1.4.1-1 [6844 B] 722s Get:229 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-isodate all 0.6.1-3 [24.3 kB] 722s Get:230 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-kiwisolver armhf 1.4.7-2 [57.0 kB] 722s Get:231 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 722s Get:232 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-matplotlib armhf 3.8.3-3 [4500 kB] 722s Get:233 http://ftpmaster.internal/ubuntu plucky/main armhf python3-msgpack armhf 1.0.3-3build2 [76.1 kB] 722s Get:234 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB] 722s Get:235 http://ftpmaster.internal/ubuntu plucky/main armhf python3-mysqldb armhf 1.4.6-2build3 [44.2 kB] 722s Get:236 http://ftpmaster.internal/ubuntu plucky/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 723s Get:237 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-common all 7.4.7-4 [775 kB] 723s Get:238 http://ftpmaster.internal/ubuntu plucky/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB] 723s Get:239 http://ftpmaster.internal/ubuntu plucky/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 723s Get:240 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sphinx all 7.4.7-4 [593 kB] 723s Get:241 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tabulate all 0.9.0-1 [45.3 kB] 723s Get:242 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-numpydoc all 1.6.0-2 [50.5 kB] 723s Get:243 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rdflib all 7.0.0-1 [405 kB] 723s Get:244 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 723s Get:245 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 723s Get:246 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 723s Get:247 http://ftpmaster.internal/ubuntu plucky/universe armhf t-coffee armhf 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [968 kB] 723s Get:248 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-fonts-recommended all 2024.20241102-1 [4974 kB] 723s Get:249 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-latex-base all 2024.20241102-1 [1260 kB] 723s Get:250 http://ftpmaster.internal/ubuntu plucky/universe armhf libfontbox-java all 1:1.8.16-5 [208 kB] 723s Get:251 http://ftpmaster.internal/ubuntu plucky/universe armhf libpdfbox-java all 1:1.8.16-5 [5521 kB] 723s Get:252 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-latex-recommended all 2024.20241102-1 [8739 kB] 724s Get:253 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-pictures all 2024.20241102-1 [17.0 MB] 725s Get:254 http://ftpmaster.internal/ubuntu plucky/universe armhf texlive-latex-extra all 2024.20241102-1 [24.2 MB] 726s Get:255 http://ftpmaster.internal/ubuntu plucky/universe armhf wise-data all 2.4.1-25 [83.0 kB] 726s Get:256 http://ftpmaster.internal/ubuntu plucky/universe armhf wise armhf 2.4.1-25 [917 kB] 726s Get:257 http://ftpmaster.internal/ubuntu plucky/universe armhf fasttree armhf 2.1.11-2 [162 kB] 727s Preconfiguring packages ... 727s Fetched 324 MB in 14s (22.6 MB/s) 727s Selecting previously unselected package m4. 727s (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 ... 59567 files and directories currently installed.) 727s Preparing to unpack .../000-m4_1.4.19-4build1_armhf.deb ... 727s Unpacking m4 (1.4.19-4build1) ... 727s Selecting previously unselected package flex. 727s Preparing to unpack .../001-flex_2.6.4-8.2build1_armhf.deb ... 727s Unpacking flex (2.6.4-8.2build1) ... 727s Selecting previously unselected package fonts-lato. 727s Preparing to unpack .../002-fonts-lato_2.015-1_all.deb ... 727s Unpacking fonts-lato (2.015-1) ... 727s Selecting previously unselected package libgomp1:armhf. 727s Preparing to unpack .../003-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 727s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 727s Selecting previously unselected package libfftw3-double3:armhf. 727s Preparing to unpack .../004-libfftw3-double3_3.3.10-1ubuntu4_armhf.deb ... 727s Unpacking libfftw3-double3:armhf (3.3.10-1ubuntu4) ... 727s Selecting previously unselected package libfreetype6:armhf. 727s Preparing to unpack .../005-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 727s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 727s Selecting previously unselected package fonts-dejavu-mono. 727s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 727s Unpacking fonts-dejavu-mono (2.37-8) ... 727s Selecting previously unselected package fonts-dejavu-core. 727s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 727s Unpacking fonts-dejavu-core (2.37-8) ... 727s Selecting previously unselected package libfontenc1:armhf. 727s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 727s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 727s Selecting previously unselected package x11-common. 727s Preparing to unpack .../009-x11-common_1%3a7.7+23ubuntu3_all.deb ... 727s Unpacking x11-common (1:7.7+23ubuntu3) ... 727s Selecting previously unselected package xfonts-encodings. 727s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 727s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 728s Selecting previously unselected package xfonts-utils. 728s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_armhf.deb ... 728s Unpacking xfonts-utils (1:7.7+7) ... 728s Selecting previously unselected package fonts-urw-base35. 728s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 728s Unpacking fonts-urw-base35 (20200910-8) ... 728s Selecting previously unselected package fontconfig-config. 728s Preparing to unpack .../013-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 728s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 728s Selecting previously unselected package libfontconfig1:armhf. 728s Preparing to unpack .../014-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 728s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 728s Selecting previously unselected package libsharpyuv0:armhf. 728s Preparing to unpack .../015-libsharpyuv0_1.4.0-0.1_armhf.deb ... 728s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 728s Selecting previously unselected package libaom3:armhf. 728s Preparing to unpack .../016-libaom3_3.11.0~rc1-1_armhf.deb ... 728s Unpacking libaom3:armhf (3.11.0~rc1-1) ... 729s Selecting previously unselected package libheif-plugin-aomdec:armhf. 729s Preparing to unpack .../017-libheif-plugin-aomdec_1.18.1-2_armhf.deb ... 729s Unpacking libheif-plugin-aomdec:armhf (1.18.1-2) ... 729s Selecting previously unselected package libde265-0:armhf. 729s Preparing to unpack .../018-libde265-0_1.0.15-1build4_armhf.deb ... 729s Unpacking libde265-0:armhf (1.0.15-1build4) ... 729s Selecting previously unselected package libheif-plugin-libde265:armhf. 729s Preparing to unpack .../019-libheif-plugin-libde265_1.18.1-2_armhf.deb ... 729s Unpacking libheif-plugin-libde265:armhf (1.18.1-2) ... 729s Selecting previously unselected package libheif1:armhf. 729s Preparing to unpack .../020-libheif1_1.18.1-2_armhf.deb ... 729s Unpacking libheif1:armhf (1.18.1-2) ... 729s Selecting previously unselected package libjbig0:armhf. 729s Preparing to unpack .../021-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 729s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 729s Selecting previously unselected package libjpeg-turbo8:armhf. 729s Preparing to unpack .../022-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 729s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 729s Selecting previously unselected package libjpeg8:armhf. 729s Preparing to unpack .../023-libjpeg8_8c-2ubuntu11_armhf.deb ... 729s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 729s Selecting previously unselected package liblcms2-2:armhf. 729s Preparing to unpack .../024-liblcms2-2_2.16-2_armhf.deb ... 729s Unpacking liblcms2-2:armhf (2.16-2) ... 729s Selecting previously unselected package liblqr-1-0:armhf. 729s Preparing to unpack .../025-liblqr-1-0_0.4.2-2.1build2_armhf.deb ... 729s Unpacking liblqr-1-0:armhf (0.4.2-2.1build2) ... 729s Selecting previously unselected package libltdl7:armhf. 729s Preparing to unpack .../026-libltdl7_2.4.7-7build1_armhf.deb ... 729s Unpacking libltdl7:armhf (2.4.7-7build1) ... 729s Selecting previously unselected package libopenjp2-7:armhf. 729s Preparing to unpack .../027-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 729s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 729s Selecting previously unselected package libraw23t64:armhf. 729s Preparing to unpack .../028-libraw23t64_0.21.3-1_armhf.deb ... 729s Unpacking libraw23t64:armhf (0.21.3-1) ... 729s Selecting previously unselected package libdeflate0:armhf. 729s Preparing to unpack .../029-libdeflate0_1.22-1_armhf.deb ... 729s Unpacking libdeflate0:armhf (1.22-1) ... 729s Selecting previously unselected package liblerc4:armhf. 729s Preparing to unpack .../030-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 729s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 729s Selecting previously unselected package libwebp7:armhf. 729s Preparing to unpack .../031-libwebp7_1.4.0-0.1_armhf.deb ... 729s Unpacking libwebp7:armhf (1.4.0-0.1) ... 729s Selecting previously unselected package libtiff6:armhf. 729s Preparing to unpack .../032-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 729s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 729s Selecting previously unselected package libwebpdemux2:armhf. 729s Preparing to unpack .../033-libwebpdemux2_1.4.0-0.1_armhf.deb ... 729s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 729s Selecting previously unselected package libwebpmux3:armhf. 730s Preparing to unpack .../034-libwebpmux3_1.4.0-0.1_armhf.deb ... 730s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 730s Selecting previously unselected package imagemagick-6-common. 730s Preparing to unpack .../035-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1build1_all.deb ... 730s Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 730s Selecting previously unselected package libmagickcore-6.q16-7t64:armhf. 730s Preparing to unpack .../036-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_armhf.deb ... 730s Unpacking libmagickcore-6.q16-7t64:armhf (8:6.9.13.12+dfsg1-1build1) ... 730s Selecting previously unselected package libmagickwand-6.q16-7t64:armhf. 730s Preparing to unpack .../037-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_armhf.deb ... 730s Unpacking libmagickwand-6.q16-7t64:armhf (8:6.9.13.12+dfsg1-1build1) ... 730s Selecting previously unselected package poppler-data. 730s Preparing to unpack .../038-poppler-data_0.4.12-1_all.deb ... 730s Unpacking poppler-data (0.4.12-1) ... 730s Selecting previously unselected package libpython3.13-minimal:armhf. 730s Preparing to unpack .../039-libpython3.13-minimal_3.13.0-2_armhf.deb ... 730s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 730s Selecting previously unselected package python3.13-minimal. 730s Preparing to unpack .../040-python3.13-minimal_3.13.0-2_armhf.deb ... 730s Unpacking python3.13-minimal (3.13.0-2) ... 730s Selecting previously unselected package sgml-base. 730s Preparing to unpack .../041-sgml-base_1.31_all.deb ... 730s Unpacking sgml-base (1.31) ... 730s Selecting previously unselected package autoconf. 730s Preparing to unpack .../042-autoconf_2.72-3_all.deb ... 730s Unpacking autoconf (2.72-3) ... 730s Selecting previously unselected package autotools-dev. 730s Preparing to unpack .../043-autotools-dev_20220109.1_all.deb ... 730s Unpacking autotools-dev (20220109.1) ... 730s Selecting previously unselected package automake. 730s Preparing to unpack .../044-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 730s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 730s Selecting previously unselected package autopoint. 730s Preparing to unpack .../045-autopoint_0.22.5-2_all.deb ... 730s Unpacking autopoint (0.22.5-2) ... 730s Selecting previously unselected package libtcl8.6:armhf. 730s Preparing to unpack .../046-libtcl8.6_8.6.15+dfsg-2_armhf.deb ... 730s Unpacking libtcl8.6:armhf (8.6.15+dfsg-2) ... 731s Selecting previously unselected package libxrender1:armhf. 731s Preparing to unpack .../047-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 731s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 731s Selecting previously unselected package libxft2:armhf. 731s Preparing to unpack .../048-libxft2_2.3.6-1build1_armhf.deb ... 731s Unpacking libxft2:armhf (2.3.6-1build1) ... 731s Selecting previously unselected package libxss1:armhf. 731s Preparing to unpack .../049-libxss1_1%3a1.2.3-1build3_armhf.deb ... 731s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 731s Selecting previously unselected package libtk8.6:armhf. 731s Preparing to unpack .../050-libtk8.6_8.6.15-1_armhf.deb ... 731s Unpacking libtk8.6:armhf (8.6.15-1) ... 731s Selecting previously unselected package tk8.6-blt2.5. 731s Preparing to unpack .../051-tk8.6-blt2.5_2.5.3+dfsg-7build1_armhf.deb ... 731s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 731s Selecting previously unselected package blt. 731s Preparing to unpack .../052-blt_2.5.3+dfsg-7build1_armhf.deb ... 731s Unpacking blt (2.5.3+dfsg-7build1) ... 731s Selecting previously unselected package libc-dev-bin. 731s Preparing to unpack .../053-libc-dev-bin_2.40-1ubuntu3_armhf.deb ... 731s Unpacking libc-dev-bin (2.40-1ubuntu3) ... 731s Selecting previously unselected package linux-libc-dev:armhf. 731s Preparing to unpack .../054-linux-libc-dev_6.11.0-8.8_armhf.deb ... 731s Unpacking linux-libc-dev:armhf (6.11.0-8.8) ... 731s Selecting previously unselected package libcrypt-dev:armhf. 731s Preparing to unpack .../055-libcrypt-dev_1%3a4.4.36-4build1_armhf.deb ... 731s Unpacking libcrypt-dev:armhf (1:4.4.36-4build1) ... 731s Selecting previously unselected package rpcsvc-proto. 731s Preparing to unpack .../056-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 731s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 731s Selecting previously unselected package libc6-dev:armhf. 731s Preparing to unpack .../057-libc6-dev_2.40-1ubuntu3_armhf.deb ... 731s Unpacking libc6-dev:armhf (2.40-1ubuntu3) ... 732s Selecting previously unselected package libisl23:armhf. 732s Preparing to unpack .../058-libisl23_0.27-1_armhf.deb ... 732s Unpacking libisl23:armhf (0.27-1) ... 732s Selecting previously unselected package libmpc3:armhf. 732s Preparing to unpack .../059-libmpc3_1.3.1-1build2_armhf.deb ... 732s Unpacking libmpc3:armhf (1.3.1-1build2) ... 732s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 732s Preparing to unpack .../060-cpp-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 732s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 732s Selecting previously unselected package cpp-14. 