0s autopkgtest [05:46:34]: starting date and time: 2024-11-15 05:46:34+0000 0s autopkgtest [05:46:34]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [05:46:34]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.285gvmfd/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-biopython --apt-upgrade python-treetime --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-biopython/1.84+dfsg-4build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-22.secgroup --name adt-plucky-amd64-python-treetime-20241115-054633-juju-7f2275-prod-proposed-migration-environment-15-4c363df1-bacf-4c45-bff9-8271454996c5 --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/ 39s autopkgtest [05:47:13]: testbed dpkg architecture: amd64 39s autopkgtest [05:47:13]: testbed apt version: 2.9.8 39s autopkgtest [05:47:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 40s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 40s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [97.2 kB] 40s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1055 kB] 41s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 41s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 41s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [131 kB] 41s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [198 kB] 41s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [818 kB] 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [299 kB] 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9128 B] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 41s Fetched 2737 kB in 1s (3327 kB/s) 41s Reading package lists... 43s Reading package lists... 43s Building dependency tree... 43s Reading state information... 43s Calculating upgrade... 43s The following packages will be upgraded: 43s firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0 43s libexpat1 lxd-installer man-db pastebinit python3-systemd xfsprogs 44s 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 44s Need to get 13.6 MB of archives. 44s After this operation, 477 kB of additional disk space will be used. 44s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 44s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 44s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 44s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 44s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB] 44s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB] 44s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB] 44s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB] 44s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 44s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 44s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 44s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 45s Preconfiguring packages ... 45s Fetched 13.6 MB in 1s (14.3 MB/s) 45s (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.) 45s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 45s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 45s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 45s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 45s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 45s (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 ... 75568 files and directories currently installed.) 45s Preparing to unpack .../0-libexpat1_2.6.4-1_amd64.deb ... 45s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 45s Preparing to unpack .../1-man-db_2.13.0-1_amd64.deb ... 45s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 45s Preparing to unpack .../2-grub2-common_2.12-5ubuntu7_amd64.deb ... 45s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 45s Preparing to unpack .../3-grub-pc_2.12-5ubuntu7_amd64.deb ... 45s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 45s Preparing to unpack .../4-grub-pc-bin_2.12-5ubuntu7_amd64.deb ... 45s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 45s Preparing to unpack .../5-grub-common_2.12-5ubuntu7_amd64.deb ... 45s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 45s Preparing to unpack .../6-lxd-installer_9_all.deb ... 45s Unpacking lxd-installer (9) over (8) ... 46s Preparing to unpack .../7-pastebinit_1.7.1-1_all.deb ... 46s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 46s Preparing to unpack .../8-python3-systemd_235-1build5_amd64.deb ... 46s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 46s Preparing to unpack .../9-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 46s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 46s Setting up libexpat1:amd64 (2.6.4-1) ... 46s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 46s Setting up pastebinit (1.7.1-1) ... 46s Setting up man-db (2.13.0-1) ... 46s Updating database of manual pages ... 47s man-db.service is a disabled or a static unit not running, not starting it. 47s Setting up grub-common (2.12-5ubuntu7) ... 47s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 48s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 48s update-initramfs: deferring update (trigger activated) 48s Setting up lxd-installer (9) ... 49s Setting up python3-systemd (235-1build5) ... 49s Setting up grub2-common (2.12-5ubuntu7) ... 49s Setting up grub-pc-bin (2.12-5ubuntu7) ... 49s Setting up grub-pc (2.12-5ubuntu7) ... 49s Installing for i386-pc platform. 49s Installation finished. No error reported. 49s Sourcing file `/etc/default/grub' 49s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 49s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 49s Generating grub configuration file ... 50s Found linux image: /boot/vmlinuz-6.11.0-8-generic 50s Found initrd image: /boot/initrd.img-6.11.0-8-generic 50s Warning: os-prober will not be executed to detect other bootable partitions. 