0s autopkgtest [21:28:46]: starting date and time: 2024-11-14 21:28:46+0000 0s autopkgtest [21:28:46]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [21:28:46]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uqait53w/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-biopython --apt-upgrade python-treetime --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-biopython/1.84+dfsg-4build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-33.secgroup --name adt-plucky-arm64-python-treetime-20241114-212845-juju-7f2275-prod-proposed-migration-environment-15-91d76772-ac95-4521-8110-0869c7a8802a --image adt/ubuntu-plucky-arm64-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/ 83s autopkgtest [21:30:09]: testbed dpkg architecture: arm64 83s autopkgtest [21:30:09]: testbed apt version: 2.9.8 83s autopkgtest [21:30:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 84s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 84s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.1 kB] 84s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 84s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [106 kB] 84s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1037 kB] 84s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [138 kB] 84s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 84s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [775 kB] 84s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6116 B] 84s Fetched 2210 kB in 1s (2533 kB/s) 84s Reading package lists... 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s Calculating upgrade... 88s The following packages will be upgraded: 88s libcap-ng0 pastebinit python3-systemd 88s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 76.6 kB of archives. 88s After this operation, 349 kB of additional disk space will be used. 88s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libcap-ng0 arm64 0.8.5-3build1 [15.0 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 89s Fetched 76.6 kB in 0s (219 kB/s) 89s (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 ... 79925 files and directories currently installed.) 89s Preparing to unpack .../libcap-ng0_0.8.5-3build1_arm64.deb ... 89s Unpacking libcap-ng0:arm64 (0.8.5-3build1) over (0.8.5-1) ... 89s Setting up libcap-ng0:arm64 (0.8.5-3build1) ... 90s (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 ... 79925 files and directories currently installed.) 90s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 90s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 90s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 90s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 90s Setting up pastebinit (1.7.1-1) ... 90s Setting up python3-systemd (235-1build5) ... 90s Processing triggers for man-db (2.12.1-3) ... 91s Processing triggers for libc-bin (2.40-1ubuntu3) ... 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 92s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 92s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 92s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 93s Reading package lists... 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s autopkgtest [21:30:25]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 99s autopkgtest [21:30:25]: @@@@@@@@@@@@@@@@@@@@ apt-source python-treetime 101s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (dsc) [2611 B] 101s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [5117 kB] 101s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [1291 kB] 101s Get:4 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (diff) [8028 B] 101s gpgv: Signature made Sat Nov 9 21:31:47 2024 UTC 101s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 101s gpgv: issuer "emollier@debian.org" 101s gpgv: Can't check signature: No public key 101s dpkg-source: warning: cannot verify inline signature for ./python-treetime_0.11.4-1.dsc: no acceptable signature found 102s autopkgtest [21:30:28]: testing package python-treetime version 0.11.4-1 102s autopkgtest [21:30:28]: build not needed 104s autopkgtest [21:30:30]: test run-unit-test: preparing testbed 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 112s The following additional packages will be installed: 112s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 112s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 112s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 112s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 112s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 112s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 112s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 112s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 112s python3-cairo python3-contourpy python3-cycler python3-dateutil 112s python3-decorator python3-fonttools python3-freetype python3-fs 112s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 112s python3-mpmath python3-numpy python3-packaging python3-pandas 112s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 112s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 112s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 112s python3.12-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 112s xfonts-encodings xfonts-utils xml-core 112s Suggested packages: 112s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 112s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 112s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 112s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 112s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 112s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 112s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 112s python3-gobject python3-pyqt5 python3-sip python3-tornado 112s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 112s gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 112s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 112s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 112s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-tk 112s sgml-base-doc debhelper 112s Recommended packages: 112s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 112s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 112s python3-odf python3-openpyxl python3-tables python3-olefile 112s fonts-dejavu-extra g++ | c++-compiler isympy-common 112s The following NEW packages will be installed: 112s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 112s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 112s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 112s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 112s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 112s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 112s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 112s libxslt1.1 libxss1 python-matplotlib-data python3-appdirs python3-biopython 112s python3-brotli python3-cairo python3-contourpy python3-cycler 112s python3-dateutil python3-decorator python3-fonttools python3-freetype 112s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 112s python3-mpmath python3-numpy python3-packaging python3-pandas 112s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 112s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 112s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 112s python3.12-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 112s xfonts-encodings xfonts-utils xml-core 112s 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 79.6 MB/79.6 MB of archives. 112s After this operation, 323 MB of additional disk space will be used. 112s Get:1 /tmp/autopkgtest.svENyt/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 112s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 113s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 113s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 113s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 113s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 113s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 113s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 113s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 113s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 113s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 113s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 113s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 113s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 113s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 113s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 113s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 113s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 113s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 113s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 113s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 113s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 113s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 113s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 113s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 113s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 113s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 113s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 113s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 113s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 113s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 113s Get:34 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 113s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 113s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 113s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 113s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 113s Get:39 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 113s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 114s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 114s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 114s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 114s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 114s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 114s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 114s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 114s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 114s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 114s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 114s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 114s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.6-1ubuntu1 [9806 B] 114s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 114s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 114s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 114s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 114s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 114s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 114s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 114s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 114s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 114s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-biopython arm64 1.84+dfsg-4build1 [1694 kB] 114s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 114s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 114s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 114s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 114s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 114s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 114s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 115s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 115s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 115s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 115s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 115s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 115s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 115s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 115s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 115s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 115s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 116s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 116s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 116s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 116s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 116s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 116s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-treetime all 0.11.4-1 [941 kB] 116s Fetched 79.6 MB in 4s (20.3 MB/s) 117s Selecting previously unselected package sgml-base. 