0s autopkgtest [10:58:51]: starting date and time: 2024-11-13 10:58:51+0000 0s autopkgtest [10:58:51]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [10:58:51]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mhxx27ew/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-treetime --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-46.secgroup --name adt-plucky-arm64-python-treetime-20241113-105851-juju-7f2275-prod-proposed-migration-environment-20-01271193-dd20-4ec3-81b3-49731cb60c8a --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 117s autopkgtest [11:00:48]: testbed dpkg architecture: arm64 119s autopkgtest [11:00:50]: testbed apt version: 2.9.8 119s autopkgtest [11:00:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 122s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 123s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 123s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 123s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 123s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 123s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 123s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 123s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 123s Fetched 1794 kB in 1s (2127 kB/s) 123s Reading package lists... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s Calculating upgrade... 129s The following NEW packages will be installed: 129s python3.13-gdbm 129s The following packages will be upgraded: 129s libpython3-stdlib python3 python3-gdbm python3-minimal 129s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 129s Need to get 101 kB of archives. 129s After this operation, 141 kB of additional disk space will be used. 129s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 129s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 129s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 129s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 129s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 130s Fetched 101 kB in 0s (273 kB/s) 130s (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 ... 79924 files and directories currently installed.) 130s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 130s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 131s Setting up python3-minimal (3.12.7-1) ... 131s (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 ... 79924 files and directories currently installed.) 131s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 131s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 131s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 131s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 132s Selecting previously unselected package python3.13-gdbm. 132s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 132s Unpacking python3.13-gdbm (3.13.0-2) ... 132s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 132s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 132s Setting up python3.13-gdbm (3.13.0-2) ... 132s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 132s Setting up python3 (3.12.7-1) ... 132s Setting up python3-gdbm:arm64 (3.12.7-1) ... 132s Processing triggers for man-db (2.12.1-3) ... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 135s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 135s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 135s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 137s Reading package lists... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s Calculating upgrade... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [11:01:19]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 149s autopkgtest [11:01:20]: @@@@@@@@@@@@@@@@@@@@ apt-source python-treetime 152s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (dsc) [2611 B] 152s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [5117 kB] 152s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [1291 kB] 152s Get:4 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (diff) [8028 B] 152s gpgv: Signature made Sat Nov 9 21:31:47 2024 UTC 152s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 152s gpgv: issuer "emollier@debian.org" 152s gpgv: Can't check signature: No public key 152s dpkg-source: warning: cannot verify inline signature for ./python-treetime_0.11.4-1.dsc: no acceptable signature found 153s autopkgtest [11:01:24]: testing package python-treetime version 0.11.4-1 156s autopkgtest [11:01:27]: build not needed 160s autopkgtest [11:01:31]: test run-unit-test: preparing testbed 163s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Starting pkgProblemResolver with broken count: 0 164s Starting 2 pkgProblemResolver with broken count: 0 164s Done 165s The following additional packages will be installed: 165s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 165s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 165s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 165s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 165s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 165s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 165s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 165s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 165s python3-cairo python3-contourpy python3-cycler python3-dateutil 165s python3-decorator python3-fonttools python3-freetype python3-fs 165s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 165s python3-mpmath python3-numpy python3-packaging python3-pandas 165s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 165s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 165s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 165s python3.12-tk python3.13-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib 165s x11-common xfonts-encodings xfonts-utils xml-core 165s Suggested packages: 165s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 165s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 165s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 165s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 165s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 165s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 165s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 165s python3-gobject python3-pyqt5 python3-sip python3-tornado 165s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 165s gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 165s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 165s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 165s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg sgml-base-doc 165s debhelper 165s Recommended packages: 165s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 165s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 165s python3-odf python3-openpyxl python3-tables python3-olefile 165s fonts-dejavu-extra g++ | c++-compiler isympy-common 165s The following NEW packages will be installed: 165s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 165s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 165s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 165s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 165s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 165s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 165s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 165s libxslt1.1 libxss1 python-matplotlib-data python3-appdirs python3-biopython 165s python3-brotli python3-cairo python3-contourpy python3-cycler 165s python3-dateutil python3-decorator python3-fonttools python3-freetype 165s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 165s python3-mpmath python3-numpy python3-packaging python3-pandas 165s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 165s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 165s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 165s python3.12-tk python3.13-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib 165s x11-common xfonts-encodings xfonts-utils xml-core 165s 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 79.7 MB/79.7 MB of archives. 165s After this operation, 321 MB of additional disk space will be used. 165s Get:1 /tmp/autopkgtest.HWWLdk/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 165s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 165s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 166s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 166s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 166s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 166s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 166s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 166s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 166s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 166s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 166s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 166s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 166s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 166s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 166s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 166s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 166s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 166s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 166s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 166s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 166s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 166s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 166s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 166s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 166s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 166s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 166s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 166s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 166s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 166s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 166s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 166s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 166s Get:34 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 166s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 166s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 166s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 166s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 166s Get:39 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 166s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 166s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 166s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 166s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 166s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 167s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 167s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 167s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 167s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 167s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 167s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 167s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 167s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 167s Get:53 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 167s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 167s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 167s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 167s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 167s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 167s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 167s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 167s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 167s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 167s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 167s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 167s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 167s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 167s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 167s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 167s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 167s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 167s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 167s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 167s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 167s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 167s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 167s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 167s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 167s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB] 167s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 168s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 168s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2 [50.4 kB] 168s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 168s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 168s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 168s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 168s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-treetime all 0.11.4-1 [941 kB] 169s Fetched 79.7 MB in 3s (23.9 MB/s) 169s Selecting previously unselected package sgml-base. 169s (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 ... 