50s Systems on them will not be added to the GRUB boot configuration. 50s Check GRUB_DISABLE_OS_PROBER documentation entry. 50s Adding boot menu entry for UEFI Firmware Settings ... 50s done 50s Processing triggers for libc-bin (2.40-1ubuntu3) ... 50s Processing triggers for install-info (7.1.1-1) ... 50s Processing triggers for initramfs-tools (0.142ubuntu34) ... 50s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 50s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 59s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 59s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 59s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 60s Reading package lists... 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s autopkgtest [05:47:35]: rebooting testbed after setup commands that affected boot 65s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 78s autopkgtest [05:47:52]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 81s autopkgtest [05:47:55]: @@@@@@@@@@@@@@@@@@@@ apt-source python-treetime 83s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (dsc) [2611 B] 83s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [5117 kB] 83s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [1291 kB] 83s Get:4 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (diff) [8028 B] 83s gpgv: Signature made Sat Nov 9 21:31:47 2024 UTC 83s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 83s gpgv: issuer "emollier@debian.org" 83s gpgv: Can't check signature: No public key 83s dpkg-source: warning: cannot verify inline signature for ./python-treetime_0.11.4-1.dsc: no acceptable signature found 83s autopkgtest [05:47:57]: testing package python-treetime version 0.11.4-1 83s autopkgtest [05:47:57]: build not needed 85s autopkgtest [05:47:59]: test run-unit-test: preparing testbed 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Starting pkgProblemResolver with broken count: 0 89s Starting 2 pkgProblemResolver with broken count: 0 89s Done 89s The following additional packages will be installed: 89s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 89s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 89s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 89s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 89s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 89s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 89s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 89s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 89s python3-cairo python3-contourpy python3-cycler python3-dateutil 89s python3-decorator python3-fonttools python3-freetype python3-fs 89s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 89s python3-mpmath python3-numpy python3-packaging python3-pandas 89s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 89s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 89s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 89s python3.12-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 89s xfonts-encodings xfonts-utils xml-core 89s Suggested packages: 89s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 89s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 89s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 89s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 89s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 89s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 89s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 89s python3-gobject python3-pyqt5 python3-sip python3-tornado 89s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 89s gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 89s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 89s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 89s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-tk 89s sgml-base-doc debhelper 89s Recommended packages: 89s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 89s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 89s python3-odf python3-openpyxl python3-tables python3-numba python3-olefile 89s fonts-dejavu-extra g++ | c++-compiler isympy-common 89s The following NEW packages will be installed: 89s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 89s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 89s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 89s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 89s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 89s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 89s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 89s libxslt1.1 libxss1 python-matplotlib-data python3-appdirs python3-biopython 89s python3-brotli python3-cairo python3-contourpy python3-cycler 89s python3-dateutil python3-decorator python3-fonttools python3-freetype 89s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 89s python3-mpmath python3-numpy python3-packaging python3-pandas 89s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 89s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 89s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 89s python3.12-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 89s xfonts-encodings xfonts-utils xml-core 89s 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 84.8 MB/84.8 MB of archives. 