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79930 files and directories currently installed.) 117s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 117s Unpacking sgml-base (1.31) ... 117s Selecting previously unselected package libtcl8.6:arm64. 117s Preparing to unpack .../01-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 117s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 117s Selecting previously unselected package fonts-dejavu-mono. 117s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 117s Unpacking fonts-dejavu-mono (2.37-8) ... 117s Selecting previously unselected package fonts-dejavu-core. 117s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 117s Unpacking fonts-dejavu-core (2.37-8) ... 117s Selecting previously unselected package libfontenc1:arm64. 117s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 117s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 117s Selecting previously unselected package x11-common. 117s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 117s Unpacking x11-common (1:7.7+23ubuntu3) ... 117s Selecting previously unselected package xfonts-encodings. 117s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 117s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 117s Selecting previously unselected package xfonts-utils. 117s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_arm64.deb ... 117s Unpacking xfonts-utils (1:7.7+7) ... 117s Selecting previously unselected package fonts-urw-base35. 117s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 117s Unpacking fonts-urw-base35 (20200910-8) ... 117s Selecting previously unselected package fontconfig-config. 117s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 117s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 117s Selecting previously unselected package libfontconfig1:arm64. 117s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 117s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 117s Selecting previously unselected package libxrender1:arm64. 117s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 117s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 117s Selecting previously unselected package libxft2:arm64. 117s Preparing to unpack .../12-libxft2_2.3.6-1build1_arm64.deb ... 117s Unpacking libxft2:arm64 (2.3.6-1build1) ... 117s Selecting previously unselected package libxss1:arm64. 117s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_arm64.deb ... 117s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 118s Selecting previously unselected package libtk8.6:arm64. 118s Preparing to unpack .../14-libtk8.6_8.6.15-1_arm64.deb ... 118s Unpacking libtk8.6:arm64 (8.6.15-1) ... 118s Selecting previously unselected package tk8.6-blt2.5. 118s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 118s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 118s Selecting previously unselected package blt. 118s Preparing to unpack .../16-blt_2.5.3+dfsg-7build1_arm64.deb ... 118s Unpacking blt (2.5.3+dfsg-7build1) ... 118s Selecting previously unselected package fonts-lyx. 118s Preparing to unpack .../17-fonts-lyx_2.4.2.1-1_all.deb ... 118s Unpacking fonts-lyx (2.4.2.1-1) ... 118s Selecting previously unselected package libblas3:arm64. 118s Preparing to unpack .../18-libblas3_3.12.0-3build2_arm64.deb ... 118s Unpacking libblas3:arm64 (3.12.0-3build2) ... 118s Selecting previously unselected package libpixman-1-0:arm64. 118s Preparing to unpack .../19-libpixman-1-0_0.44.0-3_arm64.deb ... 118s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 118s Selecting previously unselected package libxcb-render0:arm64. 118s Preparing to unpack .../20-libxcb-render0_1.17.0-2_arm64.deb ... 118s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 118s Selecting previously unselected package libxcb-shm0:arm64. 118s Preparing to unpack .../21-libxcb-shm0_1.17.0-2_arm64.deb ... 118s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 118s Selecting previously unselected package libcairo2:arm64. 118s Preparing to unpack .../22-libcairo2_1.18.2-2_arm64.deb ... 118s Unpacking libcairo2:arm64 (1.18.2-2) ... 118s Selecting previously unselected package libdeflate0:arm64. 118s Preparing to unpack .../23-libdeflate0_1.22-1_arm64.deb ... 118s Unpacking libdeflate0:arm64 (1.22-1) ... 118s Selecting previously unselected package libgfortran5:arm64. 118s Preparing to unpack .../24-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 118s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 118s Selecting previously unselected package libgomp1:arm64. 118s Preparing to unpack .../25-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 118s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 118s Selecting previously unselected package libgraphite2-3:arm64. 118s Preparing to unpack .../26-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 118s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 118s Selecting previously unselected package libharfbuzz0b:arm64. 118s Preparing to unpack .../27-libharfbuzz0b_10.0.1-1_arm64.deb ... 118s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 118s Selecting previously unselected package libimagequant0:arm64. 118s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_arm64.deb ... 118s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 118s Selecting previously unselected package libjpeg-turbo8:arm64. 118s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 118s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 118s Selecting previously unselected package libjpeg8:arm64. 118s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_arm64.deb ... 118s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 118s Selecting previously unselected package libjs-jquery. 118s Preparing to unpack .../31-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 118s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 118s Selecting previously unselected package libjs-jquery-ui. 118s Preparing to unpack .../32-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 118s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 118s Selecting previously unselected package liblapack3:arm64. 118s Preparing to unpack .../33-liblapack3_3.12.0-3build2_arm64.deb ... 118s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 118s Selecting previously unselected package liblbfgsb0:arm64. 118s Preparing to unpack .../34-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 118s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 118s Selecting previously unselected package liblcms2-2:arm64. 118s Preparing to unpack .../35-liblcms2-2_2.16-2_arm64.deb ... 118s Unpacking liblcms2-2:arm64 (2.16-2) ... 118s Selecting previously unselected package liblerc4:arm64. 118s Preparing to unpack .../36-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 118s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 118s Selecting previously unselected package libqhull-r8.0:arm64. 118s Preparing to unpack .../37-libqhull-r8.0_2020.2-6build1_arm64.deb ... 118s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 118s Selecting previously unselected package libraqm0:arm64. 119s Preparing to unpack .../38-libraqm0_0.10.1-1build1_arm64.deb ... 119s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 119s Selecting previously unselected package libsharpyuv0:arm64. 119s Preparing to unpack .../39-libsharpyuv0_1.4.0-0.1_arm64.deb ... 119s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 119s Selecting previously unselected package libjbig0:arm64. 119s Preparing to unpack .../40-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 119s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 119s Selecting previously unselected package libwebp7:arm64. 119s Preparing to unpack .../41-libwebp7_1.4.0-0.1_arm64.deb ... 119s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 119s Selecting previously unselected package libtiff6:arm64. 119s Preparing to unpack .../42-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 119s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 119s Selecting previously unselected package libwebpdemux2:arm64. 119s Preparing to unpack .../43-libwebpdemux2_1.4.0-0.1_arm64.deb ... 119s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 119s Selecting previously unselected package libwebpmux3:arm64. 119s Preparing to unpack .../44-libwebpmux3_1.4.0-0.1_arm64.deb ... 119s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 119s Selecting previously unselected package libxslt1.1:arm64. 119s Preparing to unpack .../45-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 119s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 119s Selecting previously unselected package python-matplotlib-data. 119s Preparing to unpack .../46-python-matplotlib-data_3.8.3-3_all.deb ... 119s Unpacking python-matplotlib-data (3.8.3-3) ... 119s Selecting previously unselected package python3-appdirs. 119s Preparing to unpack .../47-python3-appdirs_1.4.4-4_all.deb ... 119s Unpacking python3-appdirs (1.4.4-4) ... 119s Selecting previously unselected package python3-numpy. 119s Preparing to unpack .../48-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 119s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 119s Selecting previously unselected package python3.12-tk. 119s Preparing to unpack .../49-python3.12-tk_3.12.7-3_arm64.deb ... 119s Unpacking python3.12-tk (3.12.7-3) ... 119s Selecting previously unselected package python3-tk:arm64. 119s Preparing to unpack .../50-python3-tk_3.12.6-1ubuntu1_arm64.deb ... 