0s autopkgtest [02:08:59]: starting date: 2024-03-18 0s autopkgtest [02:08:59]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt 0s autopkgtest [02:08:59]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3f7kyb94/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ncbi-blast+,src:mbedtls --apt-upgrade python-pyani --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-5.secgroup --name adt-noble-arm64-python-pyani-20240318-020859-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 65s autopkgtest [02:10:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 65s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 65s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 65s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 66s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 66s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 66s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 66s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 66s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 66s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB] 66s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 66s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 66s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 68s Fetched 9189 kB in 2s (5732 kB/s) 68s Reading package lists... 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 72s Calculating upgrade... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 78s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 79s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 80s Calculating upgrade... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s autopkgtest [02:10:21]: testbed dpkg architecture: arm64 91s autopkgtest [02:10:30]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 91s autopkgtest [02:10:30]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pyani 95s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-pyani 0.2.12-3 (dsc) [2404 B] 95s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-pyani 0.2.12-3 (tar) [49.0 MB] 95s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-pyani 0.2.12-3 (diff) [11.4 kB] 95s gpgv: Signature made Fri Nov 24 20:24:53 2023 UTC 95s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 95s gpgv: issuer "tille@debian.org" 95s gpgv: Can't check signature: No public key 95s dpkg-source: warning: cannot verify inline signature for ./python-pyani_0.2.12-3.dsc: no acceptable signature found 96s autopkgtest [02:10:35]: testing package python-pyani version 0.2.12-3 96s autopkgtest [02:10:35]: build not needed 103s autopkgtest [02:10:42]: test run-unit-test: preparing testbed 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 107s Starting 2 pkgProblemResolver with broken count: 0 107s Done 107s Done 107s Starting pkgProblemResolver with broken count: 0 107s Starting 2 pkgProblemResolver with broken count: 0 107s Done 108s The following additional packages will be installed: 108s blt fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 108s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 108s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 108s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 108s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libmbedcrypto7t64 libmbedtls14t64 108s libmbedx509-1t64 libopenjp2-7 libpixman-1-0 libpython3.11-minimal 108s libpython3.11-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 108s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 108s libxft2 libxrender1 libxslt1.1 libxss1 mummer ncbi-blast+ ncbi-data 108s python-matplotlib-data python3-all python3-appdirs python3-biopython 108s python3-brotli python3-cairo python3-contourpy python3-cycler 108s python3-dateutil python3-decorator python3-distutils python3-fonttools 108s python3-freetype python3-fs python3-iniconfig python3-kiwisolver 108s python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-mpmath 108s python3-numpy python3-packaging python3-pandas python3-pandas-lib 108s python3-pil python3-pil.imagetk python3-pluggy python3-pyani python3-pytest 108s python3-reportlab python3-rlpycairo python3-scipy python3-seaborn 108s python3-setuptools python3-sympy python3-tk python3-ufolib2 108s python3-unicodedata2 python3.11 python3.11-minimal sgml-base tk8.6-blt2.5 108s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 108s Suggested packages: 108s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 108s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 108s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 108s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 108s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 108s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 108s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 108s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 108s texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran python3-dev 108s python-pandas-doc python3-statsmodels python-pil-doc pdf-viewer 108s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 108s python-scipy-doc python-setuptools-doc texlive-fonts-extra python-sympy-doc 108s tix python3-tk-dbg python3.11-venv python3.11-doc binfmt-support 108s sgml-base-doc debhelper 108s Recommended packages: 108s javascript-common python-biopython-doc python3-bs4 python3-cssselect 108s python3-html5lib python3-bottleneck python3-numexpr python3-odf 108s python3-openpyxl python3-tables python3-olefile g++ | c++-compiler 108s python3-patsy isympy-common 108s The following NEW packages will be installed: 108s blt fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 108s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 108s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 108s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 108s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libmbedcrypto7t64 libmbedtls14t64 108s libmbedx509-1t64 libopenjp2-7 libpixman-1-0 libpython3.11-minimal 108s libpython3.11-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 108s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 108s libxft2 libxrender1 libxslt1.1 libxss1 mummer ncbi-blast+ ncbi-data 108s python-matplotlib-data python3-all python3-appdirs python3-biopython 108s python3-brotli python3-cairo python3-contourpy python3-cycler 108s python3-dateutil python3-decorator python3-distutils python3-fonttools 108s python3-freetype python3-fs python3-iniconfig python3-kiwisolver 108s python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-mpmath 108s python3-numpy python3-packaging python3-pandas python3-pandas-lib 108s python3-pil python3-pil.imagetk python3-pluggy python3-pyani python3-pytest 108s python3-reportlab python3-rlpycairo python3-scipy python3-seaborn 108s python3-setuptools python3-sympy python3-tk python3-ufolib2 108s python3-unicodedata2 python3.11 python3.11-minimal sgml-base tk8.6-blt2.5 108s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 108s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 108s 1 not fully installed or removed. 108s Need to get 114 MB of archives. 