0s autopkgtest [10:05:50]: starting date and time: 2024-10-30 10:05:50+0000 0s autopkgtest [10:05:50]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [10:05:50]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.21kbfyam/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:setuptools --apt-upgrade python-biopython --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/75.2.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-17.secgroup --name adt-plucky-amd64-python-biopython-20241030-100549-juju-7f2275-prod-proposed-migration-environment-15-bcb38b63-e53e-4bbc-9035-bdbd6cd2b2a9 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 575s autopkgtest [10:15:25]: testbed dpkg architecture: amd64 575s autopkgtest [10:15:25]: testbed apt version: 2.9.8 575s autopkgtest [10:15:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 576s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 576s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [212 kB] 576s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 576s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [2840 B] 576s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [28.1 kB] 576s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [65.6 kB] 576s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [24.6 kB] 576s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 576s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [81.5 kB] 576s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [255 kB] 576s Fetched 783 kB in 0s (3542 kB/s) 576s Reading package lists... 578s Reading package lists... 578s Building dependency tree... 578s Reading state information... 578s Calculating upgrade... 579s The following NEW packages will be installed: 579s python3-jaraco.text 579s The following packages will be upgraded: 579s python3-pkg-resources python3-setuptools 579s 2 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 579s Need to get 802 kB of archives. 579s After this operation, 12.3 kB of additional disk space will be used. 579s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jaraco.text all 4.0.0-1 [11.5 kB] 579s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-pkg-resources all 75.2.0-1 [134 kB] 579s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-setuptools all 75.2.0-1 [657 kB] 579s Fetched 802 kB in 0s (12.6 MB/s) 579s Selecting previously unselected package python3-jaraco.text. 580s (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 ... 75315 files and directories currently installed.) 580s Preparing to unpack .../python3-jaraco.text_4.0.0-1_all.deb ... 580s Unpacking python3-jaraco.text (4.0.0-1) ... 580s Preparing to unpack .../python3-pkg-resources_75.2.0-1_all.deb ... 580s Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-1) ... 580s Preparing to unpack .../python3-setuptools_75.2.0-1_all.deb ... 580s Unpacking python3-setuptools (75.2.0-1) over (74.1.2-1) ... 580s Setting up python3-pkg-resources (75.2.0-1) ... 581s Setting up python3-jaraco.text (4.0.0-1) ... 581s Setting up python3-setuptools (75.2.0-1) ... 582s Reading package lists... 583s Building dependency tree... 583s Reading state information... 583s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 583s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 583s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 583s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 583s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 585s Reading package lists... 585s Reading package lists... 585s Building dependency tree... 585s Reading state information... 586s Calculating upgrade... 586s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 586s Reading package lists... 587s Building dependency tree... 587s Reading state information... 587s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 588s autopkgtest [10:15:38]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 588s autopkgtest [10:15:38]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biopython 590s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.83+dfsg1-3 (dsc) [3437 B] 590s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.83+dfsg1-3 (tar) [11.5 MB] 590s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biopython 1.83+dfsg1-3 (diff) [21.7 kB] 590s gpgv: Signature made Wed May 22 13:59:24 2024 UTC 590s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 590s gpgv: issuer "emollier@debian.org" 590s gpgv: Can't check signature: No public key 590s dpkg-source: warning: cannot verify inline signature for ./python-biopython_1.83+dfsg1-3.dsc: no acceptable signature found 591s autopkgtest [10:15:41]: testing package python-biopython version 1.83+dfsg1-3 591s autopkgtest [10:15:41]: build not needed 592s autopkgtest [10:15:42]: test dependencies: preparing testbed 593s Reading package lists... 593s Building dependency tree... 593s Reading state information... 594s Starting pkgProblemResolver with broken count: 0 594s Starting 2 pkgProblemResolver with broken count: 0 594s Done 594s The following additional packages will be installed: 594s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 594s libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 libgfortran5 594s libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 594s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 594s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 594s libxcb-shm0 libxrender1 python-biopython-doc python3-all python3-biopython 594s python3-biopython-sql python3-cairo python3-freetype python3-numpy 594s python3-pil python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 594s x11-common xfonts-encodings xfonts-utils xml-core 594s Suggested packages: 594s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 594s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 594s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 594s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 594s gcc gfortran python-numpy-doc python3-dev python3-pytest python-pil-doc 594s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 594s rl-renderpm sgml-base-doc debhelper 594s Recommended packages: 594s ncbi-blast+ python3-olefile fonts-dejavu-extra 594s The following NEW packages will be installed: 594s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono 594s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 594s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 594s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 594s libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 594s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python-biopython-doc 594s python3-all python3-biopython python3-biopython-sql python3-cairo 594s python3-freetype python3-numpy python3-pil python3-reportlab 594s python3-rlpycairo sgml-base w3c-sgml-lib x11-common xfonts-encodings 594s xfonts-utils xml-core 594s 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. 594s Need to get 45.6 MB/45.6 MB of archives. 594s After this operation, 109 MB of additional disk space will be used. 594s Get:1 /tmp/autopkgtest.04pS5H/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [740 B] 594s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 594s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 594s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 594s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 594s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 594s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 594s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 594s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 594s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 594s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 594s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 594s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.42.2-1build1 [279 kB] 594s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 594s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 594s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 594s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 594s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 594s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-7ubuntu1 [909 kB] 594s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-7ubuntu1 [148 kB] 594s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 594s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 9.0.0-1 [487 kB] 594s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 594s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 594s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 594s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 595s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB] 595s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 595s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 595s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 595s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 595s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 595s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 595s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 595s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 595s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biopython-doc all 1.83+dfsg1-3 [17.4 MB] 595s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 595s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 595s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 595s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 595s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 595s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.4.0-2 [81.3 kB] 595s Get:43 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 595s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.2-1 [1130 kB] 595s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 595s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 595s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.83+dfsg1-3 [1653 kB] 595s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython-sql all 1.83+dfsg1-3 [25.7 kB] 595s Fetched 45.6 MB in 0s (102 MB/s) 595s Selecting previously unselected package sgml-base. 595s (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 ... 75324 files and directories currently installed.) 595s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 595s Unpacking sgml-base (1.31) ... 595s Selecting previously unselected package fonts-dejavu-mono. 595s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 595s Unpacking fonts-dejavu-mono (2.37-8) ... 595s Selecting previously unselected package fonts-dejavu-core. 595s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 595s Unpacking fonts-dejavu-core (2.37-8) ... 595s Selecting previously unselected package libfontenc1:amd64. 595s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 595s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 595s Selecting previously unselected package x11-common. 595s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 595s Unpacking x11-common (1:7.7+23ubuntu3) ... 595s Selecting previously unselected package xfonts-encodings. 595s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 595s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 596s Selecting previously unselected package xfonts-utils. 596s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_amd64.deb ... 596s Unpacking xfonts-utils (1:7.7+7) ... 596s Selecting previously unselected package fonts-urw-base35. 596s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 596s Unpacking fonts-urw-base35 (20200910-8) ... 596s Selecting previously unselected package fontconfig-config. 596s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 596s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 596s Selecting previously unselected package libblas3:amd64. 596s Preparing to unpack .../09-libblas3_3.12.0-3build2_amd64.deb ... 596s Unpacking libblas3:amd64 (3.12.0-3build2) ... 596s Selecting previously unselected package libfontconfig1:amd64. 596s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 596s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 596s Selecting previously unselected package libpixman-1-0:amd64. 596s Preparing to unpack .../11-libpixman-1-0_0.42.2-1build1_amd64.deb ... 596s Unpacking libpixman-1-0:amd64 (0.42.2-1build1) ... 596s Selecting previously unselected package libxcb-render0:amd64. 596s Preparing to unpack .../12-libxcb-render0_1.17.0-2_amd64.deb ... 596s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 596s Selecting previously unselected package libxcb-shm0:amd64. 596s Preparing to unpack .../13-libxcb-shm0_1.17.0-2_amd64.deb ... 596s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 596s Selecting previously unselected package libxrender1:amd64. 596s Preparing to unpack .../14-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 596s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 596s Selecting previously unselected package libcairo2:amd64. 596s Preparing to unpack .../15-libcairo2_1.18.2-2_amd64.deb ... 596s Unpacking libcairo2:amd64 (1.18.2-2) ... 596s Selecting previously unselected package libdeflate0:amd64. 596s Preparing to unpack .../16-libdeflate0_1.21-1_amd64.deb ... 596s Unpacking libdeflate0:amd64 (1.21-1) ... 596s Selecting previously unselected package libgfortran5:amd64. 596s Preparing to unpack .../17-libgfortran5_14.2.0-7ubuntu1_amd64.deb ... 596s Unpacking libgfortran5:amd64 (14.2.0-7ubuntu1) ... 596s Selecting previously unselected package libgomp1:amd64. 597s Preparing to unpack .../18-libgomp1_14.2.0-7ubuntu1_amd64.deb ... 597s Unpacking libgomp1:amd64 (14.2.0-7ubuntu1) ... 597s Selecting previously unselected package libgraphite2-3:amd64. 597s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 597s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 597s Selecting previously unselected package libharfbuzz0b:amd64. 597s Preparing to unpack .../20-libharfbuzz0b_9.0.0-1_amd64.deb ... 597s Unpacking libharfbuzz0b:amd64 (9.0.0-1) ... 597s Selecting previously unselected package libimagequant0:amd64. 597s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_amd64.deb ... 597s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 597s Selecting previously unselected package libjpeg-turbo8:amd64. 597s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 597s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 597s Selecting previously unselected package libjpeg8:amd64. 597s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_amd64.deb ... 597s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 597s Selecting previously unselected package liblapack3:amd64. 597s Preparing to unpack .../24-liblapack3_3.12.0-3build2_amd64.deb ... 