79931 files and directories currently installed.) 169s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 169s Unpacking sgml-base (1.31) ... 169s Selecting previously unselected package libtcl8.6:arm64. 169s Preparing to unpack .../01-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 169s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 169s Selecting previously unselected package fonts-dejavu-mono. 169s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 169s Unpacking fonts-dejavu-mono (2.37-8) ... 169s Selecting previously unselected package fonts-dejavu-core. 169s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 169s Unpacking fonts-dejavu-core (2.37-8) ... 169s Selecting previously unselected package libfontenc1:arm64. 169s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 169s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 169s Selecting previously unselected package x11-common. 169s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 169s Unpacking x11-common (1:7.7+23ubuntu3) ... 169s Selecting previously unselected package xfonts-encodings. 169s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 169s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 169s Selecting previously unselected package xfonts-utils. 169s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_arm64.deb ... 169s Unpacking xfonts-utils (1:7.7+7) ... 169s Selecting previously unselected package fonts-urw-base35. 170s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 170s Unpacking fonts-urw-base35 (20200910-8) ... 170s Selecting previously unselected package fontconfig-config. 170s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 170s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 170s Selecting previously unselected package libfontconfig1:arm64. 170s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 170s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 170s Selecting previously unselected package libxrender1:arm64. 170s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 170s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 170s Selecting previously unselected package libxft2:arm64. 170s Preparing to unpack .../12-libxft2_2.3.6-1build1_arm64.deb ... 170s Unpacking libxft2:arm64 (2.3.6-1build1) ... 170s Selecting previously unselected package libxss1:arm64. 170s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_arm64.deb ... 170s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 170s Selecting previously unselected package libtk8.6:arm64. 170s Preparing to unpack .../14-libtk8.6_8.6.15-1_arm64.deb ... 170s Unpacking libtk8.6:arm64 (8.6.15-1) ... 170s Selecting previously unselected package tk8.6-blt2.5. 170s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 170s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 170s Selecting previously unselected package blt. 170s Preparing to unpack .../16-blt_2.5.3+dfsg-7build1_arm64.deb ... 170s Unpacking blt (2.5.3+dfsg-7build1) ... 170s Selecting previously unselected package fonts-lyx. 170s Preparing to unpack .../17-fonts-lyx_2.4.2.1-1_all.deb ... 170s Unpacking fonts-lyx (2.4.2.1-1) ... 171s Selecting previously unselected package libblas3:arm64. 171s Preparing to unpack .../18-libblas3_3.12.0-3build2_arm64.deb ... 171s Unpacking libblas3:arm64 (3.12.0-3build2) ... 171s Selecting previously unselected package libpixman-1-0:arm64. 171s Preparing to unpack .../19-libpixman-1-0_0.44.0-3_arm64.deb ... 171s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 171s Selecting previously unselected package libxcb-render0:arm64. 171s Preparing to unpack .../20-libxcb-render0_1.17.0-2_arm64.deb ... 171s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 171s Selecting previously unselected package libxcb-shm0:arm64. 171s Preparing to unpack .../21-libxcb-shm0_1.17.0-2_arm64.deb ... 171s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 171s Selecting previously unselected package libcairo2:arm64. 171s Preparing to unpack .../22-libcairo2_1.18.2-2_arm64.deb ... 171s Unpacking libcairo2:arm64 (1.18.2-2) ... 171s Selecting previously unselected package libdeflate0:arm64. 171s Preparing to unpack .../23-libdeflate0_1.22-1_arm64.deb ... 171s Unpacking libdeflate0:arm64 (1.22-1) ... 171s Selecting previously unselected package libgfortran5:arm64. 171s Preparing to unpack .../24-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 171s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 171s Selecting previously unselected package libgomp1:arm64. 171s Preparing to unpack .../25-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 171s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 171s Selecting previously unselected package libgraphite2-3:arm64. 171s Preparing to unpack .../26-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 171s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 171s Selecting previously unselected package libharfbuzz0b:arm64. 171s Preparing to unpack .../27-libharfbuzz0b_10.0.1-1_arm64.deb ... 171s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 171s Selecting previously unselected package libimagequant0:arm64. 171s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_arm64.deb ... 171s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 171s Selecting previously unselected package libjpeg-turbo8:arm64. 171s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 171s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 171s Selecting previously unselected package libjpeg8:arm64. 171s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_arm64.deb ... 171s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 171s Selecting previously unselected package libjs-jquery. 171s Preparing to unpack .../31-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 171s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 171s Selecting previously unselected package libjs-jquery-ui. 171s Preparing to unpack .../32-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 171s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 171s Selecting previously unselected package liblapack3:arm64. 171s Preparing to unpack .../33-liblapack3_3.12.0-3build2_arm64.deb ... 171s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 171s Selecting previously unselected package liblbfgsb0:arm64. 171s Preparing to unpack .../34-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 171s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 171s Selecting previously unselected package liblcms2-2:arm64. 171s Preparing to unpack .../35-liblcms2-2_2.16-2_arm64.deb ... 171s Unpacking liblcms2-2:arm64 (2.16-2) ... 171s Selecting previously unselected package liblerc4:arm64. 172s Preparing to unpack .../36-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 172s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 172s Selecting previously unselected package libqhull-r8.0:arm64. 172s Preparing to unpack .../37-libqhull-r8.0_2020.2-6build1_arm64.deb ... 172s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 172s Selecting previously unselected package libraqm0:arm64. 172s Preparing to unpack .../38-libraqm0_0.10.1-1build1_arm64.deb ... 172s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 172s Selecting previously unselected package libsharpyuv0:arm64. 172s Preparing to unpack .../39-libsharpyuv0_1.4.0-0.1_arm64.deb ... 172s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 172s Selecting previously unselected package libjbig0:arm64. 172s Preparing to unpack .../40-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 172s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 172s Selecting previously unselected package libwebp7:arm64. 172s Preparing to unpack .../41-libwebp7_1.4.0-0.1_arm64.deb ... 172s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 172s Selecting previously unselected package libtiff6:arm64. 172s Preparing to unpack .../42-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 172s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 172s Selecting previously unselected package libwebpdemux2:arm64. 172s Preparing to unpack .../43-libwebpdemux2_1.4.0-0.1_arm64.deb ... 172s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 172s Selecting previously unselected package libwebpmux3:arm64. 172s Preparing to unpack .../44-libwebpmux3_1.4.0-0.1_arm64.deb ... 172s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 172s Selecting previously unselected package libxslt1.1:arm64. 172s Preparing to unpack .../45-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 172s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 172s Selecting previously unselected package python-matplotlib-data. 172s Preparing to unpack .../46-python-matplotlib-data_3.8.3-3_all.deb ... 172s Unpacking python-matplotlib-data (3.8.3-3) ... 172s Selecting previously unselected package python3-appdirs. 172s Preparing to unpack .../47-python3-appdirs_1.4.4-4_all.deb ... 172s Unpacking python3-appdirs (1.4.4-4) ... 172s Selecting previously unselected package python3-numpy. 172s Preparing to unpack .../48-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 172s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 172s Selecting previously unselected package python3.12-tk. 172s Preparing to unpack .../49-python3.12-tk_3.12.7-3_arm64.deb ... 172s Unpacking python3.12-tk (3.12.7-3) ... 172s Selecting previously unselected package python3.13-tk. 172s Preparing to unpack .../50-python3.13-tk_3.13.0-2_arm64.deb ... 172s Unpacking python3.13-tk (3.13.0-2) ... 172s Selecting previously unselected package python3-tk:arm64. 173s Preparing to unpack .../51-python3-tk_3.12.7-1_arm64.deb ... 173s Unpacking python3-tk:arm64 (3.12.7-1) ... 173s Selecting previously unselected package python3-pil.imagetk:arm64. 173s Preparing to unpack .../52-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 173s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 173s Selecting previously unselected package libopenjp2-7:arm64. 173s Preparing to unpack .../53-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 173s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 173s Selecting previously unselected package python3-pil:arm64. 