89s After this operation, 341 MB of additional disk space will be used. 89s Get:1 /tmp/autopkgtest.sHJI2r/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 89s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 90s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 90s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 90s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 90s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 90s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 90s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 90s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 90s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 90s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 90s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 90s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 90s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 90s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 90s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 90s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 90s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 90s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 90s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 90s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 90s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 90s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 90s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 90s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 90s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 90s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 90s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 90s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 90s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 90s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 90s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 90s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 90s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 90s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 90s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 90s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 90s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 90s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 90s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 90s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 90s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 90s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 90s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 90s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 90s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 90s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 90s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 90s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 90s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 90s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.6-1ubuntu1 [9806 B] 90s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 90s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 90s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 90s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 90s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 90s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 90s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 91s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 91s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 91s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB] 91s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 91s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 91s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 91s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 91s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 91s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 91s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 91s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 91s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 91s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 91s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 91s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 91s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 91s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 91s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB] 91s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 91s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 91s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 91s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 91s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 92s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 92s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 92s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 93s Fetched 84.8 MB in 3s (29.8 MB/s) 93s Selecting previously unselected package sgml-base. 93s (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 ... 75575 files and directories currently installed.) 93s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 93s Unpacking sgml-base (1.31) ... 93s Selecting previously unselected package libtcl8.6:amd64. 93s Preparing to unpack .../01-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 93s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 93s Selecting previously unselected package fonts-dejavu-mono. 93s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 93s Unpacking fonts-dejavu-mono (2.37-8) ... 93s Selecting previously unselected package fonts-dejavu-core. 93s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 93s Unpacking fonts-dejavu-core (2.37-8) ... 93s Selecting previously unselected package libfontenc1:amd64. 93s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 93s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 93s Selecting previously unselected package x11-common. 93s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 93s Unpacking x11-common (1:7.7+23ubuntu3) ... 93s Selecting previously unselected package xfonts-encodings. 