597s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 597s Selecting previously unselected package liblcms2-2:amd64. 597s Preparing to unpack .../25-liblcms2-2_2.14-2build1_amd64.deb ... 597s Unpacking liblcms2-2:amd64 (2.14-2build1) ... 597s Selecting previously unselected package liblerc4:amd64. 597s Preparing to unpack .../26-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 597s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 597s Selecting previously unselected package libraqm0:amd64. 597s Preparing to unpack .../27-libraqm0_0.10.1-1build1_amd64.deb ... 597s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 597s Selecting previously unselected package libsharpyuv0:amd64. 597s Preparing to unpack .../28-libsharpyuv0_1.4.0-0.1_amd64.deb ... 597s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 597s Selecting previously unselected package libjbig0:amd64. 597s Preparing to unpack .../29-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 597s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 597s Selecting previously unselected package libwebp7:amd64. 597s Preparing to unpack .../30-libwebp7_1.4.0-0.1_amd64.deb ... 597s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 597s Selecting previously unselected package libtiff6:amd64. 597s Preparing to unpack .../31-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 597s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 597s Selecting previously unselected package libwebpdemux2:amd64. 597s Preparing to unpack .../32-libwebpdemux2_1.4.0-0.1_amd64.deb ... 597s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 597s Selecting previously unselected package libwebpmux3:amd64. 597s Preparing to unpack .../33-libwebpmux3_1.4.0-0.1_amd64.deb ... 597s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 597s Selecting previously unselected package python-biopython-doc. 597s Preparing to unpack .../34-python-biopython-doc_1.83+dfsg1-3_all.deb ... 597s Unpacking python-biopython-doc (1.83+dfsg1-3) ... 597s Selecting previously unselected package python3-all. 597s Preparing to unpack .../35-python3-all_3.12.6-0ubuntu1_amd64.deb ... 597s Unpacking python3-all (3.12.6-0ubuntu1) ... 597s Selecting previously unselected package python3-numpy. 597s Preparing to unpack .../36-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 597s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 598s Selecting previously unselected package libopenjp2-7:amd64. 598s Preparing to unpack .../37-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 598s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 598s Selecting previously unselected package python3-pil:amd64. 598s Preparing to unpack .../38-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 598s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 598s Selecting previously unselected package python3-cairo. 598s Preparing to unpack .../39-python3-cairo_1.26.1-2_amd64.deb ... 598s Unpacking python3-cairo (1.26.1-2) ... 598s Selecting previously unselected package python3-freetype. 598s Preparing to unpack .../40-python3-freetype_2.4.0-2_all.deb ... 598s Unpacking python3-freetype (2.4.0-2) ... 598s Selecting previously unselected package python3-rlpycairo. 598s Preparing to unpack .../41-python3-rlpycairo_0.3.0-3_all.deb ... 598s Unpacking python3-rlpycairo (0.3.0-3) ... 598s Selecting previously unselected package python3-reportlab. 598s Preparing to unpack .../42-python3-reportlab_4.2.2-1_all.deb ... 598s Unpacking python3-reportlab (4.2.2-1) ... 598s Selecting previously unselected package xml-core. 598s Preparing to unpack .../43-xml-core_0.19_all.deb ... 598s Unpacking xml-core (0.19) ... 598s Selecting previously unselected package w3c-sgml-lib. 598s Preparing to unpack .../44-w3c-sgml-lib_1.3-3_all.deb ... 598s Unpacking w3c-sgml-lib (1.3-3) ... 598s Selecting previously unselected package python3-biopython. 598s Preparing to unpack .../45-python3-biopython_1.83+dfsg1-3_amd64.deb ... 598s Unpacking python3-biopython (1.83+dfsg1-3) ... 598s Selecting previously unselected package python3-biopython-sql. 598s Preparing to unpack .../46-python3-biopython-sql_1.83+dfsg1-3_all.deb ... 598s Unpacking python3-biopython-sql (1.83+dfsg1-3) ... 598s Selecting previously unselected package autopkgtest-satdep. 598s Preparing to unpack .../47-1-autopkgtest-satdep.deb ... 598s Unpacking autopkgtest-satdep (0) ... 599s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 599s Setting up liblcms2-2:amd64 (2.14-2build1) ... 599s Setting up libpixman-1-0:amd64 (0.42.2-1build1) ... 599s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 599s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 599s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 599s Setting up libxcb-render0:amd64 (1.17.0-2) ... 599s Setting up x11-common (1:7.7+23ubuntu3) ... 599s Setting up libdeflate0:amd64 (1.21-1) ... 599s Setting up python3-all (3.12.6-0ubuntu1) ... 599s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 599s Setting up libgomp1:amd64 (14.2.0-7ubuntu1) ... 599s Setting up python3-freetype (2.4.0-2) ... 599s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 599s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 599s Setting up libblas3:amd64 (3.12.0-3build2) ... 599s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 599s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 599s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 599s Setting up fonts-dejavu-mono (2.37-8) ... 599s Setting up fonts-dejavu-core (2.37-8) ... 599s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 599s Setting up libgfortran5:amd64 (14.2.0-7ubuntu1) ... 599s Setting up libwebp7:amd64 (1.4.0-0.1) ... 599s Setting up python-biopython-doc (1.83+dfsg1-3) ... 599s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 599s Setting up libharfbuzz0b:amd64 (9.0.0-1) ... 599s Setting up sgml-base (1.31) ... 599s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 599s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 599s Setting up liblapack3:amd64 (3.12.0-3build2) ... 599s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 599s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 599s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 599s Setting up xfonts-utils (1:7.7+7) ... 599s Setting up libraqm0:amd64 (0.10.1-1build1) ... 599s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 601s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 601s Setting up xml-core (0.19) ... 602s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 602s Setting up fonts-urw-base35 (20200910-8) ... 602s Setting up libcairo2:amd64 (1.18.2-2) ... 602s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 602s Setting up python3-cairo (1.26.1-2) ... 602s Setting up python3-rlpycairo (0.3.0-3) ... 602s Setting up python3-reportlab (4.2.2-1) ... 603s Processing triggers for libc-bin (2.40-1ubuntu3) ... 603s Processing triggers for man-db (2.12.1-3) ... 605s Processing triggers for sgml-base (1.31) ... 605s Setting up w3c-sgml-lib (1.3-3) ... 640s Setting up python3-biopython (1.83+dfsg1-3) ... 642s Setting up python3-biopython-sql (1.83+dfsg1-3) ... 642s Setting up autopkgtest-satdep (0) ... 645s (Reading database ... 80339 files and directories currently installed.) 645s Removing autopkgtest-satdep (0) ... 645s autopkgtest [10:16:35]: test dependencies: sh debian/tests/run-unit-test 645s autopkgtest [10:16:35]: test dependencies: [----------------------- 648s mkdir: created directory 'Bio' 648s mkdir: created directory 'Bio/Align' 648s mkdir: created directory 'Bio/Align/substitution_matrices' 648s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 648s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 648s Remove test test_Tutorial.py which is bound to fail 648s test_Ace ... ok 648s test_Affy ... ok 651s test_AlignIO ... ok 652s test_AlignIO_ClustalIO ... ok 652s test_AlignIO_EmbossIO ... ok 652s test_AlignIO_FastaIO ... ok 652s test_AlignIO_MauveIO ... ok 652s test_AlignIO_PhylipIO ... ok 652s test_AlignIO_convert ... ok 652s test_AlignInfo ... ok 652s test_Align_Alignment ... ok 652s test_Align_a2m ... ok 652s test_Align_bed ... ok 653s test_Align_bigbed ... ok 653s test_Align_bigmaf ... ok 654s test_Align_bigpsl ... ok 654s test_Align_chain ... ok 654s test_Align_clustal ... ok 657s test_Align_codonalign ... ok 658s test_Align_emboss ... ok 658s test_Align_exonerate ... ok 658s test_Align_fasta ... ok 658s test_Align_hhr ... ok 659s test_Align_maf ... ok 659s test_Align_mauve ... ok 659s test_Align_msf ... ok 659s test_Align_nexus ... ok 659s test_Align_phylip ... ok 659s test_Align_psl ... ok 660s test_Align_sam ... ok 662s test_Align_stockholm ... ok 662s test_Align_tabular ... ok 662s test_Application ... ok 662s test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython 663s test_BioSQL_MySQLdb_online ... skipping. internet not available 663s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 663s test_BioSQL_mysql_connector_online ... skipping. internet not available 663s test_BioSQL_psycopg2_online ... skipping. internet not available 668s test_BioSQL_sqlite3 ... ok 668s test_BioSQL_sqlite3_online ... skipping. internet not available 668s test_Blast_Record ... ok 668s test_CAPS ... ok 669s test_Chi2 ... ok 669s test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. 669s test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. 669s test_Cluster ... ok 669s test_CodonTable ... ok 669s test_ColorSpiral ... ok 669s test_Compass ... ok 670s test_Consensus ... ok 671s test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. 671s test_EMBL_unittest ... ok 671s test_Emboss ... skipping. $EMBOSS_ROOT='/usr/lib/emboss' which does not exist! 671s test_EmbossPrimer ... ok 675s test_Entrez ... ok 675s test_Entrez_online ... skipping. internet not available 675s test_Entrez_parser ... ok 675s test_Enzyme ... ok 675s test_ExPASy ... skipping. internet not available 675s test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. 675s test_File ... ok 676s test_GenBank ... ok 678s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 680s ok 681s test_GraphicsChromosome ... ok 681s test_GraphicsDistribution ... ok 682s test_GraphicsGeneral ... ok 682s test_HMMCasino ... ok 682s test_HMMGeneral ... ok 683s test_KEGG ... ok 683s test_KEGG_online ... skipping. internet not available 689s test_KGML_graphics ... ok 689s test_KGML_graphics_online ... skipping. internet not available 690s test_KGML_nographics ... ok 690s test_KeyWList ... ok 690s test_LogisticRegression ... ok 691s test_MafIO_index ... ok 691s test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. 692s test_MarkovModel ... ok 692s test_Medline ... ok 692s test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. 692s test_NCBIXML ... ok 693s test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. 693s test_NCBI_qblast ... ok 693s test_NMR ... ok 693s test_NaiveBayes ... ok 693s test_Nexus ... ok 693s test_PAML_baseml ... ok 694s test_PAML_codeml ... ok 694s test_PAML_yn00 ... ok 694s test_PDBList ... skipping. internet not available 697s test_PDB_CEAligner ... ok 697s test_PDB_DSSP ... ok 697s test_PDB_Dice ... ok 697s test_PDB_Disordered ... ok 698s test_PDB_Exposure ... ok 698s test_PDB_FragmentMapper ... ok 699s test_PDB_KDTree ... ok 700s test_PDB_MMCIF2Dict ... ok 700s test_PDB_MMCIFIO ... ok 701s test_PDB_MMCIFParser ... ok 701s test_PDB_NACCESS ... ok 701s test_PDB_PDBIO ... ok 702s test_PDB_PDBParser ... ok 702s 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 702s test_PDB_Polypeptide ... ok 702s test_PDB_QCPSuperimposer ... ok 706s test_PDB_SASA ... ok 706s test_PDB_SMCRA ... ok 706s test_PDB_Selection ... ok 707s test_PDB_StructureAlignment ... ok 707s test_PDB_Superimposer ... ok 707s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 707s 707s test_PDB_parse_pdb_header ... ok 707s test_PDB_vectors ... ok 707s test_PQR ... ok 707s test_Pathway ... ok 707s test_Phd ... ok 708s test_Phylo ... ok 708s test_PhyloXML ... ok 708s test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. 709s test_Phylo_NeXML ... ok 709s test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. 709s test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo 709s test_PopGen_GenePop_nodepend ... ok 709s test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. 709s test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. 709s test_ProtParam ... ok 709s test_RCSBFormats ... ok 710s test_Restriction ... ok 710s test_SCOP_Astral ... ok 710s test_SCOP_Cla ... ok 710s test_SCOP_Des ... ok 710s test_SCOP_Dom ... ok 710s test_SCOP_Hie ... ok 710s test_SCOP_Raf ... ok 710s test_SCOP_Residues ... ok 710s test_SCOP_Scop ... ok 710s test_SCOP_online ... skipping. internet not available 710s test_SVDSuperimposer ... ok 710s test_SearchIO_blast_tab ... ok 710s test_SearchIO_blast_tab_index ... ok 711s test_SearchIO_blast_xml ... ok 712s test_SearchIO_blast_xml_index ... ok 712s test_SearchIO_blat_psl ... ok 712s test_SearchIO_blat_psl_index ... ok 712s test_SearchIO_exonerate ... ok 712s test_SearchIO_exonerate_text_index ... ok 713s test_SearchIO_exonerate_vulgar_index ... ok 713s test_SearchIO_fasta_m10 ... ok 713s test_SearchIO_fasta_m10_index ... ok 713s test_SearchIO_hhsuite2_text ... ok 713s test_SearchIO_hmmer2_text ... ok 713s test_SearchIO_hmmer2_text_index ... ok 713s test_SearchIO_hmmer3_domtab ... ok 713s test_SearchIO_hmmer3_domtab_index ... ok 714s test_SearchIO_hmmer3_tab ... ok 714s test_SearchIO_hmmer3_tab_index ... ok 714s test_SearchIO_hmmer3_text ... ok 714s test_SearchIO_hmmer3_text_index ... ok 714s test_SearchIO_interproscan_xml ... ok 714s test_SearchIO_model ... ok 714s test_SearchIO_write ... ok 715s test_SeqFeature ... /usr/lib/python3/dist-packages/Bio/SeqFeature.py:1040: BiopythonParserWarning: Attempting to fix invalid location '3..2' as it looks like incorrect origin wrapping. Please fix input file, this could have unintended behavior. 715s warnings.warn( 715s ok 735s test_SeqIO ... ok 736s test_SeqIO_AbiIO ... ok 736s test_SeqIO_FastaIO ... ok 736s test_SeqIO_Gck ... ok 736s test_SeqIO_Insdc ... ok 736s test_SeqIO_NibIO ... ok 738s test_SeqIO_PdbIO ... ok 739s test_SeqIO_QualityIO ... ok 739s test_SeqIO_SeqXML ... ok 739s test_SeqIO_SnapGene ... ok 740s test_SeqIO_TwoBitIO ... ok 740s test_SeqIO_Xdna ... ok 741s test_SeqIO_features ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line 741s warnings.warn( 741s ok 758s test_SeqIO_index ... ok 758s test_SeqIO_online ... skipping. internet not available 758s test_SeqIO_write ... ok 759s test_SeqRecord ... ok 759s test_SeqUtils ... ok 760s test_Seq_objs ... ok 760s test_SffIO ... ok 760s test_SwissProt ... ok 760s test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. 