119s Unpacking python3-tk:arm64 (3.12.6-1ubuntu1) ... 119s Selecting previously unselected package python3-pil.imagetk:arm64. 119s Preparing to unpack .../51-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 119s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 119s Selecting previously unselected package libopenjp2-7:arm64. 119s Preparing to unpack .../52-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 119s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 119s Selecting previously unselected package python3-pil:arm64. 119s Preparing to unpack .../53-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 119s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 119s Selecting previously unselected package python3-cairo. 119s Preparing to unpack .../54-python3-cairo_1.26.1-2_arm64.deb ... 119s Unpacking python3-cairo (1.26.1-2) ... 119s Selecting previously unselected package python3-freetype. 119s Preparing to unpack .../55-python3-freetype_2.5.1-1_all.deb ... 119s Unpacking python3-freetype (2.5.1-1) ... 119s Selecting previously unselected package python3-rlpycairo. 119s Preparing to unpack .../56-python3-rlpycairo_0.3.0-3_all.deb ... 119s Unpacking python3-rlpycairo (0.3.0-3) ... 119s Selecting previously unselected package python3-reportlab. 119s Preparing to unpack .../57-python3-reportlab_4.2.5-1_all.deb ... 119s Unpacking python3-reportlab (4.2.5-1) ... 120s Selecting previously unselected package xml-core. 120s Preparing to unpack .../58-xml-core_0.19_all.deb ... 120s Unpacking xml-core (0.19) ... 120s Selecting previously unselected package w3c-sgml-lib. 120s Preparing to unpack .../59-w3c-sgml-lib_1.3-3_all.deb ... 120s Unpacking w3c-sgml-lib (1.3-3) ... 120s Selecting previously unselected package python3-biopython. 120s Preparing to unpack .../60-python3-biopython_1.84+dfsg-4build1_arm64.deb ... 120s Unpacking python3-biopython (1.84+dfsg-4build1) ... 120s Selecting previously unselected package python3-brotli. 120s Preparing to unpack .../61-python3-brotli_1.1.0-2build2_arm64.deb ... 120s Unpacking python3-brotli (1.1.0-2build2) ... 120s Selecting previously unselected package python3-contourpy. 120s Preparing to unpack .../62-python3-contourpy_1.3.0-2_arm64.deb ... 120s Unpacking python3-contourpy (1.3.0-2) ... 120s Selecting previously unselected package python3-cycler. 120s Preparing to unpack .../63-python3-cycler_0.12.1-1_all.deb ... 120s Unpacking python3-cycler (0.12.1-1) ... 120s Selecting previously unselected package python3-six. 120s Preparing to unpack .../64-python3-six_1.16.0-7_all.deb ... 120s Unpacking python3-six (1.16.0-7) ... 120s Selecting previously unselected package python3-dateutil. 120s Preparing to unpack .../65-python3-dateutil_2.9.0-2_all.deb ... 120s Unpacking python3-dateutil (2.9.0-2) ... 120s Selecting previously unselected package python3-decorator. 120s Preparing to unpack .../66-python3-decorator_5.1.1-5_all.deb ... 120s Unpacking python3-decorator (5.1.1-5) ... 120s Selecting previously unselected package python3-scipy. 120s Preparing to unpack .../67-python3-scipy_1.13.1-5_arm64.deb ... 120s Unpacking python3-scipy (1.13.1-5) ... 120s Selecting previously unselected package python3-ufolib2. 120s Preparing to unpack .../68-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 120s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 120s Selecting previously unselected package python3-mpmath. 120s Preparing to unpack .../69-python3-mpmath_1.3.0-1_all.deb ... 120s Unpacking python3-mpmath (1.3.0-1) ... 121s Selecting previously unselected package python3-sympy. 121s Preparing to unpack .../70-python3-sympy_1.13.3-1_all.deb ... 121s Unpacking python3-sympy (1.13.3-1) ... 121s Selecting previously unselected package python3-tz. 121s Preparing to unpack .../71-python3-tz_2024.1-2_all.deb ... 121s Unpacking python3-tz (2024.1-2) ... 121s Selecting previously unselected package python3-fs. 121s Preparing to unpack .../72-python3-fs_2.4.16-4_all.deb ... 121s Unpacking python3-fs (2.4.16-4) ... 121s Selecting previously unselected package python3-lxml:arm64. 121s Preparing to unpack .../73-python3-lxml_5.3.0-1_arm64.deb ... 121s Unpacking python3-lxml:arm64 (5.3.0-1) ... 121s Selecting previously unselected package python3-lz4. 121s Preparing to unpack .../74-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 121s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 121s Selecting previously unselected package python3-unicodedata2. 121s Preparing to unpack .../75-python3-unicodedata2_15.1.0+ds-1build2_arm64.deb ... 121s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 121s Selecting previously unselected package unicode-data. 121s Preparing to unpack .../76-unicode-data_15.1.0-1_all.deb ... 121s Unpacking unicode-data (15.1.0-1) ... 121s Selecting previously unselected package python3-fonttools. 121s Preparing to unpack .../77-python3-fonttools_4.46.0-1build2_arm64.deb ... 121s Unpacking python3-fonttools (4.46.0-1build2) ... 121s Selecting previously unselected package python3-kiwisolver. 121s Preparing to unpack .../78-python3-kiwisolver_1.4.7-2build1_arm64.deb ... 121s Unpacking python3-kiwisolver (1.4.7-2build1) ... 121s Selecting previously unselected package python3-packaging. 121s Preparing to unpack .../79-python3-packaging_24.1-1_all.deb ... 121s Unpacking python3-packaging (24.1-1) ... 121s Selecting previously unselected package python3-matplotlib. 121s Preparing to unpack .../80-python3-matplotlib_3.8.3-3_arm64.deb ... 121s Unpacking python3-matplotlib (3.8.3-3) ... 122s Selecting previously unselected package python3-pandas-lib:arm64. 122s Preparing to unpack .../81-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 122s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 122s Selecting previously unselected package python3-pandas. 122s Preparing to unpack .../82-python3-pandas_2.2.3+dfsg-5_all.deb ... 122s Unpacking python3-pandas (2.2.3+dfsg-5) ... 122s Selecting previously unselected package python3-treetime. 122s Preparing to unpack .../83-python3-treetime_0.11.4-1_all.deb ... 122s Unpacking python3-treetime (0.11.4-1) ... 122s Selecting previously unselected package autopkgtest-satdep. 122s Preparing to unpack .../84-1-autopkgtest-satdep.deb ... 122s Unpacking autopkgtest-satdep (0) ... 122s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 122s Setting up liblcms2-2:arm64 (2.16-2) ... 122s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 122s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 122s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 122s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 122s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 122s Setting up libxcb-render0:arm64 (1.17.0-2) ... 122s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 122s Setting up fonts-lyx (2.4.2.1-1) ... 122s Setting up x11-common (1:7.7+23ubuntu3) ... 123s Setting up libdeflate0:arm64 (1.22-1) ... 123s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 123s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 123s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 123s Setting up python3-freetype (2.5.1-1) ... 123s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 123s Setting up python3-tz (2024.1-2) ... 123s Setting up unicode-data (15.1.0-1) ... 123s Setting up python3-six (1.16.0-7) ... 123s Setting up python3-decorator (5.1.1-5) ... 123s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 123s Setting up libblas3:arm64 (3.12.0-3build2) ... 123s 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 123s Setting up python3-packaging (24.1-1) ... 123s Setting up python3-brotli (1.1.0-2build2) ... 123s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 123s Setting up python3-cycler (0.12.1-1) ... 123s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 123s Setting up fonts-dejavu-mono (2.37-8) ... 123s Setting up python3-kiwisolver (1.4.7-2build1) ... 124s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 124s Setting up fonts-dejavu-core (2.37-8) ... 124s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 124s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 124s Setting up libwebp7:arm64 (1.4.0-0.1) ... 124s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 124s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 124s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 124s Setting up python3-dateutil (2.9.0-2) ... 124s Setting up sgml-base (1.31) ... 124s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 124s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 124s Setting up python3-mpmath (1.3.0-1) ... 124s Setting up python-matplotlib-data (3.8.3-3) ... 124s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 124s Setting up python3-appdirs (1.4.4-4) ... 124s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 124s Setting up python3-sympy (1.13.3-1) ... 131s Setting up liblapack3:arm64 (3.12.0-3build2) ... 131s 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 131s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 132s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 132s Setting up xfonts-utils (1:7.7+7) ... 132s Setting up python3-fs (2.4.16-4) ... 132s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 132s Setting up libraqm0:arm64 (0.10.1-1build1) ... 132s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 134s Setting up python3-lxml:arm64 (5.3.0-1) ... 134s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 134s Setting up xml-core (0.19) ... 134s Setting up python3-contourpy (1.3.0-2) ... 134s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 134s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 134s Setting up libxft2:arm64 (2.3.6-1build1) ... 135s Setting up python3-scipy (1.13.1-5) ... 139s Setting up libtk8.6:arm64 (8.6.15-1) ... 139s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 139s Setting up python3.12-tk (3.12.7-3) ... 139s Setting up fonts-urw-base35 (20200910-8) ... 139s Setting up libcairo2:arm64 (1.18.2-2) ... 139s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 139s Setting up python3-pandas (2.2.3+dfsg-5) ... 144s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 144s Setting up python3-cairo (1.26.1-2) ... 144s Setting up blt (2.5.3+dfsg-7build1) ... 144s Setting up python3-tk:arm64 (3.12.6-1ubuntu1) ... 144s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 144s Setting up python3-rlpycairo (0.3.0-3) ... 145s Setting up python3-reportlab (4.2.5-1) ... 145s Setting up python3-fonttools (4.46.0-1build2) ... 146s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 147s Setting up python3-matplotlib (3.8.3-3) ... 148s Processing triggers for libc-bin (2.40-1ubuntu3) ... 148s Processing triggers for man-db (2.12.1-3) ... 149s Processing triggers for sgml-base (1.31) ... 149s Setting up w3c-sgml-lib (1.3-3) ... 177s Setting up python3-biopython (1.84+dfsg-4build1) ... 179s Setting up python3-treetime (0.11.4-1) ... 179s Setting up autopkgtest-satdep (0) ... 183s (Reading database ... 90676 files and directories currently installed.) 183s Removing autopkgtest-satdep (0) ... 