93s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 93s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 93s Selecting previously unselected package xfonts-utils. 93s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_amd64.deb ... 93s Unpacking xfonts-utils (1:7.7+7) ... 93s Selecting previously unselected package fonts-urw-base35. 93s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 93s Unpacking fonts-urw-base35 (20200910-8) ... 93s Selecting previously unselected package fontconfig-config. 93s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 93s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 93s Selecting previously unselected package libfontconfig1:amd64. 93s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 93s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 93s Selecting previously unselected package libxrender1:amd64. 93s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 93s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 93s Selecting previously unselected package libxft2:amd64. 93s Preparing to unpack .../12-libxft2_2.3.6-1build1_amd64.deb ... 93s Unpacking libxft2:amd64 (2.3.6-1build1) ... 93s Selecting previously unselected package libxss1:amd64. 93s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_amd64.deb ... 93s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 93s Selecting previously unselected package libtk8.6:amd64. 93s Preparing to unpack .../14-libtk8.6_8.6.15-1_amd64.deb ... 93s Unpacking libtk8.6:amd64 (8.6.15-1) ... 93s Selecting previously unselected package tk8.6-blt2.5. 93s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 93s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 93s Selecting previously unselected package blt. 93s Preparing to unpack .../16-blt_2.5.3+dfsg-7build1_amd64.deb ... 93s Unpacking blt (2.5.3+dfsg-7build1) ... 93s Selecting previously unselected package fonts-lyx. 93s Preparing to unpack .../17-fonts-lyx_2.4.2.1-1_all.deb ... 93s Unpacking fonts-lyx (2.4.2.1-1) ... 93s Selecting previously unselected package libblas3:amd64. 93s Preparing to unpack .../18-libblas3_3.12.0-3build2_amd64.deb ... 93s Unpacking libblas3:amd64 (3.12.0-3build2) ... 93s Selecting previously unselected package libpixman-1-0:amd64. 93s Preparing to unpack .../19-libpixman-1-0_0.44.0-3_amd64.deb ... 93s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 93s Selecting previously unselected package libxcb-render0:amd64. 93s Preparing to unpack .../20-libxcb-render0_1.17.0-2_amd64.deb ... 93s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 93s Selecting previously unselected package libxcb-shm0:amd64. 93s Preparing to unpack .../21-libxcb-shm0_1.17.0-2_amd64.deb ... 93s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 93s Selecting previously unselected package libcairo2:amd64. 93s Preparing to unpack .../22-libcairo2_1.18.2-2_amd64.deb ... 93s Unpacking libcairo2:amd64 (1.18.2-2) ... 93s Selecting previously unselected package libdeflate0:amd64. 93s Preparing to unpack .../23-libdeflate0_1.22-1_amd64.deb ... 93s Unpacking libdeflate0:amd64 (1.22-1) ... 93s Selecting previously unselected package libgfortran5:amd64. 93s Preparing to unpack .../24-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 93s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 93s Selecting previously unselected package libgomp1:amd64. 93s Preparing to unpack .../25-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 93s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 93s Selecting previously unselected package libgraphite2-3:amd64. 93s Preparing to unpack .../26-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 93s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 94s Selecting previously unselected package libharfbuzz0b:amd64. 94s Preparing to unpack .../27-libharfbuzz0b_10.0.1-1_amd64.deb ... 94s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 94s Selecting previously unselected package libimagequant0:amd64. 94s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_amd64.deb ... 94s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 94s Selecting previously unselected package libjpeg-turbo8:amd64. 94s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 94s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 94s Selecting previously unselected package libjpeg8:amd64. 94s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_amd64.deb ... 94s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 94s Selecting previously unselected package libjs-jquery. 94s Preparing to unpack .../31-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 94s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 94s Selecting previously unselected package libjs-jquery-ui. 94s Preparing to unpack .../32-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 94s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 94s Selecting previously unselected package liblapack3:amd64. 94s Preparing to unpack .../33-liblapack3_3.12.0-3build2_amd64.deb ... 94s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 94s Selecting previously unselected package liblbfgsb0:amd64. 94s Preparing to unpack .../34-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 94s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 94s Selecting previously unselected package liblcms2-2:amd64. 94s Preparing to unpack .../35-liblcms2-2_2.16-2_amd64.deb ... 94s Unpacking liblcms2-2:amd64 (2.16-2) ... 94s Selecting previously unselected package liblerc4:amd64. 94s Preparing to unpack .../36-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 94s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 94s Selecting previously unselected package libqhull-r8.0:amd64. 