761s test_TogoWS ... skipping. internet not available 761s test_TreeConstruction ... ok 761s test_UniGene ... ok 761s test_UniProt_GOA ... ok 761s test_Uniprot ... ok 762s test_align ... ok 762s test_align_substitution_matrices ... ok 765s test_bgzf ... ok 765s test_cellosaurus ... ok 770s test_codonalign ... ok 770s test_geo ... ok 770s test_kNN ... ok 770s test_motifs ... ok 770s test_motifs_online ... skipping. internet not available 770s 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. 770s warnings.warn( 770s ok 771s test_pairwise2_no_C ... ok 771s test_pairwise_aligner ... ok 771s test_pairwise_alignment_map ... ok 780s test_phenotype ... ok 780s test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. 780s 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. 780s test_prodoc ... ok 781s test_prosite ... ok 781s test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. 781s test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython 781s test_seq ... ok 781s test_translate ... ok 781s ---------------------------------------------------------------------- 781s Ran 212 tests in 132.829 seconds 781s 781s Skipping any tests requiring internet access 781s Python version: 3.12.7 (main, Oct 3 2024, 15:15:22) [GCC 14.2.0] 781s Operating system: posix linux 782s autopkgtest [10:18:52]: test dependencies: -----------------------] 782s autopkgtest [10:18:52]: test dependencies: - - - - - - - - - - results - - - - - - - - - - 782s dependencies PASS 782s autopkgtest [10:18:52]: test full_suite: preparing testbed 935s autopkgtest [10:21:25]: testbed dpkg architecture: amd64 935s autopkgtest [10:21:25]: testbed apt version: 2.9.8 935s autopkgtest [10:21:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 936s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 936s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [28.1 kB] 936s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [212 kB] 936s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 936s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [2840 B] 936s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [65.6 kB] 936s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [24.6 kB] 936s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 936s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [81.5 kB] 936s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [255 kB] 936s Fetched 783 kB in 0s (4323 kB/s) 936s Reading package lists... 937s Reading package lists... 937s Building dependency tree... 937s Reading state information... 938s Calculating upgrade... 938s The following NEW packages will be installed: 938s python3-jaraco.text 938s The following packages will be upgraded: 938s python3-pkg-resources python3-setuptools 938s 2 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 938s Need to get 802 kB of archives. 938s After this operation, 12.3 kB of additional disk space will be used. 938s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jaraco.text all 4.0.0-1 [11.5 kB] 938s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-pkg-resources all 75.2.0-1 [134 kB] 938s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-setuptools all 75.2.0-1 [657 kB] 938s Fetched 802 kB in 0s (21.8 MB/s) 938s Selecting previously unselected package python3-jaraco.text. 938s (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 ... 75315 files and directories currently installed.) 938s Preparing to unpack .../python3-jaraco.text_4.0.0-1_all.deb ... 938s Unpacking python3-jaraco.text (4.0.0-1) ... 938s Preparing to unpack .../python3-pkg-resources_75.2.0-1_all.deb ... 938s Unpacking python3-pkg-resources (75.2.0-1) over (74.1.2-1) ... 938s Preparing to unpack .../python3-setuptools_75.2.0-1_all.deb ... 939s Unpacking python3-setuptools (75.2.0-1) over (74.1.2-1) ... 939s Setting up python3-pkg-resources (75.2.0-1) ... 939s Setting up python3-jaraco.text (4.0.0-1) ... 939s Setting up python3-setuptools (75.2.0-1) ... 940s Reading package lists... 940s Building dependency tree... 940s Reading state information... 941s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 941s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 941s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 941s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 941s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 942s Reading package lists... 942s Reading package lists... 942s Building dependency tree... 942s Reading state information... 942s Calculating upgrade... 942s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 942s Reading package lists... 943s Building dependency tree... 943s Reading state information... 943s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 945s Reading package lists... 945s Building dependency tree... 945s Reading state information... 946s Starting pkgProblemResolver with broken count: 0 946s Starting 2 pkgProblemResolver with broken count: 0 946s Done 946s The following additional packages will be installed: 946s autoconf automake autopoint autotools-dev blt build-essential bwa clustalo 946s clustalw cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper 946s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dialign dssp dwz 946s emboss emboss-data emboss-lib fasttree flex fontconfig-config 946s fonts-dejavu-core fonts-dejavu-mono fonts-lmodern fonts-lyx fonts-urw-base35 946s g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 946s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext ghostscript hevea 946s hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 946s intltool-debian libamd-comgr2 libamdhip64-5 libaom3 libapache-pom-java 946s libarchive-zip-perl libargtable2-0 libasan8 libavahi-client3 946s libavahi-common-data libavahi-common3 libblas3 libcairo2 libcc1-0 946s libcifpp-data libcifpp5 libcommons-logging-java libcommons-parent-java 946s libcups2t64 libde265-0 libdebhelper-perl libdeflate0 libdrm-amdgpu1 946s libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 libfftw3-double3 946s libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 946s libgcc-14-dev libgd3 libgfortran5 libgomp1 libgraphite2-3 libgs-common 946s libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec 946s libheif-plugin-libde265 libheif1 libhpdf-2.3.0 libhsa-runtime64-1 libhsakmt1 946s libhts3t64 libhtscodecs2 libhwasan0 libhwloc-plugins libhwloc15 libibmad5 946s libibumad3 libice6 libidn12 libijs-0.35 libimagequant0 libisl23 libitm1 946s libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 946s libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 946s liblcms2-2 liblerc4 libllvm17t64 liblqr-1-0 liblsan0 libltdl7 946s libmagickcore-6.q16-7t64 libmagickwand-6.q16-7t64 libmbedcrypto7t64 946s libmbedtls14t64 libmbedx509-1t64 libmpc3 libmpfi0 libmunge2 libmysqlclient21 946s libnetpbm11t64 libopenjp2-7 libopenmpi3t64 libpaper-utils libpaper1 946s libpciaccess0 libpdfbox-java libpixman-1-0 libpmix2t64 libpotrace0 libpq5 946s libpsm-infinipath1 libpsm2-2 libptexenc1 libpython3-all-dev libpython3-dev 946s libpython3.12-dev libqhull-r8.0 libquadmath0 libraqm0 libraw23t64 946s librdmacm1t64 libsharpyuv0 libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 946s libteckit0 libtexlua53-5 libtiff6 libtk8.6 libtool libtsan2 libubsan1 946s libucx0 libwebp7 libwebpdemux2 libwebpmux3 libxaw7 libxcb-render0 946s libxcb-shm0 libxft2 libxi6 libxmu6 libxnvctrl0 libxpm4 libxrender1 946s libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 m4 mafft muscle3 mysql-common 946s ncbi-blast+ ncbi-data netpbm ocl-icd-libopencl1 openmpi-bin openmpi-common 946s phylip phyml po-debconf poppler-data prank preview-latex-style probcons 946s python-biopython-doc python-matplotlib-data python3-all python3-all-dev 946s python3-appdirs python3-biopython python3-biopython-sql python3-brotli 946s python3-cairo python3-contourpy python3-cycler python3-dateutil 946s python3-decorator python3-dev python3-fonttools python3-freetype python3-fs 946s python3-isodate python3-kiwisolver python3-lxml python3-lz4 946s python3-matplotlib python3-mmtf python3-mpmath python3-msgpack 946s python3-mysqldb python3-networkx python3-numpy python3-packaging python3-pil 946s python3-pil.imagetk python3-psycopg2 python3-rdflib python3-reportlab 946s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 946s python3-tz python3-ufolib2 python3.12-dev python3.12-tk raxml samtools 946s sgml-base t-coffee t1utils tex-common texlive-base texlive-binaries 946s texlive-fonts-recommended texlive-latex-base texlive-latex-extra 946s texlive-latex-recommended texlive-pictures tk8.6-blt2.5 unicode-data 946s w3c-sgml-lib wise wise-data x11-common xdg-utils xfonts-encodings 946s xfonts-utils xml-core zlib1g-dev 946s Suggested packages: 946s autoconf-archive gnu-standards autoconf-doc blt-demo clustalx seaview 946s cpp-doc gcc-14-locales cpp-14-doc dh-make flit python3-build 946s python3-installer python3-wheel emboss-doc emboss-test embassy bison 946s flex-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre g++-multilib 946s g++-14-multilib gcc-14-doc gcc-multilib manpages-dev gdb gcc-doc 946s gcc-14-multilib gdb-x86-64-linux-gnu gettext-doc libasprintf-dev 946s libgettextpo-dev hevea-doc imagemagick-6-doc autotrace cups-bsd | lpr 946s | lprng enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin 946s mplayer povray radiance sane-utils transfig libraw-bin 946s libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java 946s cups-common libfftw3-bin libfftw3-dev libgd-tools libheif-plugin-x265 946s libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc 946s libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar 946s libheif-plugin-rav1e libheif-plugin-svtenc libhwloc-contrib-plugins 946s libjs-jquery-ui-docs liblcms2-utils libmagickcore-6.q16-7-extra libmpfi-doc 946s libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler 946s gcj-jdk m4-doc opencl-icd gfortran | fortran-compiler phylip-doc 946s libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho 946s fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai 946s fonts-arphic-uming fonts-nanum probcons-extra python-cycler-doc 946s python-lxml-doc cm-super-minimal dvipng fonts-staypuft gir1.2-gtk-3.0 946s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 946s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 946s texlive-extra-utils python-mpmath-doc python3-gmpy2 default-mysql-server 946s | virtual-mysql-server python3-gdal python3-pydot python3-pygraphviz 946s gfortran python-numpy-doc python3-pytest python-pil-doc python-psycopg2-doc 946s python-rdflib-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc 946s rl-accel rl-renderpm python-scipy-doc texlive-fonts-extra python-sympy-doc 946s tix python3-tk-dbg python3.13-tk cwltool sgml-base-doc boxshade 946s t-coffee-examples perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 946s hintview texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex 946s icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-science 946s texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex 946s texlive-pictures-doc vprerex wise-doc 946s Recommended packages: 946s primer3 libfl-dev libmagickcore-6.q16-7-extra libarchive-cpio-perl 946s fonts-droid-fallback libheif-plugin-aomenc javascript-common libltdl-dev 946s blast2 libwww-perl lynx ruby libmail-sendmail-perl python3-bs4 946s python3-cssselect python3-html5lib python3-olefile python3-sparqlwrapper 946s fonts-dejavu-extra isympy-common amap-align dialign-tx fsa kalign 946s libsoap-lite-perl libxml-simple-perl muscle mustang poa proda tm-align 946s lmodern dvisvgm tex-gyre tipa default-jre libspreadsheet-parseexcel-perl 946s texlive-plain-generic tk libfile-mimeinfo-perl libnet-dbus-perl 946s libx11-protocol-perl x11-utils x11-xserver-utils 946s The following NEW packages will be installed: 946s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 946s build-essential bwa clustalo clustalw cpp cpp-14 cpp-14-x86-64-linux-gnu 946s cpp-x86-64-linux-gnu debhelper debugedit dh-autoreconf dh-python 946s dh-strip-nondeterminism dialign dssp dwz emboss emboss-data emboss-lib 946s fasttree flex fontconfig-config fonts-dejavu-core fonts-dejavu-mono 946s fonts-lmodern fonts-lyx fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu 946s g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu 946s gettext ghostscript hevea hicolor-icon-theme imagemagick 946s imagemagick-6-common imagemagick-6.q16 intltool-debian libamd-comgr2 946s libamdhip64-5 libaom3 libapache-pom-java libarchive-zip-perl libargtable2-0 946s libasan8 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 946s libcairo2 libcc1-0 libcifpp-data libcifpp5 libcommons-logging-java 946s libcommons-parent-java libcups2t64 libde265-0 libdebhelper-perl libdeflate0 946s libdrm-amdgpu1 libevent-pthreads-2.1-7t64 libexpat1-dev libfabric1 946s libfftw3-double3 libfile-stripnondeterminism-perl libfontbox-java 946s libfontconfig1 libfontenc1 libgcc-14-dev libgd3 libgfortran5 libgomp1 946s libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b 946s libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libhpdf-2.3.0 946s libhsa-runtime64-1 libhsakmt1 libhts3t64 libhtscodecs2 libhwasan0 946s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libice6 libidn12 946s libijs-0.35 libimagequant0 libisl23 libitm1 libjbig0 libjbig2dec0 946s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc 946s libjs-underscore libkpathsea6 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 946s libllvm17t64 liblqr-1-0 liblsan0 libltdl7 libmagickcore-6.q16-7t64 946s libmagickwand-6.q16-7t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 946s libmpc3 libmpfi0 libmunge2 libmysqlclient21 libnetpbm11t64 libopenjp2-7 946s libopenmpi3t64 libpaper-utils libpaper1 libpciaccess0 libpdfbox-java 946s libpixman-1-0 libpmix2t64 libpotrace0 libpq5 libpsm-infinipath1 libpsm2-2 946s libptexenc1 libpython3-all-dev libpython3-dev libpython3.12-dev 946s libqhull-r8.0 libquadmath0 libraqm0 libraw23t64 librdmacm1t64 libsharpyuv0 946s libsm6 libstdc++-14-dev libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 946s libtiff6 libtk8.6 libtool libtsan2 libubsan1 libucx0 libwebp7 libwebpdemux2 946s libwebpmux3 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 946s libxnvctrl0 libxpm4 libxrender1 libxslt1.1 libxss1 libxt6t64 libzzip-0-13t64 946s m4 mafft muscle3 mysql-common ncbi-blast+ ncbi-data netpbm 946s ocl-icd-libopencl1 openmpi-bin openmpi-common phylip phyml po-debconf 946s poppler-data prank preview-latex-style probcons python-biopython-doc 946s python-matplotlib-data python3-all python3-all-dev python3-appdirs 946s python3-biopython python3-biopython-sql python3-brotli python3-cairo 946s python3-contourpy python3-cycler python3-dateutil python3-decorator 946s python3-dev python3-fonttools python3-freetype python3-fs python3-isodate 946s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mmtf 946s python3-mpmath python3-msgpack python3-mysqldb python3-networkx 946s python3-numpy python3-packaging python3-pil python3-pil.imagetk 946s python3-psycopg2 python3-rdflib python3-reportlab python3-rlpycairo 946s python3-scipy python3-six python3-sympy python3-tk python3-tz 946s python3-ufolib2 python3.12-dev python3.12-tk raxml samtools sgml-base 946s t-coffee t1utils tex-common texlive-base texlive-binaries 946s texlive-fonts-recommended texlive-latex-base texlive-latex-extra 946s texlive-latex-recommended texlive-pictures tk8.6-blt2.5 unicode-data 946s w3c-sgml-lib wise wise-data x11-common xdg-utils xfonts-encodings 946s xfonts-utils xml-core zlib1g-dev 946s 0 upgraded, 268 newly installed, 0 to remove and 0 not upgraded. 