0s autopkgtest [21:03:20]: starting date and time: 2024-11-14 21:03:20+0000 0s autopkgtest [21:03:20]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [21:03:20]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6q9f5f6w/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-22.secgroup --name adt-plucky-amd64-python-treetime-20241114-210320-juju-7f2275-prod-proposed-migration-environment-15-3048aa0a-77fe-459b-a39c-6c672357ec35 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/ 41s autopkgtest [21:04:01]: testbed dpkg architecture: amd64 42s autopkgtest [21:04:01]: testbed apt version: 2.9.8 42s autopkgtest [21:04:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 42s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 42s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 42s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1044 kB] 43s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.7 kB] 43s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 43s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.4 kB] 43s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [144 kB] 43s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 43s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [805 kB] 43s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [295 kB] 43s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 43s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9660 B] 43s Fetched 2613 kB in 1s (3147 kB/s) 43s Reading package lists... 45s Reading package lists... 45s Building dependency tree... 45s Reading state information... 46s Calculating upgrade... 46s The following NEW packages will be installed: 46s python3.13-gdbm 46s The following packages will be upgraded: 46s libcap-ng0 libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal 46s python3-systemd 46s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 46s Need to get 178 kB of archives. 46s After this operation, 256 kB of additional disk space will be used. 46s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 46s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 46s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 46s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 46s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 46s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 46s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 46s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 46s Fetched 178 kB in 0s (434 kB/s) 47s (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 ... 75542 files and directories currently installed.) 47s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 47s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 47s Setting up python3-minimal (3.12.7-1) ... 47s (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 ... 75542 files and directories currently installed.) 47s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 47s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 47s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 47s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 47s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 47s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 47s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 47s Selecting previously unselected package python3.13-gdbm. 47s (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 ... 75542 files and directories currently installed.) 47s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 47s Unpacking python3.13-gdbm (3.13.0-2) ... 47s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 47s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 47s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 47s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 47s Preparing to unpack .../python3-systemd_235-1build5_amd64.deb ... 47s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 47s Setting up python3.13-gdbm (3.13.0-2) ... 47s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 47s Setting up python3 (3.12.7-1) ... 48s Setting up python3-systemd (235-1build5) ... 48s Setting up python3-gdbm:amd64 (3.12.7-1) ... 48s Setting up pastebinit (1.7.1-1) ... 48s Processing triggers for libc-bin (2.40-1ubuntu3) ... 48s Processing triggers for man-db (2.12.1-3) ... 48s Reading package lists... 48s Building dependency tree... 48s Reading state information... 49s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 49s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 49s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 49s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 49s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 50s Reading package lists... 50s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Calculating upgrade... 50s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s autopkgtest [21:04:14]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 54s autopkgtest [21:04:14]: @@@@@@@@@@@@@@@@@@@@ apt-source python-treetime 56s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (dsc) [2611 B] 56s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [5117 kB] 56s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [1291 kB] 56s Get:4 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (diff) [8028 B] 56s gpgv: Signature made Sat Nov 9 21:31:47 2024 UTC 56s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 56s gpgv: issuer "emollier@debian.org" 56s gpgv: Can't check signature: No public key 56s dpkg-source: warning: cannot verify inline signature for ./python-treetime_0.11.4-1.dsc: no acceptable signature found 56s autopkgtest [21:04:16]: testing package python-treetime version 0.11.4-1 57s autopkgtest [21:04:17]: build not needed 58s autopkgtest [21:04:18]: test run-unit-test: preparing testbed 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Starting pkgProblemResolver with broken count: 0 67s Starting 2 pkgProblemResolver with broken count: 0 67s Done 68s The following additional packages will be installed: 68s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 68s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 68s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 68s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 68s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 68s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 68s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 68s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 68s python3-cairo python3-contourpy python3-cycler python3-dateutil 68s python3-decorator python3-fonttools python3-freetype python3-fs 68s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 68s python3-mpmath python3-numpy python3-packaging python3-pandas 68s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 68s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 68s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 68s python3.12-tk python3.13-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib 68s x11-common xfonts-encodings xfonts-utils xml-core 68s Suggested packages: 68s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 68s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 68s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 68s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 68s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 68s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 68s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 68s python3-gobject python3-pyqt5 python3-sip python3-tornado 68s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 68s gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 68s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 68s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 68s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg sgml-base-doc 68s debhelper 68s Recommended packages: 68s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 68s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 68s python3-odf python3-openpyxl python3-tables python3-numba python3-olefile 68s fonts-dejavu-extra g++ | c++-compiler isympy-common 68s The following NEW packages will be installed: 68s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 68s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 68s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 68s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 68s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 68s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 68s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 68s libxslt1.1 libxss1 python-matplotlib-data python3-appdirs python3-biopython 68s python3-brotli python3-cairo python3-contourpy python3-cycler 68s python3-dateutil python3-decorator python3-fonttools python3-freetype 68s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 68s python3-mpmath python3-numpy python3-packaging python3-pandas 68s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 68s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 68s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 68s python3.12-tk python3.13-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib 68s x11-common xfonts-encodings xfonts-utils xml-core 68s 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. 68s Need to get 84.9 MB/84.9 MB of archives. 68s After this operation, 340 MB of additional disk space will be used. 68s Get:1 /tmp/autopkgtest.uRPnbJ/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [724 B] 68s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 68s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 68s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 68s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 68s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 68s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 68s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 68s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 68s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 69s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 69s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 69s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 69s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 69s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 69s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 69s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 69s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 69s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 69s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 69s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 69s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 69s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 69s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 69s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 69s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 69s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 69s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 69s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 