732s Preparing to unpack .../061-cpp-14_14.2.0-8ubuntu1_armhf.deb ... 732s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 732s Selecting previously unselected package cpp-arm-linux-gnueabihf. 732s Preparing to unpack .../062-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 732s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 732s Selecting previously unselected package cpp. 732s Preparing to unpack .../063-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ... 732s Unpacking cpp (4:14.1.0-2ubuntu1) ... 732s Selecting previously unselected package libcc1-0:armhf. 732s Preparing to unpack .../064-libcc1-0_14.2.0-8ubuntu1_armhf.deb ... 732s Unpacking libcc1-0:armhf (14.2.0-8ubuntu1) ... 732s Selecting previously unselected package libasan8:armhf. 732s Preparing to unpack .../065-libasan8_14.2.0-8ubuntu1_armhf.deb ... 732s Unpacking libasan8:armhf (14.2.0-8ubuntu1) ... 732s Selecting previously unselected package libubsan1:armhf. 732s Preparing to unpack .../066-libubsan1_14.2.0-8ubuntu1_armhf.deb ... 732s Unpacking libubsan1:armhf (14.2.0-8ubuntu1) ... 732s Selecting previously unselected package libgcc-14-dev:armhf. 732s Preparing to unpack .../067-libgcc-14-dev_14.2.0-8ubuntu1_armhf.deb ... 732s Unpacking libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 732s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 732s Preparing to unpack .../068-gcc-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 732s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 733s Selecting previously unselected package gcc-14. 733s Preparing to unpack .../069-gcc-14_14.2.0-8ubuntu1_armhf.deb ... 733s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 733s Selecting previously unselected package gcc-arm-linux-gnueabihf. 733s Preparing to unpack .../070-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 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Unpacking dh-strip-nondeterminism (1.14.0-1) ... 734s Selecting previously unselected package debugedit. 734s Preparing to unpack .../087-debugedit_1%3a5.1-1_armhf.deb ... 734s Unpacking debugedit (1:5.1-1) ... 734s Selecting previously unselected package dwz. 734s Preparing to unpack .../088-dwz_0.15-1build6_armhf.deb ... 734s Unpacking dwz (0.15-1build6) ... 735s Selecting previously unselected package gettext. 735s Preparing to unpack .../089-gettext_0.22.5-2_armhf.deb ... 735s Unpacking gettext (0.22.5-2) ... 735s Selecting previously unselected package intltool-debian. 735s Preparing to unpack .../090-intltool-debian_0.35.0+20060710.6_all.deb ... 735s Unpacking intltool-debian (0.35.0+20060710.6) ... 735s Selecting previously unselected package po-debconf. 735s Preparing to unpack .../091-po-debconf_1.0.21+nmu1_all.deb ... 735s Unpacking po-debconf (1.0.21+nmu1) ... 735s Selecting previously unselected package debhelper. 735s Preparing to unpack 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previously unselected package libgs10-common. 736s Preparing to unpack .../104-libgs10-common_10.03.1~dfsg1-0ubuntu2_all.deb ... 736s Unpacking libgs10-common (10.03.1~dfsg1-0ubuntu2) ... 736s Selecting previously unselected package libavahi-common-data:armhf. 736s Preparing to unpack .../105-libavahi-common-data_0.8-13ubuntu6_armhf.deb ... 736s Unpacking libavahi-common-data:armhf (0.8-13ubuntu6) ... 736s Selecting previously unselected package libavahi-common3:armhf. 736s Preparing to unpack .../106-libavahi-common3_0.8-13ubuntu6_armhf.deb ... 736s Unpacking libavahi-common3:armhf (0.8-13ubuntu6) ... 736s Selecting previously unselected package libavahi-client3:armhf. 736s Preparing to unpack .../107-libavahi-client3_0.8-13ubuntu6_armhf.deb ... 736s Unpacking libavahi-client3:armhf (0.8-13ubuntu6) ... 736s Selecting previously unselected package libcups2t64:armhf. 736s Preparing to unpack .../108-libcups2t64_2.4.10-1ubuntu2_armhf.deb ... 736s Unpacking libcups2t64:armhf 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Preparing to unpack .../114-libsm6_2%3a1.2.4-1_armhf.deb ... 736s Unpacking libsm6:armhf (2:1.2.4-1) ... 736s Selecting previously unselected package libxt6t64:armhf. 736s Preparing to unpack .../115-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 736s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 736s Selecting previously unselected package libgs10:armhf. 736s Preparing to unpack .../116-libgs10_10.03.1~dfsg1-0ubuntu2_armhf.deb ... 736s Unpacking libgs10:armhf (10.03.1~dfsg1-0ubuntu2) ... 736s Selecting previously unselected package ghostscript. 736s Preparing to unpack .../117-ghostscript_10.03.1~dfsg1-0ubuntu2_armhf.deb ... 736s Unpacking ghostscript (10.03.1~dfsg1-0ubuntu2) ... 736s Selecting previously unselected package libnetpbm11t64:armhf. 736s Preparing to unpack .../118-libnetpbm11t64_2%3a11.08.01-1_armhf.deb ... 736s Unpacking libnetpbm11t64:armhf (2:11.08.01-1) ... 736s Selecting previously unselected package netpbm. 736s Preparing to unpack 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737s Unpacking libsynctex2:armhf (2024.20240313.70630+ds-5) ... 737s Selecting previously unselected package libtexlua53-5:armhf. 737s Preparing to unpack .../125-libtexlua53-5_2024.20240313.70630+ds-5_armhf.deb ... 737s Unpacking libtexlua53-5:armhf (2024.20240313.70630+ds-5) ... 737s Selecting previously unselected package t1utils. 737s Preparing to unpack .../126-t1utils_1.41-4build3_armhf.deb ... 737s Unpacking t1utils (1.41-4build3) ... 737s Selecting previously unselected package libpixman-1-0:armhf. 737s Preparing to unpack .../127-libpixman-1-0_0.44.0-3_armhf.deb ... 737s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 737s Selecting previously unselected package libxcb-render0:armhf. 737s Preparing to unpack .../128-libxcb-render0_1.17.0-2_armhf.deb ... 737s Unpacking libxcb-render0:armhf (1.17.0-2) ... 737s Selecting previously unselected package libxcb-shm0:armhf. 737s Preparing to unpack .../129-libxcb-shm0_1.17.0-2_armhf.deb ... 737s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 737s Selecting previously unselected package libcairo2:armhf. 737s Preparing to unpack .../130-libcairo2_1.18.2-2_armhf.deb ... 737s Unpacking libcairo2:armhf (1.18.2-2) ... 737s Selecting previously unselected package libgraphite2-3:armhf. 737s Preparing to unpack .../131-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 737s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 737s Selecting previously unselected package libharfbuzz0b:armhf. 737s Preparing to unpack .../132-libharfbuzz0b_10.0.1-1_armhf.deb ... 737s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 737s Selecting previously unselected package libmpfi0:armhf. 737s Preparing to unpack .../133-libmpfi0_1.5.4+ds-4_armhf.deb ... 737s Unpacking libmpfi0:armhf (1.5.4+ds-4) ... 737s Selecting previously unselected package libpotrace0:armhf. 737s Preparing to unpack .../134-libpotrace0_1.16-2build1_armhf.deb ... 737s Unpacking libpotrace0:armhf (1.16-2build1) ... 738s Selecting previously unselected package libteckit0:armhf. 738s Preparing to unpack .../135-libteckit0_2.5.12+ds1-1_armhf.deb ... 738s Unpacking libteckit0:armhf (2.5.12+ds1-1) ... 738s Selecting previously unselected package libxmu6:armhf. 738s Preparing to unpack .../136-libxmu6_2%3a1.1.3-3build2_armhf.deb ... 738s Unpacking libxmu6:armhf (2:1.1.3-3build2) ... 738s Selecting previously unselected package libxpm4:armhf. 738s Preparing to unpack .../137-libxpm4_1%3a3.5.17-1build2_armhf.deb ... 738s Unpacking libxpm4:armhf (1:3.5.17-1build2) ... 738s Selecting previously unselected package libxaw7:armhf. 738s Preparing to unpack .../138-libxaw7_2%3a1.0.16-1_armhf.deb ... 738s Unpacking libxaw7:armhf (2:1.0.16-1) ... 738s Selecting previously unselected package libxi6:armhf. 738s Preparing to unpack .../139-libxi6_2%3a1.8.2-1_armhf.deb ... 738s Unpacking libxi6:armhf (2:1.8.2-1) ... 738s Selecting previously unselected package libzzip-0-13t64:armhf. 738s Preparing to unpack .../140-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_armhf.deb ... 738s Unpacking libzzip-0-13t64:armhf (0.13.72+dfsg.1-1.2build1) ... 738s Selecting previously unselected package texlive-binaries. 738s Preparing to unpack .../141-texlive-binaries_2024.20240313.70630+ds-5_armhf.deb ... 738s Unpacking texlive-binaries (2024.20240313.70630+ds-5) ... 739s Selecting previously unselected package xdg-utils. 739s Preparing to unpack .../142-xdg-utils_1.2.1-0ubuntu1_all.deb ... 739s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 739s Selecting previously unselected package texlive-base. 739s Preparing to unpack .../143-texlive-base_2024.20241102-1_all.deb ... 739s Unpacking texlive-base (2024.20241102-1) ... 740s Selecting previously unselected package hicolor-icon-theme. 740s Preparing to unpack .../144-hicolor-icon-theme_0.18-1_all.deb ... 740s Unpacking hicolor-icon-theme (0.18-1) ... 740s Selecting previously unselected package imagemagick-6.q16. 740s Preparing to unpack .../145-imagemagick-6.q16_8%3a6.9.13.12+dfsg1-1build1_armhf.deb ... 740s Unpacking imagemagick-6.q16 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libcommons-logging-java. 740s Preparing to unpack .../151-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ... 740s Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ... 740s Selecting previously unselected package libexpat1-dev:armhf. 740s Preparing to unpack .../152-libexpat1-dev_2.6.2-2_armhf.deb ... 740s Unpacking libexpat1-dev:armhf (2.6.2-2) ... 740s Selecting previously unselected package libgfortran5:armhf. 740s Preparing to unpack .../153-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 740s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 741s Selecting previously unselected package libimagequant0:armhf. 741s Preparing to unpack .../154-libimagequant0_2.18.0-1build1_armhf.deb ... 741s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 741s Selecting previously unselected package libjs-jquery. 741s Preparing to unpack .../155-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 741s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 741s Selecting previously unselected package libjs-jquery-ui. 741s Preparing to unpack .../156-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 741s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 741s Selecting previously unselected package libjs-underscore. 741s Preparing to unpack .../157-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 741s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 741s Selecting previously unselected package libjs-sphinxdoc. 741s Preparing to unpack .../158-libjs-sphinxdoc_7.4.7-4_all.deb ... 741s Unpacking libjs-sphinxdoc (7.4.7-4) ... 741s Selecting previously unselected package libjson-perl. 741s Preparing to unpack .../159-libjson-perl_4.10000-1_all.deb ... 741s Unpacking libjson-perl (4.10000-1) ... 741s Selecting previously unselected package liblapack3:armhf. 741s Preparing to unpack .../160-liblapack3_3.12.0-3build2_armhf.deb ... 741s Unpacking liblapack3:armhf (3.12.0-3build2) ... 741s Selecting previously unselected package liblbfgsb0:armhf. 741s Preparing to unpack .../161-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 741s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 741s Selecting previously unselected package libmbedcrypto7t64:armhf. 741s Preparing to unpack .../162-libmbedcrypto7t64_2.28.8-1_armhf.deb ... 741s Unpacking libmbedcrypto7t64:armhf (2.28.8-1) ... 741s Selecting previously unselected package libmbedx509-1t64:armhf. 741s Preparing to unpack .../163-libmbedx509-1t64_2.28.8-1_armhf.deb ... 741s Unpacking libmbedx509-1t64:armhf (2.28.8-1) ... 741s Selecting previously unselected package libmbedtls14t64:armhf. 741s Preparing to unpack .../164-libmbedtls14t64_2.28.8-1_armhf.deb ... 741s Unpacking libmbedtls14t64:armhf (2.28.8-1) ... 741s Selecting previously unselected package mysql-common. 741s Preparing to unpack .../165-mysql-common_5.8+1.1.1_all.deb ... 741s Unpacking mysql-common (5.8+1.1.1) ... 741s Selecting previously unselected package libmysqlclient21:armhf. 741s Preparing to unpack .../166-libmysqlclient21_8.0.40-1_armhf.deb ... 741s Unpacking libmysqlclient21:armhf (8.0.40-1) ... 741s Selecting previously unselected package libpython3.12t64:armhf. 741s Preparing to unpack .../167-libpython3.12t64_3.12.7-3_armhf.deb ... 741s Unpacking libpython3.12t64:armhf (3.12.7-3) ... 742s Selecting previously unselected package zlib1g-dev:armhf. 742s Preparing to unpack .../168-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 742s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 742s Selecting previously unselected package libpython3.12-dev:armhf. 742s Preparing to unpack .../169-libpython3.12-dev_3.12.7-3_armhf.deb ... 742s Unpacking libpython3.12-dev:armhf (3.12.7-3) ... 742s Selecting previously unselected package libpython3-dev:armhf. 742s Preparing to unpack .../170-libpython3-dev_3.12.7-1_armhf.deb ... 742s Unpacking libpython3-dev:armhf (3.12.7-1) ... 742s Selecting previously unselected package libpython3.13-stdlib:armhf. 742s Preparing to unpack .../171-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 742s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 742s Selecting previously unselected package libpython3.13:armhf. 742s Preparing to unpack .../172-libpython3.13_3.13.0-2_armhf.deb ... 742s Unpacking libpython3.13:armhf (3.13.0-2) ... 742s Selecting previously unselected package libpython3.13-dev:armhf. 742s Preparing to unpack .../173-libpython3.13-dev_3.13.0-2_armhf.deb ... 742s Unpacking libpython3.13-dev:armhf (3.13.0-2) ... 742s Selecting previously unselected package libpython3-all-dev:armhf. 742s Preparing to unpack .../174-libpython3-all-dev_3.12.7-1_armhf.deb ... 742s Unpacking libpython3-all-dev:armhf (3.12.7-1) ... 742s Selecting previously unselected package libqhull-r8.0:armhf. 742s Preparing to unpack .../175-libqhull-r8.0_2020.2-6build1_armhf.deb ... 742s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 743s Selecting previously unselected package libraqm0:armhf. 743s Preparing to unpack .../176-libraqm0_0.10.1-1build1_armhf.deb ... 743s Unpacking libraqm0:armhf (0.10.1-1build1) ... 743s Selecting previously unselected package libxslt1.1:armhf. 743s Preparing to unpack .../177-libxslt1.1_1.1.39-0exp1ubuntu1_armhf.deb ... 743s Unpacking libxslt1.1:armhf (1.1.39-0exp1ubuntu1) ... 743s Selecting previously unselected package mafft. 743s Preparing to unpack .../178-mafft_7.505-1_armhf.deb ... 743s Unpacking mafft (7.505-1) ... 743s Selecting previously unselected package ncbi-data. 743s Preparing to unpack .../179-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 743s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 743s Selecting previously unselected package ncbi-blast+. 