184s autopkgtest [21:31:50]: test run-unit-test: [----------------------- 185s 185s 0.00 -TreeAnc: set-up 185s read alignment from file h3n2_na/h3n2_na_20.fasta with 19 sequences of length 1407 185s read tree from file h3n2_na/h3n2_na_20.nwk with 19 leaves 185s 185s inferring ancestral sequences... 185s ...done. 185s 185s The TOTAL tree length is 1.311e-01 and 183 mutations were observed. 185s Of these 183 mutations, 185s - 148 occur 1 times 185s - 16 occur 2 times 185s - 1 occur 3 times 185s 185s Of the 1407 positions in the genome, 185s - 1237 were hit 0 times (expected 1235.40) 185s - 124 were hit 1 times (expected 160.68) 185s - 25 were hit 2 times (expected 10.45) 185s - 3 were hit 3 times (expected 0.45) 185s 185s log-likelihood difference to Poisson distribution with same mean: -1.226e+01 185s 185s 185s The ten most homoplasic mutations are: 185s mut multiplicity 185s G27A 3 185s A88G 2 185s A267G 2 185s G451R 2 185s G629A 2 185s C763T 2 185s G780A 2 185s C825T 2 185s C891A 2 185s C906T 2 186s homoplasy_scanning ok 186s 186s 0.00 -TreeAnc: set-up 186s 186s Inferred sequence evolution model (saved as 2024-11-14_ancestral/sequence_evolution_model.txt): 186s Substitution rate (mu): 1.0 186s 186s Equilibrium frequencies (pi_i): 186s A: 0.3062 186s C: 0.1925 186s G: 0.2336 186s T: 0.2577 186s -: 0.01 186s 186s Symmetrized rates from j->i (W_ij): 186s A C G T - 186s A 0 0.8311 2.7926 0.4496 1.0287 186s C 0.8311 0 0.577 2.8797 1.0535 186s G 2.7926 0.577 0 0.612 1.0437 186s T 0.4496 2.8797 0.612 0 1.0394 186s - 1.0287 1.0535 1.0437 1.0394 0 186s 186s Actual rates from j->i (Q_ij): 186s A C G T - 186s A 0 0.2545 0.8551 0.1377 0.315 186s C 0.16 0 0.1111 0.5543 0.2028 186s G 0.6523 0.1348 0 0.143 0.2438 186s T 0.1159 0.7421 0.1577 0 0.2678 186s - 0.0103 0.0106 0.0105 0.0104 0 186s 186s 186s --- alignment including ancestral nodes saved as 186s 2024-11-14_ancestral/ancestral_sequences.fasta 186s 186s --- tree saved in nexus format as 186s 2024-11-14_ancestral/annotated_tree.nexus 186s 186s --- tree saved in auspice json format as 186s 2024-11-14_ancestral/auspice_tree.json 186s 187s ancestral_reconstruction ok 189s 189s 0.00 -TreeAnc: set-up 189s 189s Attempting to parse dates... 189s Using column 'name' as name. This needs match the taxon names in the tree!! 189s Using column 'date' as date. 189s 189s 0.00 TreeTime.reroot: with method or node: least-squares 189s 189s 0.00 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 189s 189s 0.03 TreeTime.reroot: with method or node: least-squares 189s 189s 0.03 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 189s 189s 0.05 TreeTime.reroot: with method or node: least-squares 189s 189s 0.05 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 189s 189s Root-Tip-Regression: 189s --rate: 2.826e-03 189s --r^2: 0.98 189s 189s The R^2 value indicates the fraction of variation inroot-to-tip 189s distance explained by the sampling times.Higher values corresponds 189s more clock-like behavior (max 1.0). 189s 189s The rate is the slope of the best fit of the date tothe root-to-tip 189s distance and provides an estimate ofthe substitution rate. The rate 189s needs to be positive!Negative rates suggest an inappropriate root. 189s 189s 189s The estimated rate and tree correspond to a root date: 189s 189s --- root-date: 1996.75 189s 189s 189s --- new tree written to 189s 2024-11-14_clock/rerooted.newick 189s 189s --- wrote dates and root-to-tip distances to 189s 2024-11-14_clock/rtt.csv 189s 189s --- root-to-tip plot saved to 189s 2024-11-14_clock/root_to_tip_regression.pdf 189s temporal_signal ok 195s 195s Attempting to parse dates... 195s Using column 'name' as name. This needs match the taxon names in the tree!! 195s Using column 'date' as date. 195s 195s 0.00 -TreeAnc: set-up 195s 195s 0.10 TreeTime.reroot: with method or node: least-squares 195s 195s 0.10 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 195s 195s 0.13 TreeTime.reroot: with method or node: least-squares 195s 195s 0.13 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 195s 195s 0.20 ###TreeTime.run: INITIAL ROUND 195s 195s 0.77 TreeTime.reroot: with method or node: least-squares 195s 195s 0.77 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 195s 195s 0.79 ###TreeTime.run: rerunning timetree after rerooting 195s 195s 1.42 ###TreeTime.run: ITERATION 1 out of 2 iterations 195s 195s 1.42 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 195s polytomies using the old 'greedy' mode. This is not well suited for large 195s polytomies. Stochastic resolution will become the default in future 195s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 195s keep using the greedy method in the future, run with `--greedy-resolve` 195s 195s 2.06 ###TreeTime.run: CONVERGED 195s 195s 3.80 ###TreeTime.run: FINAL ROUND - confidence estimation via marginal 195s reconstruction 195s 195s Inferred sequence evolution model (saved as 2024-11-14_treetime/sequence_evolution_model.txt): 195s Substitution rate (mu): 1.0 195s 195s Equilibrium frequencies (pi_i): 195s A: 0.3088 195s C: 0.1897 195s G: 0.2335 195s T: 0.2581 195s -: 0.0099 195s 195s Symmetrized rates from j->i (W_ij): 195s A C G T - 195s A 0 0.7003 3.0669 0.2651 0.9742 195s C 0.7003 0 0.3354 3.399 0.999 195s G 3.0669 0.3354 0 0.4258 0.9892 195s T 0.2651 3.399 0.4258 0 0.9848 195s - 0.9742 0.999 0.9892 0.9848 0 195s 195s Actual rates from j->i (Q_ij): 195s A C G T - 195s A 0 0.2163 0.9472 0.0819 0.3009 195s C 0.1328 0 0.0636 0.6448 0.1895 195s G 0.716 0.0783 0 0.0994 0.2309 195s T 0.0684 0.8772 0.1099 0 0.2541 195s - 0.0097 0.0099 0.0098 0.0098 0 195s 195s 195s Inferred sequence evolution model (saved as 2024-11-14_treetime/molecular_clock.txt): 195s Root-Tip-Regression: 195s --rate: 2.674e-03 +/- 3.99e-04 (one std-dev) 195s --chi^2: 8.62 195s --r^2: 0.98 195s 195s --- saved tree as 195s 2024-11-14_treetime/timetree.pdf 195s 195s --- root-to-tip plot saved to 195s 2024-11-14_treetime/root_to_tip_regression.pdf 195s 195s --- alignment including ancestral nodes saved as 195s 2024-11-14_treetime/ancestral_sequences.fasta 195s 195s --- saved divergence times in 195s 2024-11-14_treetime/dates.tsv 195s 195s --- tree saved in nexus format as 195s 2024-11-14_treetime/timetree.nexus 195s 195s --- tree saved in auspice json format as 195s 2024-11-14_treetime/auspice_tree.json 195s 195s --- divergence tree saved in nexus format as 195s 2024-11-14_treetime/divergence_tree.nexus 195s 195s timetree_inference ok 196s /usr/lib/python3/dist-packages/treetime/wrappers.py:587: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 196s weight_dict = {row[0]:row[1] for ri,row in tmp_weights.iterrows() if not np.isnan(row[1])} 197s Using column '#name' as taxon name. This needs to match the taxa in the tree! 197s Assigned discrete traits to 86 out of 86 taxa. 197s 197s 197s Completed mugration model inference of attribute 'country' for zika/zika.nwk 197s 197s Saved inferred mugration model as: 2024-11-14_mugration/GTR.txt 197s Saved annotated tree as: 2024-11-14_mugration/annotated_tree.nexus 197s ---Done! 197s 197s mugration ok 248s 248s Attempting to parse dates... 248s Using column 'strain' as name. This needs match the taxon names in the tree!! 248s Using column 'date' as date. 248s 248s 0.00 -TreeAnc: set-up 248s 248s 5.97 TreeTime.reroot: with method or node: least-squares 248s 248s 5.97 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 248s 248s 6.16 TreeTime.reroot: with method or node: least-squares 248s 248s 6.16 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 248s 248s 7.27 ###TreeTime.run: INITIAL ROUND 248s 248s 14.54 TreeTime.reroot: with method or node: least-squares 248s 248s 14.54 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 248s 248s 14.71 ###TreeTime.run: rerunning timetree after rerooting 248s 248s 22.38 ###TreeTime.run: ITERATION 1 out of 2 iterations 248s 248s 22.38 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 248s polytomies using the old 'greedy' mode. This is not well suited for large 248s polytomies. Stochastic resolution will become the default in future 248s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 248s keep using the greedy method in the future, run with `--greedy-resolve` 248s 248s 33.25 ###TreeTime.run: ITERATION 2 out of 2 iterations 248s 248s 42.74 TreeTime: the following tips have been marked as outliers. Their date 248s constraints were not used. Please remove them from the tree. Their dates 248s have been reset: 248s 248s 42.74 G22619, input date: [2011.0013698630137, 2011.9986301369863], apparent 248s date: 1985.75 248s 248s 42.74 G22703, input date: [2004.0013661202186, 2004.9986338797814], apparent 248s date: 2012.13 248s 248s Inferred sequence evolution model (saved as 2024-11-14-0001_treetime/sequence_evolution_model.txt): 248s Substitution rate (mu): 1.0 248s 248s Equilibrium frequencies (pi_i): 248s A: 0.1669 248s C: 0.3286 248s G: 0.3273 248s T: 0.1669 248s -: 0.0103 248s 248s Symmetrized rates from j->i (W_ij): 248s A C G T - 248s A 0 0.768 1.6494 0.3119 35.7056 248s C 0.768 0 0.3143 1.4203 35.672 248s G 1.6494 0.3143 0 0.7442 49.1856 248s T 0.3119 1.4203 0.7442 0 31.9338 248s - 35.7056 35.672 49.1856 31.9338 0 248s 248s Actual rates from j->i (Q_ij): 248s A C G T - 248s A 0 0.1282 0.2753 0.0521 5.9597 248s C 0.2524 0 0.1033 0.4667 11.721 248s G 0.5399 0.1029 0 0.2436 16.0996 248s T 0.0521 0.237 0.1242 0 5.3291 248s - 0.3681 0.3678 0.5071 0.3292 0 248s 248s 248s Inferred sequence evolution model (saved as 2024-11-14-0001_treetime/molecular_clock.txt): 248s Root-Tip-Regression: 248s --rate: 1.000e-07 248s --r^2: 0.45 248s 248s --- saved tree as 248s 2024-11-14-0001_treetime/timetree.pdf 248s 248s --- root-to-tip plot saved to 248s 2024-11-14-0001_treetime/root_to_tip_regression.pdf 248s Sites that were constant except for ambiguous bases were made constant 248s by TreeTime. This happened 1343 times. These sites are now excluded 248s from the VCF. 248s 248s ***WARNING: vcf_utils.py 248s 52 sites were found that had no alternative bases. If this data has 248s been run through TreeTime and contains ambiguous bases, try calling 248s get_tree_dict with var_ambigs=True to see if this clears the error. 248s Alternative causes: - Not all sequences in your alignment are in the 248s tree (if you are running TreeTime via commandline this is most likely) 248s - In TreeTime, can be caused by overwriting variants in tips with 248s small branch lengths (debug) These are the positions affected 248s (numbering starts at 0): 248s 46593, 52473, 165918, 304891, 662240, 954864, 954865, 954866, 954867, 248s 963561, 1046706, 1145470, 1321893, 1468105, 1468106, 1512661, 1704463, 248s 1716723, 1743968, 1951837, 2129868, 2215816, 2274543, 2515984, 248s 2580886, 2626512, 2626513, 2626599, 2686156, 2736331, 2823901, 248s 2869282, 2894207, 2911378, 3047997, 3160385, 3314001, 3321447, 248s 3336505, 3461793, 3490408, 3618189, 3734466, 3764813, 3828626, 248s 3842630, 3894439, 3912292, 3913650, 3956227, 4149358, 4183687 248s 248s --- alignment including ancestral nodes saved as 248s 2024-11-14-0001_treetime/ancestral_sequences.vcf 248s 248s --- saved divergence times in 248s 2024-11-14-0001_treetime/dates.tsv 248s 248s --- tree saved in nexus format as 248s 2024-11-14-0001_treetime/timetree.nexus 248s 248s --- tree saved in auspice json format as 248s 2024-11-14-0001_treetime/auspice_tree.json 248s 248s --- divergence tree saved in nexus format as 248s 2024-11-14-0001_treetime/divergence_tree.nexus 248s 248s --- saved detected outliers as 2024-11-14-0001_treetime/outliers.tsv 248s timetree_inference on vcf data ok 359s 359s Attempting to parse dates... 