69s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 69s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 69s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 69s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 69s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 69s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 69s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 69s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 69s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 69s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 69s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 69s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 69s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 69s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 69s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 69s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 69s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 69s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 69s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 69s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 69s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 69s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 69s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 69s Get:53 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 69s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 69s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 69s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 69s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 69s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 69s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 69s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 70s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 70s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 70s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 70s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 70s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 70s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 70s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 70s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 70s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 70s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 70s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 70s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 70s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 70s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 70s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 70s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 70s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 70s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 70s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 70s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 70s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 70s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 70s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 71s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 71s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 71s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 71s Fetched 84.9 MB in 3s (27.3 MB/s) 71s Selecting previously unselected package sgml-base. 71s (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 ... 75554 files and directories currently installed.) 71s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 71s Unpacking sgml-base (1.31) ... 71s Selecting previously unselected package libtcl8.6:amd64. 71s Preparing to unpack .../01-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 71s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 71s Selecting previously unselected package fonts-dejavu-mono. 71s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 71s Unpacking fonts-dejavu-mono (2.37-8) ... 71s Selecting previously unselected package fonts-dejavu-core. 71s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 71s Unpacking fonts-dejavu-core (2.37-8) ... 71s Selecting previously unselected package libfontenc1:amd64. 71s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 71s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 71s Selecting previously unselected package x11-common. 71s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 71s Unpacking x11-common (1:7.7+23ubuntu3) ... 71s Selecting previously unselected package xfonts-encodings. 71s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 71s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 71s Selecting previously unselected package xfonts-utils. 71s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_amd64.deb ... 71s Unpacking xfonts-utils (1:7.7+7) ... 71s Selecting previously unselected package fonts-urw-base35. 71s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 72s Unpacking fonts-urw-base35 (20200910-8) ... 72s Selecting previously unselected package fontconfig-config. 72s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 72s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 72s Selecting previously unselected package libfontconfig1:amd64. 72s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 72s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 72s Selecting previously unselected package libxrender1:amd64. 72s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 72s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 72s Selecting previously unselected package libxft2:amd64. 72s Preparing to unpack .../12-libxft2_2.3.6-1build1_amd64.deb ... 72s Unpacking libxft2:amd64 (2.3.6-1build1) ... 72s Selecting previously unselected package libxss1:amd64. 72s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_amd64.deb ... 72s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 72s Selecting previously unselected package libtk8.6:amd64. 72s Preparing to unpack .../14-libtk8.6_8.6.15-1_amd64.deb ... 72s Unpacking libtk8.6:amd64 (8.6.15-1) ... 72s Selecting previously unselected package tk8.6-blt2.5. 72s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 72s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 72s Selecting previously unselected package blt. 72s Preparing to unpack .../16-blt_2.5.3+dfsg-7build1_amd64.deb ... 72s Unpacking blt (2.5.3+dfsg-7build1) ... 72s Selecting previously unselected package fonts-lyx. 72s Preparing to unpack .../17-fonts-lyx_2.4.2.1-1_all.deb ... 72s Unpacking fonts-lyx (2.4.2.1-1) ... 72s Selecting previously unselected package libblas3:amd64. 72s Preparing to unpack .../18-libblas3_3.12.0-3build2_amd64.deb ... 72s Unpacking libblas3:amd64 (3.12.0-3build2) ... 72s Selecting previously unselected package libpixman-1-0:amd64. 72s Preparing to unpack .../19-libpixman-1-0_0.44.0-3_amd64.deb ... 72s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 72s Selecting previously unselected package libxcb-render0:amd64. 72s Preparing to unpack .../20-libxcb-render0_1.17.0-2_amd64.deb ... 72s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 72s Selecting previously unselected package libxcb-shm0:amd64. 72s Preparing to unpack .../21-libxcb-shm0_1.17.0-2_amd64.deb ... 72s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 72s Selecting previously unselected package libcairo2:amd64. 72s Preparing to unpack .../22-libcairo2_1.18.2-2_amd64.deb ... 72s Unpacking libcairo2:amd64 (1.18.2-2) ... 72s Selecting previously unselected package libdeflate0:amd64. 72s Preparing to unpack .../23-libdeflate0_1.22-1_amd64.deb ... 72s Unpacking libdeflate0:amd64 (1.22-1) ... 72s Selecting previously unselected package libgfortran5:amd64. 72s Preparing to unpack .../24-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 72s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 72s Selecting previously unselected package libgomp1:amd64. 72s Preparing to unpack .../25-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 72s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 72s Selecting previously unselected package libgraphite2-3:amd64. 72s Preparing to unpack .../26-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 72s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 72s Selecting previously unselected package libharfbuzz0b:amd64. 72s Preparing to unpack .../27-libharfbuzz0b_10.0.1-1_amd64.deb ... 72s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 72s Selecting previously unselected package libimagequant0:amd64. 72s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_amd64.deb ... 72s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 73s Selecting previously unselected package libjpeg-turbo8:amd64. 73s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 73s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 73s Selecting previously unselected package libjpeg8:amd64. 73s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_amd64.deb ... 73s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 73s Selecting previously unselected package libjs-jquery. 73s Preparing to unpack .../31-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 73s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 73s Selecting previously unselected package libjs-jquery-ui. 73s Preparing to unpack .../32-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 73s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 73s Selecting previously unselected package liblapack3:amd64. 73s Preparing to unpack .../33-liblapack3_3.12.0-3build2_amd64.deb ... 73s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 73s Selecting previously unselected package liblbfgsb0:amd64. 73s Preparing to unpack .../34-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 73s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 73s Selecting previously unselected package liblcms2-2:amd64. 73s Preparing to unpack .../35-liblcms2-2_2.16-2_amd64.deb ... 73s Unpacking liblcms2-2:amd64 (2.16-2) ... 73s Selecting previously unselected package liblerc4:amd64. 73s Preparing to unpack .../36-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 73s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 73s Selecting previously unselected package libqhull-r8.0:amd64. 73s Preparing to unpack .../37-libqhull-r8.0_2020.2-6build1_amd64.deb ... 73s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 73s Selecting previously unselected package libraqm0:amd64. 73s Preparing to unpack .../38-libraqm0_0.10.1-1build1_amd64.deb ... 73s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 73s Selecting previously unselected package libsharpyuv0:amd64. 73s Preparing to unpack .../39-libsharpyuv0_1.4.0-0.1_amd64.deb ... 73s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 73s Selecting previously unselected package libjbig0:amd64. 73s Preparing to unpack .../40-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 73s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 73s Selecting previously unselected package libwebp7:amd64. 73s Preparing to unpack .../41-libwebp7_1.4.0-0.1_amd64.deb ... 