946s Need to get 448 MB/448 MB of archives. 946s After this operation, 1939 MB of additional disk space will be used. 946s Get:1 /tmp/autopkgtest.04pS5H/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [1004 B] 946s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 946s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 flex amd64 2.6.4-8.2build1 [301 kB] 946s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-7ubuntu1 [148 kB] 946s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu4 [839 kB] 946s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 946s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 946s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 946s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 946s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 946s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 946s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 946s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 946s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 946s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 946s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libaom3 amd64 3.9.1-1 [1933 kB] 946s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-aomdec amd64 1.18.1-2 [11.1 kB] 946s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libde265-0 amd64 1.0.15-1build4 [168 kB] 946s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-libde265 amd64 1.18.1-2 [8758 B] 946s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif1 amd64 1.18.1-2 [293 kB] 946s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 946s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 946s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 946s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB] 946s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblqr-1-0 amd64 0.4.2-2.1build2 [28.5 kB] 946s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.4.7-7build1 [40.3 kB] 946s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 946s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libraw23t64 amd64 0.21.2-2.1build1 [378 kB] 946s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 946s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 946s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 946s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 946s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 946s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 946s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick-6-common all 8:6.9.13.12+dfsg1-1build1 [69.6 kB] 946s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmagickcore-6.q16-7t64 amd64 8:6.9.13.12+dfsg1-1build1 [1851 kB] 946s Get:37 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmagickwand-6.q16-7t64 amd64 8:6.9.13.12+dfsg1-1build1 [316 kB] 946s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-data all 0.4.12-1 [2060 kB] 946s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 946s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 946s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 946s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 946s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 946s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 946s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 946s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 946s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 946s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 946s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 946s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 946s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 946s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 946s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-7ubuntu1 [11.9 MB] 947s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-7ubuntu1 [1026 B] 947s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 947s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 947s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-7ubuntu1 [47.6 kB] 947s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-7ubuntu1 [29.1 kB] 947s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-7ubuntu1 [2998 kB] 947s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-7ubuntu1 [1316 kB] 947s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-7ubuntu1 [2733 kB] 947s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-7ubuntu1 [1177 kB] 947s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-7ubuntu1 [1634 kB] 947s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-7ubuntu1 [153 kB] 947s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-7ubuntu1 [2814 kB] 947s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-7ubuntu1 [23.4 MB] 947s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-7ubuntu1 [526 kB] 947s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 947s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 947s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-7ubuntu1 [2503 kB] 947s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-7ubuntu1 [13.4 MB] 947s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-7ubuntu1 [19.8 kB] 947s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 947s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 947s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 947s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 bwa amd64 0.7.17-7 [195 kB] 947s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 libargtable2-0 amd64 13-2 [14.6 kB] 947s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 clustalo amd64 1.2.4-8build1 [202 kB] 947s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 clustalw amd64 2.1+lgpl-7 [275 kB] 947s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 947s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 947s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 947s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 947s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 947s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 947s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.0-6 [46.1 kB] 947s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 947s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 947s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 947s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 947s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 947s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20240824 [112 kB] 947s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 dialign amd64 2.2.1-13 [154 kB] 947s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcifpp-data all 5.0.7.1-3build1 [450 kB] 947s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcifpp5 amd64 5.0.7.1-3build1 [936 kB] 947s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 dssp amd64 4.2.2-2 [670 kB] 947s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 947s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 947s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 9.0.0-1 [487 kB] 947s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 947s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB] 947s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libgd3 amd64 2.3.3-12ubuntu3 [127 kB] 947s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhpdf-2.3.0 amd64 2.3.0+dfsg-1build3 [432 kB] 947s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 mysql-common all 5.8+1.1.1 [6800 B] 947s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libmysqlclient21 amd64 8.0.39-1 [1250 kB] 947s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libpq5 amd64 17.0-1 [249 kB] 947s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss-lib amd64 6.6.0+dfsg-12ubuntu2 [2976 kB] 947s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss-data all 6.6.0+dfsg-12ubuntu2 [61.0 MB] 948s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 emboss amd64 6.6.0+dfsg-12ubuntu2 [980 kB] 948s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lmodern all 2.005-1 [4799 kB] 948s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.1-2 [171 kB] 948s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs-common all 10.03.1~dfsg1-0ubuntu2 [175 kB] 948s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs10-common all 10.03.1~dfsg1-0ubuntu2 [488 kB] 948s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common-data amd64 0.8-13ubuntu6 [29.7 kB] 948s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-common3 amd64 0.8-13ubuntu6 [23.3 kB] 948s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libavahi-client3 amd64 0.8-13ubuntu6 [26.8 kB] 948s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libcups2t64 amd64 2.4.10-1ubuntu2 [271 kB] 948s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libidn12 amd64 1.42-2 [55.9 kB] 948s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libijs-0.35 amd64 0.35-15.1build1 [15.3 kB] 948s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig2dec0 amd64 0.20-1build3 [65.0 kB] 948s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB] 948s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.0.10-1build3 [41.4 kB] 948s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.3-1build3 [15.7 kB] 948s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 948s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 libgs10 amd64 10.03.1~dfsg1-0ubuntu2 [3672 kB] 948s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 ghostscript amd64 10.03.1~dfsg1-0ubuntu2 [43.5 kB] 948s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetpbm11t64 amd64 2:11.07.00-2 [114 kB] 948s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 netpbm amd64 2:11.07.00-2 [2067 kB] 948s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 tex-common all 6.18 [32.8 kB] 948s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B] 948s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-4 [64.3 kB] 948s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-4 [41.9 kB] 948s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-4 [59.9 kB] 948s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-4 [123 kB] 948s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 t1utils amd64 1.41-4build3 [61.3 kB] 948s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.42.2-1build1 [279 kB] 948s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 948s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 948s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 948s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpfi0 amd64 1.5.4+ds-3 [35.1 kB] 948s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpotrace0 amd64 1.16-2build1 [17.7 kB] 948s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 libteckit0 amd64 2.5.12+ds1-1 [411 kB] 948s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB] 948s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libxaw7 amd64 2:1.0.14-1build2 [187 kB] 948s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 948s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2build1 [28.1 kB] 948s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-binaries amd64 2024.20240313.70630+ds-4 [8478 kB] 948s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 948s Get:149 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-base all 2024.20240706-1 [22.5 MB] 948s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-1 [13.5 kB] 948s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick-6.q16 amd64 8:6.9.13.12+dfsg1-1build1 [254 kB] 948s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 imagemagick amd64 8:6.9.13.12+dfsg1-1build1 [14.2 kB] 948s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 hevea amd64 2.36-2 [2023 kB] 948s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-18 [26.0 MB] 948s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 948s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-amdgpu1 amd64 2.4.122-1 [20.9 kB] 948s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 948s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 948s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-4build1 [9627 kB] 948s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 29-2 [5284 B] 948s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 948s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB] 948s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB] 948s Get:164 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 948s Get:165 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.2-2 [140 kB] 948s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 948s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 948s Get:168 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 52.0-2ubuntu1 [70.8 kB] 948s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3ubuntu1 [658 kB] 948s Get:170 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-7ubuntu1 [909 kB] 948s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 948s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 948s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.11.0-2 [173 kB] 948s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 948s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 948s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 948s Get:177 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-3 [157 kB] 948s Get:178 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 948s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 948s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto7t64 