359s Using column 'name' as name. This needs match the taxon names in the tree!! 359s Using column 'date' as date. 359s 359s 0.00 -TreeAnc: set-up 359s 359s 3.62 -WARNING: character U is unknown. Treating it as missing information 359s 359s 14.81 TreeTime.reroot: with method or node: least-squares 359s 359s 14.81 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 359s 359s 15.29 TreeTime.reroot: with method or node: least-squares 359s 359s 15.29 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 359s 359s 21.55 ###TreeTime.run: INITIAL ROUND 359s 359s 31.56 TreeTime.reroot: with method or node: least-squares 359s 359s 31.56 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 359s 359s 31.97 ###TreeTime.run: rerunning timetree after rerooting 359s 359s 45.05 ###TreeTime.run: ITERATION 1 out of 2 iterations 359s 359s 45.74 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 359s polytomies using the old 'greedy' mode. This is not well suited for large 359s polytomies. Stochastic resolution will become the default in future 359s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 359s keep using the greedy method in the future, run with `--greedy-resolve` 359s 359s 66.35 ###TreeTime.run: ITERATION 2 out of 2 iterations 359s 359s 104.59 TreeTime: the following tips have been marked as outliers. Their date 359s constraints were not used. Please remove them from the tree. Their dates 359s have been reset: 359s 359s 104.59 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.10 359s 359s 104.59 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.10 359s 359s 104.59 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.10 359s 359s 104.59 NZG_0381, input date: 2016.23, apparent date: 2015.10 359s 359s 104.59 NZG_0393, input date: 2016.24, apparent date: 2015.17 359s 359s 104.59 NZG_0358, input date: 2016.22, apparent date: 2015.17 359s 359s 104.59 NZG_0422, input date: 2016.25, apparent date: 2015.17 359s 359s 104.59 2607_C2_12855_EMLH, input date: 2015.28, apparent date: 2015.48 359s 359s 104.59 2607_C2_12916_EMLH, input date: 2015.32, apparent date: 2015.48 359s 359s 104.59 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.58 359s 359s 104.59 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.84 359s 359s 104.59 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.84 359s 359s 104.59 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.84 359s 359s 104.59 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2015.98 359s 359s 104.59 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.91 359s 359s 104.59 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.91 359s 359s 104.59 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.78 359s 359s 104.59 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.91 359s 359s 104.59 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2015.98 359s 359s 104.59 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2015.98 359s 359s Inferred sequence evolution model (saved as 2024-11-14-0002_treetime/sequence_evolution_model.txt): 359s Substitution rate (mu): 1.0 359s 359s Equilibrium frequencies (pi_i): 359s A: 0.3139 359s C: 0.2144 359s G: 0.1978 359s T: 0.2638 359s -: 0.01 359s 359s Symmetrized rates from j->i (W_ij): 359s A C G T - 359s A 0 0.3826 2.5277 0.2294 6.7951 359s C 0.3826 0 0.1691 3.5602 12.1804 359s G 2.5277 0.1691 0 0.3724 5.2953 359s T 0.2294 3.5602 0.3724 0 27.743 359s - 6.7951 12.1804 5.2953 27.743 0 359s 359s Actual rates from j->i (Q_ij): 359s A C G T - 359s A 0 0.1201 0.7935 0.072 2.1332 359s C 0.082 0 0.0363 0.7635 2.612 359s G 0.5001 0.0335 0 0.0737 1.0476 359s T 0.0605 0.9393 0.0983 0 7.3197 359s - 0.0676 0.1212 0.0527 0.2761 0 359s 359s 359s Inferred sequence evolution model (saved as 2024-11-14-0002_treetime/molecular_clock.txt): 359s Root-Tip-Regression: 359s --rate: 7.885e-04 359s --r^2: 0.80 359s 359s Inferred coalescent model 359s Skyline assuming 100.0 gen/year and approximate confidence bounds (+/- 2.000000 standard deviations of the LH) 359s date N_e lower upper 359s 2013.968 3.736e+01 1.526e+01 9.147e+01 359s 2014.065 6.120e+01 3.318e+01 1.129e+02 359s 2014.162 1.334e+02 8.103e+01 2.197e+02 359s 2014.259 1.447e+02 8.735e+01 2.397e+02 359s 2014.356 1.422e+02 9.349e+01 2.164e+02 359s 2014.453 3.147e+02 2.206e+02 4.491e+02 359s 2014.550 9.308e+02 6.321e+02 1.371e+03 359s 2014.647 1.092e+03 7.046e+02 1.693e+03 359s 2014.744 1.099e+03 7.122e+02 1.695e+03 359s 2014.840 9.957e+02 6.104e+02 1.624e+03 359s 2014.937 8.203e+02 5.111e+02 1.317e+03 359s 2015.034 3.210e+02 1.948e+02 5.291e+02 359s 2015.131 2.652e+02 1.748e+02 4.024e+02 359s 2015.228 2.757e+02 1.734e+02 4.384e+02 359s 2015.325 1.837e+02 1.138e+02 2.965e+02 359s 2015.422 1.520e+02 9.971e+01 2.318e+02 359s 2015.519 1.079e+02 6.593e+01 1.766e+02 359s 2015.616 1.083e+02 6.720e+01 1.747e+02 359s 2015.713 3.536e+01 1.874e+01 6.670e+01 359s 2015.810 1.032e+01 4.177e+00 2.552e+01 359s 359s --- written skyline to 2024-11-14-0002_treetime/skyline.tsv 359s 359s --- saved tree as 359s 2024-11-14-0002_treetime/timetree.pdf 359s 359s --- root-to-tip plot saved to 359s 2024-11-14-0002_treetime/root_to_tip_regression.pdf 359s 359s --- alignment including ancestral nodes saved as 359s 2024-11-14-0002_treetime/ancestral_sequences.fasta 359s 359s --- saved divergence times in 359s 2024-11-14-0002_treetime/dates.tsv 359s 359s --- tree saved in nexus format as 359s 2024-11-14-0002_treetime/timetree.nexus 359s 359s --- tree saved in auspice json format as 359s 2024-11-14-0002_treetime/auspice_tree.json 359s 359s --- divergence tree saved in nexus format as 359s 2024-11-14-0002_treetime/divergence_tree.nexus 359s 359s --- saved detected outliers as 2024-11-14-0002_treetime/outliers.tsv 360s skyline approximation ok 388s 388s Attempting to parse dates... 388s Using column 'name' as name. This needs match the taxon names in the tree!! 388s Using column 'date' as date. 388s 388s 0.00 -TreeAnc: set-up 388s 388s 0.06 TreeTime.reroot: with method or node: least-squares 388s 388s 0.06 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 388s 388s 0.63 TreeTime.reroot: with method or node: least-squares 388s 388s 0.63 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 388s 388s 1.05 ###TreeTime.run: INITIAL ROUND 388s 388s 9.03 TreeTime.reroot: with method or node: least-squares 388s 388s 9.03 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 388s 388s 9.46 ###TreeTime.run: rerunning timetree after rerooting 388s 388s 17.59 ###TreeTime.run: ITERATION 1 out of 2 iterations 388s 388s 17.59 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 388s polytomies using the old 'greedy' mode. This is not well suited for large 388s polytomies. Stochastic resolution will become the default in future 388s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 388s keep using the greedy method in the future, run with `--greedy-resolve` 388s 388s 25.76 ###TreeTime.run: CONVERGED 388s 388s 25.77 TreeTime: the following tips have been marked as outliers. Their date 388s constraints were not used. Please remove them from the tree. Their dates 388s have been reset: 388s 388s 25.77 NZG_0393, input date: 2016.24, apparent date: 2015.26 388s 388s 25.77 NZG_0422, input date: 2016.25, apparent date: 2015.26 388s 388s 25.77 NZG_0358, input date: 2016.22, apparent date: 2015.26 388s 388s 25.77 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.19 388s 388s 25.77 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.19 388s 388s 25.77 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.19 388s 388s 25.77 NZG_0381, input date: 2016.23, apparent date: 2015.19 388s 388s 25.77 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.40 388s 388s 25.77 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.81 388s 388s 25.77 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.81 388s 388s 25.77 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2015.87 388s 388s 25.77 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2015.87 388s 388s 25.77 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.74 388s 388s 25.77 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.81 388s 388s 25.77 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.68 388s 388s 25.77 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.74 388s 388s 25.77 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.74 388s 388s 25.77 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2015.87 388s 388s Inferred sequence evolution model (saved as 2024-11-14-0003_treetime/sequence_evolution_model.txt): 388s Substitution rate (mu): 1.0 388s 388s Equilibrium frequencies (pi_i): 388s A: 0.2 388s C: 0.2 388s G: 0.2 388s T: 0.2 388s -: 0.2 388s 388s Symmetrized rates from j->i (W_ij): 388s A C G T - 388s A 0 1.25 1.25 1.25 1.25 388s C 1.25 0 1.25 1.25 1.25 388s G 1.25 1.25 0 1.25 1.25 388s T 1.25 1.25 1.25 0 1.25 388s - 1.25 1.25 1.25 1.25 0 388s 388s Actual rates from j->i (Q_ij): 388s A C G T - 388s A 0 0.25 0.25 0.25 0.25 388s C 0.25 0 0.25 0.25 0.25 388s G 0.25 0.25 0 0.25 0.25 388s T 0.25 0.25 0.25 0 0.25 388s - 0.25 0.25 0.25 0.25 0 388s 388s 388s Inferred sequence evolution model (saved as 2024-11-14-0003_treetime/molecular_clock.txt): 388s Root-Tip-Regression: 388s --rate: 8.047e-04 388s --r^2: 0.79 388s 388s --- saved tree as 388s 2024-11-14-0003_treetime/timetree.pdf 388s 388s --- root-to-tip plot saved to 388s 2024-11-14-0003_treetime/root_to_tip_regression.pdf 388s --- saved divergence times in 388s 2024-11-14-0003_treetime/dates.tsv 388s 388s --- tree saved in nexus format as 388s 2024-11-14-0003_treetime/timetree.nexus 388s 388s --- tree saved in auspice json format as 388s 2024-11-14-0003_treetime/auspice_tree.json 388s 388s --- divergence tree saved in nexus format as 388s 2024-11-14-0003_treetime/divergence_tree.nexus 388s 388s --- saved detected outliers as 2024-11-14-0003_treetime/outliers.tsv 389s sequence length only ok 389s All tests passed 389s autopkgtest [21:35:15]: test run-unit-test: -----------------------] 390s autopkgtest [21:35:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 390s run-unit-test PASS 390s autopkgtest [21:35:16]: test autodep8-python3: preparing testbed 474s autopkgtest [21:36:40]: testbed dpkg architecture: arm64 474s autopkgtest [21:36:40]: testbed apt version: 2.9.8 474s autopkgtest [21:36:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 475s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 476s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1037 kB] 476s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [106 kB] 476s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 476s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.1 kB] 476s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [138 kB] 476s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 476s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [775 kB] 476s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6116 B] 476s Fetched 2210 kB in 1s (2318 kB/s) 476s Reading package lists... 