73s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 73s Selecting previously unselected package libtiff6:amd64. 73s Preparing to unpack .../42-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 73s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 73s Selecting previously unselected package libwebpdemux2:amd64. 73s Preparing to unpack .../43-libwebpdemux2_1.4.0-0.1_amd64.deb ... 73s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 73s Selecting previously unselected package libwebpmux3:amd64. 73s Preparing to unpack .../44-libwebpmux3_1.4.0-0.1_amd64.deb ... 73s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 73s Selecting previously unselected package libxslt1.1:amd64. 73s Preparing to unpack .../45-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 73s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 73s Selecting previously unselected package python-matplotlib-data. 73s Preparing to unpack .../46-python-matplotlib-data_3.8.3-3_all.deb ... 73s Unpacking python-matplotlib-data (3.8.3-3) ... 73s Selecting previously unselected package python3-appdirs. 73s Preparing to unpack .../47-python3-appdirs_1.4.4-4_all.deb ... 73s Unpacking python3-appdirs (1.4.4-4) ... 73s Selecting previously unselected package python3-numpy. 73s Preparing to unpack .../48-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 73s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 73s Selecting previously unselected package python3.12-tk. 73s Preparing to unpack .../49-python3.12-tk_3.12.7-3_amd64.deb ... 73s Unpacking python3.12-tk (3.12.7-3) ... 73s Selecting previously unselected package python3.13-tk. 73s Preparing to unpack .../50-python3.13-tk_3.13.0-2_amd64.deb ... 73s Unpacking python3.13-tk (3.13.0-2) ... 73s Selecting previously unselected package python3-tk:amd64. 73s Preparing to unpack .../51-python3-tk_3.12.7-1_amd64.deb ... 73s Unpacking python3-tk:amd64 (3.12.7-1) ... 73s Selecting previously unselected package python3-pil.imagetk:amd64. 73s Preparing to unpack .../52-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 73s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 74s Selecting previously unselected package libopenjp2-7:amd64. 74s Preparing to unpack .../53-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 74s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 74s Selecting previously unselected package python3-pil:amd64. 74s Preparing to unpack .../54-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 74s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 74s Selecting previously unselected package python3-cairo. 74s Preparing to unpack .../55-python3-cairo_1.26.1-2_amd64.deb ... 74s Unpacking python3-cairo (1.26.1-2) ... 74s Selecting previously unselected package python3-freetype. 74s Preparing to unpack .../56-python3-freetype_2.5.1-1_all.deb ... 74s Unpacking python3-freetype (2.5.1-1) ... 74s Selecting previously unselected package python3-rlpycairo. 74s Preparing to unpack .../57-python3-rlpycairo_0.3.0-3_all.deb ... 74s Unpacking python3-rlpycairo (0.3.0-3) ... 74s Selecting previously unselected package python3-reportlab. 74s Preparing to unpack .../58-python3-reportlab_4.2.5-1_all.deb ... 74s Unpacking python3-reportlab (4.2.5-1) ... 74s Selecting previously unselected package xml-core. 74s Preparing to unpack .../59-xml-core_0.19_all.deb ... 74s Unpacking xml-core (0.19) ... 74s Selecting previously unselected package w3c-sgml-lib. 74s Preparing to unpack .../60-w3c-sgml-lib_1.3-3_all.deb ... 74s Unpacking w3c-sgml-lib (1.3-3) ... 74s Selecting previously unselected package python3-biopython. 74s Preparing to unpack .../61-python3-biopython_1.84+dfsg-4_amd64.deb ... 74s Unpacking python3-biopython (1.84+dfsg-4) ... 74s Selecting previously unselected package python3-brotli. 74s Preparing to unpack .../62-python3-brotli_1.1.0-2build2_amd64.deb ... 74s Unpacking python3-brotli (1.1.0-2build2) ... 74s Selecting previously unselected package python3-contourpy. 74s Preparing to unpack .../63-python3-contourpy_1.3.0-2_amd64.deb ... 74s Unpacking python3-contourpy (1.3.0-2) ... 74s Selecting previously unselected package python3-cycler. 74s Preparing to unpack .../64-python3-cycler_0.12.1-1_all.deb ... 74s Unpacking python3-cycler (0.12.1-1) ... 74s Selecting previously unselected package python3-six. 74s Preparing to unpack .../65-python3-six_1.16.0-7_all.deb ... 74s Unpacking python3-six (1.16.0-7) ... 74s Selecting previously unselected package python3-dateutil. 74s Preparing to unpack .../66-python3-dateutil_2.9.0-2_all.deb ... 74s Unpacking python3-dateutil (2.9.0-2) ... 74s Selecting previously unselected package python3-decorator. 74s Preparing to unpack .../67-python3-decorator_5.1.1-5_all.deb ... 74s Unpacking python3-decorator (5.1.1-5) ... 74s Selecting previously unselected package python3-scipy. 74s Preparing to unpack .../68-python3-scipy_1.13.1-5_amd64.deb ... 74s Unpacking python3-scipy (1.13.1-5) ... 75s Selecting previously unselected package python3-ufolib2. 75s Preparing to unpack .../69-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 75s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 75s Selecting previously unselected package python3-mpmath. 75s Preparing to unpack .../70-python3-mpmath_1.3.0-1_all.deb ... 75s Unpacking python3-mpmath (1.3.0-1) ... 75s Selecting previously unselected package python3-sympy. 75s Preparing to unpack .../71-python3-sympy_1.13.3-1_all.deb ... 75s Unpacking python3-sympy (1.13.3-1) ... 75s Selecting previously unselected package python3-tz. 75s Preparing to unpack .../72-python3-tz_2024.1-2_all.deb ... 75s Unpacking python3-tz (2024.1-2) ... 75s Selecting previously unselected package python3-fs. 75s Preparing to unpack .../73-python3-fs_2.4.16-4_all.deb ... 75s Unpacking python3-fs (2.4.16-4) ... 75s Selecting previously unselected package python3-lxml:amd64. 75s Preparing to unpack .../74-python3-lxml_5.3.0-1_amd64.deb ... 75s Unpacking python3-lxml:amd64 (5.3.0-1) ... 75s Selecting previously unselected package python3-lz4. 75s Preparing to unpack .../75-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 75s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 75s Selecting previously unselected package python3-unicodedata2. 75s Preparing to unpack .../76-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 75s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 75s Selecting previously unselected package unicode-data. 75s Preparing to unpack .../77-unicode-data_15.1.0-1_all.deb ... 75s Unpacking unicode-data (15.1.0-1) ... 75s Selecting previously unselected package python3-fonttools. 75s Preparing to unpack .../78-python3-fonttools_4.46.0-1build2_amd64.deb ... 75s Unpacking python3-fonttools (4.46.0-1build2) ... 75s Selecting previously unselected package python3-kiwisolver. 76s Preparing to unpack .../79-python3-kiwisolver_1.4.7-2build1_amd64.deb ... 76s Unpacking python3-kiwisolver (1.4.7-2build1) ... 76s Selecting previously unselected package python3-packaging. 76s Preparing to unpack .../80-python3-packaging_24.1-1_all.deb ... 76s Unpacking python3-packaging (24.1-1) ... 76s Selecting previously unselected package python3-matplotlib. 76s Preparing to unpack .../81-python3-matplotlib_3.8.3-3_amd64.deb ... 76s Unpacking python3-matplotlib (3.8.3-3) ... 76s Selecting previously unselected package python3-pandas-lib:amd64. 76s Preparing to unpack .../82-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ... 76s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 76s Selecting previously unselected package python3-pandas. 76s Preparing to unpack .../83-python3-pandas_2.2.3+dfsg-5_all.deb ... 76s Unpacking python3-pandas (2.2.3+dfsg-5) ... 76s Selecting previously unselected package python3-treetime. 76s Preparing to unpack .../84-python3-treetime_0.11.4-1_all.deb ... 76s Unpacking python3-treetime (0.11.4-1) ... 76s Selecting previously unselected package autopkgtest-satdep. 76s Preparing to unpack .../85-1-autopkgtest-satdep.deb ... 76s Unpacking autopkgtest-satdep (0) ... 76s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 76s Setting up liblcms2-2:amd64 (2.16-2) ... 76s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 76s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 76s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 76s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 76s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 76s Setting up libxcb-render0:amd64 (1.17.0-2) ... 76s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 76s Setting up fonts-lyx (2.4.2.1-1) ... 76s Setting up x11-common (1:7.7+23ubuntu3) ... 77s Setting up libdeflate0:amd64 (1.22-1) ... 77s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 77s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 77s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 77s Setting up python3-freetype (2.5.1-1) ... 77s Setting up libjbig0:amd64 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currently installed.) 122s Removing autopkgtest-satdep (0) ... 122s autopkgtest [21:05:22]: test run-unit-test: [----------------------- 124s 124s 0.00 -TreeAnc: set-up 124s read alignment from file h3n2_na/h3n2_na_20.fasta with 19 sequences of length 1407 124s read tree from file h3n2_na/h3n2_na_20.nwk with 19 leaves 124s 124s inferring ancestral sequences... 124s ...done. 124s 124s The TOTAL tree length is 1.311e-01 and 183 mutations were observed. 124s Of these 183 mutations, 124s - 148 occur 1 times 124s - 16 occur 2 times 124s - 1 occur 3 times 124s 124s Of the 1407 positions in the genome, 124s - 1237 were hit 0 times (expected 1235.40) 124s - 124 were hit 1 times (expected 160.68) 124s - 25 were hit 2 times (expected 10.45) 124s - 3 were hit 3 times (expected 0.45) 124s 124s log-likelihood difference to Poisson distribution with same mean: -1.226e+01 124s 124s 124s The ten most homoplasic mutations are: 124s mut multiplicity 124s G27A 3 124s A88G 2 124s A267G 2 124s G451R 2 124s G629A 2 124s C763T 2 124s G780A 2 124s C825T 2 124s C891A 2 124s C906T 2 124s homoplasy_scanning ok 124s 124s 0.00 -TreeAnc: set-up 124s 124s Inferred sequence evolution model (saved as 2024-11-14_ancestral/sequence_evolution_model.txt): 124s Substitution rate (mu): 1.0 124s 124s Equilibrium frequencies (pi_i): 124s A: 0.3062 124s C: 0.1925 124s G: 0.2336 124s T: 0.2577 124s -: 0.01 124s 124s Symmetrized rates from j->i (W_ij): 124s A C G T - 124s A 0 0.8311 2.7926 0.4496 1.0287 124s C 0.8311 0 0.577 2.8797 1.0535 124s G 2.7926 0.577 0 0.612 1.0437 124s T 0.4496 2.8797 0.612 0 1.0394 124s - 1.0287 1.0535 1.0437 1.0394 0 124s 124s Actual rates from j->i (Q_ij): 124s A C G T - 124s A 0 0.2545 0.8551 0.1377 0.315 124s C 0.16 0 0.1111 0.5543 0.2028 124s G 0.6523 0.1348 0 0.143 0.2438 124s T 0.1159 0.7421 0.1577 0 0.2678 124s - 0.0103 0.0106 0.0105 0.0104 0 124s 124s 124s --- alignment including ancestral nodes saved as 124s 2024-11-14_ancestral/ancestral_sequences.fasta 124s 124s --- tree saved in nexus format as 124s 2024-11-14_ancestral/annotated_tree.nexus 124s 124s --- tree saved in auspice json format as 124s 2024-11-14_ancestral/auspice_tree.json 124s 124s ancestral_reconstruction ok 126s 126s 0.00 -TreeAnc: set-up 126s 126s Attempting to parse dates... 