108s After this operation, 509 MB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 108s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 108s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 108s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 108s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 108s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 108s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 109s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 109s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 109s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 109s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 109s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 109s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 109s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 109s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 109s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 109s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 109s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 109s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 109s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 109s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 109s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 109s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB] 109s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B] 109s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB] 109s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B] 109s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 109s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 109s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 109s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 109s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 109s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 109s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 109s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 109s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 109s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 109s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 109s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 109s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 109s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 109s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 109s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 109s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 109s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 109s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 109s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 109s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 109s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 109s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 109s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 109s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 109s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 109s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 109s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 109s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 109s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 109s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 109s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 109s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 109s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC3-1 [170 kB] 109s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 110s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 110s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB] 110s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B] 110s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB] 110s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 110s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 110s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 110s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 110s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] 110s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB] 110s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 110s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB] 110s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.35-1 [161 kB] 110s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB] 110s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB] 110s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1 [362 kB] 110s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 110s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 110s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 110s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 110s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB] 110s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-1build2 [65.4 kB] 110s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 110s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] 110s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB] 111s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 111s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 111s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-seaborn all 0.13.2-2 [225 kB] 111s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2 [396 kB] 111s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 111s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 111s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB] 111s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB] 111s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB] 111s Get:96 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB] 111s Get:97 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyani arm64 0.2.12-3 [46.6 kB] 111s Get:98 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 111s Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 111s Get:100 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 112s Fetched 114 MB in 4s (32.2 MB/s) 112s Selecting previously unselected package libpython3.11-minimal:arm64. 113s (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 ... 74758 files and directories currently installed.) 113s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ... 113s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 113s Selecting previously unselected package python3.11-minimal. 115s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ... 115s Unpacking python3.11-minimal (3.11.8-1) ... 116s Selecting previously unselected package libpython3.11-stdlib:arm64. 119s 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129s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 129s Setting up liblcms2-2:arm64 (2.14-2) ... 129s Setting up python3-iniconfig (1.1.1-2) ... 129s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 129s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 129s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 129s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 129s Setting up libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 129s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 129s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 130s Setting up libxcb-render0:arm64 (1.15-1) ... 130s Setting up python3-unicodedata2 (15.1.0+ds-1) ... 130s Setting up fonts-lyx (2.4.0~RC3-1) ... 130s Setting up x11-common (1:7.7+23ubuntu2) ... 130s Setting up libdeflate0:arm64 (1.19-1) ... 130s Setting up libqhull-r8.0:arm64 (2020.2-6) ... 130s Setting up libxcb-shm0:arm64 (1.15-1) ... 130s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 130s Setting up python3-freetype (2.4.0-1) ... 130s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 130s Setting up unicode-data (15.1.0-1) ... 130s Setting up python3-decorator (5.1.1-5) ... 130s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 130s Setting up libblas3:arm64 (3.12.0-3) ... 130s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 130s Setting up python3-packaging (23.2-1) ... 130s Setting up python3-brotli (1.1.0-2) ... 131s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 131s Setting up python3-cycler (0.11.0-2) ... 131s Setting up libimagequant0:arm64 (2.18.0-1) ... 131s Setting up fonts-dejavu-mono (2.37-8) ... 131s Setting up python3-kiwisolver (1.4.4-1build2) ... 131s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 131s Setting up fonts-dejavu-core (2.37-8) ... 