479s Reading package lists... 479s Building dependency tree... 479s Reading state information... 480s Calculating upgrade... 481s The following packages will be upgraded: 481s libcap-ng0 pastebinit python3-systemd 481s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 481s Need to get 76.6 kB of archives. 481s After this operation, 349 kB of additional disk space will be used. 481s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libcap-ng0 arm64 0.8.5-3build1 [15.0 kB] 481s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 481s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 482s Fetched 76.6 kB in 0s (208 kB/s) 482s (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 ... 79925 files and directories currently installed.) 482s Preparing to unpack .../libcap-ng0_0.8.5-3build1_arm64.deb ... 482s Unpacking libcap-ng0:arm64 (0.8.5-3build1) over (0.8.5-1) ... 482s Setting up libcap-ng0:arm64 (0.8.5-3build1) ... 483s (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 ... 79925 files and directories currently installed.) 483s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 483s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 483s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 483s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 483s Setting up pastebinit (1.7.1-1) ... 483s Setting up python3-systemd (235-1build5) ... 483s Processing triggers for man-db (2.12.1-3) ... 484s Processing triggers for libc-bin (2.40-1ubuntu3) ... 484s Reading package lists... 485s Building dependency tree... 485s Reading state information... 486s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 486s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 486s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 486s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 486s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 488s Reading package lists... 488s Reading package lists... 488s Building dependency tree... 488s Reading state information... 489s Calculating upgrade... 491s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 491s Reading package lists... 491s Building dependency tree... 491s Reading state information... 492s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 498s Reading package lists... 499s Building dependency tree... 499s Reading state information... 499s Starting pkgProblemResolver with broken count: 0 500s Starting 2 pkgProblemResolver with broken count: 0 500s Done 501s The following additional packages will be installed: 501s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 501s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 501s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 501s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 501s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 501s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 501s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 501s python-matplotlib-data python3-all python3-appdirs python3-biopython 501s python3-brotli python3-cairo python3-contourpy python3-cycler 501s python3-dateutil python3-decorator python3-fonttools python3-freetype 501s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 501s python3-mpmath python3-numpy python3-packaging python3-pandas 501s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 501s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 501s python3-treetime python3-tz python3-ufolib2 python3.12-tk sgml-base 501s tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 501s xfonts-utils xml-core 501s Suggested packages: 501s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 501s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 501s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 501s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 501s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 501s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 501s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 501s python3-gobject python3-pyqt5 python3-sip python3-tornado 501s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 501s gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 501s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 501s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 501s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-tk 501s sgml-base-doc debhelper 501s Recommended packages: 501s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 501s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 501s python3-odf python3-openpyxl python3-tables python3-olefile 501s fonts-dejavu-extra g++ | c++-compiler isympy-common 501s The following NEW packages will be installed: 501s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 501s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 501s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 501s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 501s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 501s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 501s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 501s libxslt1.1 libxss1 python-matplotlib-data python3-all python3-appdirs 501s python3-biopython python3-brotli python3-cairo python3-contourpy 501s python3-cycler python3-dateutil python3-decorator python3-fonttools 501s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 501s python3-matplotlib python3-mpmath python3-numpy python3-packaging 501s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 501s python3-reportlab python3-rlpycairo python3-scipy python3-six python3-sympy 501s python3-tk python3-treetime python3-tz python3-ufolib2 python3.12-tk 501s sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 501s xfonts-utils xml-core 501s 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 501s Need to get 79.3 MB/79.3 MB of archives. 501s After this operation, 320 MB of additional disk space will be used. 501s Get:1 /tmp/autopkgtest.svENyt/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 501s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 501s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 504s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 505s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 506s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 506s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 506s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 506s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 506s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 511s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 511s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 511s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 511s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 511s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 511s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 512s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 512s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 512s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 512s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 512s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 512s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 512s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 512s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 512s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 512s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 512s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 512s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 512s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 512s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 512s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 512s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 512s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 512s Get:34 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 512s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 513s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 513s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 513s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 513s Get:39 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 513s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 513s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 513s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 513s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 513s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 513s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 513s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 513s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 513s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 513s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 513s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 513s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 513s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 514s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.6-1ubuntu1 [9806 B] 514s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 514s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 514s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 514s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 514s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 514s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 514s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 514s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 514s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 514s Get:63 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-biopython arm64 1.84+dfsg-4build1 [1694 kB] 514s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 514s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 514s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 514s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 514s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 514s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 514s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 516s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 516s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 516s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 516s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 516s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 516s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 516s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 516s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 517s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 517s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 517s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 517s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 518s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 518s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 518s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-treetime all 0.11.4-1 [941 kB] 519s Fetched 79.3 MB in 18s (4488 kB/s) 519s Selecting previously unselected package sgml-base. 519s (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 ... 