173s Preparing to unpack .../54-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 173s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 173s Selecting previously unselected package python3-cairo. 173s Preparing to unpack .../55-python3-cairo_1.26.1-2_arm64.deb ... 173s Unpacking python3-cairo (1.26.1-2) ... 173s Selecting previously unselected package python3-freetype. 173s Preparing to unpack .../56-python3-freetype_2.5.1-1_all.deb ... 173s Unpacking python3-freetype (2.5.1-1) ... 173s Selecting previously unselected package python3-rlpycairo. 173s Preparing to unpack .../57-python3-rlpycairo_0.3.0-3_all.deb ... 173s Unpacking python3-rlpycairo (0.3.0-3) ... 173s Selecting previously unselected package python3-reportlab. 173s Preparing to unpack .../58-python3-reportlab_4.2.5-1_all.deb ... 173s Unpacking python3-reportlab (4.2.5-1) ... 173s Selecting previously unselected package xml-core. 173s Preparing to unpack .../59-xml-core_0.19_all.deb ... 173s Unpacking xml-core (0.19) ... 173s Selecting previously unselected package w3c-sgml-lib. 173s Preparing to unpack .../60-w3c-sgml-lib_1.3-3_all.deb ... 173s Unpacking w3c-sgml-lib (1.3-3) ... 173s Selecting previously unselected package python3-biopython. 173s Preparing to unpack .../61-python3-biopython_1.84+dfsg-4_arm64.deb ... 173s Unpacking python3-biopython (1.84+dfsg-4) ... 173s Selecting previously unselected package python3-brotli. 173s Preparing to unpack .../62-python3-brotli_1.1.0-2build2_arm64.deb ... 173s Unpacking python3-brotli (1.1.0-2build2) ... 173s Selecting previously unselected package python3-contourpy. 173s Preparing to unpack .../63-python3-contourpy_1.3.0-2_arm64.deb ... 173s Unpacking python3-contourpy (1.3.0-2) ... 173s Selecting previously unselected package python3-cycler. 174s Preparing to unpack .../64-python3-cycler_0.12.1-1_all.deb ... 174s Unpacking python3-cycler (0.12.1-1) ... 174s Selecting previously unselected package python3-six. 174s Preparing to unpack .../65-python3-six_1.16.0-7_all.deb ... 174s Unpacking python3-six (1.16.0-7) ... 174s Selecting previously unselected package python3-dateutil. 174s Preparing to unpack .../66-python3-dateutil_2.9.0-2_all.deb ... 174s Unpacking python3-dateutil (2.9.0-2) ... 174s Selecting previously unselected package python3-decorator. 174s Preparing to unpack .../67-python3-decorator_5.1.1-5_all.deb ... 174s Unpacking python3-decorator (5.1.1-5) ... 174s Selecting previously unselected package python3-scipy. 174s Preparing to unpack .../68-python3-scipy_1.13.1-5_arm64.deb ... 174s Unpacking python3-scipy (1.13.1-5) ... 174s Selecting previously unselected package python3-ufolib2. 174s Preparing to unpack .../69-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 174s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 174s Selecting previously unselected package python3-mpmath. 174s Preparing to unpack .../70-python3-mpmath_1.3.0-1_all.deb ... 174s Unpacking python3-mpmath (1.3.0-1) ... 174s Selecting previously unselected package python3-sympy. 174s Preparing to unpack .../71-python3-sympy_1.13.3-1_all.deb ... 174s Unpacking python3-sympy (1.13.3-1) ... 175s Selecting previously unselected package python3-tz. 175s Preparing to unpack .../72-python3-tz_2024.1-2_all.deb ... 175s Unpacking python3-tz (2024.1-2) ... 175s Selecting previously unselected package python3-fs. 175s Preparing to unpack .../73-python3-fs_2.4.16-4_all.deb ... 175s Unpacking python3-fs (2.4.16-4) ... 175s Selecting previously unselected package python3-lxml:arm64. 175s Preparing to unpack .../74-python3-lxml_5.3.0-1_arm64.deb ... 175s Unpacking python3-lxml:arm64 (5.3.0-1) ... 175s Selecting previously unselected package python3-lz4. 175s Preparing to unpack .../75-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 175s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 175s Selecting previously unselected package python3-unicodedata2. 175s Preparing to unpack .../76-python3-unicodedata2_15.1.0+ds-1build1_arm64.deb ... 175s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 175s Selecting previously unselected package unicode-data. 175s Preparing to unpack .../77-unicode-data_15.1.0-1_all.deb ... 175s Unpacking unicode-data (15.1.0-1) ... 175s Selecting previously unselected package python3-fonttools. 175s Preparing to unpack .../78-python3-fonttools_4.46.0-1build2_arm64.deb ... 175s Unpacking python3-fonttools (4.46.0-1build2) ... 176s Selecting previously unselected package python3-kiwisolver. 176s Preparing to unpack .../79-python3-kiwisolver_1.4.7-2_arm64.deb ... 176s Unpacking python3-kiwisolver (1.4.7-2) ... 176s Selecting previously unselected package python3-packaging. 176s Preparing to unpack .../80-python3-packaging_24.1-1_all.deb ... 176s Unpacking python3-packaging (24.1-1) ... 176s Selecting previously unselected package python3-matplotlib. 176s Preparing to unpack .../81-python3-matplotlib_3.8.3-3_arm64.deb ... 176s Unpacking python3-matplotlib (3.8.3-3) ... 176s Selecting previously unselected package python3-pandas-lib:arm64. 176s Preparing to unpack .../82-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 176s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 176s Selecting previously unselected package python3-pandas. 176s Preparing to unpack .../83-python3-pandas_2.2.3+dfsg-5_all.deb ... 176s Unpacking python3-pandas (2.2.3+dfsg-5) ... 176s Selecting previously unselected package python3-treetime. 176s Preparing to unpack .../84-python3-treetime_0.11.4-1_all.deb ... 176s Unpacking python3-treetime (0.11.4-1) ... 176s Selecting previously unselected package autopkgtest-satdep. 176s Preparing to unpack .../85-1-autopkgtest-satdep.deb ... 176s Unpacking autopkgtest-satdep (0) ... 176s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 176s Setting up liblcms2-2:arm64 (2.16-2) ... 176s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 176s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 176s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 176s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 176s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 177s Setting up libxcb-render0:arm64 (1.17.0-2) ... 177s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 177s Setting up fonts-lyx (2.4.2.1-1) ... 177s Setting up x11-common (1:7.7+23ubuntu3) ... 177s Setting up libdeflate0:arm64 (1.22-1) ... 177s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 177s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 177s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 177s Setting up python3-freetype (2.5.1-1) ... 177s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 177s Setting up python3-tz (2024.1-2) ... 177s Setting up unicode-data (15.1.0-1) ... 177s Setting up python3-six (1.16.0-7) ... 177s Setting up python3-decorator (5.1.1-5) ... 178s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 178s Setting up libblas3:arm64 (3.12.0-3build2) ... 178s 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 178s Setting up python3-packaging (24.1-1) ... 178s Setting up python3-brotli (1.1.0-2build2) ... 178s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 178s Setting up python3-cycler (0.12.1-1) ... 178s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 178s Setting up fonts-dejavu-mono (2.37-8) ... 178s Setting up python3-kiwisolver (1.4.7-2) ... 178s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 178s Setting up fonts-dejavu-core (2.37-8) ... 178s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 178s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 178s Setting up libwebp7:arm64 (1.4.0-0.1) ... 178s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 178s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 178s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 178s Setting up python3-dateutil (2.9.0-2) ... 178s Setting up sgml-base (1.31) ... 178s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 178s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 178s Setting up python3-mpmath (1.3.0-1) ... 179s Setting up python-matplotlib-data (3.8.3-3) ... 179s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 179s Setting up python3-appdirs (1.4.4-4) ... 179s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 179s Setting up python3-sympy (1.13.3-1) ... 187s Setting up liblapack3:arm64 (3.12.0-3build2) ... 187s 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 187s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 187s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 187s Setting up xfonts-utils (1:7.7+7) ... 187s Setting up python3-fs (2.4.16-4) ... 187s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 187s Setting up libraqm0:arm64 (0.10.1-1build1) ... 187s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 189s Setting up python3-lxml:arm64 (5.3.0-1) ... 189s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 189s Setting up xml-core (0.19) ... 190s Setting up python3-contourpy (1.3.0-2) ... 190s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 190s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 190s Setting up libxft2:arm64 (2.3.6-1build1) ... 190s Setting up python3-scipy (1.13.1-5) ... 194s Setting up libtk8.6:arm64 (8.6.15-1) ... 194s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 194s Setting up python3.12-tk (3.12.7-3) ... 194s Setting up fonts-urw-base35 (20200910-8) ... 194s Setting up libcairo2:arm64 (1.18.2-2) ... 194s Setting up python3.13-tk (3.13.0-2) ... 194s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 195s Setting up python3-pandas (2.2.3+dfsg-5) ... 200s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 200s Setting up python3-cairo (1.26.1-2) ... 201s Setting up blt (2.5.3+dfsg-7build1) ... 201s Setting up python3-tk:arm64 (3.12.7-1) ... 201s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 201s Setting up python3-rlpycairo (0.3.0-3) ... 201s Setting up python3-reportlab (4.2.5-1) ... 202s Setting up python3-fonttools (4.46.0-1build2) ... 203s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 203s Setting up python3-matplotlib (3.8.3-3) ... 205s Processing triggers for libc-bin (2.40-1ubuntu3) ... 205s Processing triggers for man-db (2.12.1-3) ... 206s Processing triggers for sgml-base (1.31) ... 206s Setting up w3c-sgml-lib (1.3-3) ... 234s Setting up python3-biopython (1.84+dfsg-4) ... 235s Setting up python3-treetime (0.11.4-1) ... 235s Setting up autopkgtest-satdep (0) ... 241s (Reading database ... 90686 files and directories currently installed.) 241s Removing autopkgtest-satdep (0) ... 242s autopkgtest [11:02:53]: test run-unit-test: [----------------------- 243s 243s 0.00 -TreeAnc: set-up 243s read alignment from file h3n2_na/h3n2_na_20.fasta with 19 sequences of length 1407 243s read tree from file h3n2_na/h3n2_na_20.nwk with 19 leaves 243s 243s inferring ancestral sequences... 243s ...done. 243s 243s The TOTAL tree length is 1.311e-01 and 183 mutations were observed. 