131s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 131s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 131s Setting up python3-pluggy (1.4.0-1) ... 131s Setting up libwebp7:arm64 (1.3.2-0.4) ... 131s Setting up fonts-dejavu-extra (2.37-8) ... 131s Setting up libxslt1.1:arm64 (1.1.35-1) ... 131s Setting up mummer (3.23+dfsg-8) ... 131s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 131s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 131s Setting up python3-dateutil (2.8.2-3) ... 131s Setting up sgml-base (1.31) ... 131s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 131s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 131s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 131s Setting up python3-mpmath (1.2.1-3) ... 132s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... 132s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 132s Setting up python3-lib2to3 (3.11.5-1) ... 132s Setting up python3-appdirs (1.4.4-4) ... 132s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 132s Setting up python3-distutils (3.11.5-1) ... 132s python3.12: can't get files for byte-compilation 132s Setting up python3.11-minimal (3.11.8-1) ... 133s Setting up python3-sympy (1.12-7) ... 138s Setting up liblapack3:arm64 (3.12.0-3) ... 138s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 138s Setting up libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 138s Setting up python3-setuptools (68.1.2-2) ... 138s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 138s Setting up python3-pytest (7.4.4-1) ... 139s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 139s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 139s Setting up python3-all (3.12.1-0ubuntu2) ... 139s Setting up xfonts-utils (1:7.7+6build2) ... 139s Setting up python3-fs (2.4.16-3) ... 139s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 139s Setting up libraqm0:arm64 (0.10.1-1) ... 139s Setting up libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 139s Setting up python3-lxml:arm64 (5.1.0-1) ... 139s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 139s Setting up xml-core (0.19) ... 139s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 139s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 139s Setting up python3.11 (3.11.8-1) ... 140s Setting up libxft2:arm64 (2.3.6-1) ... 140s Setting up libtk8.6:arm64 (8.6.13-2) ... 140s Setting up fonts-urw-base35 (20200910-8) ... 140s Setting up libcairo2:arm64 (1.18.0-1) ... 140s Setting up ncbi-blast+ (2.12.0+ds-4build1) ... 141s Setting up python3-pil:arm64 (10.2.0-1) ... 141s Setting up python3-numpy (1:1.24.2-2) ... 142s Setting up python3-contourpy (1.0.7-1build2) ... 143s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 143s Setting up python3-scipy (1.11.4-6) ... 145s Setting up python3-cairo (1.25.1-2) ... 145s Setting up blt (2.5.3+dfsg-7) ... 145s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 145s Setting up python3-tk:arm64 (3.11.5-1) ... 146s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 150s Setting up python3-pil.imagetk:arm64 (10.2.0-1) ... 150s Setting up python3-rlpycairo (0.3.0-3) ... 150s Setting up python3-reportlab (4.1.0-1) ... 151s Setting up python3-fonttools (4.46.0-1) ... 152s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 152s Setting up python3-matplotlib (3.6.3-1ubuntu3) ... 153s Setting up python3-seaborn (0.13.2-2) ... 153s Processing triggers for systemd (255.2-3ubuntu2) ... 153s Processing triggers for man-db (2.12.0-3) ... 154s Processing triggers for libc-bin (2.39-0ubuntu2) ... 155s Processing triggers for sgml-base (1.31) ... 155s Setting up w3c-sgml-lib (1.3-3) ... 179s Setting up python3-biopython (1.81+dfsg-3) ... 180s Setting up python3-pyani (0.2.12-3) ... 180s Setting up autopkgtest-satdep (0) ... 185s (Reading database ... 87016 files and directories currently installed.) 185s Removing autopkgtest-satdep (0) ... 186s autopkgtest [02:12:05]: test run-unit-test: [----------------------- 186s Testing with python3.12 in /tmp/autopkgtest.jnK1Ne/build.Kq5/src: 186s ============================= test session starts ============================== 186s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3 186s cachedir: .pytest_cache 186s rootdir: /tmp/autopkgtest.jnK1Ne/build.Kq5/src 190s collecting ... collected 56 items 190s 190s tests/test_anib.py::TestBLASTCmdline::test_blastall_dbjobdict SKIPPED [ 1%] 190s tests/test_anib.py::TestBLASTCmdline::test_blastall_generation SKIPPED [ 3%] 190s tests/test_anib.py::TestBLASTCmdline::test_blastall_graph SKIPPED (l...) [ 5%] 190s tests/test_anib.py::TestBLASTCmdline::test_blastdb_commands PASSED [ 7%] 190s tests/test_anib.py::TestBLASTCmdline::test_blastn_commands PASSED [ 8%] 190s tests/test_anib.py::TestBLASTCmdline::test_blastn_dbjobdict PASSED [ 10%] 190s tests/test_anib.py::TestBLASTCmdline::test_blastn_generation PASSED [ 12%] 192s tests/test_anib.py::TestBLASTCmdline::test_blastn_graph PASSED [ 14%] 192s tests/test_anib.py::TestBLASTCmdline::test_formatdb_generation SKIPPED [ 16%] 192s tests/test_anib.py::TestBLASTCmdline::test_legacy_blastdb_commands SKIPPED [ 17%] 192s tests/test_anib.py::TestBLASTCmdline::test_legacy_blastn_commands SKIPPED [ 19%] 192s tests/test_anib.py::TestBLASTCmdline::test_makeblastdb_generation PASSED [ 21%] 194s tests/test_anib.py::TestFragments::test_fragment_files PASSED [ 23%] 195s tests/test_anib.py::TestParsing::test_blastdir_processing PASSED [ 25%] 195s tests/test_anib.py::TestParsing::test_legacy_blastdir_processing SKIPPED [ 26%] 195s tests/test_anib.py::TestParsing::test_parse_blasttab SKIPPED (legacy...) [ 28%] 195s tests/test_anim.py::TestNUCmerCmdline::test_maxmatch_cmd_generation PASSED [ 30%] 195s tests/test_anim.py::TestNUCmerCmdline::test_multi_cmd_generation PASSED [ 32%] 195s tests/test_anim.py::TestNUCmerCmdline::test_nucmer_job_generation PASSED [ 33%] 195s tests/test_anim.py::TestNUCmerCmdline::test_single_cmd_generation PASSED [ 35%] 195s tests/test_anim.py::TestDeltafileProcessing::test_deltafile_import PASSED [ 37%] 195s tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir PASSED [ 39%] 212s tests/test_concordance.py::TestConcordance::test_anib_concordance PASSED [ 41%] 212s tests/test_concordance.py::TestConcordance::test_aniblastall_concordance SKIPPED [ 42%] 222s tests/test_concordance.py::TestConcordance::test_anim_concordance PASSED [ 44%] 233s tests/test_concordance.py::TestConcordance::test_tetra_concordance PASSED [ 46%] 233s tests/test_dependencies.py::test_import_biopython PASSED [ 48%] 233s tests/test_dependencies.py::test_import_matplotlib PASSED [ 50%] 233s tests/test_dependencies.py::test_import_numpy PASSED [ 51%] 233s tests/test_dependencies.py::test_import_pandas PASSED [ 53%] 233s tests/test_dependencies.py::test_import_scipy PASSED [ 55%] 234s tests/test_dependencies.py::test_run_blast PASSED [ 57%] 234s tests/test_dependencies.py::test_run_blastall SKIPPED (unconditional...) [ 58%] 234s tests/test_dependencies.py::test_run_nucmer PASSED [ 60%] 234s tests/test_graphics.py::test_png_mpl PASSED [ 62%] 234s tests/test_graphics.py::test_svg_mpl PASSED [ 64%] 235s tests/test_graphics.py::test_pdf_mpl PASSED [ 66%] 235s tests/test_graphics.py::test_png_seaborn PASSED [ 67%] 236s tests/test_graphics.py::test_svg_seaborn PASSED [ 69%] 236s tests/test_graphics.py::test_pdf_seaborn PASSED [ 71%] 236s tests/test_jobs.py::TestJob::test_add_dependency PASSED [ 73%] 236s tests/test_jobs.py::TestJob::test_create_job PASSED [ 75%] 236s tests/test_jobs.py::TestJob::test_create_job_with_command PASSED [ 76%] 236s tests/test_jobs.py::TestJob::test_remove_dependency PASSED [ 78%] 236s tests/test_jobs.py::TestJobGroup::test_1d_jobgroup PASSED [ 80%] 236s tests/test_jobs.py::TestJobGroup::test_2d_jobgroup PASSED [ 82%] 236s tests/test_jobs.py::TestJobGroup::test_add_dependency