79930 files and directories currently installed.) 519s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 519s Unpacking sgml-base (1.31) ... 519s Selecting previously unselected package libtcl8.6:arm64. 519s Preparing to unpack .../01-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 519s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 519s Selecting previously unselected package fonts-dejavu-mono. 519s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 519s Unpacking fonts-dejavu-mono (2.37-8) ... 519s Selecting previously unselected package fonts-dejavu-core. 519s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 519s Unpacking fonts-dejavu-core (2.37-8) ... 520s Selecting previously unselected package libfontenc1:arm64. 520s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 520s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 520s Selecting previously unselected package x11-common. 520s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 520s Unpacking x11-common (1:7.7+23ubuntu3) ... 520s Selecting previously unselected package xfonts-encodings. 520s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 520s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 520s Selecting previously unselected package xfonts-utils. 520s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_arm64.deb ... 520s Unpacking xfonts-utils (1:7.7+7) ... 520s Selecting previously unselected package fonts-urw-base35. 520s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 520s Unpacking fonts-urw-base35 (20200910-8) ... 520s Selecting previously unselected package fontconfig-config. 520s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 520s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 521s Selecting previously unselected package libfontconfig1:arm64. 521s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 521s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 521s Selecting previously unselected package libxrender1:arm64. 521s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 521s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 521s Selecting previously unselected package libxft2:arm64. 521s Preparing to unpack .../12-libxft2_2.3.6-1build1_arm64.deb ... 521s Unpacking libxft2:arm64 (2.3.6-1build1) ... 521s Selecting previously unselected package libxss1:arm64. 521s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_arm64.deb ... 521s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 521s Selecting previously unselected package libtk8.6:arm64. 521s Preparing to unpack .../14-libtk8.6_8.6.15-1_arm64.deb ... 521s Unpacking libtk8.6:arm64 (8.6.15-1) ... 521s Selecting previously unselected package tk8.6-blt2.5. 521s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 521s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 521s Selecting previously unselected package blt. 521s Preparing to unpack .../16-blt_2.5.3+dfsg-7build1_arm64.deb ... 521s Unpacking blt (2.5.3+dfsg-7build1) ... 521s Selecting previously unselected package fonts-lyx. 521s Preparing to unpack .../17-fonts-lyx_2.4.2.1-1_all.deb ... 521s Unpacking fonts-lyx (2.4.2.1-1) ... 521s Selecting previously unselected package libblas3:arm64. 521s Preparing to unpack .../18-libblas3_3.12.0-3build2_arm64.deb ... 521s Unpacking libblas3:arm64 (3.12.0-3build2) ... 521s Selecting previously unselected package libpixman-1-0:arm64. 521s Preparing to unpack .../19-libpixman-1-0_0.44.0-3_arm64.deb ... 521s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 521s Selecting previously unselected package libxcb-render0:arm64. 521s Preparing to unpack .../20-libxcb-render0_1.17.0-2_arm64.deb ... 521s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 521s Selecting previously unselected package libxcb-shm0:arm64. 521s Preparing to unpack .../21-libxcb-shm0_1.17.0-2_arm64.deb ... 521s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 521s Selecting previously unselected package libcairo2:arm64. 521s Preparing to unpack .../22-libcairo2_1.18.2-2_arm64.deb ... 521s Unpacking libcairo2:arm64 (1.18.2-2) ... 521s Selecting previously unselected package libdeflate0:arm64. 521s Preparing to unpack .../23-libdeflate0_1.22-1_arm64.deb ... 521s Unpacking libdeflate0:arm64 (1.22-1) ... 521s Selecting previously unselected package libgfortran5:arm64. 521s Preparing to unpack .../24-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 521s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 521s Selecting previously unselected package libgomp1:arm64. 521s Preparing to unpack .../25-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 521s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 521s Selecting previously unselected package libgraphite2-3:arm64. 521s Preparing to unpack .../26-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 521s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 521s Selecting previously unselected package libharfbuzz0b:arm64. 522s Preparing to unpack .../27-libharfbuzz0b_10.0.1-1_arm64.deb ... 522s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 522s Selecting previously unselected package libimagequant0:arm64. 522s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_arm64.deb ... 522s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 522s Selecting previously unselected package libjpeg-turbo8:arm64. 522s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 522s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 522s Selecting previously unselected package libjpeg8:arm64. 522s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_arm64.deb ... 522s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 522s Selecting previously unselected package libjs-jquery. 522s Preparing to unpack .../31-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 522s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 522s Selecting previously unselected package libjs-jquery-ui. 522s Preparing to unpack .../32-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 522s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 522s Selecting previously unselected package liblapack3:arm64. 522s Preparing to unpack .../33-liblapack3_3.12.0-3build2_arm64.deb ... 522s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 522s Selecting previously unselected package liblbfgsb0:arm64. 522s Preparing to unpack .../34-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 522s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 522s Selecting previously unselected package liblcms2-2:arm64. 522s Preparing to unpack .../35-liblcms2-2_2.16-2_arm64.deb ... 522s Unpacking liblcms2-2:arm64 (2.16-2) ... 522s Selecting previously unselected package liblerc4:arm64. 522s Preparing to unpack .../36-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 522s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 522s Selecting previously unselected package libqhull-r8.0:arm64. 522s Preparing to unpack .../37-libqhull-r8.0_2020.2-6build1_arm64.deb ... 522s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 522s Selecting previously unselected package libraqm0:arm64. 522s Preparing to unpack .../38-libraqm0_0.10.1-1build1_arm64.deb ... 522s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 522s Selecting previously unselected package libsharpyuv0:arm64. 522s Preparing to unpack .../39-libsharpyuv0_1.4.0-0.1_arm64.deb ... 522s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 522s Selecting previously unselected package libjbig0:arm64. 522s Preparing to unpack .../40-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 522s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 522s Selecting previously unselected package libwebp7:arm64. 522s Preparing to unpack .../41-libwebp7_1.4.0-0.1_arm64.deb ... 522s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 522s Selecting previously unselected package libtiff6:arm64. 522s Preparing to unpack .../42-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 522s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 523s Selecting previously unselected package libwebpdemux2:arm64. 523s Preparing to unpack .../43-libwebpdemux2_1.4.0-0.1_arm64.deb ... 523s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 523s Selecting previously unselected package libwebpmux3:arm64. 523s Preparing to unpack .../44-libwebpmux3_1.4.0-0.1_arm64.deb ... 523s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 523s Selecting previously unselected package libxslt1.1:arm64. 523s Preparing to unpack .../45-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 523s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 523s Selecting previously unselected package python-matplotlib-data. 523s Preparing to unpack .../46-python-matplotlib-data_3.8.3-3_all.deb ... 523s Unpacking python-matplotlib-data (3.8.3-3) ... 523s Selecting previously unselected package python3-all. 523s Preparing to unpack .../47-python3-all_3.12.6-0ubuntu1_arm64.deb ... 523s Unpacking python3-all (3.12.6-0ubuntu1) ... 523s Selecting previously unselected package python3-appdirs. 523s Preparing to unpack .../48-python3-appdirs_1.4.4-4_all.deb ... 523s Unpacking python3-appdirs (1.4.4-4) ... 523s Selecting previously unselected package python3-numpy. 523s Preparing to unpack .../49-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 523s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 523s Selecting previously unselected package python3.12-tk. 523s Preparing to unpack .../50-python3.12-tk_3.12.7-3_arm64.deb ... 523s Unpacking python3.12-tk (3.12.7-3) ... 523s Selecting previously unselected package python3-tk:arm64. 523s Preparing to unpack .../51-python3-tk_3.12.6-1ubuntu1_arm64.deb ... 523s Unpacking python3-tk:arm64 (3.12.6-1ubuntu1) ... 523s Selecting previously unselected package python3-pil.imagetk:arm64. 523s Preparing to unpack .../52-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 523s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 523s Selecting previously unselected package libopenjp2-7:arm64. 523s Preparing to unpack .../53-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 523s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 523s Selecting previously unselected package python3-pil:arm64. 523s Preparing to unpack .../54-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 523s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 524s Selecting previously unselected package python3-cairo. 524s Preparing to unpack .../55-python3-cairo_1.26.1-2_arm64.deb ... 524s Unpacking python3-cairo (1.26.1-2) ... 