243s Of these 183 mutations, 243s - 148 occur 1 times 243s - 16 occur 2 times 243s - 1 occur 3 times 243s 243s Of the 1407 positions in the genome, 243s - 1237 were hit 0 times (expected 1235.40) 243s - 124 were hit 1 times (expected 160.68) 243s - 25 were hit 2 times (expected 10.45) 243s - 3 were hit 3 times (expected 0.45) 243s 243s log-likelihood difference to Poisson distribution with same mean: -1.226e+01 243s 243s 243s The ten most homoplasic mutations are: 243s mut multiplicity 243s G27A 3 243s A88G 2 243s A267G 2 243s G451R 2 243s G629A 2 243s C763T 2 243s G780A 2 243s C825T 2 243s C891A 2 243s C906T 2 244s homoplasy_scanning ok 244s 244s 0.00 -TreeAnc: set-up 244s 244s Inferred sequence evolution model (saved as 2024-11-13_ancestral/sequence_evolution_model.txt): 244s Substitution rate (mu): 1.0 244s 244s Equilibrium frequencies (pi_i): 244s A: 0.3062 244s C: 0.1925 244s G: 0.2336 244s T: 0.2577 244s -: 0.01 244s 244s Symmetrized rates from j->i (W_ij): 244s A C G T - 244s A 0 0.8311 2.7926 0.4496 1.0287 244s C 0.8311 0 0.577 2.8797 1.0535 244s G 2.7926 0.577 0 0.612 1.0437 244s T 0.4496 2.8797 0.612 0 1.0394 244s - 1.0287 1.0535 1.0437 1.0394 0 244s 244s Actual rates from j->i (Q_ij): 244s A C G T - 244s A 0 0.2545 0.8551 0.1377 0.315 244s C 0.16 0 0.1111 0.5543 0.2028 244s G 0.6523 0.1348 0 0.143 0.2438 244s T 0.1159 0.7421 0.1577 0 0.2678 244s - 0.0103 0.0106 0.0105 0.0104 0 244s 244s 244s --- alignment including ancestral nodes saved as 244s 2024-11-13_ancestral/ancestral_sequences.fasta 244s 244s --- tree saved in nexus format as 244s 2024-11-13_ancestral/annotated_tree.nexus 244s 244s --- tree saved in auspice json format as 244s 2024-11-13_ancestral/auspice_tree.json 244s 245s ancestral_reconstruction ok 247s 247s 0.00 -TreeAnc: set-up 247s 247s Attempting to parse dates... 247s Using column 'name' as name. This needs match the taxon names in the tree!! 247s Using column 'date' as date. 247s 247s 0.00 TreeTime.reroot: with method or node: least-squares 247s 247s 0.01 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 247s 247s 0.03 TreeTime.reroot: with method or node: least-squares 247s 247s 0.03 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 247s 247s 0.05 TreeTime.reroot: with method or node: least-squares 247s 247s 0.05 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 247s 247s Root-Tip-Regression: 247s --rate: 2.826e-03 247s --r^2: 0.98 247s 247s The R^2 value indicates the fraction of variation inroot-to-tip 247s distance explained by the sampling times.Higher values corresponds 247s more clock-like behavior (max 1.0). 247s 247s The rate is the slope of the best fit of the date tothe root-to-tip 247s distance and provides an estimate ofthe substitution rate. The rate 247s needs to be positive!Negative rates suggest an inappropriate root. 247s 247s 247s The estimated rate and tree correspond to a root date: 247s 247s --- root-date: 1996.75 247s 247s 247s --- new tree written to 247s 2024-11-13_clock/rerooted.newick 247s 247s --- wrote dates and root-to-tip distances to 247s 2024-11-13_clock/rtt.csv 247s 247s --- root-to-tip plot saved to 247s 2024-11-13_clock/root_to_tip_regression.pdf 247s temporal_signal ok 253s 253s Attempting to parse dates... 253s Using column 'name' as name. This needs match the taxon names in the tree!! 253s Using column 'date' as date. 253s 253s 0.00 -TreeAnc: set-up 253s 253s 0.11 TreeTime.reroot: with method or node: least-squares 253s 253s 0.11 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 253s 253s 0.14 TreeTime.reroot: with method or node: least-squares 253s 253s 0.14 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 253s 253s 0.25 ###TreeTime.run: INITIAL ROUND 253s 253s 0.87 TreeTime.reroot: with method or node: least-squares 253s 253s 0.87 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 253s 253s 0.89 ###TreeTime.run: rerunning timetree after rerooting 253s 253s 1.57 ###TreeTime.run: ITERATION 1 out of 2 iterations 253s 253s 1.57 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 253s polytomies using the old 'greedy' mode. This is not well suited for large 253s polytomies. Stochastic resolution will become the default in future 253s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 253s keep using the greedy method in the future, run with `--greedy-resolve` 253s 253s 2.29 ###TreeTime.run: CONVERGED 253s 253s 4.24 ###TreeTime.run: FINAL ROUND - confidence estimation via marginal 253s reconstruction 253s 253s Inferred sequence evolution model (saved as 2024-11-13_treetime/sequence_evolution_model.txt): 253s Substitution rate (mu): 1.0 253s 253s Equilibrium frequencies (pi_i): 253s A: 0.3088 253s C: 0.1897 253s G: 0.2335 253s T: 0.2581 253s -: 0.0099 253s 253s Symmetrized rates from j->i (W_ij): 253s A C G T - 253s A 0 0.7003 3.0669 0.2651 0.9742 253s C 0.7003 0 0.3354 3.399 0.999 253s G 3.0669 0.3354 0 0.4258 0.9892 253s T 0.2651 3.399 0.4258 0 0.9848 253s - 0.9742 0.999 0.9892 0.9848 0 253s 253s Actual rates from j->i (Q_ij): 253s A C G T - 253s A 0 0.2163 0.9472 0.0819 0.3009 253s C 0.1328 0 0.0636 0.6448 0.1895 253s G 0.716 0.0783 0 0.0994 0.2309 253s T 0.0684 0.8772 0.1099 0 0.2541 253s - 0.0097 0.0099 0.0098 0.0098 0 253s 253s 253s Inferred sequence evolution model (saved as 2024-11-13_treetime/molecular_clock.txt): 253s Root-Tip-Regression: 253s --rate: 2.638e-03 +/- 3.97e-04 (one std-dev) 253s --chi^2: 8.32 253s --r^2: 0.98 253s 253s --- saved tree as 253s 2024-11-13_treetime/timetree.pdf 253s 253s --- root-to-tip plot saved to 253s 2024-11-13_treetime/root_to_tip_regression.pdf 253s 253s --- alignment including ancestral nodes saved as 253s 2024-11-13_treetime/ancestral_sequences.fasta 253s 253s --- saved divergence times in 253s 2024-11-13_treetime/dates.tsv 253s 253s --- tree saved in nexus format as 253s 2024-11-13_treetime/timetree.nexus 253s 253s --- tree saved in auspice json format as 253s 2024-11-13_treetime/auspice_tree.json 253s 253s --- divergence tree saved in nexus format as 253s 2024-11-13_treetime/divergence_tree.nexus 253s 254s timetree_inference ok 255s /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]` 255s weight_dict = {row[0]:row[1] for ri,row in tmp_weights.iterrows() if not np.isnan(row[1])} 256s Using column '#name' as taxon name. This needs to match the taxa in the tree! 256s Assigned discrete traits to 86 out of 86 taxa. 256s 256s 256s Completed mugration model inference of attribute 'country' for zika/zika.nwk 256s 256s Saved inferred mugration model as: 2024-11-13_mugration/GTR.txt 256s Saved annotated tree as: 2024-11-13_mugration/annotated_tree.nexus 256s ---Done! 256s 256s mugration ok 307s 307s Attempting to parse dates... 307s Using column 'strain' as name. This needs match the taxon names in the tree!! 307s Using column 'date' as date. 307s 307s 0.00 -TreeAnc: set-up 307s 307s 6.29 TreeTime.reroot: with method or node: least-squares 307s 307s 6.29 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 307s 307s 6.49 TreeTime.reroot: with method or node: least-squares 307s 307s 6.50 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 307s 307s 7.67 ###TreeTime.run: INITIAL ROUND 307s 307s 14.95 TreeTime.reroot: with method or node: least-squares 307s 307s 14.95 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 307s 307s 15.13 ###TreeTime.run: rerunning timetree after rerooting 307s 307s 22.96 ###TreeTime.run: ITERATION 1 out of 2 iterations 307s 307s 22.96 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 307s polytomies using the old 'greedy' mode. This is not well suited for large 307s polytomies. Stochastic resolution will become the default in future 307s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 307s keep using the greedy method in the future, run with `--greedy-resolve` 307s 307s 33.60 ###TreeTime.run: ITERATION 2 out of 2 iterations 307s 307s 43.33 TreeTime: the following tips have been marked as outliers. Their date 307s constraints were not used. Please remove them from the tree. Their dates 307s have been reset: 307s 307s 43.33 G22619, input date: [2011.0013698630137, 2011.9986301369863], apparent 307s date: 1987.93 307s 307s 43.33 G22703, input date: [2004.0013661202186, 2004.9986338797814], apparent 307s date: 2012.13 307s 307s Inferred sequence evolution model (saved as 2024-11-13-0001_treetime/sequence_evolution_model.txt): 307s Substitution rate (mu): 1.0 307s 307s Equilibrium frequencies (pi_i): 307s A: 0.1669 307s C: 0.3286 307s G: 0.3273 307s T: 0.1669 307s -: 0.0103 307s 307s Symmetrized rates from j->i (W_ij): 307s A C G T - 307s A 0 0.7501 1.6494 0.3119 35.7049 307s C 0.7501 0 0.3189 1.4202 35.6713 307s G 1.6494 0.3189 0 0.7442 49.4052 307s T 0.3119 1.4202 0.7442 0 32.0732 307s - 35.7049 35.6713 49.4052 32.0732 0 307s 307s Actual rates from j->i (Q_ij): 307s A C G T - 307s A 0 0.1252 0.2753 0.0521 5.9595 307s C 0.2465 0 0.1048 0.4667 11.7208 307s G 0.5399 0.1044 0 0.2436 16.1715 307s T 0.0521 0.237 0.1242 0 5.3524 307s - 0.3681 0.3677 0.5093 0.3307 0 307s 307s 307s Inferred sequence evolution model (saved as 2024-11-13-0001_treetime/molecular_clock.txt): 307s Root-Tip-Regression: 307s --rate: 1.000e-07 307s --r^2: 0.46 307s 307s --- saved tree as 307s 2024-11-13-0001_treetime/timetree.pdf 307s 307s --- root-to-tip plot saved to 307s 2024-11-13-0001_treetime/root_to_tip_regression.pdf 307s Sites that were constant except for ambiguous bases were made constant 307s by TreeTime. This happened 1343 times. These sites are now excluded 307s from the VCF. 307s 307s ***WARNING: vcf_utils.py 307s 52 sites were found that had no alternative bases. If this data has 307s been run through TreeTime and contains ambiguous bases, try calling 307s get_tree_dict with var_ambigs=True to see if this clears the error. 307s Alternative causes: - Not all sequences in your alignment are in the 307s tree (if you are running TreeTime via commandline this is most likely) 307s - In TreeTime, can be caused by overwriting variants in tips with 307s small branch lengths (debug) These are the positions affected 307s (numbering starts at 0): 307s 46593, 52473, 165918, 304891, 662240, 954864, 954865, 954866, 954867, 307s 963561, 1046706, 1145470, 1321893, 1468105, 1468106, 1512661, 1704463, 307s 1716723, 1743968, 1951837, 2129868, 2215816, 2274543, 2515984, 307s 2580886, 2626512, 2626513, 2626599, 2686156, 2736331, 2823901, 307s 2869282, 2894207, 2911378, 3047997, 3160385, 3314001, 3321447, 307s 3336505, 3461793, 3490408, 3618189, 3734466, 3764813, 3828626, 307s 3842630, 3894439, 3912292, 3913650, 3956227, 4149358, 4183687 307s 307s --- alignment including ancestral nodes saved as 307s 2024-11-13-0001_treetime/ancestral_sequences.vcf 307s 307s --- saved divergence times in 307s 2024-11-13-0001_treetime/dates.tsv 307s 307s --- tree saved in nexus format as 307s 2024-11-13-0001_treetime/timetree.nexus 307s 307s --- tree saved in auspice json format as 307s 2024-11-13-0001_treetime/auspice_tree.json 307s 307s --- divergence tree saved in nexus format as 307s 2024-11-13-0001_treetime/divergence_tree.nexus 307s 307s --- saved detected outliers as 2024-11-13-0001_treetime/outliers.tsv 307s timetree_inference on vcf data ok 427s 427s Attempting to parse dates... 