PASSED [ 83%] 236s tests/test_jobs.py::TestJobGroup::test_create_jobgroup PASSED [ 85%] 236s tests/test_jobs.py::TestJobGroup::test_remove_dependency PASSED [ 87%] 236s tests/test_multiprocessing.py::TestMultiprocessing::test_cmdsets PASSED [ 89%] 310s tests/test_multiprocessing.py::TestMultiprocessing::test_dependency_graph_run PASSED [ 91%] 310s tests/test_multiprocessing.py::TestMultiprocessing::test_multiprocessing_run PASSED [ 92%] 310s tests/test_parsing.py::test_anim_delta PASSED [ 94%] 323s tests/test_tetra.py::TestTETRA::test_correlations PASSED [ 96%] 323s tests/test_tetra.py::TestTETRA::test_tetraclean PASSED [ 98%] 328s tests/test_tetra.py::TestTETRA::test_zscore PASSED [100%] 328s 328s =============================== warnings summary =============================== 328s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 328s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 328s EPOCH = datetime.datetime.utcfromtimestamp(0) 328s 328s ../../../../usr/lib/python3/dist-packages/pyani/pyani_graphics.py:70 328s /usr/lib/python3/dist-packages/pyani/pyani_graphics.py:70: PendingDeprecationWarning: The register_cmap function will be deprecated in a future version. Use ``matplotlib.colormaps.register(name)`` instead. 328s plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD) 328s 328s ../../../../usr/lib/python3/dist-packages/pyani/pyani_graphics.py:71 328s /usr/lib/python3/dist-packages/pyani/pyani_graphics.py:71: PendingDeprecationWarning: The register_cmap function will be deprecated in a future version. Use ``matplotlib.colormaps.register(name)`` instead. 328s plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD) 328s 328s ../../../../usr/lib/python3/dist-packages/pyani/pyani_graphics.py:72 328s /usr/lib/python3/dist-packages/pyani/pyani_graphics.py:72: PendingDeprecationWarning: The register_cmap function will be deprecated in a future version. Use ``matplotlib.colormaps.register(name)`` instead. 328s plt.register_cmap(cmap=pyani_config.CMAP_BURD) 328s 328s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 328s ============ 46 passed, 10 skipped, 4 warnings in 141.85s (0:02:21) ============ 331s autopkgtest [02:14:30]: test run-unit-test: -----------------------] 331s autopkgtest [02:14:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 331s run-unit-test PASS 332s autopkgtest [02:14:31]: test autodep8-python3: preparing testbed 461s autopkgtest [02:16:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 461s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 462s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 462s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 462s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 462s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 462s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 462s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 462s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 462s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 462s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB] 462s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 462s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 462s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 464s Fetched 9189 kB in 2s (5138 kB/s) 464s Reading package lists... 467s Reading package lists... 467s Building dependency tree... 467s Reading state information... 468s Calculating upgrade... 468s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 469s Reading package lists... 469s Building dependency tree... 469s Reading state information... 469s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 470s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 470s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 470s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 470s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 471s Reading package lists... 472s Reading package lists... 472s Building dependency tree... 472s Reading state information... 472s Calculating upgrade... 473s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 473s Reading package lists... 473s Building dependency tree... 473s Reading state information... 474s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 474s autopkgtest [02:16:53]: testbed dpkg architecture: arm64 477s Reading package lists... 478s Building dependency tree... 478s Reading state information... 478s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 478s Starting 2 pkgProblemResolver with broken count: 0 478s Done 478s Done 479s Starting pkgProblemResolver with broken count: 0 479s Starting 2 pkgProblemResolver with broken count: 0 479s Done 479s The following additional packages will be installed: 479s blt fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 479s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 479s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 479s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 479s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libmbedcrypto7t64 libmbedtls14t64 479s libmbedx509-1t64 libopenjp2-7 libpixman-1-0 libpython3.11-minimal 479s libpython3.11-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 479s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 479s libxft2 libxrender1 libxslt1.1 libxss1 mummer ncbi-blast+ ncbi-data 479s python-matplotlib-data python3-all python3-appdirs python3-biopython 479s python3-brotli python3-cairo python3-contourpy python3-cycler 479s python3-dateutil python3-decorator python3-distutils python3-fonttools 479s python3-freetype python3-fs python3-kiwisolver python3-lib2to3 python3-lxml 479s python3-lz4 python3-matplotlib python3-mpmath python3-numpy 479s python3-packaging python3-pandas python3-pandas-lib python3-pil 479s python3-pil.imagetk python3-pyani python3-reportlab python3-rlpycairo 479s python3-scipy python3-seaborn python3-setuptools python3-sympy python3-tk 479s python3-ufolib2 python3.11 python3.11-minimal sgml-base tk8.6-blt2.5 479s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 479s Suggested packages: 479s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 479s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 479s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 479s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 479s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 479s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 479s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 479s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 479s texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc gfortran python3-dev 479s python3-pytest python-pandas-doc python3-statsmodels python-pil-doc 479s pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel 479s rl-renderpm python-scipy-doc python-setuptools-doc texlive-fonts-extra 479s python-sympy-doc tix python3-tk-dbg python3.11-venv python3.11-doc 479s binfmt-support sgml-base-doc debhelper 479s Recommended packages: 479s javascript-common python-biopython-doc python3-bs4 python3-cssselect 479s python3-html5lib python3-bottleneck python3-numexpr python3-odf 479s python3-openpyxl python3-tables python3-olefile g++ | c++-compiler 479s python3-patsy isympy-common 479s The following NEW packages will be installed: 479s blt fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 479s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 479s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 479s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 479s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libmbedcrypto7t64 libmbedtls14t64 479s libmbedx509-1t64 libopenjp2-7 libpixman-1-0 libpython3.11-minimal 479s libpython3.11-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 479s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 479s libxft2 libxrender1 libxslt1.1 libxss1 mummer ncbi-blast+ ncbi-data 479s python-matplotlib-data python3-all python3-appdirs python3-biopython 479s python3-brotli python3-cairo python3-contourpy python3-cycler 479s python3-dateutil python3-decorator python3-distutils python3-fonttools 479s python3-freetype python3-fs python3-kiwisolver python3-lib2to3 python3-lxml 479s python3-lz4 python3-matplotlib python3-mpmath python3-numpy 479s python3-packaging python3-pandas python3-pandas-lib python3-pil 479s python3-pil.imagetk python3-pyani python3-reportlab python3-rlpycairo 479s python3-scipy python3-seaborn python3-setuptools python3-sympy python3-tk 479s python3-ufolib2 python3.11 python3.11-minimal sgml-base tk8.6-blt2.5 479s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 479s 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 479s 1 not fully installed or removed. 