743s Preparing to unpack .../180-ncbi-blast+_2.16.0+ds-6_armhf.deb ... 743s Unpacking ncbi-blast+ (2.16.0+ds-6) ... 744s Selecting previously unselected package phylip. 744s Preparing to unpack .../181-phylip_1%3a3.697+dfsg-4build1_armhf.deb ... 744s Unpacking phylip (1:3.697+dfsg-4build1) ... 744s Selecting previously unselected package prank. 744s Preparing to unpack .../182-prank_0.0.170427+dfsg-3_armhf.deb ... 744s Unpacking prank (0.0.170427+dfsg-3) ... 744s Selecting previously unselected package preview-latex-style. 744s Preparing to unpack .../183-preview-latex-style_13.2-1_all.deb ... 744s Unpacking preview-latex-style (13.2-1) ... 744s Selecting previously unselected package probcons. 744s Preparing to unpack .../184-probcons_1.12-14_armhf.deb ... 744s Unpacking probcons (1.12-14) ... 744s Selecting previously unselected package python-biopython-doc. 744s Preparing to unpack .../185-python-biopython-doc_1.84+dfsg-4_all.deb ... 744s Unpacking python-biopython-doc (1.84+dfsg-4) ... 744s Selecting previously unselected package python-matplotlib-data. 744s Preparing to unpack .../186-python-matplotlib-data_3.8.3-3_all.deb ... 744s Unpacking python-matplotlib-data (3.8.3-3) ... 745s Selecting previously unselected package python3.13. 745s Preparing to unpack .../187-python3.13_3.13.0-2_armhf.deb ... 745s Unpacking python3.13 (3.13.0-2) ... 745s Selecting previously unselected package python3-all. 745s Preparing to unpack .../188-python3-all_3.12.7-1_armhf.deb ... 745s Unpacking python3-all (3.12.7-1) ... 745s Selecting previously unselected package python3.12-dev. 745s Preparing to unpack .../189-python3.12-dev_3.12.7-3_armhf.deb ... 745s Unpacking python3.12-dev (3.12.7-3) ... 745s Selecting previously unselected package python3-dev. 745s Preparing to unpack .../190-python3-dev_3.12.7-1_armhf.deb ... 745s Unpacking python3-dev (3.12.7-1) ... 745s Selecting previously unselected package python3.13-dev. 745s Preparing to unpack .../191-python3.13-dev_3.13.0-2_armhf.deb ... 745s Unpacking python3.13-dev (3.13.0-2) ... 745s Selecting previously unselected package python3-all-dev. 745s Preparing to unpack .../192-python3-all-dev_3.12.7-1_armhf.deb ... 745s Unpacking python3-all-dev (3.12.7-1) ... 745s Selecting previously unselected package python3-appdirs. 745s Preparing to unpack .../193-python3-appdirs_1.4.4-4_all.deb ... 745s Unpacking python3-appdirs (1.4.4-4) ... 745s Selecting previously unselected package python3-numpy. 745s Preparing to unpack .../194-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 745s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 745s Selecting previously unselected package python3.12-tk. 745s Preparing to unpack .../195-python3.12-tk_3.12.7-3_armhf.deb ... 745s Unpacking python3.12-tk (3.12.7-3) ... 745s Selecting previously unselected package python3.13-tk. 745s Preparing to unpack .../196-python3.13-tk_3.13.0-2_armhf.deb ... 745s Unpacking python3.13-tk (3.13.0-2) ... 745s Selecting previously unselected package python3-tk:armhf. 745s Preparing to unpack .../197-python3-tk_3.12.7-1_armhf.deb ... 745s Unpacking python3-tk:armhf (3.12.7-1) ... 745s Selecting previously unselected package python3-pil.imagetk:armhf. 745s Preparing to unpack .../198-python3-pil.imagetk_10.4.0-1ubuntu1_armhf.deb ... 745s Unpacking python3-pil.imagetk:armhf (10.4.0-1ubuntu1) ... 745s Selecting previously unselected package python3-pil:armhf. 745s Preparing to unpack .../199-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 745s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 745s Selecting previously unselected package python3-cairo. 745s Preparing to unpack .../200-python3-cairo_1.26.1-2_armhf.deb ... 745s Unpacking python3-cairo (1.26.1-2) ... 745s Selecting previously unselected package python3-freetype. 746s Preparing to unpack .../201-python3-freetype_2.5.1-1_all.deb ... 746s Unpacking python3-freetype (2.5.1-1) ... 746s Selecting previously unselected package python3-rlpycairo. 746s Preparing to unpack .../202-python3-rlpycairo_0.3.0-3_all.deb ... 746s Unpacking python3-rlpycairo (0.3.0-3) ... 746s Selecting previously unselected package python3-reportlab. 746s Preparing to unpack .../203-python3-reportlab_4.2.5-1_all.deb ... 746s Unpacking python3-reportlab (4.2.5-1) ... 746s Selecting previously unselected package w3c-sgml-lib. 746s Preparing to unpack .../204-w3c-sgml-lib_1.3-3_all.deb ... 746s Unpacking w3c-sgml-lib (1.3-3) ... 746s Selecting previously unselected package python3-biopython. 746s Preparing to unpack .../205-python3-biopython_1.84+dfsg-4_armhf.deb ... 746s Unpacking python3-biopython (1.84+dfsg-4) ... 746s Selecting previously unselected package python3-biopython-sql. 746s Preparing to unpack .../206-python3-biopython-sql_1.84+dfsg-4_all.deb ... 746s Unpacking python3-biopython-sql (1.84+dfsg-4) ... 746s Selecting previously unselected package python3-brotli. 746s Preparing to unpack .../207-python3-brotli_1.1.0-2build2_armhf.deb ... 746s Unpacking python3-brotli (1.1.0-2build2) ... 746s Selecting previously unselected package python3-contourpy. 746s Preparing to unpack .../208-python3-contourpy_1.3.0-2_armhf.deb ... 746s Unpacking python3-contourpy (1.3.0-2) ... 746s Selecting previously unselected package python3-cycler. 746s Preparing to unpack .../209-python3-cycler_0.12.1-1_all.deb ... 746s Unpacking python3-cycler (0.12.1-1) ... 746s Selecting previously unselected package python3-six. 746s Preparing to unpack .../210-python3-six_1.16.0-7_all.deb ... 746s Unpacking python3-six (1.16.0-7) ... 747s Selecting previously unselected package python3-dateutil. 747s Preparing to unpack .../211-python3-dateutil_2.9.0-2_all.deb ... 747s Unpacking python3-dateutil (2.9.0-2) ... 747s Selecting previously unselected package python3-decorator. 747s Preparing to unpack .../212-python3-decorator_5.1.1-5_all.deb ... 747s Unpacking python3-decorator (5.1.1-5) ... 747s Selecting previously unselected package python3-defusedxml. 747s Preparing to unpack .../213-python3-defusedxml_0.7.1-2_all.deb ... 747s Unpacking python3-defusedxml (0.7.1-2) ... 747s Selecting previously unselected package python3-roman. 747s Preparing to unpack .../214-python3-roman_4.2-1_all.deb ... 747s Unpacking python3-roman (4.2-1) ... 747s Selecting previously unselected package python3-docutils. 747s Preparing to unpack .../215-python3-docutils_0.21.2+dfsg-2_all.deb ... 747s Unpacking python3-docutils (0.21.2+dfsg-2) ... 747s Selecting previously unselected package python3-scipy. 747s Preparing to unpack .../216-python3-scipy_1.13.1-5_armhf.deb ... 747s Unpacking python3-scipy (1.13.1-5) ... 748s Selecting previously unselected package python3-ufolib2. 748s Preparing to unpack .../217-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 748s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 748s Selecting previously unselected package python3-mpmath. 748s Preparing to unpack .../218-python3-mpmath_1.3.0-1_all.deb ... 748s Unpacking python3-mpmath (1.3.0-1) ... 748s Selecting previously unselected package python3-sympy. 748s Preparing to unpack .../219-python3-sympy_1.13.3-1_all.deb ... 748s Unpacking python3-sympy (1.13.3-1) ... 749s Selecting previously unselected package python3-tz. 749s Preparing to unpack .../220-python3-tz_2024.1-2_all.deb ... 749s Unpacking python3-tz (2024.1-2) ... 749s Selecting previously unselected package python3-fs. 749s Preparing to unpack .../221-python3-fs_2.4.16-4_all.deb ... 749s Unpacking python3-fs (2.4.16-4) ... 749s Selecting previously unselected package python3-lxml:armhf. 749s Preparing to unpack .../222-python3-lxml_5.3.0-1_armhf.deb ... 749s Unpacking python3-lxml:armhf (5.3.0-1) ... 749s Selecting previously unselected package python3-lz4. 749s Preparing to unpack .../223-python3-lz4_4.0.2+dfsg-1build4_armhf.deb ... 749s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 749s Selecting previously unselected package unicode-data. 749s Preparing to unpack .../224-unicode-data_15.1.0-1_all.deb ... 749s Unpacking unicode-data (15.1.0-1) ... 749s Selecting previously unselected package python3-fonttools. 749s Preparing to unpack .../225-python3-fonttools_4.46.0-1build2_armhf.deb ... 749s Unpacking python3-fonttools (4.46.0-1build2) ... 749s Selecting previously unselected package python3-imagesize. 749s Preparing to unpack .../226-python3-imagesize_1.4.1-1_all.deb ... 749s Unpacking python3-imagesize (1.4.1-1) ... 749s Selecting previously unselected package python3-isodate. 749s Preparing to unpack .../227-python3-isodate_0.6.1-3_all.deb ... 749s Unpacking python3-isodate (0.6.1-3) ... 749s Selecting previously unselected package python3-kiwisolver. 749s Preparing to unpack .../228-python3-kiwisolver_1.4.7-2_armhf.deb ... 749s Unpacking python3-kiwisolver (1.4.7-2) ... 750s Selecting previously unselected package python3-packaging. 750s Preparing to unpack .../229-python3-packaging_24.1-1_all.deb ... 750s Unpacking python3-packaging (24.1-1) ... 750s Selecting previously unselected package python3-matplotlib. 750s Preparing to unpack .../230-python3-matplotlib_3.8.3-3_armhf.deb ... 750s Unpacking python3-matplotlib (3.8.3-3) ... 750s Selecting previously unselected package python3-msgpack. 750s Preparing to unpack .../231-python3-msgpack_1.0.3-3build2_armhf.deb ... 750s Unpacking python3-msgpack (1.0.3-3build2) ... 750s Selecting previously unselected package python3-mmtf. 750s Preparing to unpack .../232-python3-mmtf_1.1.3-1_all.deb ... 750s Unpacking python3-mmtf (1.1.3-1) ... 750s Selecting previously unselected package python3-mysqldb. 750s Preparing to unpack .../233-python3-mysqldb_1.4.6-2build3_armhf.deb ... 750s Unpacking python3-mysqldb (1.4.6-2build3) ... 750s Selecting previously unselected package python3-networkx. 750s Preparing to unpack .../234-python3-networkx_3.2.1-4ubuntu1_all.deb ... 750s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 751s Selecting previously unselected package sphinx-common. 751s Preparing to unpack .../235-sphinx-common_7.4.7-4_all.deb ... 751s Unpacking sphinx-common (7.4.7-4) ... 752s Selecting previously unselected package python3-alabaster. 752s Preparing to unpack .../236-python3-alabaster_0.7.16-0.1_all.deb ... 752s Unpacking python3-alabaster 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texlive-fonts-recommended (2024.20241102-1) ... 753s Selecting previously unselected package texlive-latex-base. 753s Preparing to unpack .../247-texlive-latex-base_2024.20241102-1_all.deb ... 753s Unpacking texlive-latex-base (2024.20241102-1) ... 753s Selecting previously unselected package libfontbox-java. 753s Preparing to unpack .../248-libfontbox-java_1%3a1.8.16-5_all.deb ... 753s Unpacking libfontbox-java (1:1.8.16-5) ... 753s Selecting previously unselected package libpdfbox-java. 753s Preparing to unpack .../249-libpdfbox-java_1%3a1.8.16-5_all.deb ... 753s Unpacking libpdfbox-java (1:1.8.16-5) ... 754s Selecting previously unselected package texlive-latex-recommended. 754s Preparing to unpack .../250-texlive-latex-recommended_2024.20241102-1_all.deb ... 754s Unpacking texlive-latex-recommended (2024.20241102-1) ... 754s Selecting previously unselected package texlive-pictures. 754s Preparing to unpack .../251-texlive-pictures_2024.20241102-1_all.deb ... 754s Unpacking texlive-pictures (2024.20241102-1) ... 756s Selecting previously unselected package texlive-latex-extra. 756s Preparing to unpack .../252-texlive-latex-extra_2024.20241102-1_all.deb ... 756s Unpacking texlive-latex-extra (2024.20241102-1) ... 758s Selecting previously unselected package wise-data. 758s Preparing to unpack .../253-wise-data_2.4.1-25_all.deb ... 758s Unpacking wise-data (2.4.1-25) ... 758s Selecting previously unselected package wise. 758s Preparing to unpack .../254-wise_2.4.1-25_armhf.deb ... 758s Unpacking wise (2.4.1-25) ... 758s Selecting previously unselected package fasttree. 758s Preparing to unpack .../255-fasttree_2.1.11-2_armhf.deb ... 758s Unpacking fasttree (2.1.11-2) ... 758s Selecting previously unselected package autopkgtest-satdep. 758s Preparing to unpack .../256-2-autopkgtest-satdep.deb ... 758s Unpacking autopkgtest-satdep (0) ... 758s Setting up dh-python (6.20241024) ... 758s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 758s Setting up liblcms2-2:armhf (2.16-2) ... 758s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 758s Setting up libpixman-1-0:armhf (0.44.0-3) ... 758s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 758s Setting up libpaper1:armhf (1.1.29build1) ... 759s 759s Creating config file /etc/papersize with new version 759s Setting up libaom3:armhf (3.11.0~rc1-1) ... 759s Setting up mysql-common (5.8+1.1.1) ... 759s update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode 759s Setting up libmysqlclient21:armhf (8.0.40-1) ... 759s Setting up imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 759s Setting up fonts-lato (2.015-1) ... 759s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 759s Setting up libxpm4:armhf (1:3.5.17-1build2) ... 759s Setting up hicolor-icon-theme (0.18-1) ... 759s Setting up libxi6:armhf (2:1.8.2-1) ... 759s Setting up probcons (1.12-14) ... 759s Setting up libmbedcrypto7t64:armhf (2.28.8-1) ... 759s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 759s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 759s Setting up libxcb-render0:armhf (1.17.0-2) ... 759s Setting up python3-defusedxml (0.7.1-2) ... 759s Setting up mafft (7.505-1) ... 759s Setting up libarchive-zip-perl (1.68-1) ... 759s Setting up bwa (0.7.18-1) ... 759s Setting up python3-alabaster (0.7.16-0.1) ... 760s Setting up fonts-lyx (2.4.2.1-1) ... 760s Setting up libijs-0.35:armhf (0.35-15.1build1) ... 760s Setting up libdebhelper-perl (13.20ubuntu1) ... 760s Setting up libgs-common (10.03.1~dfsg1-0ubuntu2) ... 760s Setting up libfontbox-java (1:1.8.16-5) ... 760s Setting up phylip (1:3.697+dfsg-4build1) ... 760s Setting up x11-common (1:7.7+23ubuntu3) ... 760s Setting up libdeflate0:armhf (1.22-1) ... 760s Setting up linux-libc-dev:armhf (6.11.0-8.8) ... 760s Setting up python3-tabulate (0.9.0-1) ... 760s Setting up m4 (1.4.19-4build1) ... 760s Setting up libqhull-r8.0:armhf (2020.2-6build1) ... 760s Setting up libxcb-shm0:armhf (1.17.0-2) ... 760s Setting up libpaper-utils (1.1.29build1) ... 760s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 760s Setting up python3-networkx (3.2.1-4ubuntu1) ... 765s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 765s Setting up libnetpbm11t64:armhf (2:11.08.01-1) ... 