126s Using column 'name' as name. This needs match the taxon names in the tree!! 126s Using column 'date' as date. 126s 126s 0.00 TreeTime.reroot: with method or node: least-squares 126s 126s 0.00 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 126s 126s 0.02 TreeTime.reroot: with method or node: least-squares 126s 126s 0.02 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 126s 126s 0.04 TreeTime.reroot: with method or node: least-squares 126s 126s 0.04 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 126s 126s Root-Tip-Regression: 126s --rate: 2.826e-03 126s --r^2: 0.98 126s 126s The R^2 value indicates the fraction of variation inroot-to-tip 126s distance explained by the sampling times.Higher values corresponds 126s more clock-like behavior (max 1.0). 126s 126s The rate is the slope of the best fit of the date tothe root-to-tip 126s distance and provides an estimate ofthe substitution rate. The rate 126s needs to be positive!Negative rates suggest an inappropriate root. 126s 126s 126s The estimated rate and tree correspond to a root date: 126s 126s --- root-date: 1996.75 126s 126s 126s --- new tree written to 126s 2024-11-14_clock/rerooted.newick 126s 126s --- wrote dates and root-to-tip distances to 126s 2024-11-14_clock/rtt.csv 126s 126s --- root-to-tip plot saved to 126s 2024-11-14_clock/root_to_tip_regression.pdf 126s temporal_signal ok 132s 132s Attempting to parse dates... 132s Using column 'name' as name. This needs match the taxon names in the tree!! 132s Using column 'date' as date. 132s 132s 0.00 -TreeAnc: set-up 132s 132s 0.08 TreeTime.reroot: with method or node: least-squares 132s 132s 0.08 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 132s 132s 0.09 TreeTime.reroot: with method or node: least-squares 132s 132s 0.09 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 132s 132s 0.15 ###TreeTime.run: INITIAL ROUND 132s 132s 0.65 TreeTime.reroot: with method or node: least-squares 132s 132s 0.65 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 132s 132s 0.67 ###TreeTime.run: rerunning timetree after rerooting 132s 132s 1.20 ###TreeTime.run: ITERATION 1 out of 2 iterations 132s 132s 1.20 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 132s polytomies using the old 'greedy' mode. This is not well suited for large 132s polytomies. Stochastic resolution will become the default in future 132s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 132s keep using the greedy method in the future, run with `--greedy-resolve` 132s 132s 1.76 ###TreeTime.run: ITERATION 2 out of 2 iterations 132s 132s 3.79 ###TreeTime.run: FINAL ROUND - confidence estimation via marginal 132s reconstruction 132s 132s Inferred sequence evolution model (saved as 2024-11-14_treetime/sequence_evolution_model.txt): 132s Substitution rate (mu): 1.0 132s 132s Equilibrium frequencies (pi_i): 132s A: 0.3088 132s C: 0.1897 132s G: 0.2335 132s T: 0.2581 132s -: 0.0099 132s 132s Symmetrized rates from j->i (W_ij): 132s A C G T - 132s A 0 0.7003 3.0669 0.2651 0.9742 132s C 0.7003 0 0.3354 3.399 0.999 132s G 3.0669 0.3354 0 0.4258 0.9892 132s T 0.2651 3.399 0.4258 0 0.9848 132s - 0.9742 0.999 0.9892 0.9848 0 132s 132s Actual rates from j->i (Q_ij): 132s A C G T - 132s A 0 0.2163 0.9472 0.0819 0.3009 132s C 0.1328 0 0.0636 0.6448 0.1895 132s G 0.716 0.0783 0 0.0994 0.2309 132s T 0.0684 0.8772 0.1099 0 0.2541 132s - 0.0097 0.0099 0.0098 0.0098 0 132s 132s 132s Inferred sequence evolution model (saved as 2024-11-14_treetime/molecular_clock.txt): 132s Root-Tip-Regression: 132s --rate: 2.612e-03 +/- 3.98e-04 (one std-dev) 132s --chi^2: 8.37 132s --r^2: 0.98 132s 132s --- saved tree as 132s 2024-11-14_treetime/timetree.pdf 132s 132s --- root-to-tip plot saved to 132s 2024-11-14_treetime/root_to_tip_regression.pdf 132s 132s --- alignment including ancestral nodes saved as 132s 2024-11-14_treetime/ancestral_sequences.fasta 132s 132s --- saved divergence times in 132s 2024-11-14_treetime/dates.tsv 132s 132s --- tree saved in nexus format as 132s 2024-11-14_treetime/timetree.nexus 132s 132s --- tree saved in auspice json format as 132s 2024-11-14_treetime/auspice_tree.json 132s 132s --- divergence tree saved in nexus format as 132s 2024-11-14_treetime/divergence_tree.nexus 132s 132s /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]` 132s weight_dict = {row[0]:row[1] for ri,row in tmp_weights.iterrows() if not np.isnan(row[1])} 132s timetree_inference ok 132s Using column '#name' as taxon name. This needs to match the taxa in the tree! 132s Assigned discrete traits to 86 out of 86 taxa. 132s 132s 132s Completed mugration model inference of attribute 'country' for zika/zika.nwk 132s 132s Saved inferred mugration model as: 2024-11-14_mugration/GTR.txt 132s Saved annotated tree as: 2024-11-14_mugration/annotated_tree.nexus 132s ---Done! 132s 132s mugration ok 171s 171s Attempting to parse dates... 171s Using column 'strain' as name. This needs match the taxon names in the tree!! 171s Using column 'date' as date. 171s 171s 0.00 -TreeAnc: set-up 171s 171s 4.22 TreeTime.reroot: with method or node: least-squares 171s 171s 4.22 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 171s 171s 4.36 TreeTime.reroot: with method or node: least-squares 171s 171s 4.36 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 171s 171s 5.17 ###TreeTime.run: INITIAL ROUND 171s 171s 11.16 TreeTime.reroot: with method or node: least-squares 171s 171s 11.17 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 171s 171s 11.28 ###TreeTime.run: rerunning timetree after rerooting 171s 171s 17.84 ###TreeTime.run: ITERATION 1 out of 2 iterations 171s 171s 17.84 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 171s polytomies using the old 'greedy' mode. This is not well suited for large 171s polytomies. Stochastic resolution will become the default in future 171s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 171s keep using the greedy method in the future, run with `--greedy-resolve` 171s 171s 26.40 ###TreeTime.run: ITERATION 2 out of 2 iterations 171s 171s 34.25 TreeTime: the following tips have been marked as outliers. Their date 171s constraints were not used. Please remove them from the tree. Their dates 171s have been reset: 171s 171s 34.25 G22619, input date: [2011.0013698630137, 2011.9986301369863], apparent 171s date: 1989.25 171s 171s 34.25 G22625, input date: [2009.0013698630137, 2009.9986301369863], apparent 171s date: 2025.24 171s 171s 34.25 G22703, input date: [2004.0013661202186, 2004.9986338797814], apparent 171s date: 2027.50 171s 171s Inferred sequence evolution model (saved as 2024-11-14-0001_treetime/sequence_evolution_model.txt): 171s Substitution rate (mu): 1.0 171s 171s Equilibrium frequencies (pi_i): 171s A: 0.1669 171s C: 0.3286 171s G: 0.3273 171s T: 0.1669 171s -: 0.0103 171s 171s Symmetrized rates from j->i (W_ij): 171s A C G T - 171s A 0 0.7509 1.66 0.3122 35.7409 171s C 0.7509 0 0.3146 1.4127 35.8539 171s G 1.66 0.3146 0 0.7449 49.3079 171s T 0.3122 1.4127 0.7449 0 32.1055 171s - 35.7409 35.8539 49.3079 32.1055 0 171s 171s Actual rates from j->i (Q_ij): 171s A C G T - 171s A 0 0.1253 0.2771 0.0521 5.9656 171s C 0.2467 0 0.1034 0.4642 11.7808 171s G 0.5434 0.103 0 0.2438 16.1396 171s T 0.0521 0.2358 0.1243 0 5.3578 171s - 0.3685 0.3696 0.5083 0.331 0 171s 171s 171s Inferred sequence evolution model (saved as 2024-11-14-0001_treetime/molecular_clock.txt): 171s Root-Tip-Regression: 171s --rate: 1.000e-07 171s --r^2: 0.24 171s 171s --- saved tree as 171s 2024-11-14-0001_treetime/timetree.pdf 171s 171s --- root-to-tip plot saved to 171s 2024-11-14-0001_treetime/root_to_tip_regression.pdf 171s Sites that were constant except for ambiguous bases were made constant 171s by TreeTime. This happened 1343 times. These sites are now excluded 171s from the VCF. 171s 171s ***WARNING: vcf_utils.py 171s 52 sites were found that had no alternative bases. If this data has 171s been run through TreeTime and contains ambiguous bases, try calling 171s get_tree_dict with var_ambigs=True to see if this clears the error. 171s Alternative causes: - Not all sequences in your alignment are in the 171s tree (if you are running TreeTime via commandline this is most likely) 171s - In TreeTime, can be caused by overwriting variants in tips with 171s small branch lengths (debug) These are the positions affected 171s (numbering starts at 0): 171s 46593, 52473, 165918, 304891, 662240, 954864, 954865, 954866, 954867, 171s 963561, 1046706, 1145470, 1321893, 1468105, 1468106, 1512661, 1704463, 171s 1716723, 1743968, 1951837, 2129868, 2215816, 2274543, 2515984, 171s 2580886, 2626512, 2626513, 2626599, 2686156, 2736331, 2823901, 171s 2869282, 2894207, 2911378, 3047997, 3160385, 3314001, 3321447, 171s 3336505, 3461793, 3490408, 3618189, 3734466, 3764813, 3828626, 171s 3842630, 3894439, 3912292, 3913650, 3956227, 4149358, 4183687 171s 171s --- alignment including ancestral nodes saved as 171s 2024-11-14-0001_treetime/ancestral_sequences.vcf 171s 171s --- saved divergence times in 171s 2024-11-14-0001_treetime/dates.tsv 171s 171s --- tree saved in nexus format as 171s 2024-11-14-0001_treetime/timetree.nexus 171s 171s --- tree saved in auspice json format as 171s 2024-11-14-0001_treetime/auspice_tree.json 171s 171s --- divergence tree saved in nexus format as 171s 2024-11-14-0001_treetime/divergence_tree.nexus 171s 171s --- saved detected outliers as 2024-11-14-0001_treetime/outliers.tsv 171s timetree_inference on vcf data ok 256s 256s Attempting to parse dates... 