524s Selecting previously unselected package python3-freetype. 524s Preparing to unpack .../56-python3-freetype_2.5.1-1_all.deb ... 524s Unpacking python3-freetype (2.5.1-1) ... 524s Selecting previously unselected package python3-rlpycairo. 524s Preparing to unpack .../57-python3-rlpycairo_0.3.0-3_all.deb ... 524s Unpacking python3-rlpycairo (0.3.0-3) ... 524s Selecting previously unselected package python3-reportlab. 524s Preparing to unpack .../58-python3-reportlab_4.2.5-1_all.deb ... 524s Unpacking python3-reportlab (4.2.5-1) ... 524s Selecting previously unselected package xml-core. 524s Preparing to unpack .../59-xml-core_0.19_all.deb ... 524s Unpacking xml-core (0.19) ... 524s Selecting previously unselected package w3c-sgml-lib. 524s Preparing to unpack .../60-w3c-sgml-lib_1.3-3_all.deb ... 524s Unpacking w3c-sgml-lib (1.3-3) ... 524s Selecting previously unselected package python3-biopython. 524s Preparing to unpack .../61-python3-biopython_1.84+dfsg-4build1_arm64.deb ... 524s Unpacking python3-biopython (1.84+dfsg-4build1) ... 524s Selecting previously unselected package python3-brotli. 524s Preparing to unpack .../62-python3-brotli_1.1.0-2build2_arm64.deb ... 524s Unpacking python3-brotli (1.1.0-2build2) ... 524s Selecting previously unselected package python3-contourpy. 524s Preparing to unpack .../63-python3-contourpy_1.3.0-2_arm64.deb ... 524s Unpacking python3-contourpy (1.3.0-2) ... 524s Selecting previously unselected package python3-cycler. 524s Preparing to unpack .../64-python3-cycler_0.12.1-1_all.deb ... 524s Unpacking python3-cycler (0.12.1-1) ... 524s Selecting previously unselected package python3-six. 524s Preparing to unpack .../65-python3-six_1.16.0-7_all.deb ... 524s Unpacking python3-six (1.16.0-7) ... 525s Selecting previously unselected package python3-dateutil. 525s Preparing to unpack .../66-python3-dateutil_2.9.0-2_all.deb ... 525s Unpacking python3-dateutil (2.9.0-2) ... 525s Selecting previously unselected package python3-decorator. 525s Preparing to unpack .../67-python3-decorator_5.1.1-5_all.deb ... 525s Unpacking python3-decorator (5.1.1-5) ... 525s Selecting previously unselected package python3-scipy. 525s Preparing to unpack .../68-python3-scipy_1.13.1-5_arm64.deb ... 525s Unpacking python3-scipy (1.13.1-5) ... 525s Selecting previously unselected package python3-ufolib2. 525s Preparing to unpack .../69-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 525s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 525s Selecting previously unselected package python3-mpmath. 525s Preparing to unpack .../70-python3-mpmath_1.3.0-1_all.deb ... 525s Unpacking python3-mpmath (1.3.0-1) ... 525s Selecting previously unselected package python3-sympy. 525s Preparing to unpack .../71-python3-sympy_1.13.3-1_all.deb ... 525s Unpacking python3-sympy (1.13.3-1) ... 526s Selecting previously unselected package python3-tz. 526s Preparing to unpack .../72-python3-tz_2024.1-2_all.deb ... 526s Unpacking python3-tz (2024.1-2) ... 526s Selecting previously unselected package python3-fs. 526s Preparing to unpack .../73-python3-fs_2.4.16-4_all.deb ... 526s Unpacking python3-fs (2.4.16-4) ... 526s Selecting previously unselected package python3-lxml:arm64. 526s Preparing to unpack .../74-python3-lxml_5.3.0-1_arm64.deb ... 526s Unpacking python3-lxml:arm64 (5.3.0-1) ... 526s Selecting previously unselected package python3-lz4. 526s Preparing to unpack .../75-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 526s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 526s Selecting previously unselected package unicode-data. 526s Preparing to unpack .../76-unicode-data_15.1.0-1_all.deb ... 526s Unpacking unicode-data (15.1.0-1) ... 526s Selecting previously unselected package python3-fonttools. 526s Preparing to unpack .../77-python3-fonttools_4.46.0-1build2_arm64.deb ... 526s Unpacking python3-fonttools (4.46.0-1build2) ... 526s Selecting previously unselected package python3-kiwisolver. 526s Preparing to unpack .../78-python3-kiwisolver_1.4.7-2build1_arm64.deb ... 526s Unpacking python3-kiwisolver (1.4.7-2build1) ... 526s Selecting previously unselected package python3-packaging. 527s Preparing to unpack .../79-python3-packaging_24.1-1_all.deb ... 527s Unpacking python3-packaging (24.1-1) ... 527s Selecting previously unselected package python3-matplotlib. 527s Preparing to unpack .../80-python3-matplotlib_3.8.3-3_arm64.deb ... 527s Unpacking python3-matplotlib (3.8.3-3) ... 527s Selecting previously unselected package python3-pandas-lib:arm64. 527s Preparing to unpack .../81-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 527s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 527s Selecting previously unselected package python3-pandas. 527s Preparing to unpack .../82-python3-pandas_2.2.3+dfsg-5_all.deb ... 527s Unpacking python3-pandas (2.2.3+dfsg-5) ... 527s Selecting previously unselected package python3-treetime. 527s Preparing to unpack .../83-python3-treetime_0.11.4-1_all.deb ... 527s Unpacking python3-treetime (0.11.4-1) ... 527s Selecting previously unselected package autopkgtest-satdep. 527s Preparing to unpack .../84-2-autopkgtest-satdep.deb ... 527s Unpacking autopkgtest-satdep (0) ... 527s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 527s Setting up liblcms2-2:arm64 (2.16-2) ... 527s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 527s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 527s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 527s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 527s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 528s Setting up libxcb-render0:arm64 (1.17.0-2) ... 528s Setting up fonts-lyx (2.4.2.1-1) ... 528s Setting up x11-common (1:7.7+23ubuntu3) ... 528s Setting up libdeflate0:arm64 (1.22-1) ... 528s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 528s Setting up python3-all (3.12.6-0ubuntu1) ... 528s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 528s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 528s Setting up python3-freetype (2.5.1-1) ... 528s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 528s Setting up python3-tz (2024.1-2) ... 529s Setting up unicode-data (15.1.0-1) ... 529s Setting up python3-six (1.16.0-7) ... 529s Setting up python3-decorator (5.1.1-5) ... 529s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 529s Setting up libblas3:arm64 (3.12.0-3build2) ... 529s 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 529s Setting up python3-packaging (24.1-1) ... 529s Setting up python3-brotli (1.1.0-2build2) ... 529s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 529s Setting up python3-cycler (0.12.1-1) ... 530s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 530s Setting up fonts-dejavu-mono (2.37-8) ... 530s Setting up python3-kiwisolver (1.4.7-2build1) ... 530s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 530s Setting up fonts-dejavu-core (2.37-8) ... 530s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 530s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 530s Setting up libwebp7:arm64 (1.4.0-0.1) ... 530s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 530s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 530s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 530s Setting up python3-dateutil (2.9.0-2) ... 530s Setting up sgml-base (1.31) ... 530s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 530s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 530s Setting up python3-mpmath (1.3.0-1) ... 532s Setting up python-matplotlib-data (3.8.3-3) ... 532s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 532s Setting up python3-appdirs (1.4.4-4) ... 532s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 532s Setting up python3-sympy (1.13.3-1) ... 541s Setting up liblapack3:arm64 (3.12.0-3build2) ... 541s 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 541s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 541s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 541s Setting up xfonts-utils (1:7.7+7) ... 541s Setting up python3-fs (2.4.16-4) ... 542s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 542s Setting up libraqm0:arm64 (0.10.1-1build1) ... 542s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 544s Setting up python3-lxml:arm64 (5.3.0-1) ... 544s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 544s Setting up xml-core (0.19) ... 544s Setting up python3-contourpy (1.3.0-2) ... 545s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 545s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 545s Setting up libxft2:arm64 (2.3.6-1build1) ... 545s Setting up python3-scipy (1.13.1-5) ... 549s Setting up libtk8.6:arm64 (8.6.15-1) ... 549s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 549s Setting up python3.12-tk (3.12.7-3) ... 549s Setting up fonts-urw-base35 (20200910-8) ... 549s Setting up libcairo2:arm64 (1.18.2-2) ... 549s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 549s Setting up python3-pandas (2.2.3+dfsg-5) ... 555s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 555s Setting up python3-cairo (1.26.1-2) ... 555s Setting up blt (2.5.3+dfsg-7build1) ... 555s Setting up python3-tk:arm64 (3.12.6-1ubuntu1) ... 555s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 555s Setting up python3-rlpycairo (0.3.0-3) ... 555s Setting up python3-reportlab (4.2.5-1) ... 556s Setting up python3-fonttools (4.46.0-1build2) ... 557s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 557s Setting up python3-matplotlib (3.8.3-3) ... 559s Processing triggers for libc-bin (2.40-1ubuntu3) ... 559s Processing triggers for man-db (2.12.1-3) ... 560s Processing triggers for sgml-base (1.31) ... 560s Setting up w3c-sgml-lib (1.3-3) ... 588s Setting up python3-biopython (1.84+dfsg-4build1) ... 590s Setting up python3-treetime (0.11.4-1) ... 590s Setting up autopkgtest-satdep (0) ... 594s (Reading database ... 90667 files and directories currently installed.) 594s Removing autopkgtest-satdep (0) ... 598s autopkgtest [21:38:44]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import treetime; print(treetime)" ; done 598s autopkgtest [21:38:44]: test autodep8-python3: [----------------------- 598s Testing with python3.12: 599s 599s autopkgtest [21:38:45]: test autodep8-python3: -----------------------] 600s autodep8-python3 PASS (superficial) 600s autopkgtest [21:38:46]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 600s autopkgtest [21:38:46]: @@@@@@@@@@@@@@@@@@@@ summary 600s run-unit-test PASS 600s autodep8-python3 PASS (superficial) 605s nova [W] Skipping flock in bos03-arm64 605s Creating nova instance adt-plucky-arm64-python-treetime-20241114-212845-juju-7f2275-prod-proposed-migration-environment-15-91d76772-ac95-4521-8110-0869c7a8802a from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)... 605s nova [W] Skipping flock in bos03-arm64 605s Creating nova instance adt-plucky-arm64-python-treetime-20241114-212845-juju-7f2275-prod-proposed-migration-environment-15-91d76772-ac95-4521-8110-0869c7a8802a from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...