94s Preparing to unpack .../37-libqhull-r8.0_2020.2-6build1_amd64.deb ... 94s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 94s Selecting previously unselected package libraqm0:amd64. 94s Preparing to unpack .../38-libraqm0_0.10.1-1build1_amd64.deb ... 94s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 94s Selecting previously unselected package libsharpyuv0:amd64. 94s Preparing to unpack .../39-libsharpyuv0_1.4.0-0.1_amd64.deb ... 94s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 94s Selecting previously unselected package libjbig0:amd64. 94s Preparing to unpack .../40-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 94s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 94s Selecting previously unselected package libwebp7:amd64. 94s Preparing to unpack .../41-libwebp7_1.4.0-0.1_amd64.deb ... 94s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 94s Selecting previously unselected package libtiff6:amd64. 94s Preparing to unpack .../42-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 94s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 94s Selecting previously unselected package libwebpdemux2:amd64. 94s Preparing to unpack .../43-libwebpdemux2_1.4.0-0.1_amd64.deb ... 94s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 94s Selecting previously unselected package libwebpmux3:amd64. 94s Preparing to unpack .../44-libwebpmux3_1.4.0-0.1_amd64.deb ... 94s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 94s Selecting previously unselected package libxslt1.1:amd64. 94s Preparing to unpack .../45-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 94s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 94s Selecting previously unselected package python-matplotlib-data. 94s Preparing to unpack .../46-python-matplotlib-data_3.8.3-3_all.deb ... 94s Unpacking python-matplotlib-data (3.8.3-3) ... 94s Selecting previously unselected package python3-appdirs. 94s Preparing to unpack .../47-python3-appdirs_1.4.4-4_all.deb ... 94s Unpacking python3-appdirs (1.4.4-4) ... 94s Selecting previously unselected package python3-numpy. 94s Preparing to unpack .../48-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 94s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 94s Selecting previously unselected package python3.12-tk. 94s Preparing to unpack .../49-python3.12-tk_3.12.7-3_amd64.deb ... 94s Unpacking python3.12-tk (3.12.7-3) ... 94s Selecting previously unselected package python3-tk:amd64. 94s Preparing to unpack .../50-python3-tk_3.12.6-1ubuntu1_amd64.deb ... 94s Unpacking python3-tk:amd64 (3.12.6-1ubuntu1) ... 94s Selecting previously unselected package python3-pil.imagetk:amd64. 94s Preparing to unpack .../51-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 94s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 94s Selecting previously unselected package libopenjp2-7:amd64. 94s Preparing to unpack .../52-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 94s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 94s Selecting previously unselected package python3-pil:amd64. 94s Preparing to unpack .../53-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 94s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 94s Selecting previously unselected package python3-cairo. 94s Preparing to unpack .../54-python3-cairo_1.26.1-2_amd64.deb ... 94s Unpacking python3-cairo (1.26.1-2) ... 94s Selecting previously unselected package python3-freetype. 94s Preparing to unpack .../55-python3-freetype_2.5.1-1_all.deb ... 94s Unpacking python3-freetype (2.5.1-1) ... 94s Selecting previously unselected package python3-rlpycairo. 94s Preparing to unpack .../56-python3-rlpycairo_0.3.0-3_all.deb ... 94s Unpacking python3-rlpycairo (0.3.0-3) ... 94s Selecting previously unselected package python3-reportlab. 94s Preparing to unpack .../57-python3-reportlab_4.2.5-1_all.deb ... 94s Unpacking python3-reportlab (4.2.5-1) ... 95s Selecting previously unselected package xml-core. 95s Preparing to unpack .../58-xml-core_0.19_all.deb ... 95s Unpacking xml-core (0.19) ... 95s Selecting previously unselected package w3c-sgml-lib. 95s Preparing to unpack .../59-w3c-sgml-lib_1.3-3_all.deb ... 95s Unpacking w3c-sgml-lib (1.3-3) ... 95s Selecting previously unselected package python3-biopython. 95s Preparing to unpack .../60-python3-biopython_1.84+dfsg-4build1_amd64.deb ... 95s Unpacking python3-biopython (1.84+dfsg-4build1) ... 95s Selecting previously unselected package python3-brotli. 95s Preparing to unpack .../61-python3-brotli_1.1.0-2build2_amd64.deb ... 95s Unpacking python3-brotli (1.1.0-2build2) ... 95s Selecting previously unselected package python3-contourpy. 95s Preparing to unpack .../62-python3-contourpy_1.3.0-2_amd64.deb ... 95s Unpacking python3-contourpy (1.3.0-2) ... 95s Selecting previously unselected package python3-cycler. 95s Preparing to unpack .../63-python3-cycler_0.12.1-1_all.deb ... 95s Unpacking python3-cycler (0.12.1-1) ... 95s Selecting previously unselected package python3-six. 95s Preparing to unpack .../64-python3-six_1.16.0-7_all.deb ... 95s Unpacking python3-six (1.16.0-7) ... 95s Selecting previously unselected package python3-dateutil. 95s Preparing to unpack .../65-python3-dateutil_2.9.0-2_all.deb ... 95s Unpacking python3-dateutil (2.9.0-2) ... 95s Selecting previously unselected package python3-decorator. 95s Preparing to unpack .../66-python3-decorator_5.1.1-5_all.deb ... 95s Unpacking python3-decorator (5.1.1-5) ... 95s Selecting previously unselected package python3-scipy. 95s Preparing to unpack .../67-python3-scipy_1.13.1-5_amd64.deb ... 95s Unpacking python3-scipy (1.13.1-5) ... 95s Selecting previously unselected package python3-ufolib2. 