256s Using column 'name' as name. This needs match the taxon names in the tree!! 256s Using column 'date' as date. 256s 256s 0.00 -TreeAnc: set-up 256s 256s 2.67 -WARNING: character U is unknown. Treating it as missing information 256s 256s 10.29 TreeTime.reroot: with method or node: least-squares 256s 256s 10.29 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 256s 256s 10.65 TreeTime.reroot: with method or node: least-squares 256s 256s 10.65 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 256s 256s 15.45 ###TreeTime.run: INITIAL ROUND 256s 256s 23.49 TreeTime.reroot: with method or node: least-squares 256s 256s 23.49 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 256s 256s 23.80 ###TreeTime.run: rerunning timetree after rerooting 256s 256s 34.12 ###TreeTime.run: ITERATION 1 out of 2 iterations 256s 256s 34.63 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 256s polytomies using the old 'greedy' mode. This is not well suited for large 256s polytomies. Stochastic resolution will become the default in future 256s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 256s keep using the greedy method in the future, run with `--greedy-resolve` 256s 256s 50.66 ###TreeTime.run: ITERATION 2 out of 2 iterations 256s 256s 79.21 TreeTime: the following tips have been marked as outliers. Their date 256s constraints were not used. Please remove them from the tree. Their dates 256s have been reset: 256s 256s 79.21 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.10 256s 256s 79.21 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.10 256s 256s 79.21 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.10 256s 256s 79.21 NZG_0381, input date: 2016.23, apparent date: 2015.10 256s 256s 79.21 NZG_0393, input date: 2016.24, apparent date: 2015.17 256s 256s 79.21 NZG_0358, input date: 2016.22, apparent date: 2015.17 256s 256s 79.21 NZG_0422, input date: 2016.25, apparent date: 2015.17 256s 256s 79.21 2607_C2_12855_EMLH, input date: 2015.28, apparent date: 2015.48 256s 256s 79.21 2607_C2_12916_EMLH, input date: 2015.32, apparent date: 2015.48 256s 256s 79.21 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.58 256s 256s 79.21 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.83 256s 256s 79.21 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.83 256s 256s 79.21 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.83 256s 256s 79.21 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2015.97 256s 256s 79.21 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.90 256s 256s 79.21 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.90 256s 256s 79.21 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.77 256s 256s 79.21 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.90 256s 256s 79.21 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2015.97 256s 256s 79.21 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2015.97 256s 256s Inferred sequence evolution model (saved as 2024-11-14-0002_treetime/sequence_evolution_model.txt): 256s Substitution rate (mu): 1.0 256s 256s Equilibrium frequencies (pi_i): 256s A: 0.3139 256s C: 0.2144 256s G: 0.1978 256s T: 0.2639 256s -: 0.01 256s 256s Symmetrized rates from j->i (W_ij): 256s A C G T - 256s A 0 0.3826 2.5279 0.2294 6.7953 256s C 0.3826 0 0.1691 3.5597 12.1802 256s G 2.5279 0.1691 0 0.3724 5.2952 256s T 0.2294 3.5597 0.3724 0 27.7409 256s - 6.7953 12.1802 5.2952 27.7409 0 256s 256s Actual rates from j->i (Q_ij): 256s A C G T - 256s A 0 0.1201 0.7935 0.072 2.1329 256s C 0.0821 0 0.0363 0.7633 2.6119 256s G 0.5001 0.0335 0 0.0737 1.0476 256s T 0.0605 0.9394 0.0983 0 7.3206 256s - 0.0676 0.1212 0.0527 0.276 0 256s 256s 256s Inferred sequence evolution model (saved as 2024-11-14-0002_treetime/molecular_clock.txt): 256s Root-Tip-Regression: 256s --rate: 7.885e-04 256s --r^2: 0.80 256s 256s Inferred coalescent model 256s Skyline assuming 100.0 gen/year and approximate confidence bounds (+/- 2.000000 standard deviations of the LH) 256s date N_e lower upper 256s 2013.978 3.745e+01 1.531e+01 9.160e+01 256s 2014.074 6.390e+01 3.529e+01 1.157e+02 256s 2014.171 1.371e+02 8.464e+01 2.221e+02 256s 2014.267 1.388e+02 8.278e+01 2.327e+02 256s 2014.363 1.504e+02 1.011e+02 2.238e+02 256s 2014.460 3.445e+02 2.412e+02 4.920e+02 256s 2014.556 9.564e+02 6.459e+02 1.416e+03 256s 2014.653 1.060e+03 6.850e+02 1.642e+03 256s 2014.749 1.112e+03 7.232e+02 1.710e+03 256s 2014.846 9.706e+02 5.943e+02 1.585e+03 256s 2014.942 8.080e+02 5.037e+02 1.296e+03 256s 2015.039 3.111e+02 1.892e+02 5.114e+02 256s 2015.135 2.686e+02 1.777e+02 4.060e+02 256s 2015.231 2.701e+02 1.698e+02 4.298e+02 256s 2015.328 1.801e+02 1.115e+02 2.910e+02 256s 2015.424 1.514e+02 9.909e+01 2.313e+02 256s 2015.521 1.086e+02 6.627e+01 1.779e+02 256s 2015.617 1.075e+02 6.658e+01 1.737e+02 256s 2015.714 3.443e+01 1.825e+01 6.494e+01 256s 2015.810 1.007e+01 4.080e+00 2.487e+01 256s 256s --- written skyline to 2024-11-14-0002_treetime/skyline.tsv 256s 256s --- saved tree as 256s 2024-11-14-0002_treetime/timetree.pdf 256s 256s --- root-to-tip plot saved to 256s 2024-11-14-0002_treetime/root_to_tip_regression.pdf 256s 256s --- alignment including ancestral nodes saved as 256s 2024-11-14-0002_treetime/ancestral_sequences.fasta 256s 256s --- saved divergence times in 256s 2024-11-14-0002_treetime/dates.tsv 256s 256s --- tree saved in nexus format as 256s 2024-11-14-0002_treetime/timetree.nexus 256s 256s --- tree saved in auspice json format as 256s 2024-11-14-0002_treetime/auspice_tree.json 256s 256s --- divergence tree saved in nexus format as 256s 2024-11-14-0002_treetime/divergence_tree.nexus 256s 256s --- saved detected outliers as 2024-11-14-0002_treetime/outliers.tsv 256s skyline approximation ok 280s 280s Attempting to parse dates... 280s Using column 'name' as name. This needs match the taxon names in the tree!! 280s Using column 'date' as date. 280s 280s 0.00 -TreeAnc: set-up 280s 280s 0.05 TreeTime.reroot: with method or node: least-squares 280s 280s 0.05 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 280s 280s 0.47 TreeTime.reroot: with method or node: least-squares 280s 280s 0.47 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 280s 280s 0.79 ###TreeTime.run: INITIAL ROUND 280s 280s 7.67 TreeTime.reroot: with method or node: least-squares 280s 280s 7.67 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 280s 280s 7.99 ###TreeTime.run: rerunning timetree after rerooting 280s 280s 14.97 ###TreeTime.run: ITERATION 1 out of 2 iterations 280s 280s 14.97 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 280s polytomies using the old 'greedy' mode. This is not well suited for large 280s polytomies. Stochastic resolution will become the default in future 280s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 280s keep using the greedy method in the future, run with `--greedy-resolve` 280s 280s 21.92 ###TreeTime.run: CONVERGED 280s 280s 21.92 TreeTime: the following tips have been marked as outliers. Their date 280s constraints were not used. Please remove them from the tree. Their dates 280s have been reset: 280s 280s 21.92 NZG_0393, input date: 2016.24, apparent date: 2015.26 280s 280s 21.92 NZG_0422, input date: 2016.25, apparent date: 2015.26 280s 280s 21.92 NZG_0358, input date: 2016.22, apparent date: 2015.26 280s 280s 21.92 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.19 280s 280s 21.92 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.19 280s 280s 21.92 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.19 280s 280s 21.92 NZG_0381, input date: 2016.23, apparent date: 2015.19 280s 280s 21.92 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.40 280s 280s 21.92 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.81 280s 280s 21.92 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.81 280s 280s 21.92 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2015.87 280s 280s 21.92 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2015.87 280s 280s 21.92 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.74 280s 280s 21.92 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.81 280s 280s 21.92 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.68 280s 280s 21.92 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.74 280s 280s 21.92 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.74 280s 280s 21.92 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2015.87 280s 280s Inferred sequence evolution model (saved as 2024-11-14-0003_treetime/sequence_evolution_model.txt): 280s Substitution rate (mu): 1.0 280s 280s Equilibrium frequencies (pi_i): 280s A: 0.2 280s C: 0.2 280s G: 0.2 280s T: 0.2 280s -: 0.2 280s 280s Symmetrized rates from j->i (W_ij): 280s A C G T - 280s A 0 1.25 1.25 1.25 1.25 280s C 1.25 0 1.25 1.25 1.25 280s G 1.25 1.25 0 1.25 1.25 280s T 1.25 1.25 1.25 0 1.25 280s - 1.25 1.25 1.25 1.25 0 280s 280s Actual rates from j->i (Q_ij): 280s A C G T - 280s A 0 0.25 0.25 0.25 0.25 280s C 0.25 0 0.25 0.25 0.25 280s G 0.25 0.25 0 0.25 0.25 280s T 0.25 0.25 0.25 0 0.25 280s - 0.25 0.25 0.25 0.25 0 280s 280s 280s Inferred sequence evolution model (saved as 2024-11-14-0003_treetime/molecular_clock.txt): 280s Root-Tip-Regression: 280s --rate: 8.047e-04 280s --r^2: 0.79 280s 280s --- saved tree as 280s 2024-11-14-0003_treetime/timetree.pdf 280s 280s --- root-to-tip plot saved to 280s 2024-11-14-0003_treetime/root_to_tip_regression.pdf 280s --- saved divergence times in 280s 2024-11-14-0003_treetime/dates.tsv 280s 280s --- tree saved in nexus format as 280s 2024-11-14-0003_treetime/timetree.nexus 280s 280s --- tree saved in auspice json format as 280s 2024-11-14-0003_treetime/auspice_tree.json 280s 280s --- divergence tree saved in nexus format as 280s 2024-11-14-0003_treetime/divergence_tree.nexus 280s 280s --- saved detected outliers as 2024-11-14-0003_treetime/outliers.tsv 280s sequence length only ok 280s All tests passed 280s autopkgtest [21:08:00]: test run-unit-test: -----------------------] 281s autopkgtest [21:08:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 281s run-unit-test PASS 281s autopkgtest [21:08:01]: test autodep8-python3: preparing testbed 341s autopkgtest [21:09:01]: testbed dpkg architecture: amd64 341s autopkgtest [21:09:01]: testbed apt version: 2.9.8 341s autopkgtest [21:09:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 342s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 343s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.7 kB] 343s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 343s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 343s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1044 kB] 343s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.4 kB] 343s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [144 kB] 343s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 343s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [805 kB] 343s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [295 kB] 343s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 343s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9660 B] 343s Fetched 2613 kB in 1s (3114 kB/s) 343s Reading package lists... 345s Reading package lists... 346s Building dependency tree... 346s Reading state information... 346s Calculating upgrade... 346s The following NEW packages will be installed: 346s python3.13-gdbm 346s The following packages will be upgraded: 346s libcap-ng0 libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal 346s python3-systemd 346s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 346s Need to get 178 kB of archives. 346s After this operation, 256 kB of additional disk space will be used. 346s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 346s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 346s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 346s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 346s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 346s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 346s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 346s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 347s Fetched 178 kB in 0s (422 kB/s) 347s (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 ... 75542 files and directories currently installed.) 347s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 347s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 347s Setting up python3-minimal (3.12.7-1) ... 