479s Need to get 114 MB of archives. 479s After this operation, 505 MB of additional disk space will be used. 479s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 479s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 479s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 479s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 480s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 480s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 480s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 480s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 480s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 480s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 480s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 480s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 480s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 480s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 480s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 480s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 480s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 480s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 480s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 481s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 481s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 481s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 481s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 481s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 481s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 481s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB] 481s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B] 481s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB] 481s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B] 481s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 481s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 481s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 481s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 481s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 481s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 481s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 481s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 481s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 481s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 481s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 481s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 481s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 481s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 481s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 481s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 481s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 481s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 481s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 481s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 481s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 481s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 481s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 481s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 481s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 481s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 481s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 481s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 481s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 481s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 481s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 481s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 481s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 481s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC3-1 [170 kB] 481s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 481s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 481s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB] 481s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B] 481s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB] 481s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 481s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 481s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 482s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 482s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] 482s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB] 482s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 482s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB] 482s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.35-1 [161 kB] 482s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB] 482s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB] 482s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 482s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB] 482s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-1build2 [65.4 kB] 482s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 482s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] 482s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB] 483s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 483s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 483s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-seaborn all 0.13.2-2 [225 kB] 483s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2 [396 kB] 483s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 483s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 483s Get:92 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB] 483s Get:93 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB] 483s Get:94 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB] 483s Get:95 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB] 484s Get:96 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyani arm64 0.2.12-3 [46.6 kB] 484s Fetched 114 MB in 5s (23.9 MB/s) 485s Selecting previously unselected package python3-lib2to3. 485s (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 ... 74758 files and directories currently installed.) 485s Preparing to unpack .../00-python3-lib2to3_3.11.5-1_all.deb ... 485s Unpacking python3-lib2to3 (3.11.5-1) ... 485s Selecting previously unselected package python3-distutils. 485s Preparing to unpack .../01-python3-distutils_3.11.5-1_all.deb ... 485s Unpacking python3-distutils (3.11.5-1) ... 485s Selecting previously unselected package python3-all. 485s Preparing to unpack .../02-python3-all_3.12.1-0ubuntu2_arm64.deb ... 485s Unpacking python3-all (3.12.1-0ubuntu2) ... 485s Selecting previously unselected package libpython3.11-minimal:arm64. 485s Preparing to unpack .../03-libpython3.11-minimal_3.11.8-1_arm64.deb ... 485s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 485s Selecting previously unselected package python3.11-minimal. 485s Preparing to unpack .../04-python3.11-minimal_3.11.8-1_arm64.deb ... 