427s Using column 'name' as name. This needs match the taxon names in the tree!! 427s Using column 'date' as date. 427s 427s 0.00 -TreeAnc: set-up 427s 427s 3.61 -WARNING: character U is unknown. Treating it as missing information 427s 427s 15.29 TreeTime.reroot: with method or node: least-squares 427s 427s 15.29 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 427s 427s 15.78 TreeTime.reroot: with method or node: least-squares 427s 427s 15.79 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 427s 427s 23.19 ###TreeTime.run: INITIAL ROUND 427s 427s 33.38 TreeTime.reroot: with method or node: least-squares 427s 427s 33.39 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 427s 427s 33.82 ###TreeTime.run: rerunning timetree after rerooting 427s 427s 47.71 ###TreeTime.run: ITERATION 1 out of 2 iterations 427s 427s 48.48 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 427s polytomies using the old 'greedy' mode. This is not well suited for large 427s polytomies. Stochastic resolution will become the default in future 427s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 427s keep using the greedy method in the future, run with `--greedy-resolve` 427s 427s 70.32 ###TreeTime.run: ITERATION 2 out of 2 iterations 427s 427s 112.39 TreeTime: the following tips have been marked as outliers. Their date 427s constraints were not used. Please remove them from the tree. Their dates 427s have been reset: 427s 427s 112.39 NZG_0393, input date: 2016.24, apparent date: 2015.23 427s 427s 112.39 NZG_0422, input date: 2016.25, apparent date: 2015.23 427s 427s 112.39 NZG_0358, input date: 2016.22, apparent date: 2015.23 427s 427s 112.39 NZG_0381, input date: 2016.23, apparent date: 2015.18 427s 427s 112.39 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.18 427s 427s 112.39 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.18 427s 427s 112.39 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.18 427s 427s 112.39 2607_C2_12916_EMLH, input date: 2015.32, apparent date: 2015.49 427s 427s 112.39 2607_C2_12855_EMLH, input date: 2015.28, apparent date: 2015.49 427s 427s 112.39 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.59 427s 427s 112.39 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.87 427s 427s 112.39 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.87 427s 427s 112.39 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.87 427s 427s 112.39 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2016.00 427s 427s 112.39 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.94 427s 427s 112.39 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.94 427s 427s 112.39 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.80 427s 427s 112.39 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.94 427s 427s 112.39 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2016.00 427s 427s 112.39 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2016.00 427s 427s Inferred sequence evolution model (saved as 2024-11-13-0002_treetime/sequence_evolution_model.txt): 427s Substitution rate (mu): 1.0 427s 427s Equilibrium frequencies (pi_i): 427s A: 0.3139 427s C: 0.2144 427s G: 0.1979 427s T: 0.2638 427s -: 0.01 427s 427s Symmetrized rates from j->i (W_ij): 427s A C G T - 427s A 0 0.3826 2.5275 0.2294 6.7953 427s C 0.3826 0 0.1691 3.5602 12.1803 427s G 2.5275 0.1691 0 0.3724 5.2949 427s T 0.2294 3.5602 0.3724 0 27.7427 427s - 6.7953 12.1803 5.2949 27.7427 0 427s 427s Actual rates from j->i (Q_ij): 427s A C G T - 427s A 0 0.1201 0.7933 0.072 2.1329 427s C 0.0821 0 0.0363 0.7634 2.6119 427s G 0.5002 0.0335 0 0.0737 1.0478 427s T 0.0605 0.9393 0.0982 0 7.3197 427s - 0.0676 0.1212 0.0527 0.2761 0 427s 427s 427s Inferred sequence evolution model (saved as 2024-11-13-0002_treetime/molecular_clock.txt): 427s Root-Tip-Regression: 427s --rate: 7.885e-04 427s --r^2: 0.80 427s 427s Inferred coalescent model 427s Skyline assuming 100.0 gen/year and approximate confidence bounds (+/- 2.000000 standard deviations of the LH) 427s date N_e lower upper 427s 2014.122 2.698e+01 1.188e+01 6.125e+01 427s 2014.211 6.398e+01 4.250e+01 9.631e+01 427s 2014.300 1.062e+02 6.293e+01 1.791e+02 427s 2014.388 1.070e+02 7.255e+01 1.577e+02 427s 2014.477 3.603e+02 2.502e+02 5.190e+02 427s 2014.566 4.756e+02 3.202e+02 7.063e+02 427s 2014.655 8.531e+02 5.793e+02 1.256e+03 427s 2014.744 2.326e+03 1.479e+03 3.657e+03 427s 2014.833 1.327e+03 7.794e+02 2.258e+03 427s 2014.922 9.962e+02 6.012e+02 1.651e+03 427s 2015.010 5.384e+02 3.289e+02 8.815e+02 427s 2015.099 5.724e+02 3.630e+02 9.026e+02 427s 2015.188 4.181e+02 2.632e+02 6.641e+02 427s 2015.277 3.048e+02 1.880e+02 4.942e+02 427s 2015.366 3.018e+02 1.928e+02 4.725e+02 427s 2015.455 1.607e+02 9.875e+01 2.616e+02 427s 2015.543 1.232e+02 7.138e+01 2.128e+02 427s 2015.632 1.452e+02 8.657e+01 2.436e+02 427s 2015.721 7.767e+01 4.100e+01 1.471e+02 427s 2015.810 2.325e+01 8.731e+00 6.191e+01 427s 427s --- written skyline to 2024-11-13-0002_treetime/skyline.tsv 427s 427s --- saved tree as 427s 2024-11-13-0002_treetime/timetree.pdf 427s 427s --- root-to-tip plot saved to 427s 2024-11-13-0002_treetime/root_to_tip_regression.pdf 427s 427s --- alignment including ancestral nodes saved as 427s 2024-11-13-0002_treetime/ancestral_sequences.fasta 427s 427s --- saved divergence times in 427s 2024-11-13-0002_treetime/dates.tsv 427s 427s --- tree saved in nexus format as 427s 2024-11-13-0002_treetime/timetree.nexus 427s 427s --- tree saved in auspice json format as 427s 2024-11-13-0002_treetime/auspice_tree.json 427s 427s --- divergence tree saved in nexus format as 427s 2024-11-13-0002_treetime/divergence_tree.nexus 427s 427s --- saved detected outliers as 2024-11-13-0002_treetime/outliers.tsv 427s skyline approximation ok 459s 459s Attempting to parse dates... 459s Using column 'name' as name. This needs match the taxon names in the tree!! 459s Using column 'date' as date. 459s 459s 0.00 -TreeAnc: set-up 459s 459s 0.07 TreeTime.reroot: with method or node: least-squares 459s 459s 0.07 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 459s 459s 0.69 TreeTime.reroot: with method or node: least-squares 459s 459s 0.69 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 459s 459s 1.15 ###TreeTime.run: INITIAL ROUND 459s 459s 9.79 TreeTime.reroot: with method or node: least-squares 459s 459s 9.79 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 459s 459s 10.25 ###TreeTime.run: rerunning timetree after rerooting 459s 459s 19.08 ###TreeTime.run: ITERATION 1 out of 2 iterations 459s 459s 19.08 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 459s polytomies using the old 'greedy' mode. This is not well suited for large 459s polytomies. Stochastic resolution will become the default in future 459s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 459s keep using the greedy method in the future, run with `--greedy-resolve` 459s 459s 27.85 ###TreeTime.run: CONVERGED 459s 459s 27.85 TreeTime: the following tips have been marked as outliers. Their date 459s constraints were not used. Please remove them from the tree. Their dates 459s have been reset: 459s 459s 27.85 NZG_0393, input date: 2016.24, apparent date: 2015.26 459s 459s 27.85 NZG_0422, input date: 2016.25, apparent date: 2015.26 459s 459s 27.85 NZG_0358, input date: 2016.22, apparent date: 2015.26 459s 459s 27.85 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.19 459s 459s 27.85 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.19 459s 459s 27.85 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.19 459s 459s 27.85 NZG_0381, input date: 2016.23, apparent date: 2015.19 459s 459s 27.85 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.40 459s 459s 27.85 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.81 459s 459s 27.85 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.81 459s 459s 27.85 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2015.87 459s 459s 27.85 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2015.87 459s 459s 27.85 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.74 459s 459s 27.85 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.81 459s 459s 27.85 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.68 459s 459s 27.85 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.74 459s 459s 27.85 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.74 459s 459s 27.85 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2015.87 459s 459s Inferred sequence evolution model (saved as 2024-11-13-0003_treetime/sequence_evolution_model.txt): 459s Substitution rate (mu): 1.0 459s 459s Equilibrium frequencies (pi_i): 459s A: 0.2 459s C: 0.2 459s G: 0.2 459s T: 0.2 459s -: 0.2 459s 459s Symmetrized rates from j->i (W_ij): 459s A C G T - 459s A 0 1.25 1.25 1.25 1.25 459s C 1.25 0 1.25 1.25 1.25 459s G 1.25 1.25 0 1.25 1.25 459s T 1.25 1.25 1.25 0 1.25 459s - 1.25 1.25 1.25 1.25 0 459s 459s Actual rates from j->i (Q_ij): 459s A C G T - 459s A 0 0.25 0.25 0.25 0.25 459s C 0.25 0 0.25 0.25 0.25 459s G 0.25 0.25 0 0.25 0.25 459s T 0.25 0.25 0.25 0 0.25 459s - 0.25 0.25 0.25 0.25 0 459s 459s 459s Inferred sequence evolution model (saved as 2024-11-13-0003_treetime/molecular_clock.txt): 459s Root-Tip-Regression: 459s --rate: 8.047e-04 459s --r^2: 0.79 459s 459s --- saved tree as 459s 2024-11-13-0003_treetime/timetree.pdf 459s 459s --- root-to-tip plot saved to 459s 2024-11-13-0003_treetime/root_to_tip_regression.pdf 459s --- saved divergence times in 459s 2024-11-13-0003_treetime/dates.tsv 459s 459s --- tree saved in nexus format as 459s 2024-11-13-0003_treetime/timetree.nexus 459s 459s --- tree saved in auspice json format as 459s 2024-11-13-0003_treetime/auspice_tree.json 459s 459s --- divergence tree saved in nexus format as 459s 2024-11-13-0003_treetime/divergence_tree.nexus 459s 459s --- saved detected outliers as 2024-11-13-0003_treetime/outliers.tsv 459s sequence length only ok 459s All tests passed 459s autopkgtest [11:06:30]: test run-unit-test: -----------------------] 460s run-unit-test PASS 460s autopkgtest [11:06:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 461s autopkgtest [11:06:32]: test autodep8-python3: preparing testbed 556s autopkgtest [11:08:07]: testbed dpkg architecture: arm64 557s autopkgtest [11:08:08]: testbed apt version: 2.9.8 557s autopkgtest [11:08:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 558s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 559s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 559s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 559s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 559s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 559s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 559s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 559s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 559s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 559s Fetched 1794 kB in 1s (1976 kB/s) 559s Reading package lists... 563s Reading package lists... 564s Building dependency tree... 564s Reading state information... 564s Calculating upgrade... 565s The following NEW packages will be installed: 565s python3.13-gdbm 565s The following packages will be upgraded: 565s libpython3-stdlib python3 python3-gdbm python3-minimal 565s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 565s Need to get 101 kB of archives. 565s After this operation, 141 kB of additional disk space will be used. 565s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 565s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 565s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 565s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 565s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 566s Fetched 101 kB in 0s (272 kB/s) 566s (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 ... 79924 files and directories currently installed.) 566s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 566s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 566s Setting up python3-minimal (3.12.7-1) ... 566s (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 ... 79924 files and directories currently installed.) 566s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 567s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 567s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 567s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 567s Selecting previously unselected package python3.13-gdbm. 567s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 567s Unpacking python3.13-gdbm (3.13.0-2) ... 567s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 567s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 567s Setting up python3.13-gdbm (3.13.0-2) ... 567s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 567s Setting up python3 (3.12.7-1) ... 567s Setting up python3-gdbm:arm64 (3.12.7-1) ... 567s Processing triggers for man-db (2.12.1-3) ... 568s Reading package lists... 569s Building dependency tree... 569s Reading state information... 