347s (Reading database ... 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.../python3-systemd_235-1build5_amd64.deb ... 347s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 347s Setting up python3.13-gdbm (3.13.0-2) ... 347s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 347s Setting up python3 (3.12.7-1) ... 348s Setting up python3-systemd (235-1build5) ... 348s Setting up python3-gdbm:amd64 (3.12.7-1) ... 348s Setting up pastebinit (1.7.1-1) ... 348s Processing triggers for libc-bin (2.40-1ubuntu3) ... 348s Processing triggers for man-db (2.12.1-3) ... 348s Reading package lists... 348s Building dependency tree... 348s Reading state information... 349s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 349s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 349s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 349s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 349s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 350s Reading package lists... 350s Reading package lists... 351s Building dependency tree... 351s Reading state information... 351s Calculating upgrade... 351s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 351s Reading package lists... 351s Building dependency tree... 351s Reading state information... 351s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 356s Reading package lists... 356s Building dependency tree... 356s Reading state information... 356s Starting pkgProblemResolver with broken count: 0 356s Starting 2 pkgProblemResolver with broken count: 0 356s Done 356s The following additional packages will be installed: 356s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 356s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 356s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 356s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 356s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libpython3.13-minimal 356s libpython3.13-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 356s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 356s libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data python3-all 356s python3-appdirs python3-biopython python3-brotli python3-cairo 356s python3-contourpy python3-cycler python3-dateutil python3-decorator 356s python3-fonttools python3-freetype python3-fs python3-kiwisolver 356s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy 356s python3-packaging python3-pandas python3-pandas-lib python3-pil 357s python3-pil.imagetk python3-reportlab python3-rlpycairo python3-scipy 357s python3-six python3-sympy python3-tk python3-treetime python3-tz 357s python3-ufolib2 python3.12-tk python3.13 python3.13-minimal python3.13-tk 357s sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 357s xfonts-utils xml-core 357s Suggested packages: 357s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 357s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 357s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 357s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 357s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 357s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 357s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 357s python3-gobject python3-pyqt5 python3-sip python3-tornado 357s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 357s gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 357s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 357s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 357s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-venv 357s python3.13-doc binfmt-support sgml-base-doc debhelper 357s Recommended packages: 357s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 357s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 357s python3-odf python3-openpyxl python3-tables python3-numba python3-olefile 357s fonts-dejavu-extra g++ | c++-compiler isympy-common 357s The following NEW packages will be installed: 357s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 357s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 357s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 357s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 357s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 357s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 357s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 357s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 357s python-matplotlib-data python3-all python3-appdirs python3-biopython 357s python3-brotli python3-cairo python3-contourpy python3-cycler 357s python3-dateutil python3-decorator python3-fonttools python3-freetype 357s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 357s python3-mpmath python3-numpy python3-packaging python3-pandas 357s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 357s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 357s python3-treetime python3-tz python3-ufolib2 python3.12-tk python3.13 357s python3.13-minimal python3.13-tk sgml-base tk8.6-blt2.5 unicode-data 357s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 357s 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. 357s Need to get 90.4 MB/90.4 MB of archives. 357s After this operation, 361 MB of additional disk space will be used. 357s Get:1 /tmp/autopkgtest.uRPnbJ/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 357s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 357s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 357s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 357s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 357s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 357s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 357s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 357s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 357s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 357s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 357s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 358s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 358s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 358s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 358s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 358s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 358s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 358s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 358s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 358s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 358s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 358s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 358s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 358s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 358s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 358s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 358s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 358s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 358s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 358s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 358s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 358s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 358s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 358s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 358s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 358s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 358s Get:38 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 358s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 358s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 358s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 358s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 358s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 358s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 358s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 358s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 358s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 358s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 358s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 358s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 358s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 358s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 358s Get:53 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 358s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 358s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 358s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 358s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 358s Get:58 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 358s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 358s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 358s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 358s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 358s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 358s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 358s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 359s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 359s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 359s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 359s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 359s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 359s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 359s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 359s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 359s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 359s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 359s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 359s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 359s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 360s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 360s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 360s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 360s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 360s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 360s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 360s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 360s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 360s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 360s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 361s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 361s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 361s Fetched 90.4 MB in 4s (21.9 MB/s) 361s Selecting previously unselected package libpython3.13-minimal:amd64. 361s (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 ... 75554 files and directories currently installed.) 361s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 361s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 361s Selecting previously unselected package python3.13-minimal. 361s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 361s Unpacking python3.13-minimal (3.13.0-2) ... 