765s Setting up python3-tz (2024.1-2) ... 765s Setting up t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) ... 765s Setting up poppler-data (0.4.12-1) ... 765s Setting up unicode-data (15.1.0-1) ... 765s Setting up python3-mysqldb (1.4.6-2build3) ... 765s Setting up python3-six (1.16.0-7) ... 766s Setting up libpython3.12t64:armhf (3.12.7-3) ... 766s Setting up libpython3.13-minimal:armhf (3.13.0-2) ... 766s Setting up tex-common (6.18) ... 766s update-language: texlive-base not installed and configured, doing nothing! 766s Setting up python3-isodate (0.6.1-3) ... 766s Setting up python3-roman (4.2-1) ... 767s Setting up python3-decorator (5.1.1-5) ... 767s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 767s Setting up autotools-dev (20220109.1) ... 767s Setting up libblas3:armhf (3.12.0-3build2) ... 767s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 767s Setting up python3-packaging (24.1-1) ... 767s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 767s Setting up libzzip-0-13t64:armhf (0.13.72+dfsg.1-1.2build1) ... 767s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 767s Setting up libjbig2dec0:armhf (0.20-1build3) ... 767s Setting up python3-snowballstemmer (2.2.0-4build1) ... 768s Setting up libteckit0:armhf (2.5.12+ds1-1) ... 768s Setting up python3-brotli (1.1.0-2build2) ... 768s Setting up libapache-pom-java (33-2) ... 768s Setting up libavahi-common-data:armhf (0.8-13ubuntu6) ... 768s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 768s Setting up t1utils (1.41-4build3) ... 768s Setting up python3-cycler (0.12.1-1) ... 768s Setting up libtexlua53-5:armhf (2024.20240313.70630+ds-5) ... 768s Setting up libimagequant0:armhf (2.18.0-1build1) ... 768s Setting up fonts-dejavu-mono (2.37-8) ... 768s Setting up python3-kiwisolver (1.4.7-2) ... 768s Setting up libmpc3:armhf (1.3.1-1build2) ... 768s Setting up libidn12:armhf (1.42-2) ... 768s Setting up libtcl8.6:armhf (8.6.15+dfsg-2) ... 768s Setting up autopoint (0.22.5-2) ... 768s Setting up libmpfi0:armhf (1.5.4+ds-4) ... 768s Setting up fonts-dejavu-core (2.37-8) ... 769s Setting up wise-data (2.4.1-25) ... 769s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 769s Setting up libltdl7:armhf (2.4.7-7build1) ... 769s Setting up libfftw3-double3:armhf (3.3.10-1ubuntu4) ... 769s Setting up libcifpp-data (7.0.7-3) ... 769s Setting up libkpathsea6:armhf (2024.20240313.70630+ds-5) ... 769s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 769s Setting up autoconf (2.72-3) ... 769s Setting up libwebp7:armhf (1.4.0-0.1) ... 769s Setting up libubsan1:armhf (14.2.0-8ubuntu1) ... 769s Setting up dwz (0.15-1build6) ... 769s Setting up liblqr-1-0:armhf (0.4.2-2.1build2) ... 769s Setting up python3-rdflib (7.0.0-1) ... 770s Setting up libcrypt-dev:armhf (1:4.4.36-4build1) ... 770s Setting up libasan8:armhf (14.2.0-8ubuntu1) ... 770s Setting up libjson-perl (4.10000-1) ... 770s Setting up libxslt1.1:armhf (1.1.39-0exp1ubuntu1) ... 770s Setting up debugedit (1:5.1-1) ... 770s Setting up fonts-lmodern (2.005-1) ... 770s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 770s Setting up python3.13-minimal (3.13.0-2) ... 771s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 771s Setting up python3-dateutil (2.9.0-2) ... 771s Setting up fasttree (2.1.11-2) ... 771s Setting up sgml-base (1.31) ... 771s Setting up python3-msgpack (1.0.3-3build2) ... 771s Setting up libxss1:armhf (1:1.2.3-1build3) ... 771s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 771s Setting up libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 771s Setting up python3-mpmath (1.3.0-1) ... 773s Setting up libisl23:armhf (0.27-1) ... 773s Setting up libde265-0:armhf (1.0.15-1build4) ... 773s Setting up libc-dev-bin (2.40-1ubuntu3) ... 773s Setting up python-matplotlib-data (3.8.3-3) ... 773s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 773s Setting up python3-appdirs (1.4.4-4) ... 773s Setting up dialign (2.2.1-13) ... 773s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 773s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 773s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 773s Setting up xdg-utils (1.2.1-0ubuntu1) ... 773s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 773s Setting up libcc1-0:armhf (14.2.0-8ubuntu1) ... 773s Setting up libsynctex2:armhf (2024.20240313.70630+ds-5) ... 773s Setting up prank (0.0.170427+dfsg-3) ... 773s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 773s Setting up libargtable2-0 (13-2) ... 773s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 773s Setting up python3-imagesize (1.4.1-1) ... 773s Setting up libpotrace0:armhf (1.16-2build1) ... 773s Setting up libpython3.13:armhf (3.13.0-2) ... 773s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 773s Setting up automake (1:1.16.5-1.3ubuntu1) ... 773s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 773s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 773s Setting up python3-sympy (1.13.3-1) ... 792s Setting up libice6:armhf (2:1.1.1-1) ... 792s Setting up flex (2.6.4-8.2build1) ... 792s Setting up liblapack3:armhf (3.12.0-3build2) ... 792s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 792s Setting up gettext (0.22.5-2) ... 792s Setting up libmbedx509-1t64:armhf (2.28.8-1) ... 792s Setting up libpdfbox-java (1:1.8.16-5) ... 792s Setting up python3.13 (3.13.0-2) ... 793s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 794s Setting up wise (2.4.1-25) ... 794s Setting up preview-latex-style (13.2-1) ... 794s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 794s Setting up libcommons-parent-java (56-1) ... 794s Setting up libavahi-common3:armhf (0.8-13ubuntu6) ... 794s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 794s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 794s Setting up python3-all (3.12.7-1) ... 794s Setting up libcifpp7:armhf (7.0.7-3) ... 794s Setting up clustalo (1.2.4-8build1) ... 794s Setting up dssp (4.4.10-1) ... 794s Setting up python3-freetype (2.5.1-1) ... 794s Setting up xfonts-utils (1:7.7+7) ... 794s Setting up intltool-debian (0.35.0+20060710.6) ... 794s Setting up python3-fs (2.4.16-4) ... 794s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 794s Setting up libptexenc1:armhf (2024.20240313.70630+ds-5) ... 794s Setting up libraqm0:armhf (0.10.1-1build1) ... 794s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 799s Setting up libjs-sphinxdoc (7.4.7-4) ... 799s Setting up libraw23t64:armhf (0.21.3-1) ... 799s Setting up cpp-14 (14.2.0-8ubuntu1) ... 799s Setting up dh-strip-nondeterminism (1.14.0-1) ... 799s Setting up libmbedtls14t64:armhf (2.28.8-1) ... 799s Setting up python3-lxml:armhf (5.3.0-1) ... 800s Setting up python-biopython-doc (1.84+dfsg-4) ... 800s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 800s Setting up xml-core (0.19) ... 800s Setting up libc6-dev:armhf (2.40-1ubuntu3) ... 800s Setting up python3-contourpy (1.3.0-2) ... 800s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 800s Setting up libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 800s Setting up libsm6:armhf (2:1.2.4-1) ... 800s Setting up libavahi-client3:armhf (0.8-13ubuntu6) ... 800s Setting up cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 800s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 800s Setting up gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 800s Setting up g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 800s Setting up libxft2:armhf (2.3.6-1build1) ... 800s Setting up python3-scipy (1.13.1-5) ... 808s Setting up po-debconf (1.0.21+nmu1) ... 808s Setting up libtk8.6:armhf (8.6.15-1) ... 808s Setting up python3.12-tk (3.12.7-3) ... 809s Setting up python3-mmtf (1.1.3-1) ... 809s Setting up fonts-urw-base35 (20200910-8) ... 809s Setting up libcairo2:armhf (1.18.2-2) ... 809s Setting up python3.13-tk (3.13.0-2) ... 809s Setting up gcc-14 (14.2.0-8ubuntu1) ... 809s Setting up ncbi-blast+ (2.16.0+ds-6) ... 809s Setting up python3-pil:armhf (10.4.0-1ubuntu1) ... 810s Setting up libexpat1-dev:armhf (2.6.2-2) ... 810s Setting up sphinx-common (7.4.7-4) ... 810s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 810s Setting up netpbm (2:11.08.01-1) ... 810s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 810s Setting up cpp (4:14.1.0-2ubuntu1) ... 810s Setting up g++-14 (14.2.0-8ubuntu1) ... 810s Setting up libcups2t64:armhf (2.4.10-1ubuntu2) ... 810s Setting up g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 810s Setting up libgs10-common (10.03.1~dfsg1-0ubuntu2) ... 810s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 810s Setting up libxmu6:armhf (2:1.1.3-3build2) ... 810s Setting up python3-cairo (1.26.1-2) ... 810s Setting up libtool (2.4.7-7build1) ... 810s Setting up blt (2.5.3+dfsg-7build1) ... 810s Setting up python3-tk:armhf (3.12.7-1) ... 810s Setting up libpython3.12-dev:armhf (3.12.7-3) ... 810s Setting up libxaw7:armhf (2:1.0.16-1) ... 810s Setting up gcc (4:14.1.0-2ubuntu1) ... 810s Setting up dh-autoreconf (20) ... 810s Setting up python3-pil.imagetk:armhf (10.4.0-1ubuntu1) ... 810s Setting up python3-rlpycairo (0.3.0-3) ... 810s Setting up libpython3.13-dev:armhf (3.13.0-2) ... 810s Setting up python3.12-dev (3.12.7-3) ... 810s Setting up python3-reportlab (4.2.5-1) ... 812s Setting up g++ (4:14.1.0-2ubuntu1) ... 812s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 812s Setting up texlive-binaries (2024.20240313.70630+ds-5) ... 812s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 812s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 812s Setting up build-essential (12.10ubuntu1) ... 812s Setting up texlive-base (2024.20241102-1) ... 813s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 813s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 814s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 814s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 815s Setting up libgs10:armhf (10.03.1~dfsg1-0ubuntu2) ... 815s Setting up libpython3-dev:armhf (3.12.7-1) ... 815s Setting up python3.13-dev (3.13.0-2) ... 815s Setting up debhelper (13.20ubuntu1) ... 815s Setting up ghostscript (10.03.1~dfsg1-0ubuntu2) ... 815s Setting up texlive-latex-base (2024.20241102-1) ... 815s Setting up libpython3-all-dev:armhf (3.12.7-1) ... 815s Setting up python3-dev (3.12.7-1) ... 815s Setting up texlive-latex-recommended (2024.20241102-1) ... 815s Setting up texlive-pictures (2024.20241102-1) ... 815s Setting up texlive-fonts-recommended (2024.20241102-1) ... 815s Setting up python3-all-dev (3.12.7-1) ... 815s Setting up texlive-latex-extra (2024.20241102-1) ... 815s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 815s Setting up libheif-plugin-aomdec:armhf (1.18.1-2) ... 815s Setting up libheif-plugin-libde265:armhf (1.18.1-2) ... 815s Setting up libheif1:armhf (1.18.1-2) ... 815s Setting up libmagickcore-6.q16-7t64:armhf (8:6.9.13.12+dfsg1-1build1) ... 815s Setting up python3-fonttools (4.46.0-1build2) ... 817s Setting up libmagickwand-6.q16-7t64:armhf (8:6.9.13.12+dfsg1-1build1) ... 817s Setting up imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 817s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode 817s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode 817s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode 817s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode 817s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode 817s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode 817s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode 817s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode 817s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode 817s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode 817s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode 817s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode 817s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode 817s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode 817s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode 817s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode 817s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode 817s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode 817s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode 817s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode 817s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 817s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode 817s Setting up python3-matplotlib (3.8.3-3) ... 821s Setting up hevea (2.36-2) ... 821s Setting up imagemagick (8:6.9.13.12+dfsg1-1build1) ... 821s Processing triggers for install-info (7.1.1-1) ... 821s Processing triggers for libc-bin (2.40-1ubuntu3) ... 821s Processing triggers for systemd (256.5-2ubuntu4) ... 821s Processing triggers for man-db (2.12.1-3) ... 823s Processing triggers for sgml-base (1.31) ... 823s Setting up docutils-common (0.21.2+dfsg-2) ... 823s Setting up w3c-sgml-lib (1.3-3) ... 856s Setting up python3-biopython (1.84+dfsg-4) ... 859s Setting up python3-biopython-sql (1.84+dfsg-4) ... 859s Processing triggers for sgml-base (1.31) ... 859s Setting up python3-docutils (0.21.2+dfsg-2) ... 860s Setting up python3-sphinx (7.4.7-4) ... 862s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 862s Setting up python3-numpydoc (1.6.0-2) ... 863s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 863s Setting up autopkgtest-satdep (0) ... 863s Processing triggers for tex-common (6.18) ... 864s Running updmap-sys. This may take some time... done. 864s Running mktexlsr /var/lib/texmf ... done. 864s Building format(s) --all. 996s This may take some time... done. 1041s (Reading database ... 107029 files and directories currently installed.) 1041s Removing autopkgtest-satdep (0) ... 1060s autopkgtest [21:41:09]: test full_suite: sh debian/tests/run-unit-test 1060s autopkgtest [21:41:09]: test full_suite: [----------------------- 1063s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/Tutorial': No such file or directory 1063s cp: cannot stat '/usr/share/doc/python-biopython-doc/Doc/examples': No such file or directory 1066s mkdir: created directory 'Bio' 1066s mkdir: created directory 'Bio/Align' 1066s mkdir: created directory 'Bio/Align/substitution_matrices' 1066s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 1066s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 1066s Remove test test_Tutorial.py which is bound to fail 1067s test_Ace ... ok 1067s test_Affy ... skipping. Error: Install NumPy if you want to use Bio.Affy.CelFile 1067s 1067s test_AlignIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1067s 1067s test_AlignIO_ClustalIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1067s 1067s test_AlignIO_EmbossIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1067s 1067s test_AlignIO_FastaIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1067s 1067s test_AlignIO_MauveIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1067s 1067s test_AlignIO_PhylipIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1067s 1067s test_AlignIO_convert ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1067s 1067s test_AlignInfo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1067s 1067s test_Align_Alignment ... skipping. Error: Install numpy if you want to use Bio.Align. 