amd64 2.28.8-1 [209 kB] 948s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-1t64 amd64 2.28.8-1 [46.6 kB] 948s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls14t64 amd64 2.28.8-1 [82.2 kB] 949s Get:183 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.15-4build1 [14.7 kB] 949s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 949s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 949s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 949s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.11.0-2 [15.7 kB] 949s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.3-2 [697 kB] 949s Get:189 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 52.0-2ubuntu1 [29.0 kB] 949s Get:190 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 52.0-2ubuntu1 [42.6 kB] 949s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.17.0+ds-3build1 [1162 kB] 949s Get:192 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi3t64 amd64 4.1.6-13.3ubuntu2 [2575 kB] 949s Get:193 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 949s Get:194 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.7-1 [5696 kB] 949s Get:195 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.12.6-0ubuntu1 [10.2 kB] 949s Get:196 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-all-dev amd64 3.12.6-0ubuntu1 [916 B] 949s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 949s Get:198 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 949s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 mafft amd64 7.505-1 [795 kB] 949s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 muscle3 amd64 3.8.1551-3 [198 kB] 949s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-3 [3966 kB] 949s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] 949s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-common all 4.1.6-13.3ubuntu2 [170 kB] 949s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 openmpi-bin amd64 4.1.6-13.3ubuntu2 [114 kB] 949s Get:205 http://ftpmaster.internal/ubuntu plucky/universe amd64 phylip amd64 1:3.697+dfsg-4build1 [874 kB] 949s Get:206 http://ftpmaster.internal/ubuntu plucky/universe amd64 phyml amd64 3:3.3.20220408-3build3 [965 kB] 949s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 prank amd64 0.0.170427+dfsg-3 [396 kB] 949s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 preview-latex-style all 13.2-1 [347 kB] 949s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 probcons amd64 1.12-14 [125 kB] 949s Get:210 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biopython-doc all 1.83+dfsg1-3 [17.4 MB] 949s Get:211 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 949s Get:212 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 949s Get:213 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.7-1 [505 kB] 949s Get:214 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.12.6-0ubuntu1 [26.7 kB] 949s Get:215 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all-dev amd64 3.12.6-0ubuntu1 [908 B] 949s Get:216 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 949s Get:217 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 949s Get:218 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-1 [116 kB] 949s Get:219 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.6-1ubuntu1 [9806 B] 949s Get:220 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 949s Get:221 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 949s Get:222 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 949s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.4.0-2 [81.3 kB] 949s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 949s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.2-1 [1130 kB] 949s Get:226 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 949s Get:227 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 949s Get:228 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.83+dfsg1-3 [1653 kB] 949s Get:229 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython-sql all 1.83+dfsg1-3 [25.7 kB] 949s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 949s Get:231 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.2.1-1 [191 kB] 949s Get:232 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 949s Get:233 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 949s Get:234 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 949s Get:235 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 949s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-3 [16.9 MB] 949s Get:237 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 949s Get:238 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 949s Get:239 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.1-1 [4228 kB] 949s Get:240 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 949s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 949s Get:242 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 949s Get:243 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 949s Get:244 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 949s Get:245 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 949s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-isodate all 0.6.1-3 [24.3 kB] 949s Get:247 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.5-1 [51.0 kB] 949s Get:248 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 949s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 949s Get:250 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-msgpack amd64 1.0.3-3build2 [80.1 kB] 949s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mmtf all 1.1.3-1 [16.2 kB] 949s Get:252 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-mysqldb amd64 1.4.6-2build3 [47.3 kB] 949s Get:253 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 950s Get:254 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psycopg2 amd64 2.9.9-2 [132 kB] 950s Get:255 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rdflib all 7.0.0-1 [405 kB] 950s Get:256 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB] 950s Get:257 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB] 950s Get:258 http://ftpmaster.internal/ubuntu plucky/universe amd64 t-coffee amd64 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [929 kB] 950s Get:259 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-fonts-recommended all 2024.20240706-1 [4973 kB] 950s Get:260 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-base all 2024.20240706-1 [1256 kB] 950s Get:261 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfontbox-java all 1:1.8.16-5 [208 kB] 950s Get:262 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpdfbox-java all 1:1.8.16-5 [5521 kB] 950s Get:263 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-recommended all 2024.20240706-1 [8830 kB] 950s Get:264 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-pictures all 2024.20240706-1 [17.0 MB] 950s Get:265 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-extra all 2024.20240706-2 [19.6 MB] 950s Get:266 http://ftpmaster.internal/ubuntu plucky/universe amd64 wise-data all 2.4.1-25 [83.0 kB] 950s Get:267 http://ftpmaster.internal/ubuntu plucky/universe amd64 wise amd64 2.4.1-25 [843 kB] 950s Get:268 http://ftpmaster.internal/ubuntu plucky/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 951s Preconfiguring packages ... 951s Fetched 448 MB in 4s (112 MB/s) 951s Selecting previously unselected package m4. 951s (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 ... 75324 files and directories currently installed.) 951s Preparing to unpack .../000-m4_1.4.19-4build1_amd64.deb ... 951s Unpacking m4 (1.4.19-4build1) ... 951s Selecting previously unselected package flex. 951s Preparing to unpack .../001-flex_2.6.4-8.2build1_amd64.deb ... 951s Unpacking flex (2.6.4-8.2build1) ... 951s Selecting previously unselected package libgomp1:amd64. 951s Preparing to unpack .../002-libgomp1_14.2.0-7ubuntu1_amd64.deb ... 951s Unpacking libgomp1:amd64 (14.2.0-7ubuntu1) ... 951s Selecting previously unselected package libfftw3-double3:amd64. 951s Preparing to unpack .../003-libfftw3-double3_3.3.10-1ubuntu4_amd64.deb ... 951s Unpacking libfftw3-double3:amd64 (3.3.10-1ubuntu4) ... 951s Selecting previously unselected package fonts-dejavu-mono. 951s Preparing to unpack .../004-fonts-dejavu-mono_2.37-8_all.deb ... 951s Unpacking fonts-dejavu-mono (2.37-8) ... 951s Selecting previously unselected package fonts-dejavu-core. 951s Preparing to unpack .../005-fonts-dejavu-core_2.37-8_all.deb ... 951s Unpacking fonts-dejavu-core (2.37-8) ... 951s Selecting previously unselected package libfontenc1:amd64. 951s Preparing to unpack .../006-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 951s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 951s Selecting previously unselected package x11-common. 951s Preparing to unpack .../007-x11-common_1%3a7.7+23ubuntu3_all.deb ... 951s Unpacking x11-common (1:7.7+23ubuntu3) ... 951s Selecting previously unselected package xfonts-encodings. 951s Preparing to unpack .../008-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 951s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 951s Selecting previously unselected package xfonts-utils. 951s Preparing to unpack .../009-xfonts-utils_1%3a7.7+7_amd64.deb ... 951s Unpacking xfonts-utils (1:7.7+7) ... 951s Selecting previously unselected package fonts-urw-base35. 951s Preparing to unpack .../010-fonts-urw-base35_20200910-8_all.deb ... 951s Unpacking fonts-urw-base35 (20200910-8) ... 952s Selecting previously unselected package fontconfig-config. 952s Preparing to unpack .../011-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 952s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 952s Selecting previously unselected package libfontconfig1:amd64. 952s Preparing to unpack .../012-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 952s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 952s Selecting previously unselected package libsharpyuv0:amd64. 952s Preparing to unpack .../013-libsharpyuv0_1.4.0-0.1_amd64.deb ... 952s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 952s Selecting previously unselected package libaom3:amd64. 952s Preparing to unpack .../014-libaom3_3.9.1-1_amd64.deb ... 952s Unpacking libaom3:amd64 (3.9.1-1) ... 952s Selecting previously unselected package libheif-plugin-aomdec:amd64. 952s Preparing to unpack .../015-libheif-plugin-aomdec_1.18.1-2_amd64.deb ... 952s Unpacking libheif-plugin-aomdec:amd64 (1.18.1-2) ... 952s Selecting previously unselected package libde265-0:amd64. 952s Preparing to unpack .../016-libde265-0_1.0.15-1build4_amd64.deb ... 952s Unpacking libde265-0:amd64 (1.0.15-1build4) ... 952s Selecting previously unselected package libheif-plugin-libde265:amd64. 952s Preparing to unpack .../017-libheif-plugin-libde265_1.18.1-2_amd64.deb ... 952s Unpacking libheif-plugin-libde265:amd64 (1.18.1-2) ... 952s Selecting previously unselected package libheif1:amd64. 952s Preparing to unpack .../018-libheif1_1.18.1-2_amd64.deb ... 952s Unpacking libheif1:amd64 (1.18.1-2) ... 952s Selecting previously unselected package libjbig0:amd64. 952s Preparing to unpack .../019-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 952s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 952s Selecting previously unselected package libjpeg-turbo8:amd64. 952s Preparing to unpack .../020-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 952s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 952s Selecting previously unselected package libjpeg8:amd64. 952s Preparing to unpack .../021-libjpeg8_8c-2ubuntu11_amd64.deb ... 952s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 952s Selecting previously unselected package liblcms2-2:amd64. 952s Preparing to unpack .../022-liblcms2-2_2.14-2build1_amd64.deb ... 952s Unpacking liblcms2-2:amd64 (2.14-2build1) ... 952s Selecting previously unselected package liblqr-1-0:amd64. 952s Preparing to unpack .../023-liblqr-1-0_0.4.2-2.1build2_amd64.deb ... 952s Unpacking liblqr-1-0:amd64 (0.4.2-2.1build2) ... 952s Selecting previously unselected package libltdl7:amd64. 952s Preparing to unpack .../024-libltdl7_2.4.7-7build1_amd64.deb ... 952s Unpacking libltdl7:amd64 (2.4.7-7build1) ... 952s Selecting previously unselected package libopenjp2-7:amd64. 952s Preparing to unpack .../025-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 952s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 952s Selecting previously unselected package libraw23t64:amd64. 952s Preparing to unpack .../026-libraw23t64_0.21.2-2.1build1_amd64.deb ... 952s Unpacking libraw23t64:amd64 (0.21.2-2.1build1) ... 952s Selecting previously unselected package libdeflate0:amd64. 952s Preparing to unpack .../027-libdeflate0_1.21-1_amd64.deb ... 952s Unpacking libdeflate0:amd64 (1.21-1) ... 952s Selecting previously unselected package liblerc4:amd64. 952s Preparing to unpack .../028-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 952s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 952s Selecting previously unselected package libwebp7:amd64. 952s Preparing to unpack .../029-libwebp7_1.4.0-0.1_amd64.deb ... 952s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 952s Selecting previously unselected package libtiff6:amd64. 952s Preparing to unpack .../030-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 952s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 952s Selecting previously unselected package libwebpdemux2:amd64. 952s Preparing to unpack .../031-libwebpdemux2_1.4.0-0.1_amd64.deb ... 952s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 952s Selecting previously unselected package libwebpmux3:amd64. 952s Preparing to unpack .../032-libwebpmux3_1.4.0-0.1_amd64.deb ... 952s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 952s Selecting previously unselected package imagemagick-6-common. 952s Preparing to unpack .../033-imagemagick-6-common_8%3a6.9.13.12+dfsg1-1build1_all.deb ... 952s Unpacking imagemagick-6-common (8:6.9.13.12+dfsg1-1build1) ... 952s Selecting previously unselected package libmagickcore-6.q16-7t64:amd64. 952s Preparing to unpack .../034-libmagickcore-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 952s Unpacking libmagickcore-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 953s Selecting previously unselected package libmagickwand-6.q16-7t64:amd64. 953s Preparing to unpack .../035-libmagickwand-6.q16-7t64_8%3a6.9.13.12+dfsg1-1build1_amd64.deb ... 953s Unpacking libmagickwand-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 953s Selecting previously unselected package poppler-data. 953s Preparing to unpack .../036-poppler-data_0.4.12-1_all.deb ... 