361s Selecting previously unselected package sgml-base. 361s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 361s Unpacking sgml-base (1.31) ... 361s Selecting previously unselected package libtcl8.6:amd64. 361s Preparing to unpack .../03-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 361s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 361s Selecting previously unselected package fonts-dejavu-mono. 361s Preparing to unpack .../04-fonts-dejavu-mono_2.37-8_all.deb ... 361s Unpacking fonts-dejavu-mono (2.37-8) ... 361s Selecting previously unselected package fonts-dejavu-core. 361s Preparing to unpack .../05-fonts-dejavu-core_2.37-8_all.deb ... 361s Unpacking fonts-dejavu-core (2.37-8) ... 361s Selecting previously unselected package libfontenc1:amd64. 361s Preparing to unpack .../06-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 361s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 361s Selecting previously unselected package x11-common. 361s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu3_all.deb ... 361s Unpacking x11-common (1:7.7+23ubuntu3) ... 361s Selecting previously unselected package xfonts-encodings. 361s Preparing to unpack .../08-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 361s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 361s Selecting previously unselected package xfonts-utils. 361s Preparing to unpack .../09-xfonts-utils_1%3a7.7+7_amd64.deb ... 361s Unpacking xfonts-utils (1:7.7+7) ... 362s Selecting previously unselected package fonts-urw-base35. 362s Preparing to unpack .../10-fonts-urw-base35_20200910-8_all.deb ... 362s Unpacking fonts-urw-base35 (20200910-8) ... 362s Selecting previously unselected package fontconfig-config. 362s Preparing to unpack .../11-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 362s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 362s Selecting previously unselected package libfontconfig1:amd64. 362s Preparing to unpack .../12-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 362s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 362s Selecting previously unselected package libxrender1:amd64. 362s Preparing to unpack .../13-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 362s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 362s Selecting previously unselected package libxft2:amd64. 362s Preparing to unpack .../14-libxft2_2.3.6-1build1_amd64.deb ... 362s Unpacking libxft2:amd64 (2.3.6-1build1) ... 362s Selecting previously unselected package libxss1:amd64. 362s Preparing to unpack .../15-libxss1_1%3a1.2.3-1build3_amd64.deb ... 362s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 362s Selecting previously unselected package libtk8.6:amd64. 362s Preparing to unpack .../16-libtk8.6_8.6.15-1_amd64.deb ... 362s Unpacking libtk8.6:amd64 (8.6.15-1) ... 362s Selecting previously unselected package tk8.6-blt2.5. 362s Preparing to unpack .../17-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 362s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 362s Selecting previously unselected package blt. 362s Preparing to unpack .../18-blt_2.5.3+dfsg-7build1_amd64.deb ... 362s Unpacking blt (2.5.3+dfsg-7build1) ... 362s Selecting previously unselected package fonts-lyx. 362s Preparing to unpack .../19-fonts-lyx_2.4.2.1-1_all.deb ... 362s Unpacking fonts-lyx (2.4.2.1-1) ... 362s Selecting previously unselected package libblas3:amd64. 362s Preparing to unpack .../20-libblas3_3.12.0-3build2_amd64.deb ... 362s Unpacking libblas3:amd64 (3.12.0-3build2) ... 362s Selecting previously unselected package libpixman-1-0:amd64. 362s Preparing to unpack .../21-libpixman-1-0_0.44.0-3_amd64.deb ... 362s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 362s Selecting previously unselected package libxcb-render0:amd64. 362s Preparing to unpack .../22-libxcb-render0_1.17.0-2_amd64.deb ... 362s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 362s Selecting previously unselected package libxcb-shm0:amd64. 362s Preparing to unpack .../23-libxcb-shm0_1.17.0-2_amd64.deb ... 362s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 362s Selecting previously unselected package libcairo2:amd64. 362s Preparing to unpack .../24-libcairo2_1.18.2-2_amd64.deb ... 362s Unpacking libcairo2:amd64 (1.18.2-2) ... 362s Selecting previously unselected package libdeflate0:amd64. 362s Preparing to unpack .../25-libdeflate0_1.22-1_amd64.deb ... 362s Unpacking libdeflate0:amd64 (1.22-1) ... 362s Selecting previously unselected package libgfortran5:amd64. 362s Preparing to unpack .../26-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 362s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 362s Selecting previously unselected package libgomp1:amd64. 362s Preparing to unpack .../27-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 362s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 362s Selecting previously unselected package libgraphite2-3:amd64. 362s Preparing to unpack .../28-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 362s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 362s Selecting previously unselected package libharfbuzz0b:amd64. 362s Preparing to unpack .../29-libharfbuzz0b_10.0.1-1_amd64.deb ... 362s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 362s Selecting previously unselected package libimagequant0:amd64. 362s Preparing to unpack .../30-libimagequant0_2.18.0-1build1_amd64.deb ... 362s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 362s Selecting previously unselected package libjpeg-turbo8:amd64. 362s Preparing to unpack .../31-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 362s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 362s Selecting previously unselected package libjpeg8:amd64. 362s Preparing to unpack .../32-libjpeg8_8c-2ubuntu11_amd64.deb ... 362s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 362s Selecting previously unselected package libjs-jquery. 362s Preparing to unpack .../33-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 362s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 362s Selecting previously unselected package libjs-jquery-ui. 362s Preparing to unpack .../34-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 362s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 363s Selecting previously unselected package liblapack3:amd64. 363s Preparing to unpack .../35-liblapack3_3.12.0-3build2_amd64.deb ... 363s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 363s Selecting previously unselected package liblbfgsb0:amd64. 363s Preparing to unpack .../36-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 363s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 363s Selecting previously unselected package liblcms2-2:amd64. 363s Preparing to unpack .../37-liblcms2-2_2.16-2_amd64.deb ... 363s Unpacking liblcms2-2:amd64 (2.16-2) ... 363s Selecting previously unselected package liblerc4:amd64. 363s Preparing to unpack .../38-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 363s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 363s Selecting previously unselected package libpython3.13-stdlib:amd64. 363s Preparing to unpack .../39-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 363s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 363s Selecting previously unselected package libqhull-r8.0:amd64. 363s Preparing to unpack .../40-libqhull-r8.0_2020.2-6build1_amd64.deb ... 363s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 363s Selecting previously unselected package libraqm0:amd64. 363s Preparing to unpack .../41-libraqm0_0.10.1-1build1_amd64.deb ... 363s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 363s Selecting previously unselected package libsharpyuv0:amd64. 363s Preparing to unpack .../42-libsharpyuv0_1.4.0-0.1_amd64.deb ... 363s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 363s Selecting previously unselected package libjbig0:amd64. 363s Preparing to unpack .../43-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 363s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 363s Selecting previously unselected package libwebp7:amd64. 363s Preparing to unpack .../44-libwebp7_1.4.0-0.1_amd64.deb ... 363s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 363s Selecting previously unselected package libtiff6:amd64. 363s Preparing to unpack .../45-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 363s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 363s Selecting previously unselected package libwebpdemux2:amd64. 363s Preparing to unpack .../46-libwebpdemux2_1.4.0-0.1_amd64.deb ... 363s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 363s Selecting previously unselected package libwebpmux3:amd64. 363s Preparing to unpack .../47-libwebpmux3_1.4.0-0.1_amd64.deb ... 363s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 363s Selecting previously unselected package libxslt1.1:amd64. 363s Preparing to unpack .../48-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 363s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 363s Selecting previously unselected package python-matplotlib-data. 363s Preparing to unpack .../49-python-matplotlib-data_3.8.3-3_all.deb ... 363s Unpacking python-matplotlib-data (3.8.3-3) ... 363s Selecting previously unselected package python3.13. 363s Preparing to unpack .../50-python3.13_3.13.0-2_amd64.deb ... 363s Unpacking python3.13 (3.13.0-2) ... 363s Selecting previously unselected package python3-all. 363s Preparing to unpack .../51-python3-all_3.12.7-1_amd64.deb ... 363s Unpacking python3-all (3.12.7-1) ... 363s Selecting previously unselected package python3-appdirs. 363s Preparing to unpack .../52-python3-appdirs_1.4.4-4_all.deb ... 363s Unpacking python3-appdirs (1.4.4-4) ... 363s Selecting previously unselected package python3-numpy. 363s Preparing to unpack .../53-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 363s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 363s Selecting previously unselected package python3.12-tk. 363s Preparing to unpack .../54-python3.12-tk_3.12.7-3_amd64.deb ... 363s Unpacking python3.12-tk (3.12.7-3) ... 363s Selecting previously unselected package python3.13-tk. 363s Preparing to unpack .../55-python3.13-tk_3.13.0-2_amd64.deb ... 363s Unpacking python3.13-tk (3.13.0-2) ... 363s Selecting previously unselected package python3-tk:amd64. 363s Preparing to unpack .../56-python3-tk_3.12.7-1_amd64.deb ... 363s Unpacking python3-tk:amd64 (3.12.7-1) ... 363s Selecting previously unselected package python3-pil.imagetk:amd64. 363s Preparing to unpack .../57-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 363s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 363s Selecting previously unselected package libopenjp2-7:amd64. 363s Preparing to unpack .../58-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 363s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 363s Selecting previously unselected package python3-pil:amd64. 