485s Unpacking python3.11-minimal (3.11.8-1) ... 485s Selecting previously unselected package libpython3.11-stdlib:arm64. 485s Preparing to unpack .../05-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 485s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 485s Selecting previously unselected package python3.11. 485s Preparing to unpack .../06-python3.11_3.11.8-1_arm64.deb ... 485s Unpacking python3.11 (3.11.8-1) ... 485s Selecting previously unselected package libblas3:arm64. 485s Preparing to unpack .../07-libblas3_3.12.0-3_arm64.deb ... 485s Unpacking libblas3:arm64 (3.12.0-3) ... 485s Selecting previously unselected package libgfortran5:arm64. 485s Preparing to unpack .../08-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 485s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 485s Selecting previously unselected package liblapack3:arm64. 485s Preparing to unpack .../09-liblapack3_3.12.0-3_arm64.deb ... 485s Unpacking liblapack3:arm64 (3.12.0-3) ... 485s Selecting previously unselected package python3-numpy. 485s Preparing to unpack .../10-python3-numpy_1%3a1.24.2-2_arm64.deb ... 485s Unpacking python3-numpy (1:1.24.2-2) ... 485s Selecting previously unselected package libtcl8.6:arm64. 485s Preparing to unpack .../11-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 485s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 485s Selecting previously unselected package fonts-dejavu-mono. 485s Preparing to unpack .../12-fonts-dejavu-mono_2.37-8_all.deb ... 485s Unpacking fonts-dejavu-mono (2.37-8) ... 485s Selecting previously unselected package fonts-dejavu-core. 485s Preparing to unpack .../13-fonts-dejavu-core_2.37-8_all.deb ... 485s Unpacking fonts-dejavu-core (2.37-8) ... 485s Selecting previously unselected package libfontenc1:arm64. 485s Preparing to unpack .../14-libfontenc1_1%3a1.1.8-1_arm64.deb ... 485s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 485s Selecting previously unselected package x11-common. 485s Preparing to unpack .../15-x11-common_1%3a7.7+23ubuntu2_all.deb ... 485s Unpacking x11-common (1:7.7+23ubuntu2) ... 486s Selecting previously unselected package xfonts-encodings. 486s Preparing to unpack .../16-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 486s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 486s Selecting previously unselected package xfonts-utils. 486s Preparing to unpack .../17-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 486s Unpacking xfonts-utils (1:7.7+6build2) ... 486s Selecting previously unselected package fonts-urw-base35. 486s Preparing to unpack .../18-fonts-urw-base35_20200910-8_all.deb ... 486s Unpacking fonts-urw-base35 (20200910-8) ... 486s Selecting previously unselected package fontconfig-config. 486s Preparing to unpack .../19-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 486s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 486s Selecting previously unselected package libfontconfig1:arm64. 486s Preparing to unpack .../20-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 486s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 486s Selecting previously unselected package libxrender1:arm64. 486s Preparing to unpack .../21-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 486s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 486s Selecting previously unselected package libxft2:arm64. 486s Preparing to unpack .../22-libxft2_2.3.6-1_arm64.deb ... 486s Unpacking libxft2:arm64 (2.3.6-1) ... 486s Selecting previously unselected package libxss1:arm64. 486s Preparing to unpack .../23-libxss1_1%3a1.2.3-1build2_arm64.deb ... 486s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 486s Selecting previously unselected package libtk8.6:arm64. 486s Preparing to unpack .../24-libtk8.6_8.6.13-2_arm64.deb ... 486s Unpacking libtk8.6:arm64 (8.6.13-2) ... 486s Selecting previously unselected package tk8.6-blt2.5. 486s Preparing to unpack .../25-tk8.6-blt2.5_2.5.3+dfsg-7_arm64.deb ... 486s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... 486s Selecting previously unselected package blt. 486s Preparing to unpack .../26-blt_2.5.3+dfsg-7_arm64.deb ... 486s Unpacking blt (2.5.3+dfsg-7) ... 486s Selecting previously unselected package python3-tk:arm64. 486s Preparing to unpack .../27-python3-tk_3.11.5-1_arm64.deb ... 486s Unpacking python3-tk:arm64 (3.11.5-1) ... 486s Selecting previously unselected package python3-pil.imagetk:arm64. 486s Preparing to unpack .../28-python3-pil.imagetk_10.2.0-1_arm64.deb ... 486s Unpacking python3-pil.imagetk:arm64 (10.2.0-1) ... 486s Selecting previously unselected package libgomp1:arm64. 486s Preparing to unpack .../29-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 486s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 486s Selecting previously unselected package libimagequant0:arm64. 486s Preparing to unpack .../30-libimagequant0_2.18.0-1_arm64.deb ... 486s Unpacking libimagequant0:arm64 (2.18.0-1) ... 486s Selecting previously unselected package libjpeg-turbo8:arm64. 486s Preparing to unpack .../31-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 486s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 486s Selecting previously unselected package libjpeg8:arm64. 486s Preparing to unpack .../32-libjpeg8_8c-2ubuntu11_arm64.deb ... 486s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 486s Selecting previously unselected package liblcms2-2:arm64. 486s Preparing to unpack .../33-liblcms2-2_2.14-2_arm64.deb ... 486s Unpacking liblcms2-2:arm64 (2.14-2) ... 486s Selecting previously unselected package libopenjp2-7:arm64. 486s Preparing to unpack .../34-libopenjp2-7_2.5.0-2_arm64.deb ... 486s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 486s Selecting previously unselected package libgraphite2-3:arm64. 486s Preparing to unpack .../35-libgraphite2-3_1.3.14-2_arm64.deb ... 486s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 486s Selecting previously unselected package libharfbuzz0b:arm64. 486s Preparing to unpack .../36-libharfbuzz0b_8.3.0-2_arm64.deb ... 486s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 486s Selecting previously unselected package libraqm0:arm64. 486s Preparing to unpack .../37-libraqm0_0.10.1-1_arm64.deb ... 486s Unpacking libraqm0:arm64 (0.10.1-1) ... 486s Selecting previously unselected package libdeflate0:arm64. 486s Preparing to unpack .../38-libdeflate0_1.19-1_arm64.deb ... 486s Unpacking libdeflate0:arm64 (1.19-1) ... 486s Selecting previously unselected package libjbig0:arm64. 487s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 487s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 487s Selecting previously unselected package liblerc4:arm64. 487s Preparing to unpack .../40-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 487s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 487s Selecting previously unselected package libsharpyuv0:arm64. 487s Preparing to unpack .../41-libsharpyuv0_1.3.2-0.4_arm64.deb ... 487s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 487s Selecting previously unselected package libwebp7:arm64. 487s Preparing to unpack .../42-libwebp7_1.3.2-0.4_arm64.deb ... 487s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 487s Selecting previously unselected package libtiff6:arm64. 487s Preparing to unpack .../43-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 487s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 487s Selecting previously unselected package libwebpdemux2:arm64. 487s Preparing to unpack .../44-libwebpdemux2_1.3.2-0.4_arm64.deb ... 487s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 487s Selecting previously unselected package libwebpmux3:arm64. 487s Preparing to unpack .../45-libwebpmux3_1.3.2-0.4_arm64.deb ... 