953s Unpacking poppler-data (0.4.12-1) ... 953s Selecting previously unselected package sgml-base. 953s Preparing to unpack .../037-sgml-base_1.31_all.deb ... 953s Unpacking sgml-base (1.31) ... 953s Selecting previously unselected package autoconf. 953s Preparing to unpack .../038-autoconf_2.72-3_all.deb ... 953s Unpacking autoconf (2.72-3) ... 953s Selecting previously unselected package autotools-dev. 953s Preparing to unpack .../039-autotools-dev_20220109.1_all.deb ... 953s Unpacking autotools-dev (20220109.1) ... 953s Selecting previously unselected package automake. 953s Preparing to unpack .../040-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 953s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 953s Selecting previously unselected package autopoint. 953s Preparing to unpack .../041-autopoint_0.22.5-2_all.deb ... 953s Unpacking autopoint (0.22.5-2) ... 953s Selecting previously unselected package libtcl8.6:amd64. 953s Preparing to unpack .../042-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ... 953s Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 953s Selecting previously unselected package libxrender1:amd64. 953s Preparing to unpack .../043-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 953s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 953s Selecting previously unselected package libxft2:amd64. 953s Preparing to unpack .../044-libxft2_2.3.6-1build1_amd64.deb ... 953s Unpacking libxft2:amd64 (2.3.6-1build1) ... 953s Selecting previously unselected package libxss1:amd64. 953s Preparing to unpack .../045-libxss1_1%3a1.2.3-1build3_amd64.deb ... 953s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 953s Selecting previously unselected package libtk8.6:amd64. 953s Preparing to unpack .../046-libtk8.6_8.6.14-1build1_amd64.deb ... 953s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 953s Selecting previously unselected package tk8.6-blt2.5. 953s Preparing to unpack .../047-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 953s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 953s Selecting previously unselected package blt. 953s Preparing to unpack .../048-blt_2.5.3+dfsg-7build1_amd64.deb ... 953s Unpacking blt (2.5.3+dfsg-7build1) ... 953s Selecting previously unselected package libisl23:amd64. 953s Preparing to unpack .../049-libisl23_0.27-1_amd64.deb ... 953s Unpacking libisl23:amd64 (0.27-1) ... 953s Selecting previously unselected package libmpc3:amd64. 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libubsan1:amd64 (14.2.0-7ubuntu1) ... 954s Selecting previously unselected package libhwasan0:amd64. 954s Preparing to unpack .../061-libhwasan0_14.2.0-7ubuntu1_amd64.deb ... 954s Unpacking libhwasan0:amd64 (14.2.0-7ubuntu1) ... 954s Selecting previously unselected package libquadmath0:amd64. 954s Preparing to unpack .../062-libquadmath0_14.2.0-7ubuntu1_amd64.deb ... 954s Unpacking libquadmath0:amd64 (14.2.0-7ubuntu1) ... 954s Selecting previously unselected package libgcc-14-dev:amd64. 954s Preparing to unpack .../063-libgcc-14-dev_14.2.0-7ubuntu1_amd64.deb ... 954s Unpacking libgcc-14-dev:amd64 (14.2.0-7ubuntu1) ... 954s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 954s Preparing to unpack .../064-gcc-14-x86-64-linux-gnu_14.2.0-7ubuntu1_amd64.deb ... 954s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 954s Selecting previously unselected package gcc-14. 954s Preparing to unpack .../065-gcc-14_14.2.0-7ubuntu1_amd64.deb ... 954s Unpacking gcc-14 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Selecting previously unselected package g++-x86-64-linux-gnu. 955s Preparing to unpack .../071-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 955s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 955s Selecting previously unselected package g++. 955s Preparing to unpack .../072-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 955s Unpacking g++ (4:14.1.0-2ubuntu1) ... 955s Selecting previously unselected package build-essential. 955s Preparing to unpack .../073-build-essential_12.10ubuntu1_amd64.deb ... 955s Unpacking build-essential (12.10ubuntu1) ... 955s Selecting previously unselected package bwa. 955s Preparing to unpack .../074-bwa_0.7.17-7_amd64.deb ... 955s Unpacking bwa (0.7.17-7) ... 955s Selecting previously unselected package libargtable2-0. 955s Preparing to unpack .../075-libargtable2-0_13-2_amd64.deb ... 955s Unpacking libargtable2-0 (13-2) ... 955s Selecting previously unselected package clustalo. 955s Preparing to unpack .../076-clustalo_1.2.4-8build1_amd64.deb ... 955s Unpacking clustalo (1.2.4-8build1) ... 955s Selecting previously unselected package clustalw. 955s Preparing to unpack .../077-clustalw_2.1+lgpl-7_amd64.deb ... 955s Unpacking clustalw (2.1+lgpl-7) ... 955s Selecting previously unselected package libdebhelper-perl. 955s Preparing to unpack .../078-libdebhelper-perl_13.20ubuntu1_all.deb ... 955s Unpacking libdebhelper-perl (13.20ubuntu1) ... 955s Selecting previously unselected package libtool. 955s Preparing to unpack .../079-libtool_2.4.7-7build1_all.deb ... 955s Unpacking libtool (2.4.7-7build1) ... 955s Selecting previously unselected package dh-autoreconf. 955s Preparing to unpack .../080-dh-autoreconf_20_all.deb ... 955s Unpacking dh-autoreconf (20) ... 955s Selecting previously unselected package libarchive-zip-perl. 955s Preparing to unpack .../081-libarchive-zip-perl_1.68-1_all.deb ... 955s Unpacking libarchive-zip-perl (1.68-1) ... 955s Selecting previously unselected package libfile-stripnondeterminism-perl. 955s 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unselected package libxpm4:amd64. 956s Preparing to unpack .../099-libxpm4_1%3a3.5.17-1build2_amd64.deb ... 956s Unpacking libxpm4:amd64 (1:3.5.17-1build2) ... 956s Selecting previously unselected package libgd3:amd64. 956s Preparing to unpack .../100-libgd3_2.3.3-12ubuntu3_amd64.deb ... 956s Unpacking libgd3:amd64 (2.3.3-12ubuntu3) ... 956s Selecting previously unselected package libhpdf-2.3.0:amd64. 956s Preparing to unpack .../101-libhpdf-2.3.0_2.3.0+dfsg-1build3_amd64.deb ... 956s Unpacking libhpdf-2.3.0:amd64 (2.3.0+dfsg-1build3) ... 956s Selecting previously unselected package mysql-common. 956s Preparing to unpack .../102-mysql-common_5.8+1.1.1_all.deb ... 956s Unpacking mysql-common (5.8+1.1.1) ... 956s Selecting previously unselected package libmysqlclient21:amd64. 956s Preparing to unpack .../103-libmysqlclient21_8.0.39-1_amd64.deb ... 956s Unpacking libmysqlclient21:amd64 (8.0.39-1) ... 956s Selecting previously unselected package libpq5:amd64. 956s Preparing to unpack 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package libgs-common. 959s Preparing to unpack .../110-libgs-common_10.03.1~dfsg1-0ubuntu2_all.deb ... 959s Unpacking libgs-common (10.03.1~dfsg1-0ubuntu2) ... 959s Selecting previously unselected package libgs10-common. 960s Preparing to unpack .../111-libgs10-common_10.03.1~dfsg1-0ubuntu2_all.deb ... 960s Unpacking libgs10-common (10.03.1~dfsg1-0ubuntu2) ... 960s Selecting previously unselected package libavahi-common-data:amd64. 960s Preparing to unpack .../112-libavahi-common-data_0.8-13ubuntu6_amd64.deb ... 960s Unpacking libavahi-common-data:amd64 (0.8-13ubuntu6) ... 960s Selecting previously unselected package libavahi-common3:amd64. 960s Preparing to unpack .../113-libavahi-common3_0.8-13ubuntu6_amd64.deb ... 960s Unpacking libavahi-common3:amd64 (0.8-13ubuntu6) ... 960s Selecting previously unselected package libavahi-client3:amd64. 960s Preparing to unpack .../114-libavahi-client3_0.8-13ubuntu6_amd64.deb ... 960s Unpacking libavahi-client3:amd64 (0.8-13ubuntu6) ... 960s Selecting previously unselected package libcups2t64:amd64. 960s Preparing to unpack .../115-libcups2t64_2.4.10-1ubuntu2_amd64.deb ... 960s Unpacking libcups2t64:amd64 (2.4.10-1ubuntu2) ... 960s Selecting previously unselected package libidn12:amd64. 960s Preparing to unpack .../116-libidn12_1.42-2_amd64.deb ... 960s Unpacking libidn12:amd64 (1.42-2) ... 960s Selecting previously unselected package libijs-0.35:amd64. 960s Preparing to unpack .../117-libijs-0.35_0.35-15.1build1_amd64.deb ... 960s Unpacking libijs-0.35:amd64 (0.35-15.1build1) ... 960s Selecting previously unselected package libjbig2dec0:amd64. 960s Preparing to unpack .../118-libjbig2dec0_0.20-1build3_amd64.deb ... 960s Unpacking libjbig2dec0:amd64 (0.20-1build3) ... 960s Selecting previously unselected package libpaper1:amd64. 960s Preparing to unpack .../119-libpaper1_1.1.29build1_amd64.deb ... 960s Unpacking libpaper1:amd64 (1.1.29build1) ... 960s Selecting previously unselected package libice6:amd64. 960s Preparing to unpack .../120-libice6_2%3a1.0.10-1build3_amd64.deb ... 960s Unpacking libice6:amd64 (2:1.0.10-1build3) ... 960s Selecting previously unselected package libsm6:amd64. 960s Preparing to unpack .../121-libsm6_2%3a1.2.3-1build3_amd64.deb ... 960s Unpacking libsm6:amd64 (2:1.2.3-1build3) ... 960s Selecting previously unselected package libxt6t64:amd64. 960s Preparing to unpack .../122-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 960s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 960s Selecting previously unselected package libgs10:amd64. 960s Preparing to unpack .../123-libgs10_10.03.1~dfsg1-0ubuntu2_amd64.deb ... 960s Unpacking libgs10:amd64 (10.03.1~dfsg1-0ubuntu2) ... 960s Selecting previously unselected package ghostscript. 960s Preparing to unpack .../124-ghostscript_10.03.1~dfsg1-0ubuntu2_amd64.deb ... 960s Unpacking ghostscript (10.03.1~dfsg1-0ubuntu2) ... 960s Selecting previously unselected package libnetpbm11t64:amd64. 960s Preparing to unpack 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libptexenc1:amd64 (2024.20240313.70630+ds-4) ... 960s Selecting previously unselected package libsynctex2:amd64. 960s Preparing to unpack .../131-libsynctex2_2024.20240313.70630+ds-4_amd64.deb ... 960s Unpacking libsynctex2:amd64 (2024.20240313.70630+ds-4) ... 960s Selecting previously unselected package libtexlua53-5:amd64. 960s Preparing to unpack .../132-libtexlua53-5_2024.20240313.70630+ds-4_amd64.deb ... 960s Unpacking libtexlua53-5:amd64 (2024.20240313.70630+ds-4) ... 960s Selecting previously unselected package t1utils. 960s Preparing to unpack .../133-t1utils_1.41-4build3_amd64.deb ... 960s Unpacking t1utils (1.41-4build3) ... 960s Selecting previously unselected package libpixman-1-0:amd64. 960s Preparing to unpack .../134-libpixman-1-0_0.42.2-1build1_amd64.deb ... 960s Unpacking libpixman-1-0:amd64 (0.42.2-1build1) ... 960s Selecting previously unselected package libxcb-render0:amd64. 960s Preparing to unpack .../135-libxcb-render0_1.17.0-2_amd64.deb ... 960s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 960s Selecting previously unselected package libxcb-shm0:amd64. 960s Preparing to unpack .../136-libxcb-shm0_1.17.0-2_amd64.deb ... 960s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 961s Selecting previously unselected package libcairo2:amd64. 961s Preparing to unpack .../137-libcairo2_1.18.2-2_amd64.deb ... 961s Unpacking libcairo2:amd64 (1.18.2-2) ... 961s Selecting previously unselected package libmpfi0:amd64. 961s Preparing to unpack .../138-libmpfi0_1.5.4+ds-3_amd64.deb ... 961s Unpacking libmpfi0:amd64 (1.5.4+ds-3) ... 961s Selecting previously unselected package libpotrace0:amd64. 961s Preparing to unpack .../139-libpotrace0_1.16-2build1_amd64.deb ... 961s Unpacking libpotrace0:amd64 (1.16-2build1) ... 961s Selecting previously unselected package libteckit0:amd64. 961s Preparing to unpack .../140-libteckit0_2.5.12+ds1-1_amd64.deb ... 961s Unpacking libteckit0:amd64 (2.5.12+ds1-1) ... 961s Selecting previously unselected package libxmu6:amd64. 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Unpacking hevea (2.36-2) ... 962s Selecting previously unselected package libllvm17t64:amd64. 962s Preparing to unpack .../152-libllvm17t64_1%3a17.0.6-18_amd64.deb ... 962s Unpacking libllvm17t64:amd64 (1:17.0.6-18) ... 963s Selecting previously unselected package libamd-comgr2:amd64. 963s Preparing to unpack .../153-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 963s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 963s Selecting previously unselected package libdrm-amdgpu1:amd64. 963s Preparing to unpack .../154-libdrm-amdgpu1_2.4.122-1_amd64.deb ... 963s Unpacking libdrm-amdgpu1:amd64 (2.4.122-1) ... 963s Selecting previously unselected package libhsakmt1:amd64. 963s Preparing to unpack .../155-libhsakmt1_5.7.0-1build1_amd64.deb ... 963s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 963s Selecting previously unselected package libhsa-runtime64-1. 963s Preparing to unpack .../156-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 963s Unpacking 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Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 964s Preparing to unpack .../162-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 964s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 964s Selecting previously unselected package libexpat1-dev:amd64. 964s Preparing to unpack .../163-libexpat1-dev_2.6.2-2_amd64.deb ... 964s Unpacking libexpat1-dev:amd64 (2.6.2-2) ... 964s Selecting previously unselected package libpsm-infinipath1. 964s Preparing to unpack .../164-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 964s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 964s Selecting previously unselected package libpsm2-2. 964s Preparing to unpack .../165-libpsm2-2_11.2.185-2.1_amd64.deb ... 964s Unpacking libpsm2-2 (11.2.185-2.1) ... 964s Selecting previously unselected package librdmacm1t64:amd64. 964s Preparing to unpack .../166-librdmacm1t64_52.0-2ubuntu1_amd64.deb ... 964s Unpacking librdmacm1t64:amd64 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package libjs-jquery. 964s Preparing to unpack .../172-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 964s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 964s Selecting previously unselected package libjs-jquery-ui. 964s Preparing to unpack .../173-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 964s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 964s Selecting previously unselected package libjs-underscore. 964s Preparing to unpack .../174-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 964s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 964s Selecting previously unselected package libjs-sphinxdoc. 964s Preparing to unpack .../175-libjs-sphinxdoc_7.4.7-3_all.deb ... 964s Unpacking libjs-sphinxdoc (7.4.7-3) ... 964s Selecting previously unselected package liblapack3:amd64. 