1067s 1067s test_Align_a2m ... loading tests failed: 1067s Failed to import test module: test_Align_a2m 1067s Traceback (most recent call last): 1067s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1067s from . import multiarray 1067s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1067s from . import overrides 1067s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1067s from numpy.core._multiarray_umath import ( 1067s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1067s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1067s 1067s During handling of the above exception, another exception occurred: 1067s 1067s Traceback (most recent call last): 1067s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1067s from numpy.__config__ import show as show_config 1067s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1067s from numpy.core._multiarray_umath import ( 1067s ...<3 lines>... 1067s ) 1067s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1067s raise ImportError(msg) 1067s ImportError: 1067s 1067s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1067s 1067s Importing the numpy C-extensions failed. This error can happen for 1067s many reasons, often due to issues with your setup or how NumPy was 1067s installed. 1067s 1067s We have compiled some common reasons and troubleshooting tips at: 1067s 1067s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1067s 1067s Please note and check the following: 1067s 1067s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1067s * The NumPy version is: "1.26.4" 1067s 1067s and make sure that they are the versions you expect. 1067s Please carefully study the documentation linked above for further help. 1067s 1067s Original error was: No module named 'numpy.core._multiarray_umath' 1067s 1067s 1067s The above exception was the direct cause of the following exception: 1067s 1067s Traceback (most recent call last): 1067s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1067s module = __import__(module_name) 1067s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_a2m.py", line 10, in 1067s import numpy as np 1067s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1067s raise ImportError(msg) from e 1067s ImportError: Error importing numpy: you should not try to import numpy from 1067s its source directory; please exit the numpy source tree, and relaunch 1067s your python interpreter from there. 1067s 1067s test_Align_bed ... loading tests failed: 1067s Failed to import test module: test_Align_bed 1067s Traceback (most recent call last): 1067s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1067s from . import multiarray 1067s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1067s from . import overrides 1067s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1067s from numpy.core._multiarray_umath import ( 1067s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1067s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1067s 1067s During handling of the above exception, another exception occurred: 1067s 1067s Traceback (most recent call last): 1067s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1067s from numpy.__config__ import show as show_config 1067s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1067s from numpy.core._multiarray_umath import ( 1067s ...<3 lines>... 1067s ) 1067s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1067s raise ImportError(msg) 1067s ImportError: 1067s 1067s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1067s 1067s Importing the numpy C-extensions failed. This error can happen for 1067s many reasons, often due to issues with your setup or how NumPy was 1067s installed. 1067s 1067s We have compiled some common reasons and troubleshooting tips at: 1067s 1067s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1067s 1067s Please note and check the following: 1067s 1067s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1067s * The NumPy version is: "1.26.4" 1067s 1067s and make sure that they are the versions you expect. 1067s Please carefully study the documentation linked above for further help. 1067s 1067s Original error was: No module named 'numpy.core._multiarray_umath' 1067s 1067s 1067s The above exception was the direct cause of the following exception: 1067s 1067s Traceback (most recent call last): 1067s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1067s module = __import__(module_name) 1067s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_bed.py", line 11, in 1067s import numpy as np 1067s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1067s raise ImportError(msg) from e 1067s ImportError: Error importing numpy: you should not try to import numpy from 1067s its source directory; please exit the numpy source tree, and relaunch 1067s your python interpreter from there. 1067s 1067s test_Align_bigbed ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1067s 1068s test_Align_bigmaf ... loading tests failed: 1068s Failed to import test module: test_Align_bigmaf 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1068s from . import multiarray 1068s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1068s from . import overrides 1068s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1068s from numpy.core._multiarray_umath import ( 1068s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1068s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1068s 1068s During handling of the above exception, another exception occurred: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1068s from numpy.__config__ import show as show_config 1068s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1068s from numpy.core._multiarray_umath import ( 1068s ...<3 lines>... 1068s ) 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1068s raise ImportError(msg) 1068s ImportError: 1068s 1068s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1068s 1068s Importing the numpy C-extensions failed. This error can happen for 1068s many reasons, often due to issues with your setup or how NumPy was 1068s installed. 1068s 1068s We have compiled some common reasons and troubleshooting tips at: 1068s 1068s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1068s 1068s Please note and check the following: 1068s 1068s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1068s * The NumPy version is: "1.26.4" 1068s 1068s and make sure that they are the versions you expect. 1068s Please carefully study the documentation linked above for further help. 1068s 1068s Original error was: No module named 'numpy.core._multiarray_umath' 1068s 1068s 1068s The above exception was the direct cause of the following exception: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1068s module = __import__(module_name) 1068s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_bigmaf.py", line 10, in 1068s import numpy as np 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1068s raise ImportError(msg) from e 1068s ImportError: Error importing numpy: you should not try to import numpy from 1068s its source directory; please exit the numpy source tree, and relaunch 1068s your python interpreter from there. 1068s 1068s test_Align_bigpsl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1068s 1068s test_Align_chain ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1068s 1068s test_Align_clustal ... loading tests failed: 1068s Failed to import test module: test_Align_clustal 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1068s from . import multiarray 1068s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1068s from . import overrides 1068s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1068s from numpy.core._multiarray_umath import ( 1068s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1068s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1068s 1068s During handling of the above exception, another exception occurred: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1068s from numpy.__config__ import show as show_config 1068s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1068s from numpy.core._multiarray_umath import ( 1068s ...<3 lines>... 1068s ) 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1068s raise ImportError(msg) 1068s ImportError: 1068s 1068s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1068s 1068s Importing the numpy C-extensions failed. This error can happen for 1068s many reasons, often due to issues with your setup or how NumPy was 1068s installed. 1068s 1068s We have compiled some common reasons and troubleshooting tips at: 1068s 1068s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1068s 1068s Please note and check the following: 1068s 1068s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1068s * The NumPy version is: "1.26.4" 1068s 1068s and make sure that they are the versions you expect. 1068s Please carefully study the documentation linked above for further help. 1068s 1068s Original error was: No module named 'numpy.core._multiarray_umath' 1068s 1068s 1068s The above exception was the direct cause of the following exception: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1068s module = __import__(module_name) 1068s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_clustal.py", line 9, in 1068s import numpy as np 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1068s raise ImportError(msg) from e 1068s ImportError: Error importing numpy: you should not try to import numpy from 1068s its source directory; please exit the numpy source tree, and relaunch 1068s your python interpreter from there. 1068s 1068s test_Align_codonalign ... loading tests failed: 1068s Failed to import test module: test_Align_codonalign 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1068s from . import multiarray 1068s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1068s from . import overrides 1068s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1068s from numpy.core._multiarray_umath import ( 1068s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1068s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1068s 1068s During handling of the above exception, another exception occurred: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1068s from numpy.__config__ import show as show_config 1068s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1068s from numpy.core._multiarray_umath import ( 1068s ...<3 lines>... 1068s ) 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1068s raise ImportError(msg) 1068s ImportError: 1068s 1068s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1068s 1068s Importing the numpy C-extensions failed. This error can happen for 1068s many reasons, often due to issues with your setup or how NumPy was 1068s installed. 1068s 1068s We have compiled some common reasons and troubleshooting tips at: 1068s 1068s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1068s 1068s Please note and check the following: 1068s 1068s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1068s * The NumPy version is: "1.26.4" 1068s 1068s and make sure that they are the versions you expect. 1068s Please carefully study the documentation linked above for further help. 1068s 1068s Original error was: No module named 'numpy.core._multiarray_umath' 1068s 1068s 1068s The above exception was the direct cause of the following exception: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1068s module = __import__(module_name) 1068s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_codonalign.py", line 10, in 1068s import numpy as np 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1068s raise ImportError(msg) from e 1068s ImportError: Error importing numpy: you should not try to import numpy from 1068s its source directory; please exit the numpy source tree, and relaunch 1068s your python interpreter from there. 1068s 1068s test_Align_emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1068s 1068s test_Align_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1068s 1068s test_Align_fasta ... loading tests failed: 1068s Failed to import test module: test_Align_fasta 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1068s from . import multiarray 1068s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1068s from . import overrides 1068s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1068s from numpy.core._multiarray_umath import ( 1068s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1068s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1068s 1068s During handling of the above exception, another exception occurred: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1068s from numpy.__config__ import show as show_config 1068s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1068s from numpy.core._multiarray_umath import ( 1068s ...<3 lines>... 1068s ) 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1068s raise ImportError(msg) 1068s ImportError: 1068s 1068s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1068s 1068s Importing the numpy C-extensions failed. This error can happen for 1068s many reasons, often due to issues with your setup or how NumPy was 1068s installed. 1068s 1068s We have compiled some common reasons and troubleshooting tips at: 1068s 1068s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1068s 1068s Please note and check the following: 1068s 1068s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1068s * The NumPy version is: "1.26.4" 1068s 1068s and make sure that they are the versions you expect. 1068s Please carefully study the documentation linked above for further help. 1068s 1068s Original error was: No module named 'numpy.core._multiarray_umath' 1068s 1068s 1068s The above exception was the direct cause of the following exception: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1068s module = __import__(module_name) 1068s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_fasta.py", line 10, in 1068s import numpy as np 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1068s raise ImportError(msg) from e 1068s ImportError: Error importing numpy: you should not try to import numpy from 1068s its source directory; please exit the numpy source tree, and relaunch 1068s your python interpreter from there. 