487s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 487s Selecting previously unselected package python3-pil:arm64. 487s Preparing to unpack .../46-python3-pil_10.2.0-1_arm64.deb ... 487s Unpacking python3-pil:arm64 (10.2.0-1) ... 487s Selecting previously unselected package libpixman-1-0:arm64. 487s Preparing to unpack .../47-libpixman-1-0_0.42.2-1_arm64.deb ... 487s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 487s Selecting previously unselected package libxcb-render0:arm64. 487s Preparing to unpack .../48-libxcb-render0_1.15-1_arm64.deb ... 487s Unpacking libxcb-render0:arm64 (1.15-1) ... 487s Selecting previously unselected package libxcb-shm0:arm64. 487s Preparing to unpack .../49-libxcb-shm0_1.15-1_arm64.deb ... 487s Unpacking libxcb-shm0:arm64 (1.15-1) ... 487s Selecting previously unselected package libcairo2:arm64. 487s Preparing to unpack .../50-libcairo2_1.18.0-1_arm64.deb ... 487s Unpacking libcairo2:arm64 (1.18.0-1) ... 487s Selecting previously unselected package python3-cairo. 487s Preparing to unpack .../51-python3-cairo_1.25.1-2_arm64.deb ... 487s Unpacking python3-cairo (1.25.1-2) ... 487s Selecting previously unselected package python3-freetype. 487s Preparing to unpack .../52-python3-freetype_2.4.0-1_all.deb ... 487s Unpacking python3-freetype (2.4.0-1) ... 487s Selecting previously unselected package python3-rlpycairo. 487s Preparing to unpack .../53-python3-rlpycairo_0.3.0-3_all.deb ... 487s Unpacking python3-rlpycairo (0.3.0-3) ... 487s Selecting previously unselected package fonts-dejavu-extra. 487s Preparing to unpack .../54-fonts-dejavu-extra_2.37-8_all.deb ... 487s Unpacking fonts-dejavu-extra (2.37-8) ... 487s Selecting previously unselected package python3-reportlab. 487s Preparing to unpack .../55-python3-reportlab_4.1.0-1_all.deb ... 487s Unpacking python3-reportlab (4.1.0-1) ... 487s Selecting previously unselected package sgml-base. 487s Preparing to unpack .../56-sgml-base_1.31_all.deb ... 487s Unpacking sgml-base (1.31) ... 487s Selecting previously unselected package xml-core. 487s Preparing to unpack .../57-xml-core_0.19_all.deb ... 487s Unpacking xml-core (0.19) ... 487s Selecting previously unselected package w3c-sgml-lib. 487s Preparing to unpack .../58-w3c-sgml-lib_1.3-3_all.deb ... 487s Unpacking w3c-sgml-lib (1.3-3) ... 487s Selecting previously unselected package python3-biopython. 487s Preparing to unpack .../59-python3-biopython_1.81+dfsg-3_arm64.deb ... 487s Unpacking python3-biopython (1.81+dfsg-3) ... 487s Selecting previously unselected package libjs-jquery. 487s Preparing to unpack .../60-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 487s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 487s Selecting previously unselected package libjs-jquery-ui. 487s Preparing to unpack .../61-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 487s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 487s Selecting previously unselected package fonts-lyx. 487s Preparing to unpack .../62-fonts-lyx_2.4.0~RC3-1_all.deb ... 487s Unpacking fonts-lyx (2.4.0~RC3-1) ... 487s Selecting previously unselected package python-matplotlib-data. 487s Preparing to unpack .../63-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ... 487s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ... 488s Selecting previously unselected package python3-dateutil. 488s Preparing to unpack .../64-python3-dateutil_2.8.2-3_all.deb ... 488s Unpacking python3-dateutil (2.8.2-3) ... 488s Selecting previously unselected package python3-contourpy. 488s Preparing to unpack .../65-python3-contourpy_1.0.7-1build2_arm64.deb ... 488s Unpacking python3-contourpy (1.0.7-1build2) ... 488s Selecting previously unselected package python3-cycler. 488s Preparing to unpack .../66-python3-cycler_0.11.0-2_all.deb ... 488s Unpacking python3-cycler (0.11.0-2) ... 488s Selecting previously unselected package python3-brotli. 488s Preparing to unpack .../67-python3-brotli_1.1.0-2_arm64.deb ... 488s Unpacking python3-brotli (1.1.0-2) ... 488s Selecting previously unselected package python3-decorator. 488s Preparing to unpack .../68-python3-decorator_5.1.1-5_all.deb ... 488s Unpacking python3-decorator (5.1.1-5) ... 488s Selecting previously unselected package liblbfgsb0:arm64. 488s Preparing to unpack .../69-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 488s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 488s Selecting previously unselected package python3-scipy. 488s Preparing to unpack .../70-python3-scipy_1.11.4-6_arm64.deb ... 488s Unpacking python3-scipy (1.11.4-6) ... 488s Selecting previously unselected package python3-ufolib2. 489s Preparing to unpack .../71-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 489s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 489s Selecting previously unselected package python3-mpmath. 489s Preparing to unpack .../72-python3-mpmath_1.2.1-3_all.deb ... 489s Unpacking python3-mpmath (1.2.1-3) ... 489s Selecting previously unselected package python3-sympy. 489s Preparing to unpack .../73-python3-sympy_1.12-7_all.deb ... 489s Unpacking python3-sympy (1.12-7) ... 489s Selecting previously unselected package python3-appdirs. 489s Preparing to unpack .../74-python3-appdirs_1.4.4-4_all.deb ... 489s Unpacking python3-appdirs (1.4.4-4) ... 489s Selecting previously unselected package python3-fs. 489s Preparing to unpack .../75-python3-fs_2.4.16-3_all.deb ... 489s Unpacking python3-fs (2.4.16-3) ... 489s Selecting previously unselected package libxslt1.1:arm64. 489s Preparing to unpack .../76-libxslt1.1_1.1.35-1_arm64.deb ... 489s Unpacking libxslt1.1:arm64 (1.1.35-1) ... 489s Selecting previously unselected package python3-lxml:arm64. 489s Preparing to unpack .../77-python3-lxml_5.1.0-1_arm64.deb ... 489s Unpacking python3-lxml:arm64 (5.1.0-1) ... 489s Selecting previously unselected package python3-lz4. 489s Preparing to unpack .../78-python3-lz4_4.0.2+dfsg-1build2_arm64.deb ... 489s Unpacking python3-lz4 (4.0.2+dfsg-1build2) ... 489s Selecting previously unselected package unicode-data. 489s Preparing to unpack .../79-unicode-data_15.1.0-1_all.deb ... 489s Unpacking unicode-data (15.1.0-1) ... 489s Selecting previously unselected package python3-fonttools. 489s Preparing to unpack .../80-python3-fonttools_4.46.0-1_arm64.deb ... 489s Unpacking python3-fonttools (4.46.0-1) ... 489s Selecting previously unselected package python3-kiwisolver. 489s Preparing to unpack .../81-python3-kiwisolver_1.4.4-1build2_arm64.deb ... 489s Unpacking python3-kiwisolver (1.4.4-1build2) ... 489s Selecting previously unselected package python3-packaging. 489s Preparing to unpack .../82-python3-packaging_23.2-1_all.deb ... 489s Unpacking python3-packaging (23.2-1) ... 489s Selecting previously unselected package libqhull-r8.0:arm64. 489s Preparing to unpack .../83-libqhull-r8.0_2020.2-6_arm64.deb ... 489s Unpacking libqhull-r8.0:arm64 (2020.2-6) ... 489s Selecting previously unselected package python3-matplotlib. 489s Preparing to unpack .../84-python3-matplotlib_3.6.3-1ubuntu3_arm64.deb ... 489s Unpacking python3-matplotlib (3.6.3-1ubuntu3) ... 490s Selecting previously unselected package python3-pandas-lib:arm64. 490s Preparing to unpack .../85-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 490s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 490s Selecting previously unselected package python3-pandas. 490s Preparing to unpack .../86-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 490s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 490s Selecting previously unselected package python3-seaborn. 490s Preparing to unpack .../87-python3-seaborn_0.13.2-2_all.deb ... 490s Unpacking python3-seaborn (0.13.2-2) ... 490s Selecting previously unselected package python3-setuptools. 490s Preparing to unpack .../88-python3-setuptools_68.1.2-2_all.deb ... 