571s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 571s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 571s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 571s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 571s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 573s Reading package lists... 573s Reading package lists... 573s Building dependency tree... 573s Reading state information... 574s Calculating upgrade... 576s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 576s Reading package lists... 576s Building dependency tree... 576s Reading state information... 578s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 591s Reading package lists... 592s Building dependency tree... 592s Reading state information... 592s Starting pkgProblemResolver with broken count: 0 592s Starting 2 pkgProblemResolver with broken count: 0 592s Done 593s The following additional packages will be installed: 593s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 593s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 593s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 593s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 593s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 593s libpython3.13-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 593s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 593s libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data python3-all 593s python3-appdirs python3-biopython python3-brotli python3-cairo 594s python3-contourpy python3-cycler python3-dateutil python3-decorator 594s python3-fonttools python3-freetype python3-fs python3-kiwisolver 594s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy 594s python3-packaging python3-pandas python3-pandas-lib python3-pil 594s python3-pil.imagetk python3-reportlab python3-rlpycairo python3-scipy 594s python3-six python3-sympy python3-tk python3-treetime python3-tz 594s python3-ufolib2 python3.12-tk python3.13 python3.13-minimal python3.13-tk 594s sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 594s xfonts-utils xml-core 594s Suggested packages: 594s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 594s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 594s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 594s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 594s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 594s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 594s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 594s python3-gobject python3-pyqt5 python3-sip python3-tornado 594s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 594s gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 594s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 594s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 594s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-venv 594s python3.13-doc binfmt-support sgml-base-doc debhelper 594s Recommended packages: 594s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 594s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 594s python3-odf python3-openpyxl python3-tables python3-olefile 594s fonts-dejavu-extra g++ | c++-compiler isympy-common 594s The following NEW packages will be installed: 594s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 594s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 594s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 594s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 594s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 594s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 594s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 594s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 594s python-matplotlib-data python3-all python3-appdirs python3-biopython 594s python3-brotli python3-cairo python3-contourpy python3-cycler 594s python3-dateutil python3-decorator python3-fonttools python3-freetype 594s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 594s python3-mpmath python3-numpy python3-packaging python3-pandas 594s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 594s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 594s python3-treetime python3-tz python3-ufolib2 python3.12-tk python3.13 594s python3.13-minimal python3.13-tk sgml-base tk8.6-blt2.5 unicode-data 594s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 594s 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. 594s Need to get 85.1 MB/85.1 MB of archives. 594s After this operation, 344 MB of additional disk space will be used. 594s Get:1 /tmp/autopkgtest.HWWLdk/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 594s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 594s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 594s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 594s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 594s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 594s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 594s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 594s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 594s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 594s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 594s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 595s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 595s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 595s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 595s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 595s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 595s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 595s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 595s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 595s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 595s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 595s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 595s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 595s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 595s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 595s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 595s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 595s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 595s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 595s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 595s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 595s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 595s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 595s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 595s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 595s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 595s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 595s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 595s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 595s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 595s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 595s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 595s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 595s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 595s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 595s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 595s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 595s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 595s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 595s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 595s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 595s Get:53 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 595s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 595s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 595s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 595s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 595s Get:58 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 595s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 595s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 595s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 595s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 595s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 595s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 595s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 596s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 596s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 596s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 596s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 596s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 596s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 596s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 596s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 596s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 596s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 596s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 596s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 596s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 596s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 596s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 596s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 596s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 596s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 596s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 596s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2 [50.4 kB] 596s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 596s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 596s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 597s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 597s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-treetime all 0.11.4-1 [941 kB] 597s Fetched 85.1 MB in 3s (27.9 MB/s) 597s Selecting previously unselected package libpython3.13-minimal:arm64. 598s (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 ... 79931 files and directories currently installed.) 598s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 598s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 598s Selecting previously unselected package python3.13-minimal. 598s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 598s Unpacking python3.13-minimal (3.13.0-2) ... 598s Selecting previously unselected package sgml-base. 598s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 598s Unpacking sgml-base (1.31) ... 598s Selecting previously unselected package libtcl8.6:arm64. 598s Preparing to unpack .../03-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 598s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 598s Selecting previously unselected package fonts-dejavu-mono. 598s Preparing to unpack .../04-fonts-dejavu-mono_2.37-8_all.deb ... 598s Unpacking fonts-dejavu-mono (2.37-8) ... 598s Selecting previously unselected package fonts-dejavu-core. 598s Preparing to unpack .../05-fonts-dejavu-core_2.37-8_all.deb ... 598s Unpacking fonts-dejavu-core (2.37-8) ... 598s Selecting previously unselected package libfontenc1:arm64. 598s Preparing to unpack .../06-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 598s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 598s Selecting previously unselected package x11-common. 598s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu3_all.deb ... 598s Unpacking x11-common (1:7.7+23ubuntu3) ... 599s Selecting previously unselected package xfonts-encodings. 599s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 599s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 599s Selecting previously unselected package xfonts-utils. 599s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_arm64.deb ... 599s Unpacking xfonts-utils (1:7.7+7) ... 