1068s 1068s test_Align_hhr ... loading tests failed: 1068s Failed to import test module: test_Align_hhr 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1068s from . import multiarray 1068s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1068s from . import overrides 1068s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1068s from numpy.core._multiarray_umath import ( 1068s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1068s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1068s 1068s During handling of the above exception, another exception occurred: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1068s from numpy.__config__ import show as show_config 1068s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1068s from numpy.core._multiarray_umath import ( 1068s ...<3 lines>... 1068s ) 1068s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1068s raise ImportError(msg) 1068s ImportError: 1068s 1068s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1068s 1068s Importing the numpy C-extensions failed. This error can happen for 1068s many reasons, often due to issues with your setup or how NumPy was 1068s installed. 1068s 1068s We have compiled some common reasons and troubleshooting tips at: 1068s 1068s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1068s 1068s Please note and check the following: 1068s 1068s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1068s * The NumPy version is: "1.26.4" 1068s 1068s and make sure that they are the versions you expect. 1068s Please carefully study the documentation linked above for further help. 1068s 1068s Original error was: No module named 'numpy.core._multiarray_umath' 1068s 1068s 1068s The above exception was the direct cause of the following exception: 1068s 1068s Traceback (most recent call last): 1068s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1068s module = __import__(module_name) 1068s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Align_hhr.py", line 9, in 1068s import numpy as np 1068s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1068s raise ImportError(msg) from e 1068s ImportError: Error importing numpy: you should not try to import numpy from 1068s its source directory; please exit the numpy source tree, and relaunch 1068s your python interpreter from there. 1068s 1068s test_Align_maf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1068s 1068s test_Align_mauve ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1068s 1069s test_Align_msf ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1069s test_Align_nexus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1069s test_Align_phylip ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1069s test_Align_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1069s test_Align_sam ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1069s test_Align_stockholm ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1069s test_Align_tabular ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1069s test_Application ... ok 1069s test_BioSQL_MySQLdb_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1069s test_BioSQL_mysql_connector ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1069s test_BioSQL_mysql_connector_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1069s 1070s test_BioSQL_psycopg2_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1070s 1070s test_BioSQL_sqlite3 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1070s 1070s test_BioSQL_sqlite3_online ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1070s 1070s test_Blast_Record ... loading tests failed: 1070s Failed to import test module: test_Blast_Record 1070s Traceback (most recent call last): 1070s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1070s from . import multiarray 1070s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1070s from . import overrides 1070s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1070s from numpy.core._multiarray_umath import ( 1070s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1070s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1070s 1070s During handling of the above exception, another exception occurred: 1070s 1070s Traceback (most recent call last): 1070s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1070s from numpy.__config__ import show as show_config 1070s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1070s from numpy.core._multiarray_umath import ( 1070s ...<3 lines>... 1070s ) 1070s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1070s raise ImportError(msg) 1070s ImportError: 1070s 1070s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1070s 1070s Importing the numpy C-extensions failed. This error can happen for 1070s many reasons, often due to issues with your setup or how NumPy was 1070s installed. 1070s 1070s We have compiled some common reasons and troubleshooting tips at: 1070s 1070s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1070s 1070s Please note and check the following: 1070s 1070s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1070s * The NumPy version is: "1.26.4" 1070s 1070s and make sure that they are the versions you expect. 1070s Please carefully study the documentation linked above for further help. 1070s 1070s Original error was: No module named 'numpy.core._multiarray_umath' 1070s 1070s 1070s The above exception was the direct cause of the following exception: 1070s 1070s Traceback (most recent call last): 1070s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1070s module = __import__(module_name) 1070s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Blast_Record.py", line 9, in 1070s from Bio.Blast.NCBIXML import HSP 1070s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 1070s import numpy as np 1070s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1070s raise ImportError(msg) from e 1070s ImportError: Error importing numpy: you should not try to import numpy from 1070s its source directory; please exit the numpy source tree, and relaunch 1070s your python interpreter from there. 1070s 1070s test_Blast_parser ... loading tests failed: 1070s Failed to import test module: test_Blast_parser 1070s Traceback (most recent call last): 1070s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1070s from . import multiarray 1070s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1070s from . import overrides 1070s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1070s from numpy.core._multiarray_umath import ( 1070s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1070s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1070s 1070s During handling of the above exception, another exception occurred: 1070s 1070s Traceback (most recent call last): 1070s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1070s from numpy.__config__ import show as show_config 1070s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1070s from numpy.core._multiarray_umath import ( 1070s ...<3 lines>... 1070s ) 1070s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1070s raise ImportError(msg) 1070s ImportError: 1070s 1070s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1070s 1070s Importing the numpy C-extensions failed. This error can happen for 1070s many reasons, often due to issues with your setup or how NumPy was 1070s installed. 1070s 1070s We have compiled some common reasons and troubleshooting tips at: 1070s 1070s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1070s 1070s Please note and check the following: 1070s 1070s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1070s * The NumPy version is: "1.26.4" 1070s 1070s and make sure that they are the versions you expect. 1070s Please carefully study the documentation linked above for further help. 1070s 1070s Original error was: No module named 'numpy.core._multiarray_umath' 1070s 1070s 1070s The above exception was the direct cause of the following exception: 1070s 1070s Traceback (most recent call last): 1070s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1070s module = __import__(module_name) 1070s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_Blast_parser.py", line 11, in 1070s import numpy as np 1070s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1070s raise ImportError(msg) from e 1070s ImportError: Error importing numpy: you should not try to import numpy from 1070s its source directory; please exit the numpy source tree, and relaunch 1070s your python interpreter from there. 1070s 1070s test_CAPS ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1070s 1070s 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 1070s warnings.warn( 1070s skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1070s 1070s test_ClustalOmega_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1070s 1070s test_Clustalw_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1070s 1070s test_Cluster ... skipping. Error: Install NumPy if you want to use Bio.Cluster. 1070s 1070s test_CodonTable ... ok 1070s test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 1070s 1070s test_Compass ... ok 1070s test_Consensus ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1070s 1070s test_Dialign_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1070s 1070s test_EMBL_unittest ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1070s 1071s test_Emboss ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1071s 1071s test_EmbossPrimer ... ok 1075s test_Entrez ... ok 1075s test_Entrez_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1075s 1076s test_Entrez_parser ... ok 1076s test_Enzyme ... ok 1076s test_ExPASy ... skipping. internet not available 1076s test_Fasttree_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1076s 1076s test_File ... ok 1076s test_GenBank ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1076s 1076s test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 1076s 1076s test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. 1076s 1076s test_GraphicsDistribution ... loading tests failed: 1076s Failed to import test module: test_GraphicsDistribution 1076s Traceback (most recent call last): 1076s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1076s module = __import__(module_name) 1076s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_GraphicsDistribution.py", line 29, in 1076s from Bio.Graphics.Distribution import BarChartDistribution 1076s File "/usr/lib/python3/dist-packages/Bio/Graphics/Distribution.py", line 19, in 1076s from reportlab.graphics.charts.barcharts import BarChartProperties 1076s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/barcharts.py", line 15, in 1076s from reportlab.lib import colors 1076s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 1076s from reportlab.lib.rl_accel import fp_str 1076s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 1076s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 1076s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 1076s from PIL import Image 1076s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 1076s from . import _imaging as core 1076s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 1076s 1076s test_GraphicsGeneral ... loading tests failed: 1076s Failed to import test module: test_GraphicsGeneral 1076s Traceback (most recent call last): 1076s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1076s module = __import__(module_name) 1076s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_GraphicsGeneral.py", line 24, in 1076s from Bio.Graphics.Comparative import ComparativeScatterPlot 1076s File "/usr/lib/python3/dist-packages/Bio/Graphics/Comparative.py", line 14, in 1076s from reportlab.graphics.charts.lineplots import LinePlot 1076s File "/usr/lib/python3/dist-packages/reportlab/graphics/charts/lineplots.py", line 8, in 1076s from reportlab.lib import colors 1076s File "/usr/lib/python3/dist-packages/reportlab/lib/colors.py", line 43, in 1076s from reportlab.lib.rl_accel import fp_str 1076s File "/usr/lib/python3/dist-packages/reportlab/lib/rl_accel.py", line 34, in 1076s from reportlab.lib.utils import isUnicode, isSeq, rawBytes, asNative, asBytes 1076s File "/usr/lib/python3/dist-packages/reportlab/lib/utils.py", line 15, in 1076s from PIL import Image 1076s File "/usr/lib/python3/dist-packages/PIL/Image.py", line 100, in 1076s from . import _imaging as core 1076s ImportError: cannot import name '_imaging' from 'PIL' (/usr/lib/python3/dist-packages/PIL/__init__.py) 1076s 1076s test_HMMCasino ... ok 1076s test_HMMGeneral ... ok 1077s test_KEGG ... ok 1077s test_KEGG_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1077s 1077s test_KGML_graphics ... skipping. Install reportlab if you want to use Bio.Graphics. 1077s test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. 1078s test_KGML_nographics ... ok 1078s test_KeyWList ... ok 1078s test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression. 1078s test_MafIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1078s 1078s test_Mafft_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1078s 1078s test_MarkovModel ... skipping. Error: Install NumPy if you want to use Bio.MarkovModel. 1078s 1078s test_Medline ... ok 1078s test_Muscle_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1078s 1078s test_NCBIXML ... loading tests failed: 1078s Failed to import test module: test_NCBIXML 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1078s from . import multiarray 1078s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1078s from . import overrides 1078s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1078s from numpy.core._multiarray_umath import ( 1078s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1078s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1078s 1078s During handling of the above exception, another exception occurred: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1078s from numpy.__config__ import show as show_config 1078s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1078s from numpy.core._multiarray_umath import ( 1078s ...<3 lines>... 1078s ) 1078s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1078s raise ImportError(msg) 1078s ImportError: 1078s 1078s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1078s 1078s Importing the numpy C-extensions failed. This error can happen for 1078s many reasons, often due to issues with your setup or how NumPy was 1078s installed. 