363s Preparing to unpack .../59-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 363s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 363s Selecting previously unselected package python3-cairo. 364s Preparing to unpack .../60-python3-cairo_1.26.1-2_amd64.deb ... 364s Unpacking python3-cairo (1.26.1-2) ... 364s Selecting previously unselected package python3-freetype. 364s Preparing to unpack .../61-python3-freetype_2.5.1-1_all.deb ... 364s Unpacking python3-freetype (2.5.1-1) ... 364s Selecting previously unselected package python3-rlpycairo. 364s Preparing to unpack .../62-python3-rlpycairo_0.3.0-3_all.deb ... 364s Unpacking python3-rlpycairo (0.3.0-3) ... 364s Selecting previously unselected package python3-reportlab. 364s Preparing to unpack .../63-python3-reportlab_4.2.5-1_all.deb ... 364s Unpacking python3-reportlab (4.2.5-1) ... 364s Selecting previously unselected package xml-core. 364s Preparing to unpack .../64-xml-core_0.19_all.deb ... 364s Unpacking xml-core (0.19) ... 364s Selecting previously unselected package w3c-sgml-lib. 364s Preparing to unpack .../65-w3c-sgml-lib_1.3-3_all.deb ... 364s Unpacking w3c-sgml-lib (1.3-3) ... 364s Selecting previously unselected package python3-biopython. 364s Preparing to unpack .../66-python3-biopython_1.84+dfsg-4_amd64.deb ... 364s Unpacking python3-biopython (1.84+dfsg-4) ... 364s Selecting previously unselected package python3-brotli. 364s Preparing to unpack .../67-python3-brotli_1.1.0-2build2_amd64.deb ... 364s Unpacking python3-brotli (1.1.0-2build2) ... 364s Selecting previously unselected package python3-contourpy. 364s Preparing to unpack .../68-python3-contourpy_1.3.0-2_amd64.deb ... 364s Unpacking python3-contourpy (1.3.0-2) ... 364s Selecting previously unselected package python3-cycler. 364s Preparing to unpack .../69-python3-cycler_0.12.1-1_all.deb ... 364s Unpacking python3-cycler (0.12.1-1) ... 364s Selecting previously unselected package python3-six. 364s Preparing to unpack .../70-python3-six_1.16.0-7_all.deb ... 364s Unpacking python3-six (1.16.0-7) ... 364s Selecting previously unselected package python3-dateutil. 364s Preparing to unpack .../71-python3-dateutil_2.9.0-2_all.deb ... 364s Unpacking python3-dateutil (2.9.0-2) ... 364s Selecting previously unselected package python3-decorator. 364s Preparing to unpack .../72-python3-decorator_5.1.1-5_all.deb ... 364s Unpacking 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autopkgtest-satdep. 366s Preparing to unpack .../89-2-autopkgtest-satdep.deb ... 366s Unpacking autopkgtest-satdep (0) ... 366s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 366s Setting up liblcms2-2:amd64 (2.16-2) ... 366s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 366s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 366s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 366s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 366s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 366s Setting up libxcb-render0:amd64 (1.17.0-2) ... 366s Setting up fonts-lyx (2.4.2.1-1) ... 366s Setting up x11-common (1:7.7+23ubuntu3) ... 366s Setting up libdeflate0:amd64 (1.22-1) ... 366s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 366s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 366s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 366s Setting up python3-freetype (2.5.1-1) ... 367s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 367s Setting up python3-tz (2024.1-2) ... 367s Setting up unicode-data (15.1.0-1) ... 367s Setting up python3-six (1.16.0-7) ... 367s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 367s Setting up python3-decorator (5.1.1-5) ... 367s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 367s Setting up libblas3:amd64 (3.12.0-3build2) ... 367s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 367s Setting up python3-packaging (24.1-1) ... 367s Setting up python3-brotli (1.1.0-2build2) ... 367s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 367s Setting up python3-cycler (0.12.1-1) ... 367s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 367s Setting up fonts-dejavu-mono (2.37-8) ... 367s Setting up python3-kiwisolver (1.4.7-2build1) ... 368s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 368s Setting up fonts-dejavu-core (2.37-8) ... 368s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 368s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 368s Setting up libwebp7:amd64 (1.4.0-0.1) ... 368s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 368s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 368s Setting up python3.13-minimal (3.13.0-2) ... 368s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 368s Setting up python3-dateutil (2.9.0-2) ... 368s Setting up sgml-base (1.31) ... 368s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 368s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 369s Setting up python3-mpmath (1.3.0-1) ... 369s Setting up python-matplotlib-data (3.8.3-3) ... 369s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 369s Setting up python3-appdirs (1.4.4-4) ... 369s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 369s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 369s Setting up python3-sympy (1.13.3-1) ... 379s Setting up liblapack3:amd64 (3.12.0-3build2) ... 379s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 379s Setting up python3.13 (3.13.0-2) ... 380s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 380s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 380s Setting up python3-all (3.12.7-1) ... 380s Setting up xfonts-utils (1:7.7+7) ... 380s Setting up python3-fs (2.4.16-4) ... 380s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 380s Setting up libraqm0:amd64 (0.10.1-1build1) ... 380s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 383s Setting up python3-lxml:amd64 (5.3.0-1) ... 383s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 383s Setting up xml-core (0.19) ... 383s Setting up python3-contourpy (1.3.0-2) ... 384s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 384s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 384s Setting up libxft2:amd64 (2.3.6-1build1) ... 384s Setting up python3-scipy (1.13.1-5) ... 389s Setting up libtk8.6:amd64 (8.6.15-1) ... 389s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 389s Setting up python3.12-tk (3.12.7-3) ... 389s Setting up fonts-urw-base35 (20200910-8) ... 389s Setting up libcairo2:amd64 (1.18.2-2) ... 389s Setting up python3.13-tk (3.13.0-2) ... 389s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 390s Setting up python3-pandas (2.2.3+dfsg-5) ... 397s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 397s Setting up python3-cairo (1.26.1-2) ... 398s Setting up blt (2.5.3+dfsg-7build1) ... 398s Setting up python3-tk:amd64 (3.12.7-1) ... 398s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 398s Setting up python3-rlpycairo (0.3.0-3) ... 398s Setting up python3-reportlab (4.2.5-1) ... 399s Setting up python3-fonttools (4.46.0-1build2) ... 401s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 401s Setting up python3-matplotlib (3.8.3-3) ... 403s Processing triggers for libc-bin (2.40-1ubuntu3) ... 403s Processing triggers for systemd (256.5-2ubuntu4) ... 403s Processing triggers for man-db (2.12.1-3) ... 404s Processing triggers for sgml-base (1.31) ... 404s Setting up w3c-sgml-lib (1.3-3) ... 427s Setting up python3-biopython (1.84+dfsg-4) ... 429s Setting up python3-treetime (0.11.4-1) ... 429s Setting up autopkgtest-satdep (0) ... 433s (Reading database ... 87035 files and directories currently installed.) 433s Removing autopkgtest-satdep (0) ... 435s autopkgtest [21:10:35]: 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 435s autopkgtest [21:10:35]: test autodep8-python3: [----------------------- 435s Testing with python3.13: 436s Traceback (most recent call last): 436s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 436s from . import multiarray 436s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 436s from . import overrides 436s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 436s from numpy.core._multiarray_umath import ( 436s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 436s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 436s 436s During handling of the above exception, another exception occurred: 436s 436s Traceback (most recent call last): 436s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 436s from numpy.__config__ import show as show_config 436s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 436s from numpy.core._multiarray_umath import ( 436s ...<3 lines>... 436s ) 436s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 436s raise ImportError(msg) 436s ImportError: 436s 436s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 436s 436s Importing the numpy C-extensions failed. This error can happen for 436s many reasons, often due to issues with your setup or how NumPy was 436s installed. 436s 436s We have compiled some common reasons and troubleshooting tips at: 436s 436s https://numpy.org/devdocs/user/troubleshooting-importerror.html 436s 436s Please note and check the following: 436s 436s * The Python version is: Python3.13 from "/usr/bin/python3.13" 436s * The NumPy version is: "1.26.4" 436s 436s and make sure that they are the versions you expect. 436s Please carefully study the documentation linked above for further help. 436s 436s Original error was: No module named 'numpy.core._multiarray_umath' 436s 436s 436s The above exception was the direct cause of the following exception: 436s 436s Traceback (most recent call last): 436s File "", line 1, in 436s import treetime; print(treetime) 436s ^^^^^^^^^^^^^^^ 436s File "/usr/lib/python3/dist-packages/treetime/__init__.py", line 38, in 436s from .treeanc import TreeAnc 436s File "/usr/lib/python3/dist-packages/treetime/treeanc.py", line 3, in 436s import numpy as np 436s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 436s raise ImportError(msg) from e 436s ImportError: Error importing numpy: you should not try to import numpy from 436s its source directory; please exit the numpy source tree, and relaunch 436s your python interpreter from there. 436s autopkgtest [21:10:36]: test autodep8-python3: -----------------------] 436s autodep8-python3 FAIL non-zero exit status 1 436s autopkgtest [21:10:36]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 437s autopkgtest [21:10:37]: @@@@@@@@@@@@@@@@@@@@ summary 437s run-unit-test PASS 437s autodep8-python3 FAIL non-zero exit status 1 448s nova [W] Skipping flock for amd64 448s Creating nova instance adt-plucky-amd64-python-treetime-20241114-210320-juju-7f2275-prod-proposed-migration-environment-15-3048aa0a-77fe-459b-a39c-6c672357ec35 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)... 448s nova [W] Skipping flock for amd64 448s Creating nova instance adt-plucky-amd64-python-treetime-20241114-210320-juju-7f2275-prod-proposed-migration-environment-15-3048aa0a-77fe-459b-a39c-6c672357ec35 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...