490s Unpacking python3-setuptools (68.1.2-2) ... 490s Selecting previously unselected package mummer. 490s Preparing to unpack .../89-mummer_3.23+dfsg-8_arm64.deb ... 490s Unpacking mummer (3.23+dfsg-8) ... 490s Selecting previously unselected package ncbi-data. 490s Preparing to unpack .../90-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 490s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 490s Selecting previously unselected package libmbedcrypto7t64:arm64. 490s Preparing to unpack .../91-libmbedcrypto7t64_2.28.7-1.1ubuntu1_arm64.deb ... 490s Unpacking libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 490s Selecting previously unselected package libmbedx509-1t64:arm64. 490s Preparing to unpack .../92-libmbedx509-1t64_2.28.7-1.1ubuntu1_arm64.deb ... 490s Unpacking libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 491s Selecting previously unselected package libmbedtls14t64:arm64. 491s Preparing to unpack .../93-libmbedtls14t64_2.28.7-1.1ubuntu1_arm64.deb ... 491s Unpacking libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 491s Selecting previously unselected package ncbi-blast+. 491s Preparing to unpack .../94-ncbi-blast+_2.12.0+ds-4build1_arm64.deb ... 491s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ... 491s Selecting previously unselected package python3-pyani. 491s Preparing to unpack .../95-python3-pyani_0.2.12-3_arm64.deb ... 491s Unpacking python3-pyani (0.2.12-3) ... 491s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 491s Setting up liblcms2-2:arm64 (2.14-2) ... 491s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 491s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 491s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 491s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 491s Setting up libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 491s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 491s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 491s Setting up libxcb-render0:arm64 (1.15-1) ... 491s Setting up fonts-lyx (2.4.0~RC3-1) ... 491s Setting up x11-common (1:7.7+23ubuntu2) ... 492s Setting up libdeflate0:arm64 (1.19-1) ... 492s Setting up libqhull-r8.0:arm64 (2020.2-6) ... 492s Setting up libxcb-shm0:arm64 (1.15-1) ... 492s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 492s Setting up python3-freetype (2.4.0-1) ... 492s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 492s Setting up unicode-data (15.1.0-1) ... 492s Setting up python3-decorator (5.1.1-5) ... 492s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 492s Setting up libblas3:arm64 (3.12.0-3) ... 492s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 492s Setting up python3-packaging (23.2-1) ... 492s Setting up python3-brotli (1.1.0-2) ... 492s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 492s Setting up python3-cycler (0.11.0-2) ... 492s Setting up libimagequant0:arm64 (2.18.0-1) ... 492s Setting up fonts-dejavu-mono (2.37-8) ... 492s Setting up python3-kiwisolver (1.4.4-1build2) ... 493s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 493s Setting up fonts-dejavu-core (2.37-8) ... 493s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 493s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 493s Setting up libwebp7:arm64 (1.3.2-0.4) ... 493s Setting up fonts-dejavu-extra (2.37-8) ... 493s Setting up libxslt1.1:arm64 (1.1.35-1) ... 493s Setting up mummer (3.23+dfsg-8) ... 493s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 493s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 493s Setting up python3-dateutil (2.8.2-3) ... 493s Setting up sgml-base (1.31) ... 493s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 493s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 493s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 493s Setting up python3-mpmath (1.2.1-3) ... 493s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... 493s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 493s Setting up python3-lib2to3 (3.11.5-1) ... 494s Setting up python3-appdirs (1.4.4-4) ... 494s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 494s Setting up python3-distutils (3.11.5-1) ... 494s python3.12: can't get files for byte-compilation 494s Setting up python3.11-minimal (3.11.8-1) ... 494s Setting up python3-sympy (1.12-7) ... 499s Setting up liblapack3:arm64 (3.12.0-3) ... 499s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 499s Setting up libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 499s Setting up python3-setuptools (68.1.2-2) ... 500s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 500s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 500s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 500s Setting up python3-all (3.12.1-0ubuntu2) ... 500s Setting up xfonts-utils (1:7.7+6build2) ... 500s Setting up python3-fs (2.4.16-3) ... 500s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 500s Setting up libraqm0:arm64 (0.10.1-1) ... 500s Setting up libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 500s Setting up python3-lxml:arm64 (5.1.0-1) ... 500s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 500s Setting up xml-core (0.19) ... 501s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 501s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 501s Setting up python3.11 (3.11.8-1) ... 501s Setting up libxft2:arm64 (2.3.6-1) ... 501s Setting up libtk8.6:arm64 (8.6.13-2) ... 501s Setting up fonts-urw-base35 (20200910-8) ... 501s Setting up libcairo2:arm64 (1.18.0-1) ... 501s Setting up ncbi-blast+ (2.12.0+ds-4build1) ... 501s Setting up python3-pil:arm64 (10.2.0-1) ... 502s Setting up python3-numpy (1:1.24.2-2) ... 503s Setting up python3-contourpy (1.0.7-1build2) ... 504s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 504s Setting up python3-scipy (1.11.4-6) ... 506s Setting up python3-cairo (1.25.1-2) ... 506s Setting up blt (2.5.3+dfsg-7) ... 506s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 506s Setting up python3-tk:arm64 (3.11.5-1) ... 506s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 510s Setting up python3-pil.imagetk:arm64 (10.2.0-1) ... 510s Setting up python3-rlpycairo (0.3.0-3) ... 511s Setting up python3-reportlab (4.1.0-1) ... 511s Setting up python3-fonttools (4.46.0-1) ... 513s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 513s Setting up python3-matplotlib (3.6.3-1ubuntu3) ... 514s Setting up python3-seaborn (0.13.2-2) ... 514s Processing triggers for systemd (255.2-3ubuntu2) ... 514s Processing triggers for man-db (2.12.0-3) ... 516s Processing triggers for libc-bin (2.39-0ubuntu2) ... 516s Processing triggers for sgml-base (1.31) ... 516s Setting up w3c-sgml-lib (1.3-3) ... 540s Setting up python3-biopython (1.81+dfsg-3) ... 541s Setting up python3-pyani (0.2.12-3) ... 541s Setting up autopkgtest-satdep (0) ... 546s (Reading database ... 86865 files and directories currently installed.) 546s Removing autopkgtest-satdep (0) ... 553s autopkgtest [02:18:12]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pyani; print(pyani)" ; done 553s autopkgtest [02:18:12]: test autodep8-python3: [----------------------- 553s Testing with python3.12: 553s 554s autopkgtest [02:18:13]: test autodep8-python3: -----------------------] 554s autopkgtest [02:18:13]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 554s autodep8-python3 PASS (superficial) 554s autopkgtest [02:18:13]: @@@@@@@@@@@@@@@@@@@@ summary 554s run-unit-test PASS 554s autodep8-python3 PASS (superficial) 566s Creating nova instance adt-noble-arm64-python-pyani-20240318-020859-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)... 566s Creating nova instance adt-noble-arm64-python-pyani-20240318-020859-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...