1078s 1078s We have compiled some common reasons and troubleshooting tips at: 1078s 1078s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1078s 1078s Please note and check the following: 1078s 1078s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1078s * The NumPy version is: "1.26.4" 1078s 1078s and make sure that they are the versions you expect. 1078s Please carefully study the documentation linked above for further help. 1078s 1078s Original error was: No module named 'numpy.core._multiarray_umath' 1078s 1078s 1078s The above exception was the direct cause of the following exception: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1078s module = __import__(module_name) 1078s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_NCBIXML.py", line 10, in 1078s from Bio.Blast import NCBIXML 1078s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 1078s import numpy as np 1078s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1078s raise ImportError(msg) from e 1078s ImportError: Error importing numpy: you should not try to import numpy from 1078s its source directory; please exit the numpy source tree, and relaunch 1078s your python interpreter from there. 1078s 1078s test_NCBI_BLAST_tools ... loading tests failed: 1078s Failed to import test module: test_NCBI_BLAST_tools 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1078s from . import multiarray 1078s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1078s from . import overrides 1078s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1078s from numpy.core._multiarray_umath import ( 1078s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1078s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1078s 1078s During handling of the above exception, another exception occurred: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1078s from numpy.__config__ import show as show_config 1078s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1078s from numpy.core._multiarray_umath import ( 1078s ...<3 lines>... 1078s ) 1078s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1078s raise ImportError(msg) 1078s ImportError: 1078s 1078s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1078s 1078s Importing the numpy C-extensions failed. This error can happen for 1078s many reasons, often due to issues with your setup or how NumPy was 1078s installed. 1078s 1078s We have compiled some common reasons and troubleshooting tips at: 1078s 1078s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1078s 1078s Please note and check the following: 1078s 1078s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1078s * The NumPy version is: "1.26.4" 1078s 1078s and make sure that they are the versions you expect. 1078s Please carefully study the documentation linked above for further help. 1078s 1078s Original error was: No module named 'numpy.core._multiarray_umath' 1078s 1078s 1078s The above exception was the direct cause of the following exception: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1078s module = __import__(module_name) 1078s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_NCBI_BLAST_tools.py", line 25, in 1078s from Bio.Blast import Applications 1078s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 1078s import numpy as np 1078s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1078s raise ImportError(msg) from e 1078s ImportError: Error importing numpy: you should not try to import numpy from 1078s its source directory; please exit the numpy source tree, and relaunch 1078s your python interpreter from there. 1078s 1079s test_NCBI_qblast ... loading tests failed: 1079s Failed to import test module: test_NCBI_qblast 1079s Traceback (most recent call last): 1079s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1079s from . import multiarray 1079s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1079s from . import overrides 1079s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1079s from numpy.core._multiarray_umath import ( 1079s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1079s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1079s 1079s During handling of the above exception, another exception occurred: 1079s 1079s Traceback (most recent call last): 1079s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1079s from numpy.__config__ import show as show_config 1079s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1079s from numpy.core._multiarray_umath import ( 1079s ...<3 lines>... 1079s ) 1079s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1079s raise ImportError(msg) 1079s ImportError: 1079s 1079s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1079s 1079s Importing the numpy C-extensions failed. This error can happen for 1079s many reasons, often due to issues with your setup or how NumPy was 1079s installed. 1079s 1079s We have compiled some common reasons and troubleshooting tips at: 1079s 1079s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1079s 1079s Please note and check the following: 1079s 1079s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1079s * The NumPy version is: "1.26.4" 1079s 1079s and make sure that they are the versions you expect. 1079s Please carefully study the documentation linked above for further help. 1079s 1079s Original error was: No module named 'numpy.core._multiarray_umath' 1079s 1079s 1079s The above exception was the direct cause of the following exception: 1079s 1079s Traceback (most recent call last): 1079s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1079s module = __import__(module_name) 1079s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_NCBI_qblast.py", line 38, in 1079s from Bio.Blast import NCBIWWW 1079s File "/usr/lib/python3/dist-packages/Bio/Blast/__init__.py", line 39, in 1079s import numpy as np 1079s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1079s raise ImportError(msg) from e 1079s ImportError: Error importing numpy: you should not try to import numpy from 1079s its source directory; please exit the numpy source tree, and relaunch 1079s your python interpreter from there. 1079s 1079s test_NMR ... ok 1079s test_NaiveBayes ... skipping. Error: Please install NumPy if you want to use Bio.NaiveBayes. See http://www.numpy.org/ 1079s 1079s test_Nexus ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1079s 1079s test_PAML_baseml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1079s 1079s test_PAML_codeml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1079s 1079s test_PAML_yn00 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1079s 1079s test_PDB_CEAligner ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1079s 1079s test_PDB_DSSP ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1079s 1079s test_PDB_Dice ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1079s 1079s test_PDB_Disordered ... loading tests failed: 1079s Failed to import test module: test_PDB_Disordered 1079s Traceback (most recent call last): 1079s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 1079s from . import multiarray 1079s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 1079s from . import overrides 1079s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 1079s from numpy.core._multiarray_umath import ( 1079s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 1079s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1079s 1079s During handling of the above exception, another exception occurred: 1079s 1079s Traceback (most recent call last): 1079s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 1079s from numpy.__config__ import show as show_config 1079s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 1079s from numpy.core._multiarray_umath import ( 1079s ...<3 lines>... 1079s ) 1079s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 1079s raise ImportError(msg) 1079s ImportError: 1079s 1079s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1079s 1079s Importing the numpy C-extensions failed. This error can happen for 1079s many reasons, often due to issues with your setup or how NumPy was 1079s installed. 1079s 1079s We have compiled some common reasons and troubleshooting tips at: 1079s 1079s https://numpy.org/devdocs/user/troubleshooting-importerror.html 1079s 1079s Please note and check the following: 1079s 1079s * The Python version is: Python3.13 from "/usr/bin/python3.13" 1079s * The NumPy version is: "1.26.4" 1079s 1079s and make sure that they are the versions you expect. 1079s Please carefully study the documentation linked above for further help. 1079s 1079s Original error was: No module named 'numpy.core._multiarray_umath' 1079s 1079s 1079s The above exception was the direct cause of the following exception: 1079s 1079s Traceback (most recent call last): 1079s File "/usr/lib/python3.13/unittest/loader.py", line 137, in loadTestsFromName 1079s module = __import__(module_name) 1079s File "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/Tests/test_PDB_Disordered.py", line 16, in 1079s import numpy as np 1079s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 1079s raise ImportError(msg) from e 1079s ImportError: Error importing numpy: you should not try to import numpy from 1079s its source directory; please exit the numpy source tree, and relaunch 1079s your python interpreter from there. 1079s 1079s test_PDB_Exposure ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1079s 1080s test_PDB_FragmentMapper ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1080s 1080s test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB. 1080s test_PDB_MMCIF2Dict ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1080s 1080s test_PDB_MMCIFIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1080s 1080s test_PDB_MMCIFParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1080s 1080s test_PDB_NACCESS ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1080s 1080s test_PDB_PDBIO ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1080s 1080s test_PDB_PDBList ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1080s 1080s test_PDB_PDBMLParser ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1080s 1080s test_PDB_PDBParser ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1080s 1080s test_PDB_PSEA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1080s 1080s test_PDB_Polypeptide ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1080s 1080s test_PDB_QCPSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.QCPSuperimposer. 1080s 1080s test_PDB_SASA ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1080s 1080s test_PDB_SMCRA ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1080s 1080s test_PDB_Selection ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1080s 1081s test_PDB_StructureAlignment ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1081s 1081s test_PDB_Superimposer ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1081s 1081s test_PDB_alphafold_db ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1081s 1081s test_PDB_binary_cif ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1081s 1081s test_PDB_internal_coords ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1081s 1081s test_PDB_parse_pdb_header ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1081s 1081s test_PDB_vectors ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1081s 1081s test_PQR ... skipping. Error: Please install NumPy if you want to use Bio.PDB. See http://www.numpy.org/ 1081s 1081s test_Pathway ... ok 1081s test_Phd ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1081s 1081s test_Phylo ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1081s 1082s test_PhyloXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1082s 1082s test_Phylo_CDAO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1082s 1082s test_Phylo_NeXML ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1082s 1082s test_Phylo_igraph ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1082s 1082s test_Phylo_matplotlib ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1082s 1082s test_Phylo_networkx ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1082s 1082s test_PopGen_GenePop_nodepend ... ok 1082s test_Prank_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1082s 1082s test_Probcons_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1082s 1082s test_ProtParam ... ok 1082s test_RCSBFormats ... skipping. Error: Install NumPy if you want to use Bio.PDB. 1082s 1082s test_Restriction ... ok 1082s test_SCOP_Astral ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1082s 1082s test_SCOP_Cla ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1082s 1082s test_SCOP_Des ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1082s 1082s test_SCOP_Dom ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1082s 1082s test_SCOP_Hie ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1082s 1082s test_SCOP_Raf ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1082s 1083s test_SCOP_Residues ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1083s 1083s test_SCOP_Scop ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1083s 1083s test_SVDSuperimposer ... skipping. Error: Install NumPy if you want to use Bio.SVDSuperimposer. 1083s 1083s test_SearchIO_blast_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1083s 1083s test_SearchIO_blast_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1083s 1083s test_SearchIO_blast_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1083s 1083s test_SearchIO_blast_xml_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1083s 1083s test_SearchIO_blat_psl ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1083s 1083s test_SearchIO_blat_psl_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1083s 1083s test_SearchIO_exonerate ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1083s 1083s test_SearchIO_exonerate_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1083s 1083s test_SearchIO_exonerate_vulgar_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1083s 1084s test_SearchIO_fasta_m10 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_fasta_m10_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_hhsuite2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_hmmer2_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_hmmer2_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_hmmer3_domtab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_hmmer3_domtab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_hmmer3_tab ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_hmmer3_tab_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_hmmer3_text ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_hmmer3_text_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_interproscan_xml ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1084s test_SearchIO_model ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1084s 1085s test_SearchIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1085s 1085s test_SeqFeature ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1085s 1085s test_SeqIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1085s 1085s test_SeqIO_AbiIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1085s 1085s test_SeqIO_FastaIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1085s 1085s test_SeqIO_Gck ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1085s 1085s test_SeqIO_Gfa ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1085s 1085s test_SeqIO_Insdc ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1085s 1085s test_SeqIO_NibIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1085s 1085s test_SeqIO_PdbIO ... skipping. Error: Install NumPy if you want to use PDB formats with SeqIO. 