599s Selecting previously unselected package fonts-urw-base35. 599s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 599s Unpacking fonts-urw-base35 (20200910-8) ... 599s Selecting previously unselected package fontconfig-config. 599s Preparing to unpack .../11-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 600s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 600s Selecting previously unselected package libfontconfig1:arm64. 600s Preparing to unpack .../12-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 600s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 600s Selecting previously unselected package libxrender1:arm64. 600s Preparing to unpack .../13-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 600s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 600s Selecting previously unselected package libxft2:arm64. 600s Preparing to unpack .../14-libxft2_2.3.6-1build1_arm64.deb ... 600s Unpacking libxft2:arm64 (2.3.6-1build1) ... 600s Selecting previously unselected package libxss1:arm64. 600s Preparing to unpack .../15-libxss1_1%3a1.2.3-1build3_arm64.deb ... 600s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 600s Selecting previously unselected package libtk8.6:arm64. 600s Preparing to unpack .../16-libtk8.6_8.6.15-1_arm64.deb ... 600s Unpacking libtk8.6:arm64 (8.6.15-1) ... 600s Selecting previously unselected package tk8.6-blt2.5. 600s Preparing to unpack .../17-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 600s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 600s Selecting previously unselected package blt. 600s Preparing to unpack .../18-blt_2.5.3+dfsg-7build1_arm64.deb ... 600s Unpacking blt (2.5.3+dfsg-7build1) ... 600s Selecting previously unselected package fonts-lyx. 600s Preparing to unpack .../19-fonts-lyx_2.4.2.1-1_all.deb ... 600s Unpacking fonts-lyx (2.4.2.1-1) ... 600s Selecting previously unselected package libblas3:arm64. 600s Preparing to unpack .../20-libblas3_3.12.0-3build2_arm64.deb ... 600s Unpacking libblas3:arm64 (3.12.0-3build2) ... 600s Selecting previously unselected package libpixman-1-0:arm64. 600s Preparing to unpack .../21-libpixman-1-0_0.44.0-3_arm64.deb ... 600s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 600s Selecting previously unselected package libxcb-render0:arm64. 600s Preparing to unpack .../22-libxcb-render0_1.17.0-2_arm64.deb ... 600s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 600s Selecting previously unselected package libxcb-shm0:arm64. 600s Preparing to unpack .../23-libxcb-shm0_1.17.0-2_arm64.deb ... 600s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 600s Selecting previously unselected package libcairo2:arm64. 600s Preparing to unpack .../24-libcairo2_1.18.2-2_arm64.deb ... 600s Unpacking libcairo2:arm64 (1.18.2-2) ... 601s Selecting previously unselected package libdeflate0:arm64. 601s Preparing to unpack .../25-libdeflate0_1.22-1_arm64.deb ... 601s Unpacking libdeflate0:arm64 (1.22-1) ... 601s Selecting previously unselected package libgfortran5:arm64. 601s Preparing to unpack .../26-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 601s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 601s Selecting previously unselected package libgomp1:arm64. 601s Preparing to unpack .../27-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 601s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 601s Selecting previously unselected package libgraphite2-3:arm64. 601s Preparing to unpack .../28-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 601s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 601s Selecting previously unselected package libharfbuzz0b:arm64. 601s Preparing to unpack .../29-libharfbuzz0b_10.0.1-1_arm64.deb ... 601s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 601s Selecting previously unselected package libimagequant0:arm64. 601s Preparing to unpack .../30-libimagequant0_2.18.0-1build1_arm64.deb ... 601s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 601s Selecting previously unselected package libjpeg-turbo8:arm64. 601s Preparing to unpack .../31-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 601s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 601s Selecting previously unselected package libjpeg8:arm64. 601s Preparing to unpack .../32-libjpeg8_8c-2ubuntu11_arm64.deb ... 601s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 601s Selecting previously unselected package libjs-jquery. 601s Preparing to unpack .../33-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 601s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 601s Selecting previously unselected package libjs-jquery-ui. 601s Preparing to unpack .../34-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 601s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 601s Selecting previously unselected package liblapack3:arm64. 601s Preparing to unpack .../35-liblapack3_3.12.0-3build2_arm64.deb ... 601s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 601s Selecting previously unselected package liblbfgsb0:arm64. 601s Preparing to unpack .../36-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 601s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 601s Selecting previously unselected package liblcms2-2:arm64. 601s Preparing to unpack .../37-liblcms2-2_2.16-2_arm64.deb ... 601s Unpacking liblcms2-2:arm64 (2.16-2) ... 601s Selecting previously unselected package liblerc4:arm64. 602s Preparing to unpack .../38-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 602s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 602s Selecting previously unselected package libpython3.13-stdlib:arm64. 602s Preparing to unpack .../39-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 602s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 602s Selecting previously unselected package libqhull-r8.0:arm64. 602s Preparing to unpack .../40-libqhull-r8.0_2020.2-6build1_arm64.deb ... 602s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 602s Selecting previously unselected package libraqm0:arm64. 602s Preparing to unpack .../41-libraqm0_0.10.1-1build1_arm64.deb ... 602s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 602s Selecting previously unselected package libsharpyuv0:arm64. 602s Preparing to unpack .../42-libsharpyuv0_1.4.0-0.1_arm64.deb ... 602s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 602s Selecting previously unselected package libjbig0:arm64. 602s Preparing to unpack .../43-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 602s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 602s Selecting previously unselected package libwebp7:arm64. 602s Preparing to unpack .../44-libwebp7_1.4.0-0.1_arm64.deb ... 602s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 602s Selecting previously unselected package libtiff6:arm64. 602s Preparing to unpack .../45-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 602s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 602s Selecting previously unselected package libwebpdemux2:arm64. 602s Preparing to unpack .../46-libwebpdemux2_1.4.0-0.1_arm64.deb ... 602s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 602s Selecting previously unselected package libwebpmux3:arm64. 602s Preparing to unpack .../47-libwebpmux3_1.4.0-0.1_arm64.deb ... 602s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 602s Selecting previously unselected package libxslt1.1:arm64. 602s Preparing to unpack .../48-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 602s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 602s Selecting previously unselected package python-matplotlib-data. 602s Preparing to unpack .../49-python-matplotlib-data_3.8.3-3_all.deb ... 602s Unpacking python-matplotlib-data (3.8.3-3) ... 602s Selecting previously unselected package python3.13. 602s Preparing to unpack .../50-python3.13_3.13.0-2_arm64.deb ... 602s Unpacking python3.13 (3.13.0-2) ... 602s Selecting previously unselected package python3-all. 602s Preparing to unpack .../51-python3-all_3.12.7-1_arm64.deb ... 602s Unpacking python3-all (3.12.7-1) ... 603s Selecting previously unselected package python3-appdirs. 603s Preparing to unpack .../52-python3-appdirs_1.4.4-4_all.deb ... 603s Unpacking python3-appdirs (1.4.4-4) ... 603s Selecting previously unselected package python3-numpy. 603s Preparing to unpack .../53-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 603s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 603s Selecting previously unselected package python3.12-tk. 603s Preparing to unpack .../54-python3.12-tk_3.12.7-3_arm64.deb ... 603s Unpacking python3.12-tk (3.12.7-3) ... 603s Selecting previously unselected package python3.13-tk. 603s Preparing to unpack .../55-python3.13-tk_3.13.0-2_arm64.deb ... 603s Unpacking python3.13-tk (3.13.0-2) ... 603s Selecting previously unselected package python3-tk:arm64. 603s Preparing to unpack .../56-python3-tk_3.12.7-1_arm64.deb ... 603s Unpacking python3-tk:arm64 (3.12.7-1) ... 603s Selecting previously unselected package python3-pil.imagetk:arm64. 603s Preparing to unpack .../57-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 603s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 603s Selecting previously unselected package libopenjp2-7:arm64. 603s Preparing to unpack .../58-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 603s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 603s Selecting previously unselected package python3-pil:arm64. 603s Preparing to unpack .../59-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 603s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 603s Selecting previously unselected package python3-cairo. 603s Preparing to unpack .../60-python3-cairo_1.26.1-2_arm64.deb ... 603s Unpacking python3-cairo (1.26.1-2) ... 603s Selecting previously unselected package python3-freetype. 603s Preparing to unpack .../61-python3-freetype_2.5.1-1_all.deb ... 603s Unpacking python3-freetype (2.5.1-1) ... 603s Selecting previously unselected package python3-rlpycairo. 603s Preparing to unpack .../62-python3-rlpycairo_0.3.0-3_all.deb ... 603s Unpacking python3-rlpycairo (0.3.0-3) ... 603s Selecting previously unselected package python3-reportlab. 604s Preparing to unpack .../63-python3-reportlab_4.2.5-1_all.deb ... 604s Unpacking python3-reportlab (4.2.5-1) ... 604s Selecting previously unselected package xml-core. 604s Preparing to unpack .../64-xml-core_0.19_all.deb ... 604s Unpacking xml-core (0.19) ... 604s Selecting previously unselected package w3c-sgml-lib. 604s Preparing to unpack .../65-w3c-sgml-lib_1.3-3_all.deb ... 604s Unpacking w3c-sgml-lib (1.3-3) ... 604s Selecting previously unselected package python3-biopython. 604s Preparing to unpack .../66-python3-biopython_1.84+dfsg-4_arm64.deb ... 604s Unpacking python3-biopython (1.84+dfsg-4) ... 604s Selecting previously unselected package python3-brotli. 604s Preparing to unpack .../67-python3-brotli_1.1.0-2build2_arm64.deb ... 604s Unpacking python3-brotli (1.1.0-2build2) ... 604s Selecting previously unselected package python3-contourpy. 604s Preparing to unpack .../68-python3-contourpy_1.3.0-2_arm64.deb ... 604s Unpacking python3-contourpy (1.3.0-2) ... 604s Selecting previously unselected package python3-cycler. 604s Preparing to unpack .../69-python3-cycler_0.12.1-1_all.deb ... 604s Unpacking python3-cycler (0.12.1-1) ... 604s Selecting previously unselected package python3-six. 604s Preparing to unpack .../70-python3-six_1.16.0-7_all.deb ... 604s Unpacking python3-six (1.16.0-7) ... 604s Selecting previously unselected package python3-dateutil. 604s Preparing to unpack .../71-python3-dateutil_2.9.0-2_all.deb ... 604s Unpacking python3-dateutil (2.9.0-2) ... 604s Selecting previously unselected package python3-decorator. 