964s Preparing to unpack .../176-liblapack3_3.12.0-3build2_amd64.deb ... 964s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 964s Selecting previously unselected package liblbfgsb0:amd64. 964s Preparing to unpack .../177-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 964s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 964s Selecting previously unselected package libmbedcrypto7t64:amd64. 964s Preparing to unpack .../178-libmbedcrypto7t64_2.28.8-1_amd64.deb ... 964s Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ... 964s Selecting previously unselected package libmbedx509-1t64:amd64. 964s Preparing to unpack .../179-libmbedx509-1t64_2.28.8-1_amd64.deb ... 964s Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ... 964s Selecting previously unselected package libmbedtls14t64:amd64. 964s Preparing to unpack .../180-libmbedtls14t64_2.28.8-1_amd64.deb ... 964s Unpacking libmbedtls14t64:amd64 (2.28.8-1) ... 964s Selecting previously unselected package libmunge2:amd64. 964s Preparing to unpack .../181-libmunge2_0.5.15-4build1_amd64.deb ... 964s Unpacking libmunge2:amd64 (0.5.15-4build1) ... 964s Selecting previously unselected package libpciaccess0:amd64. 964s Preparing to unpack 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unselected package phylip. 966s Preparing to unpack .../203-phylip_1%3a3.697+dfsg-4build1_amd64.deb ... 966s Unpacking phylip (1:3.697+dfsg-4build1) ... 966s Selecting previously unselected package phyml. 966s Preparing to unpack .../204-phyml_3%3a3.3.20220408-3build3_amd64.deb ... 966s Unpacking phyml (3:3.3.20220408-3build3) ... 966s Selecting previously unselected package prank. 966s Preparing to unpack .../205-prank_0.0.170427+dfsg-3_amd64.deb ... 966s Unpacking prank (0.0.170427+dfsg-3) ... 966s Selecting previously unselected package preview-latex-style. 966s Preparing to unpack .../206-preview-latex-style_13.2-1_all.deb ... 966s Unpacking preview-latex-style (13.2-1) ... 966s Selecting previously unselected package probcons. 966s Preparing to unpack .../207-probcons_1.12-14_amd64.deb ... 966s Unpacking probcons (1.12-14) ... 966s Selecting previously unselected package python-biopython-doc. 966s Preparing to unpack .../208-python-biopython-doc_1.83+dfsg1-3_all.deb ... 966s Unpacking python-biopython-doc (1.83+dfsg1-3) ... 966s Selecting previously unselected package python-matplotlib-data. 966s Preparing to unpack .../209-python-matplotlib-data_3.8.3-3_all.deb ... 966s Unpacking python-matplotlib-data (3.8.3-3) ... 966s Selecting previously unselected package python3-all. 966s Preparing to unpack .../210-python3-all_3.12.6-0ubuntu1_amd64.deb ... 966s Unpacking python3-all (3.12.6-0ubuntu1) ... 966s Selecting previously unselected package python3.12-dev. 966s Preparing to unpack .../211-python3.12-dev_3.12.7-1_amd64.deb ... 966s Unpacking python3.12-dev (3.12.7-1) ... 966s Selecting previously unselected package python3-dev. 966s Preparing to unpack .../212-python3-dev_3.12.6-0ubuntu1_amd64.deb ... 966s Unpacking python3-dev (3.12.6-0ubuntu1) ... 966s Selecting previously unselected package python3-all-dev. 966s Preparing to unpack .../213-python3-all-dev_3.12.6-0ubuntu1_amd64.deb ... 966s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 966s Selecting previously unselected package python3-appdirs. 966s Preparing to unpack .../214-python3-appdirs_1.4.4-4_all.deb ... 966s Unpacking python3-appdirs (1.4.4-4) ... 966s Selecting previously unselected package python3-numpy. 966s Preparing to unpack .../215-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 966s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 967s Selecting previously unselected package python3.12-tk. 967s Preparing to unpack .../216-python3.12-tk_3.12.7-1_amd64.deb ... 967s Unpacking python3.12-tk (3.12.7-1) ... 967s Selecting previously unselected package python3-tk:amd64. 967s Preparing to unpack .../217-python3-tk_3.12.6-1ubuntu1_amd64.deb ... 967s Unpacking python3-tk:amd64 (3.12.6-1ubuntu1) ... 967s Selecting previously unselected package python3-pil.imagetk:amd64. 967s Preparing to unpack .../218-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 967s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 967s Selecting previously unselected package 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xml-core (0.19) ... 967s Selecting previously unselected package w3c-sgml-lib. 967s Preparing to unpack .../225-w3c-sgml-lib_1.3-3_all.deb ... 967s Unpacking w3c-sgml-lib (1.3-3) ... 967s Selecting previously unselected package python3-biopython. 967s Preparing to unpack .../226-python3-biopython_1.83+dfsg1-3_amd64.deb ... 967s Unpacking python3-biopython (1.83+dfsg1-3) ... 967s Selecting previously unselected package python3-biopython-sql. 967s Preparing to unpack .../227-python3-biopython-sql_1.83+dfsg1-3_all.deb ... 967s Unpacking python3-biopython-sql (1.83+dfsg1-3) ... 967s Selecting previously unselected package python3-brotli. 967s Preparing to unpack .../228-python3-brotli_1.1.0-2build2_amd64.deb ... 967s Unpacking python3-brotli (1.1.0-2build2) ... 967s Selecting previously unselected package python3-contourpy. 967s Preparing to unpack .../229-python3-contourpy_1.2.1-1_amd64.deb ... 967s Unpacking python3-contourpy (1.2.1-1) ... 967s Selecting previously unselected package python3-cycler. 967s Preparing to unpack .../230-python3-cycler_0.12.1-1_all.deb ... 967s Unpacking python3-cycler (0.12.1-1) ... 967s Selecting previously unselected package python3-six. 967s Preparing to unpack .../231-python3-six_1.16.0-7_all.deb ... 967s Unpacking python3-six (1.16.0-7) ... 967s Selecting previously unselected package python3-dateutil. 967s Preparing to unpack .../232-python3-dateutil_2.9.0-2_all.deb ... 967s Unpacking python3-dateutil (2.9.0-2) ... 967s Selecting previously unselected package python3-decorator. 968s Preparing to unpack .../233-python3-decorator_5.1.1-5_all.deb ... 968s Unpacking python3-decorator (5.1.1-5) ... 968s Selecting previously unselected package python3-scipy. 968s Preparing to unpack .../234-python3-scipy_1.13.1-3_amd64.deb ... 968s Unpacking python3-scipy (1.13.1-3) ... 968s Selecting previously unselected package python3-ufolib2. 968s Preparing to unpack .../235-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 968s Unpacking python3-ufolib2 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python3-packaging (24.1-1) ... 969s Selecting previously unselected package python3-matplotlib. 969s Preparing to unpack .../247-python3-matplotlib_3.8.3-3_amd64.deb ... 969s Unpacking python3-matplotlib (3.8.3-3) ... 969s Selecting previously unselected package python3-msgpack. 969s Preparing to unpack .../248-python3-msgpack_1.0.3-3build2_amd64.deb ... 969s Unpacking python3-msgpack (1.0.3-3build2) ... 969s Selecting previously unselected package python3-mmtf. 969s Preparing to unpack .../249-python3-mmtf_1.1.3-1_all.deb ... 969s Unpacking python3-mmtf (1.1.3-1) ... 969s Selecting previously unselected package python3-mysqldb. 969s Preparing to unpack .../250-python3-mysqldb_1.4.6-2build3_amd64.deb ... 969s Unpacking python3-mysqldb (1.4.6-2build3) ... 969s Selecting previously unselected package python3-networkx. 969s Preparing to unpack .../251-python3-networkx_3.2.1-4ubuntu1_all.deb ... 969s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 970s Selecting previously unselected 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libdrm-amdgpu1:amd64 (2.4.122-1) ... 979s Setting up libpotrace0:amd64 (1.16-2build1) ... 979s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 979s Setting up automake (1:1.16.5-1.3ubuntu1) ... 979s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 979s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 979s Setting up libfabric1:amd64 (1.17.0-3ubuntu1) ... 979s Setting up python3-sympy (1.13.1-1) ... 985s Setting up libice6:amd64 (2:1.0.10-1build3) ... 985s Setting up flex (2.6.4-8.2build1) ... 985s Setting up liblapack3:amd64 (3.12.0-3build2) ... 985s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 985s Setting up gettext (0.22.5-2) ... 985s Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... 985s Setting up libpdfbox-java (1:1.8.16-5) ... 985s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 985s Setting up wise (2.4.1-25) ... 985s Setting up preview-latex-style (13.2-1) ... 985s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 985s Setting up libcommons-parent-java (56-1) ... 985s Setting up libavahi-common3:amd64 (0.8-13ubuntu6) ... 985s Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... 985s Setting up libpython3.12-dev:amd64 (3.12.7-1) ... 985s Setting up clustalo (1.2.4-8build1) ... 985s Setting up xfonts-utils (1:7.7+7) ... 985s Setting up libhwloc-plugins:amd64 (2.11.0-2) ... 985s Setting up samtools (1.20-3) ... 985s Setting up intltool-debian (0.35.0+20060710.6) ... 985s Setting up python3-fs (2.4.16-4) ... 985s Setting up libcifpp5:amd64 (5.0.7.1-3build1) ... 985s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 985s Setting up libptexenc1:amd64 (2024.20240313.70630+ds-4) ... 985s Setting up libraqm0:amd64 (0.10.1-1build1) ... 985s Setting up python3.12-dev (3.12.7-1) ... 985s Setting up cpp-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 985s Setting up libpmix2t64:amd64 (5.0.3-2) ... 985s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 987s Setting up libjs-sphinxdoc (7.4.7-3) ... 987s Setting up libraw23t64:amd64 (0.21.2-2.1build1) ... 987s Setting up cpp-14 (14.2.0-7ubuntu1) ... 987s Setting up dh-strip-nondeterminism (1.14.0-1) ... 987s Setting up libmbedtls14t64:amd64 (2.28.8-1) ... 987s Setting up python3-lxml:amd64 (5.3.0-1) ... 987s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 987s Setting up xml-core (0.19) ... 987s Setting up python3-contourpy (1.2.1-1) ... 987s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 987s Setting up libgcc-14-dev:amd64 (14.2.0-7ubuntu1) ... 987s Setting up libstdc++-14-dev:amd64 (14.2.0-7ubuntu1) ... 987s Setting up libsm6:amd64 (2:1.2.3-1build3) ... 987s Setting up libavahi-client3:amd64 (0.8-13ubuntu6) ... 987s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 987s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 987s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 987s Setting up libxft2:amd64 (2.3.6-1build1) ... 987s Setting up python3-scipy (1.13.1-3) ... 991s Setting up libpython3-dev:amd64 (3.12.6-0ubuntu1) ... 991s Setting up po-debconf (1.0.21+nmu1) ... 991s Setting up libtk8.6:amd64 (8.6.14-1build1) ... 991s Setting up python3.12-tk (3.12.7-1) ... 991s Setting up python3-mmtf (1.1.3-1) ... 991s Setting up fonts-urw-base35 (20200910-8) ... 991s Setting up dssp (4.2.2-2) ... 991s Setting up libcairo2:amd64 (1.18.2-2) ... 991s Setting up ncbi-blast+ (2.16.0+ds-6) ... 991s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 991s Setting up libpython3-all-dev:amd64 (3.12.6-0ubuntu1) ... 991s Setting up python3-dev (3.12.6-0ubuntu1) ... 991s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 991s Setting up netpbm (2:11.07.00-2) ... 991s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 991s Setting up cpp (4:14.1.0-2ubuntu1) ... 991s Setting up gcc-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 991s Setting up libcups2t64:amd64 (2.4.10-1ubuntu2) ... 991s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 991s Setting up libgs10-common (10.03.1~dfsg1-0ubuntu2) ... 991s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 991s Setting up libxmu6:amd64 (2:1.1.3-3build2) ... 991s Setting up python3-cairo (1.26.1-2) ... 991s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 991s Setting up blt (2.5.3+dfsg-7build1) ... 991s Setting up python3-tk:amd64 (3.12.6-1ubuntu1) ... 991s Setting up libxaw7:amd64 (2:1.0.14-1build2) ... 991s Setting up gcc-14 (14.2.0-7ubuntu1) ... 991s Setting up libamdhip64-5 (5.7.1-4build1) ... 991s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 992s Setting up python3-rlpycairo (0.3.0-3) ... 992s Setting up g++-14-x86-64-linux-gnu (14.2.0-7ubuntu1) ... 992s Setting up python3-reportlab (4.2.2-1) ... 992s Setting up texlive-binaries (2024.20240313.70630+ds-4) ... 992s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode 992s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode 992s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 992s Setting up g++-14 (14.2.0-7ubuntu1) ... 992s Setting up texlive-base (2024.20240706-1) ... 993s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps 993s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg 994s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper 994s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex 994s Setting up libgs10:amd64 (10.03.1~dfsg1-0ubuntu2) ... 994s Setting up libucx0:amd64 (1.17.0+ds-3build1) ... 994s Setting up libtool (2.4.7-7build1) ... 994s Setting up ghostscript (10.03.1~dfsg1-0ubuntu2) ... 994s Setting up gcc (4:14.1.0-2ubuntu1) ... 994s Setting up dh-autoreconf (20) ... 994s Setting up texlive-latex-base (2024.20240706-1) ... 994s Setting up texlive-latex-recommended (2024.20240706-1) ... 994s Setting up texlive-pictures (2024.20240706-1) ... 994s Setting up libopenmpi3t64:amd64 (4.1.6-13.3ubuntu2) ... 994s Setting up g++ (4:14.1.0-2ubuntu1) ... 994s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 994s Setting up texlive-fonts-recommended (2024.20240706-1) ... 994s Setting up build-essential (12.10ubuntu1) ... 994s Setting up openmpi-bin (4.1.6-13.3ubuntu2) ... 994s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 994s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 994s Setting up phyml (3:3.3.20220408-3build3) ... 994s Setting up debhelper (13.20ubuntu1) ... 994s Setting up texlive-latex-extra (2024.20240706-2) ... 994s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 995s Setting up libheif-plugin-aomdec:amd64 (1.18.1-2) ... 995s Setting up libheif-plugin-libde265:amd64 (1.18.1-2) ... 995s Setting up libheif1:amd64 (1.18.1-2) ... 995s Setting up libmagickcore-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 995s Setting up python3-fonttools (4.46.0-1build2) ... 995s Setting up libmagickwand-6.q16-7t64:amd64 (8:6.9.13.12+dfsg1-1build1) ... 995s Setting up libgd3:amd64 (2.3.3-12ubuntu3) ... 995s Setting up imagemagick-6.q16 (8:6.9.13.12+dfsg1-1build1) ... 