1085s 1086s test_SeqIO_QualityIO ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1086s 1086s test_SeqIO_SeqXML ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1086s 1086s test_SeqIO_SnapGene ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1086s 1086s test_SeqIO_TwoBitIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1086s 1086s test_SeqIO_Xdna ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1086s 1086s test_SeqIO_features ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1086s 1086s test_SeqIO_index ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1086s 1086s test_SeqIO_online ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1086s 1086s test_SeqIO_write ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1086s 1086s test_SeqRecord ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1086s 1086s test_SeqUtils ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1086s 1086s test_Seq_objs ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1086s 1086s test_SffIO ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1086s 1087s test_SwissProt ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1087s 1087s test_TCoffee_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1087s 1087s test_TogoWS ... skipping. Error: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1087s 1087s test_TreeConstruction ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1087s 1087s test_UniGene ... ok 1087s test_UniProt ... skipping. internet not available 1087s test_UniProt_GOA ... ok 1087s test_UniProt_Parser ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1087s 1087s test_align ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1087s 1087s test_align_substitution_matrices ... skipping. Install NumPy if you want to use Bio.Align.substitution_matrices. 1090s test_bgzf ... ok 1090s test_cellosaurus ... ok 1090s test_codonalign ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1090s 1090s test_geo ... ok 1090s test_kNN ... skipping. Error: Install NumPy if you want to use Bio.kNN. 1090s 1090s test_motifs ... skipping. Install numpy if you want to use Bio.motifs. 1090s test_motifs_online ... skipping. Error: Install NumPy if you want to use Bio.motifs. 1090s 1090s test_pairwise2 ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1090s 1091s test_pairwise2_no_C ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1091s 1091s test_pairwise_aligner ... skipping. Error: Install numpy if you want to use Bio.Align. 1091s 1091s test_pairwise_alignment_map ... skipping. Error: Install numpy if you want to use Bio.Align.Alignment.map. 1091s 1091s test_phenotype ... skipping. Install NumPy if you want to use Bio.phenotype. 1091s test_phenotype_fit ... skipping. Install NumPy if you want to use Bio.phenotype. 1091s test_phyml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1091s 1091s test_prodoc ... ok 1091s test_prosite ... ok 1091s test_raxml_tool ... skipping. Error: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1091s 1091s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1091s test_seq ... ok 1091s test_translate ... ok 1092s ---------------------------------------------------------------------- 1092s Ran 217 tests in 24.808 seconds 1092s 1092s FAILED (failures = 15) 1092s Skipping any tests requiring internet access 1092s Python version: 3.13.0 (main, Nov 12 2024, 09:54:22) [GCC 14.2.0] 1092s Operating system: posix linux 1092s test_Ace ... ok 1092s test_Affy ... ok 1095s test_AlignIO ... ok 1095s test_AlignIO_ClustalIO ... ok 1095s test_AlignIO_EmbossIO ... ok 1095s test_AlignIO_FastaIO ... ok 1096s test_AlignIO_MauveIO ... ok 1096s test_AlignIO_PhylipIO ... ok 1096s test_AlignIO_convert ... ok 1096s test_AlignInfo ... ok 1096s test_Align_Alignment ... ok 1096s test_Align_a2m ... ok 1096s test_Align_bed ... ok 1097s test_Align_bigbed ... ok 1097s test_Align_bigmaf ... ok 1098s test_Align_bigpsl ... ok 1098s test_Align_chain ... ok 1098s test_Align_clustal ... ok 1104s test_Align_codonalign ... ok 1104s test_Align_emboss ... ok 1105s test_Align_exonerate ... ok 1105s test_Align_fasta ... ok 1105s test_Align_hhr ... ok 1105s test_Align_maf ... ok 1105s test_Align_mauve ... ok 1105s test_Align_msf ... ok 1106s test_Align_nexus ... ok 1106s test_Align_phylip ... ok 1106s test_Align_psl ... ok 1106s test_Align_sam ... ok 1109s test_Align_stockholm ... ok 1109s test_Align_tabular ... ok 1109s test_Application ... ok 1109s test_BioSQL_MySQLdb_online ... skipping. internet not available 1109s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1109s test_BioSQL_mysql_connector_online ... skipping. internet not available 1109s test_BioSQL_psycopg2_online ... skipping. internet not available 1115s test_BioSQL_sqlite3 ... ok 1115s test_BioSQL_sqlite3_online ... skipping. internet not available 1116s test_Blast_Record ... ok 1116s test_Blast_parser ... ok 1116s test_CAPS ... ok 1117s test_Chi2 ... ok 1118s test_ClustalOmega_tool ... ok 1118s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 1118s test_Cluster ... ok 1118s test_CodonTable ... ok 1118s test_ColorSpiral ... ok 1119s test_Compass ... ok 1120s test_Consensus ... ok 1123s test_Dialign_tool ... ok 1123s test_EMBL_unittest ... ok 1123s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 1123s test_EmbossPrimer ... ok 1127s test_Entrez ... ok 1127s test_Entrez_online ... skipping. internet not available 1128s test_Entrez_parser ... ok 1128s test_Enzyme ... ok 1128s test_ExPASy ... skipping. internet not available 1128s test_Fasttree_tool ... ok 1128s test_File ... ok 1129s test_GenBank ... ok 1131s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1133s ok 1134s test_GraphicsChromosome ... ok 1134s test_GraphicsDistribution ... ok 1135s test_GraphicsGeneral ... ok 1135s test_HMMCasino ... ok 1135s test_HMMGeneral ... ok 1135s test_KEGG ... ok 1135s test_KEGG_online ... skipping. internet not available 1141s test_KGML_graphics ... ok 1141s test_KGML_graphics_online ... skipping. internet not available 1142s test_KGML_nographics ... ok 1142s test_KeyWList ... ok 1142s test_LogisticRegression ... ok 1144s test_MafIO_index ... ok 1146s test_Mafft_tool ... ok 1146s test_MarkovModel ... ok 1146s test_Medline ... ok 1146s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 1147s test_NCBIXML ... ok 1150s test_NCBI_BLAST_tools ... ok 1151s test_NCBI_qblast ... ok 1151s test_NMR ... ok 1151s test_NaiveBayes ... ok 1151s test_Nexus ... ok 1151s test_PAML_baseml ... ok 1152s test_PAML_codeml ... ok 1152s test_PAML_yn00 ... ok 1156s test_PDB_CEAligner ... ok 1157s test_PDB_DSSP ... /usr/lib/python3/dist-packages/Bio/PDB/DSSP.py:199: UserWarning: 1157s Configuration error: 1157s 1157s The attempt to retrieve compound information for "SO4" failed. 1157s 1157s This information is searched for in a CCD file called components.cif or 1157s components.cif.gz which should be located in one of the following directories: 1157s 1157s "/usr/share/libcifpp" 1157s "/var/cache/libcifpp" 1157s "/tmp/autopkgtest.5lDf21/autopkgtest_tmp/libcifpp-data" 1157s "/usr/share/libcifpp" 1157s "/usr/share/libcifpp" 1157s 1157s (Note that you can add a directory to the search paths by setting the 1157s LIBCIFPP_DATA_DIR environmental variable) 1157s 1157s On Linux an optional cron script might have been installed that automatically updates 1157s components.cif and mmCIF dictionary files. This script only works when the file 1157s libcifpp.conf contains an uncommented line with the text: 1157s 1157s update=true 1157s 1157s If you do not have a working cron script, you can manually update the files 1157s in /var/cache/libcifpp using the following commands: 1157s 1157s curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif 1157s curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic 1157s curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic 1157s 1157s The current order of compound factory objects is: 1157s 1157s CCD components.cif resource 1157s CCD components.cif resource 1157s Unknown compound: SO4 1157s Missing compound information for SO4 1157s 1157s warnings.warn(err) 1158s ok 1158s test_PDB_Dice ... ok 1158s test_PDB_Disordered ... ok 1159s test_PDB_Exposure ... ok 1159s test_PDB_FragmentMapper ... ok 1161s test_PDB_KDTree ... ok 1161s test_PDB_MMCIF2Dict ... ok 1161s test_PDB_MMCIFIO ... ok 1163s test_PDB_MMCIFParser ... ok 1163s test_PDB_NACCESS ... ok 1163s test_PDB_PDBIO ... ok 1163s test_PDB_PDBList ... skipping. internet not available 1172s test_PDB_PDBMLParser ... ok 1173s test_PDB_PDBParser ... ok 1173s 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 1173s test_PDB_Polypeptide ... ok 1173s test_PDB_QCPSuperimposer ... ok 1177s test_PDB_SASA ... ok 1178s test_PDB_SMCRA ... ok 1178s test_PDB_Selection ... ok 1178s test_PDB_StructureAlignment ... ok 1178s test_PDB_Superimposer ... ok 1178s test_PDB_alphafold_db ... skipping. internet not available 1182s test_PDB_binary_cif ... /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 7. 1182s warnings.warn( 1182s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 144. 1182s warnings.warn( 1182s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 153. 1182s warnings.warn( 1182s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 1, ' ') redefined at line 0. 1182s warnings.warn( 1182s /usr/lib/python3/dist-packages/Bio/PDB/StructureBuilder.py:137: PDBConstructionWarning: WARNING: Residue (' ', 15, ' ') redefined at line 0. 1182s warnings.warn( 1182s ok 1193s test_PDB_internal_coords ... ok 1194s test_PDB_parse_pdb_header ... ok 1194s test_PDB_vectors ... ok 1195s test_PQR ... ok 1195s test_Pathway ... ok 1196s test_Phd ... ok 1196s test_Phylo ... ok 1197s test_PhyloXML ... ok 1198s test_Phylo_CDAO ... ok 1198s test_Phylo_NeXML ... ok 1199s test_Phylo_igraph ... skipping. Install igraph if you wish to use it with Bio.Phylo 1204s test_Phylo_matplotlib ... ok 1205s test_Phylo_networkx ... ok 1206s test_PopGen_GenePop_nodepend ... ok 1209s test_Prank_tool ... ok 1210s test_Probcons_tool ... ok 1211s test_ProtParam ... ok 1212s test_RCSBFormats ... ok 1213s test_Restriction ... ok 1214s test_SCOP_Astral ... ok 1215s test_SCOP_Cla ... ok 1216s test_SCOP_Des ... ok 1217s test_SCOP_Dom ... ok 1218s test_SCOP_Hie ... ok 1219s test_SCOP_Raf ... ok 1220s test_SCOP_Residues ... ok 1221s test_SCOP_Scop ... ok 1222s test_SVDSuperimposer ... ok 1223s test_SearchIO_blast_tab ... ok 1224s test_SearchIO_blast_tab_index ... ok 1225s test_SearchIO_blast_xml ... ok 1228s test_SearchIO_blast_xml_index ... ok 1229s test_SearchIO_blat_psl ... ok 1230s test_SearchIO_blat_psl_index ... ok 1231s test_SearchIO_exonerate ... ok 1232s test_SearchIO_exonerate_text_index ... ok 1233s test_SearchIO_exonerate_vulgar_index ... ok 1234s test_SearchIO_fasta_m10 ... ok 1235s test_SearchIO_fasta_m10_index ... ok 1236s test_SearchIO_hhsuite2_text ... ok 1237s test_SearchIO_hmmer2_text ... ok 1238s test_SearchIO_hmmer2_text_index ... ok 1239s test_SearchIO_hmmer3_domtab ... ok 1240s test_SearchIO_hmmer3_domtab_index ... ok 1241s test_SearchIO_hmmer3_tab ... ok 1242s test_SearchIO_hmmer3_tab_index ... ok 1243s test_SearchIO_hmmer3_text ... ok 1244s test_SearchIO_hmmer3_text_index ... ok 1245s test_SearchIO_interproscan_xml ... ok 1246s test_SearchIO_model ... ok 1248s test_SearchIO_write ... ok 1249s test_SeqFeature ... ok 1268s test_SeqIO ... ok 1270s test_SeqIO_AbiIO ... ok 1271s test_SeqIO_FastaIO ... ok 1272s test_SeqIO_Gck ... ok 1273s test_SeqIO_Gfa ... ok 1274s test_SeqIO_Insdc ... ok 1275s test_SeqIO_NibIO ... ok 1278s test_SeqIO_PdbIO ... ok 1279s test_SeqIO_QualityIO ... ok 1280s test_SeqIO_SeqXML ... ok 1281s test_SeqIO_SnapGene ... ok 1283s test_SeqIO_TwoBitIO ... ok 1284s test_SeqIO_Xdna ... ok 1286s test_SeqIO_features ... ok 1305s test_SeqIO_index ... ok 1306s test_SeqIO_online ... skipping. internet not available 1307s test_SeqIO_write ... ok 1308s test_SeqRecord ... ok 1309s test_SeqUtils ... ok 1311s test_Seq_objs ... ok 1312s test_SffIO ... ok 1313s test_SwissProt ... ok 1316s test_TCoffee_tool ... ok 1317s test_TogoWS ... skipping. internet not available 1319s test_TreeConstruction ... ok 1320s test_UniGene ... ok 1321s test_UniProt ... skipping. internet not available 1322s test_UniProt_GOA ... ok 1323s test_UniProt_Parser ... ok 1324s test_align ... ok 1325s test_align_substitution_matrices ... ok 1329s test_bgzf ... ok 1330s test_cellosaurus ... ok 1336s test_codonalign ... ok 1337s test_geo ... ok 1339s test_kNN ... ok 1340s test_motifs ... ok 1341s test_motifs_online ... skipping. internet not available 1342s 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. 1342s warnings.warn( 1342s ok 1343s test_pairwise2_no_C ... ok 1344s test_pairwise_aligner ... ok 1346s test_pairwise_alignment_map ... ok 1356s test_phenotype ... ok 1357s test_phenotype_fit ... ok 1358s 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. 1359s test_prodoc ... ok 1360s test_prosite ... ok 1361s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 1362s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 1363s test_seq ... ok 1364s test_translate ... ok 1365s ---------------------------------------------------------------------- 1365s Ran 217 tests in 272.694 seconds 1365s 1365s Skipping any tests requiring internet access 1365s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 1365s Operating system: posix linux 1368s autopkgtest [21:46:17]: test full_suite: -----------------------] 1372s autopkgtest [21:46:21]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1372s full_suite PASS 1377s autopkgtest [21:46:26]: @@@@@@@@@@@@@@@@@@@@ summary 1377s dependencies PASS 1377s full_suite PASS