604s Preparing to unpack .../72-python3-decorator_5.1.1-5_all.deb ... 604s Unpacking python3-decorator (5.1.1-5) ... 605s Selecting previously unselected package python3-scipy. 605s Preparing to unpack .../73-python3-scipy_1.13.1-5_arm64.deb ... 605s Unpacking python3-scipy (1.13.1-5) ... 605s Selecting previously unselected package python3-ufolib2. 605s Preparing to unpack .../74-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 605s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 605s Selecting previously unselected package python3-mpmath. 605s Preparing to unpack .../75-python3-mpmath_1.3.0-1_all.deb ... 605s Unpacking python3-mpmath (1.3.0-1) ... 605s Selecting previously unselected package python3-sympy. 605s Preparing to unpack .../76-python3-sympy_1.13.3-1_all.deb ... 605s Unpacking python3-sympy (1.13.3-1) ... 606s Selecting previously unselected package python3-tz. 606s Preparing to unpack .../77-python3-tz_2024.1-2_all.deb ... 606s Unpacking python3-tz (2024.1-2) ... 606s Selecting previously unselected package python3-fs. 606s Preparing to unpack .../78-python3-fs_2.4.16-4_all.deb ... 606s Unpacking python3-fs (2.4.16-4) ... 606s Selecting previously unselected package python3-lxml:arm64. 606s Preparing to unpack .../79-python3-lxml_5.3.0-1_arm64.deb ... 606s Unpacking python3-lxml:arm64 (5.3.0-1) ... 606s Selecting previously unselected package python3-lz4. 606s Preparing to unpack .../80-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 606s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 606s Selecting previously unselected package unicode-data. 606s Preparing to unpack .../81-unicode-data_15.1.0-1_all.deb ... 606s Unpacking unicode-data (15.1.0-1) ... 606s Selecting previously unselected package python3-fonttools. 606s Preparing to unpack .../82-python3-fonttools_4.46.0-1build2_arm64.deb ... 606s Unpacking python3-fonttools (4.46.0-1build2) ... 606s Selecting previously unselected package python3-kiwisolver. 606s Preparing to unpack .../83-python3-kiwisolver_1.4.7-2_arm64.deb ... 606s Unpacking python3-kiwisolver (1.4.7-2) ... 606s Selecting previously unselected package python3-packaging. 606s Preparing to unpack .../84-python3-packaging_24.1-1_all.deb ... 606s Unpacking python3-packaging (24.1-1) ... 606s Selecting previously unselected package python3-matplotlib. 606s Preparing to unpack .../85-python3-matplotlib_3.8.3-3_arm64.deb ... 607s Unpacking python3-matplotlib (3.8.3-3) ... 607s Selecting previously unselected package python3-pandas-lib:arm64. 607s Preparing to unpack .../86-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 607s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 607s Selecting previously unselected package python3-pandas. 607s Preparing to unpack .../87-python3-pandas_2.2.3+dfsg-5_all.deb ... 607s Unpacking python3-pandas (2.2.3+dfsg-5) ... 607s Selecting previously unselected package python3-treetime. 607s Preparing to unpack .../88-python3-treetime_0.11.4-1_all.deb ... 607s Unpacking python3-treetime (0.11.4-1) ... 607s Selecting previously unselected package autopkgtest-satdep. 607s Preparing to unpack .../89-2-autopkgtest-satdep.deb ... 607s Unpacking autopkgtest-satdep (0) ... 607s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 607s Setting up liblcms2-2:arm64 (2.16-2) ... 607s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 607s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 607s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 607s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 607s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 608s Setting up libxcb-render0:arm64 (1.17.0-2) ... 608s Setting up fonts-lyx (2.4.2.1-1) ... 608s Setting up x11-common (1:7.7+23ubuntu3) ... 609s Setting up libdeflate0:arm64 (1.22-1) ... 609s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 609s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 609s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 609s Setting up python3-freetype (2.5.1-1) ... 609s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 609s Setting up python3-tz (2024.1-2) ... 609s Setting up unicode-data (15.1.0-1) ... 609s Setting up python3-six (1.16.0-7) ... 610s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 610s Setting up python3-decorator (5.1.1-5) ... 610s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 610s Setting up libblas3:arm64 (3.12.0-3build2) ... 610s 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 610s Setting up python3-packaging (24.1-1) ... 611s Setting up python3-brotli (1.1.0-2build2) ... 611s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 611s Setting up python3-cycler (0.12.1-1) ... 611s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 611s Setting up fonts-dejavu-mono (2.37-8) ... 611s Setting up python3-kiwisolver (1.4.7-2) ... 612s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 612s Setting up fonts-dejavu-core (2.37-8) ... 612s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 612s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 612s Setting up libwebp7:arm64 (1.4.0-0.1) ... 612s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 612s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 612s Setting up python3.13-minimal (3.13.0-2) ... 613s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 613s Setting up python3-dateutil (2.9.0-2) ... 613s Setting up sgml-base (1.31) ... 613s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 613s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 613s Setting up python3-mpmath (1.3.0-1) ... 615s Setting up python-matplotlib-data (3.8.3-3) ... 615s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 615s Setting up python3-appdirs (1.4.4-4) ... 615s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 615s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 615s Setting up python3-sympy (1.13.3-1) ... 632s Setting up liblapack3:arm64 (3.12.0-3build2) ... 632s 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 632s Setting up python3.13 (3.13.0-2) ... 634s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 634s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 634s Setting up python3-all (3.12.7-1) ... 634s Setting up xfonts-utils (1:7.7+7) ... 634s Setting up python3-fs (2.4.16-4) ... 635s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 635s Setting up libraqm0:arm64 (0.10.1-1build1) ... 635s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 640s Setting up python3-lxml:arm64 (5.3.0-1) ... 640s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 640s Setting up xml-core (0.19) ... 641s Setting up python3-contourpy (1.3.0-2) ... 641s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 641s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 641s Setting up libxft2:arm64 (2.3.6-1build1) ... 641s Setting up python3-scipy (1.13.1-5) ... 652s Setting up libtk8.6:arm64 (8.6.15-1) ... 652s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 652s Setting up python3.12-tk (3.12.7-3) ... 652s Setting up fonts-urw-base35 (20200910-8) ... 652s Setting up libcairo2:arm64 (1.18.2-2) ... 652s Setting up python3.13-tk (3.13.0-2) ... 653s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 654s Setting up python3-pandas (2.2.3+dfsg-5) ... 667s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 667s Setting up python3-cairo (1.26.1-2) ... 668s Setting up blt (2.5.3+dfsg-7build1) ... 668s Setting up python3-tk:arm64 (3.12.7-1) ... 668s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 668s Setting up python3-rlpycairo (0.3.0-3) ... 668s Setting up python3-reportlab (4.2.5-1) ... 671s Setting up python3-fonttools (4.46.0-1build2) ... 675s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 676s Setting up python3-matplotlib (3.8.3-3) ... 681s Processing triggers for libc-bin (2.40-1ubuntu3) ... 681s Processing triggers for systemd (256.5-2ubuntu4) ... 681s Processing triggers for man-db (2.12.1-3) ... 683s Processing triggers for sgml-base (1.31) ... 683s Setting up w3c-sgml-lib (1.3-3) ... 720s Setting up python3-biopython (1.84+dfsg-4) ... 723s Setting up python3-treetime (0.11.4-1) ... 724s Setting up autopkgtest-satdep (0) ... 735s (Reading database ... 91411 files and directories currently installed.) 735s Removing autopkgtest-satdep (0) ... 746s autopkgtest [11:11:17]: 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 746s autopkgtest [11:11:17]: test autodep8-python3: [----------------------- 746s Testing with python3.13: 747s Traceback (most recent call last): 747s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 747s from . import multiarray 747s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 747s from . import overrides 747s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 747s from numpy.core._multiarray_umath import ( 747s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 747s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 747s 747s During handling of the above exception, another exception occurred: 747s 747s Traceback (most recent call last): 747s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 747s from numpy.__config__ import show as show_config 747s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 747s from numpy.core._multiarray_umath import ( 747s ...<3 lines>... 747s ) 747s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 747s raise ImportError(msg) 747s ImportError: 747s 747s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 747s 747s Importing the numpy C-extensions failed. This error can happen for 747s many reasons, often due to issues with your setup or how NumPy was 747s installed. 747s 747s We have compiled some common reasons and troubleshooting tips at: 747s 747s https://numpy.org/devdocs/user/troubleshooting-importerror.html 747s 747s Please note and check the following: 747s 747s * The Python version is: Python3.13 from "/usr/bin/python3.13" 747s * The NumPy version is: "1.26.4" 747s 747s and make sure that they are the versions you expect. 747s Please carefully study the documentation linked above for further help. 747s 747s Original error was: No module named 'numpy.core._multiarray_umath' 747s 747s 747s The above exception was the direct cause of the following exception: 747s 747s Traceback (most recent call last): 747s File "", line 1, in 747s import treetime; print(treetime) 747s ^^^^^^^^^^^^^^^ 747s File "/usr/lib/python3/dist-packages/treetime/__init__.py", line 38, in 747s from .treeanc import TreeAnc 747s File "/usr/lib/python3/dist-packages/treetime/treeanc.py", line 3, in 747s import numpy as np 747s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 747s raise ImportError(msg) from e 747s ImportError: Error importing numpy: you should not try to import numpy from 747s its source directory; please exit the numpy source tree, and relaunch 747s your python interpreter from there. 747s autopkgtest [11:11:18]: test autodep8-python3: -----------------------] 748s autopkgtest [11:11:19]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 748s autodep8-python3 FAIL non-zero exit status 1 749s autopkgtest [11:11:20]: @@@@@@@@@@@@@@@@@@@@ summary 749s run-unit-test PASS 749s autodep8-python3 FAIL non-zero exit status 1 767s nova [W] Skipping flock in bos03-arm64 767s Creating nova instance adt-plucky-arm64-python-treetime-20241113-105851-juju-7f2275-prod-proposed-migration-environment-20-01271193-dd20-4ec3-81b3-49731cb60c8a from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)... 767s nova [W] Skipping flock in bos03-arm64 767s Creating nova instance adt-plucky-arm64-python-treetime-20241113-105851-juju-7f2275-prod-proposed-migration-environment-20-01271193-dd20-4ec3-81b3-49731cb60c8a from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...