995s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode 995s update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode 995s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode 995s update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode 995s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode 995s update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode 995s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode 995s update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode 995s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode 995s update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode 995s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode 995s update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode 995s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode 995s update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode 995s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode 995s update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode 995s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode 995s update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode 995s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode 995s update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode 995s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode 995s update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode 995s Setting up emboss-lib (6.6.0+dfsg-12ubuntu2) ... 995s Setting up python3-matplotlib (3.8.3-3) ... 997s Setting up emboss (6.6.0+dfsg-12ubuntu2) ... 997s Setting up hevea (2.36-2) ... 997s Setting up imagemagick (8:6.9.13.12+dfsg1-1build1) ... 997s Processing triggers for install-info (7.1.1-1) ... 997s Processing triggers for libc-bin (2.40-1ubuntu3) ... 997s Processing triggers for man-db (2.12.1-3) ... 999s Processing triggers for shared-mime-info (2.4-5) ... 999s Processing triggers for sgml-base (1.31) ... 999s Setting up w3c-sgml-lib (1.3-3) ... 1026s Setting up python3-biopython (1.83+dfsg1-3) ... 1027s Setting up python3-biopython-sql (1.83+dfsg1-3) ... 1027s Setting up autopkgtest-satdep (0) ... 1027s Processing triggers for tex-common (6.18) ... 1028s Running updmap-sys. This may take some time... done. 1028s Running mktexlsr /var/lib/texmf ... done. 1028s Building format(s) --all. 1085s This may take some time... done. 1092s (Reading database ... 120845 files and directories currently installed.) 1092s Removing autopkgtest-satdep (0) ... 1095s autopkgtest [10:24:05]: test full_suite: sh debian/tests/run-unit-test 1095s autopkgtest [10:24:05]: test full_suite: [----------------------- 1096s mkdir: created directory 'Bio' 1096s mkdir: created directory 'Bio/Align' 1096s mkdir: created directory 'Bio/Align/substitution_matrices' 1096s mkdir: created directory 'Bio/Align/substitution_matrices/data/' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER22' -> 'Bio/Align/substitution_matrices/data/BENNER22' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER6' -> 'Bio/Align/substitution_matrices/data/BENNER6' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BENNER74' -> 'Bio/Align/substitution_matrices/data/BENNER74' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTN' -> 'Bio/Align/substitution_matrices/data/BLASTN' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLASTP' -> 'Bio/Align/substitution_matrices/data/BLASTP' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM45' -> 'Bio/Align/substitution_matrices/data/BLOSUM45' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM50' -> 'Bio/Align/substitution_matrices/data/BLOSUM50' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM62' -> 'Bio/Align/substitution_matrices/data/BLOSUM62' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM80' -> 'Bio/Align/substitution_matrices/data/BLOSUM80' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/BLOSUM90' -> 'Bio/Align/substitution_matrices/data/BLOSUM90' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/DAYHOFF' -> 'Bio/Align/substitution_matrices/data/DAYHOFF' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/FENG' -> 'Bio/Align/substitution_matrices/data/FENG' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GENETIC' -> 'Bio/Align/substitution_matrices/data/GENETIC' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/GONNET1992' -> 'Bio/Align/substitution_matrices/data/GONNET1992' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/HOXD70' -> 'Bio/Align/substitution_matrices/data/HOXD70' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JOHNSON' -> 'Bio/Align/substitution_matrices/data/JOHNSON' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/JONES' -> 'Bio/Align/substitution_matrices/data/JONES' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/LEVIN' -> 'Bio/Align/substitution_matrices/data/LEVIN' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MCLACHLAN' -> 'Bio/Align/substitution_matrices/data/MCLACHLAN' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MDM78' -> 'Bio/Align/substitution_matrices/data/MDM78' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/MEGABLAST' -> 'Bio/Align/substitution_matrices/data/MEGABLAST' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/NUC.4.4' -> 'Bio/Align/substitution_matrices/data/NUC.4.4' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM250' -> 'Bio/Align/substitution_matrices/data/PAM250' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM30' -> 'Bio/Align/substitution_matrices/data/PAM30' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/PAM70' -> 'Bio/Align/substitution_matrices/data/PAM70' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RAO' -> 'Bio/Align/substitution_matrices/data/RAO' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/RISLER' -> 'Bio/Align/substitution_matrices/data/RISLER' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/SCHNEIDER' -> 'Bio/Align/substitution_matrices/data/SCHNEIDER' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/STR' -> 'Bio/Align/substitution_matrices/data/STR' 1096s '/usr/lib/python3/dist-packages/Bio/Align/substitution_matrices/data/TRANS' -> 'Bio/Align/substitution_matrices/data/TRANS' 1096s Remove test test_Tutorial.py which is bound to fail 1097s test_Ace ... ok 1097s test_Affy ... ok 1100s test_AlignIO ... ok 1100s test_AlignIO_ClustalIO ... ok 1100s test_AlignIO_EmbossIO ... ok 1100s test_AlignIO_FastaIO ... ok 1100s test_AlignIO_MauveIO ... ok 1100s test_AlignIO_PhylipIO ... ok 1100s test_AlignIO_convert ... ok 1100s test_AlignInfo ... ok 1100s test_Align_Alignment ... ok 1100s test_Align_a2m ... ok 1100s test_Align_bed ... ok 1100s test_Align_bigbed ... ok 1101s test_Align_bigmaf ... ok 1101s test_Align_bigpsl ... ok 1101s test_Align_chain ... ok 1101s test_Align_clustal ... ok 1106s test_Align_codonalign ... ok 1107s test_Align_emboss ... ok 1107s test_Align_exonerate ... ok 1107s test_Align_fasta ... ok 1107s test_Align_hhr ... ok 1107s test_Align_maf ... ok 1107s test_Align_mauve ... ok 1108s test_Align_msf ... ok 1108s test_Align_nexus ... ok 1108s test_Align_phylip ... ok 1108s test_Align_psl ... ok 1108s test_Align_sam ... ok 1110s test_Align_stockholm ... ok 1110s test_Align_tabular ... ok 1110s test_Application ... ok 1111s test_BWA_tool ... ok 1111s test_BioSQL_MySQLdb_online ... skipping. internet not available 1111s test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) 1111s test_BioSQL_mysql_connector_online ... skipping. internet not available 1111s test_BioSQL_psycopg2_online ... skipping. internet not available 1116s test_BioSQL_sqlite3 ... ok 1116s test_BioSQL_sqlite3_online ... skipping. internet not available 1116s test_Blast_Record ... ok 1116s test_CAPS ... ok 1116s test_Chi2 ... ok 1117s test_ClustalOmega_tool ... ok 1117s test_Clustalw_tool ... ok 1118s test_Cluster ... ok 1118s test_CodonTable ... ok 1118s test_ColorSpiral ... ok 1118s test_Compass ... ok 1119s test_Consensus ... ok 1120s test_Dialign_tool ... ok 1120s test_EMBL_unittest ... ok 1127s test_Emboss ... ok 1127s test_EmbossPrimer ... ok 1131s test_Entrez ... ok 1131s test_Entrez_online ... skipping. internet not available 1131s test_Entrez_parser ... ok 1132s test_Enzyme ... ok 1132s test_ExPASy ... skipping. internet not available 1132s test_Fasttree_tool ... ok 1132s test_File ... ok 1132s test_GenBank ... ok 1134s test_GenomeDiagram ... Warn: Can't find .pfb for face 'Helvetica' 1136s ok 1137s test_GraphicsChromosome ... ok 1137s test_GraphicsDistribution ... ok 1138s test_GraphicsGeneral ... ok 1138s test_HMMCasino ... ok 1138s test_HMMGeneral ... ok 1138s test_KEGG ... ok 1138s test_KEGG_online ... skipping. internet not available 1143s test_KGML_graphics ... ok 1144s test_KGML_graphics_online ... skipping. internet not available 1144s test_KGML_nographics ... ok 1144s test_KeyWList ... ok 1145s test_LogisticRegression ... ok 1145s test_MafIO_index ... ok 1147s test_Mafft_tool ... ok 1147s test_MarkovModel ... ok 1147s test_Medline ... ok 1147s test_Muscle_tool ... ok 1148s test_NCBIXML ... ok 1150s test_NCBI_BLAST_tools ... ok 1150s test_NCBI_qblast ... ok 1150s test_NMR ... ok 1150s test_NaiveBayes ... ok 1150s test_Nexus ... ok 1150s test_PAML_baseml ... ok 1151s test_PAML_codeml ... ok 1151s test_PAML_yn00 ... ok 1151s test_PDBList ... skipping. internet not available 1153s test_PDB_CEAligner ... ok 1155s test_PDB_DSSP ... ok 1155s test_PDB_Dice ... ok 1155s test_PDB_Disordered ... ok 1155s test_PDB_Exposure ... ok 1156s test_PDB_FragmentMapper ... ok 1157s test_PDB_KDTree ... ok 1157s test_PDB_MMCIF2Dict ... ok 1157s test_PDB_MMCIFIO ... ok 1159s test_PDB_MMCIFParser ... ok 1159s test_PDB_NACCESS ... ok 1159s test_PDB_PDBIO ... ok 1159s test_PDB_PDBParser ... ok 1159s 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 1159s test_PDB_Polypeptide ... ok 1159s test_PDB_QCPSuperimposer ... ok 1162s test_PDB_SASA ... ok 1163s test_PDB_SMCRA ... ok 1163s test_PDB_Selection ... ok 1163s test_PDB_StructureAlignment ... ok 1163s test_PDB_Superimposer ... ok 1172s test_PDB_internal_coords ... ok 1172s test_PDB_parse_pdb_header ... ok 1172s test_PDB_vectors ... ok 1172s test_PQR ... ok 1173s test_Pathway ... ok 1173s test_Phd ... ok 1173s test_Phylo ... ok 1174s test_PhyloXML ... ok 1174s test_Phylo_CDAO ... ok 1175s test_Phylo_NeXML ... ok 1178s test_Phylo_matplotlib ... ok 1178s test_Phylo_networkx ... ok 1179s test_PopGen_GenePop_nodepend ... ok 1180s test_Prank_tool ... ok 1181s test_Probcons_tool ... ok 1181s test_ProtParam ... ok 1182s test_RCSBFormats ... ok 1183s test_Restriction ... ok 1183s test_SCOP_Astral ... ok 1183s test_SCOP_Cla ... ok 1184s test_SCOP_Des ... ok 1184s test_SCOP_Dom ... ok 1185s test_SCOP_Hie ... ok 1185s test_SCOP_Raf ... ok 1186s test_SCOP_Residues ... ok 1186s test_SCOP_Scop ... ok 1186s test_SCOP_online ... skipping. internet not available 1187s test_SVDSuperimposer ... ok 1187s test_SearchIO_blast_tab ... ok 1188s test_SearchIO_blast_tab_index ... ok 1188s test_SearchIO_blast_xml ... ok 1190s test_SearchIO_blast_xml_index ... ok 1190s test_SearchIO_blat_psl ... ok 1191s test_SearchIO_blat_psl_index ... ok 1191s test_SearchIO_exonerate ... ok 1192s test_SearchIO_exonerate_text_index ... ok 1192s test_SearchIO_exonerate_vulgar_index ... ok 1192s test_SearchIO_fasta_m10 ... ok 1193s test_SearchIO_fasta_m10_index ... ok 1194s test_SearchIO_hhsuite2_text ... ok 1194s test_SearchIO_hmmer2_text ... ok 1194s test_SearchIO_hmmer2_text_index ... ok 1195s test_SearchIO_hmmer3_domtab ... ok 1195s test_SearchIO_hmmer3_domtab_index ... ok 1196s test_SearchIO_hmmer3_tab ... ok 1196s test_SearchIO_hmmer3_tab_index ... ok 1196s test_SearchIO_hmmer3_text ... ok 1197s test_SearchIO_hmmer3_text_index ... ok 1197s test_SearchIO_interproscan_xml ... ok 1198s test_SearchIO_model ... ok 1198s test_SearchIO_write ... ok 1199s test_SeqFeature ... /usr/lib/python3/dist-packages/Bio/SeqFeature.py:1040: BiopythonParserWarning: Attempting to fix invalid location '3..2' as it looks like incorrect origin wrapping. Please fix input file, this could have unintended behavior. 1199s warnings.warn( 1199s ok 1215s test_SeqIO ... ok 1215s test_SeqIO_AbiIO ... ok 1216s test_SeqIO_FastaIO ... ok 1216s test_SeqIO_Gck ... ok 1217s test_SeqIO_Insdc ... ok 1217s test_SeqIO_NibIO ... ok 1219s test_SeqIO_PdbIO ... ok 1220s test_SeqIO_QualityIO ... ok 1220s test_SeqIO_SeqXML ... ok 1221s test_SeqIO_SnapGene ... ok 1222s test_SeqIO_TwoBitIO ... ok 1223s test_SeqIO_Xdna ... ok 1223s test_SeqIO_features ... /usr/lib/python3/dist-packages/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line 1223s warnings.warn( 1223s ok 1238s test_SeqIO_index ... ok 1238s test_SeqIO_online ... skipping. internet not available 1238s test_SeqIO_write ... ok 1239s test_SeqRecord ... ok 1239s test_SeqUtils ... ok 1241s test_Seq_objs ... ok 1241s test_SffIO ... ok 1242s test_SwissProt ... ok 1245s test_TCoffee_tool ... ok 1246s test_TogoWS ... skipping. internet not available 1246s test_TreeConstruction ... ok 1247s test_UniGene ... ok 1247s test_UniProt_GOA ... ok 1248s test_Uniprot ... ok 1248s test_align ... ok 1249s test_align_substitution_matrices ... ok 1252s test_bgzf ... ok 1252s test_cellosaurus ... ok 1258s test_codonalign ... ok 1258s test_geo ... ok 1259s test_kNN ... ok 1259s test_motifs ... ok 1260s test_motifs_online ... skipping. internet not available 1260s 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. 1260s warnings.warn( 1260s ok 1261s test_pairwise2_no_C ... ok 1261s test_pairwise_aligner ... ok 1262s test_pairwise_alignment_map ... ok 1270s test_phenotype ... ok 1270s test_phenotype_fit ... ok 1271s test_phyml_tool ... ok 1271s test_prodoc ... ok 1272s test_prosite ... ok 1272s test_raxml_tool ... ok 1273s test_samtools_tool ... ok 1273s test_seq ... ok 1274s test_translate ... ok 1274s Skipping any tests requiring internet access 1274s Python version: 3.12.7 (main, Oct 3 2024, 15:15:22) [GCC 14.2.0] 1274s Operating system: posix linux 1274s ---------------------------------------------------------------------- 1274s Ran 212 tests in 177.416 seconds 1274s 1276s autopkgtest [10:27:06]: test full_suite: -----------------------] 1276s full_suite PASS 1276s autopkgtest [10:27:06]: test full_suite: - - - - - - - - - - results - - - - - - - - - - 1276s autopkgtest [10:27:06]: @@@@@@@@@@@@@@@@@@@@ summary 1276s dependencies PASS 1276s full_suite PASS 1286s nova [W] Skipping flock for amd64 1286s Creating nova instance adt-plucky-amd64-python-biopython-20241030-100549-juju-7f2275-prod-proposed-migration-environment-15-bcb38b63-e53e-4bbc-9035-bdbd6cd2b2a9 from image adt/ubuntu-plucky-amd64-server-20241029.img (UUID 38cf62dc-8d54-4e4f-bcab-db8084c89f55)... 1286s nova [W] Skipping flock for amd64 1286s Creating nova instance adt-plucky-amd64-python-biopython-20241030-100549-juju-7f2275-prod-proposed-migration-environment-15-bcb38b63-e53e-4bbc-9035-bdbd6cd2b2a9 from image adt/ubuntu-plucky-amd64-server-20241029.img (UUID 38cf62dc-8d54-4e4f-bcab-db8084c89f55)...