95s Preparing to unpack .../68-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 95s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 95s Selecting previously unselected package python3-mpmath. 95s Preparing to unpack .../69-python3-mpmath_1.3.0-1_all.deb ... 95s Unpacking python3-mpmath (1.3.0-1) ... 95s Selecting previously unselected package python3-sympy. 95s Preparing to unpack .../70-python3-sympy_1.13.3-1_all.deb ... 95s Unpacking python3-sympy (1.13.3-1) ... 96s Selecting previously unselected package python3-tz. 96s Preparing to unpack .../71-python3-tz_2024.1-2_all.deb ... 96s Unpacking python3-tz (2024.1-2) ... 96s Selecting previously unselected package python3-fs. 96s Preparing to unpack .../72-python3-fs_2.4.16-4_all.deb ... 96s Unpacking python3-fs (2.4.16-4) ... 96s Selecting previously unselected package python3-lxml:amd64. 96s Preparing to unpack .../73-python3-lxml_5.3.0-1_amd64.deb ... 96s Unpacking python3-lxml:amd64 (5.3.0-1) ... 96s Selecting previously unselected package python3-lz4. 96s Preparing to unpack .../74-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 96s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 96s Selecting previously unselected package python3-unicodedata2. 96s Preparing to unpack .../75-python3-unicodedata2_15.1.0+ds-1build2_amd64.deb ... 96s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 96s Selecting previously unselected package unicode-data. 96s Preparing to unpack .../76-unicode-data_15.1.0-1_all.deb ... 96s Unpacking unicode-data (15.1.0-1) ... 96s Selecting previously unselected package python3-fonttools. 96s Preparing to unpack .../77-python3-fonttools_4.46.0-1build2_amd64.deb ... 96s Unpacking python3-fonttools (4.46.0-1build2) ... 96s Selecting previously unselected package python3-kiwisolver. 96s Preparing to unpack .../78-python3-kiwisolver_1.4.7-2build1_amd64.deb ... 96s Unpacking python3-kiwisolver (1.4.7-2build1) ... 96s Selecting previously unselected package python3-packaging. 96s Preparing 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0.00 -TreeAnc: set-up 143s read alignment from file h3n2_na/h3n2_na_20.fasta with 19 sequences of length 1407 143s read tree from file h3n2_na/h3n2_na_20.nwk with 19 leaves 143s 143s inferring ancestral sequences... 143s ...done. 143s 143s The TOTAL tree length is 1.311e-01 and 183 mutations were observed. 143s Of these 183 mutations, 143s - 148 occur 1 times 143s - 16 occur 2 times 143s - 1 occur 3 times 143s 143s Of the 1407 positions in the genome, 143s - 1237 were hit 0 times (expected 1235.40) 143s - 124 were hit 1 times (expected 160.68) 143s - 25 were hit 2 times (expected 10.45) 143s - 3 were hit 3 times (expected 0.45) 143s 143s log-likelihood difference to Poisson distribution with same mean: -1.226e+01 143s 143s 143s The ten most homoplasic mutations are: 143s mut multiplicity 143s G27A 3 143s A88G 2 143s A267G 2 143s G451R 2 143s G629A 2 143s C763T 2 143s G780A 2 143s C825T 2 143s C891A 2 143s C906T 2 143s homoplasy_scanning ok 144s 144s 0.00 -TreeAnc: set-up 144s 144s Inferred sequence evolution model (saved as 2024-11-15_ancestral/sequence_evolution_model.txt): 144s Substitution rate (mu): 1.0 144s 144s Equilibrium frequencies (pi_i): 144s A: 0.3062 144s C: 0.1925 144s G: 0.2336 144s T: 0.2577 144s -: 0.01 144s 144s Symmetrized rates from j->i (W_ij): 144s A C G T - 144s A 0 0.8311 2.7926 0.4496 1.0287 144s C 0.8311 0 0.577 2.8797 1.0535 144s G 2.7926 0.577 0 0.612 1.0437 144s T 0.4496 2.8797 0.612 0 1.0394 144s - 1.0287 1.0535 1.0437 1.0394 0 144s 144s Actual rates from j->i (Q_ij): 144s A C G T - 144s A 0 0.2545 0.8551 0.1377 0.315 144s C 0.16 0 0.1111 0.5543 0.2028 144s G 0.6523 0.1348 0 0.143 0.2438 144s T 0.1159 0.7421 0.1577 0 0.2678 144s - 0.0103 0.0106 0.0105 0.0104 0 144s 144s 144s --- alignment including ancestral nodes saved as 144s 2024-11-15_ancestral/ancestral_sequences.fasta 144s 144s --- tree saved in nexus format as 144s 2024-11-15_ancestral/annotated_tree.nexus 144s 144s --- tree saved in auspice json format as 144s 2024-11-15_ancestral/auspice_tree.json 144s 144s ancestral_reconstruction ok 145s 145s 0.00 -TreeAnc: set-up 145s 145s Attempting to parse dates... 145s Using column 'name' as name. This needs match the taxon names in the tree!! 145s Using column 'date' as date. 145s 145s 0.00 TreeTime.reroot: with method or node: least-squares 145s 145s 0.00 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 145s 145s 0.02 TreeTime.reroot: with method or node: least-squares 145s 145s 0.02 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 145s 145s 0.04 TreeTime.reroot: with method or node: least-squares 145s 145s 0.04 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 145s 145s Root-Tip-Regression: 145s --rate: 2.826e-03 145s --r^2: 0.98 145s 145s The R^2 value indicates the fraction of variation inroot-to-tip 145s distance explained by the sampling times.Higher values corresponds 145s more clock-like behavior (max 1.0). 145s 145s The rate is the slope of the best fit of the date tothe root-to-tip 145s distance and provides an estimate ofthe substitution rate. The rate 145s needs to be positive!Negative rates suggest an inappropriate root. 145s 145s 145s The estimated rate and tree correspond to a root date: 145s 145s --- root-date: 1996.75 145s 145s 145s --- new tree written to 145s 2024-11-15_clock/rerooted.newick 145s 145s --- wrote dates and root-to-tip distances to 145s 2024-11-15_clock/rtt.csv 145s 145s --- root-to-tip plot saved to 145s 2024-11-15_clock/root_to_tip_regression.pdf 146s temporal_signal ok 150s 150s Attempting to parse dates... 150s Using column 'name' as name. This needs match the taxon names in the tree!! 150s Using column 'date' as date. 150s 150s 0.00 -TreeAnc: set-up 150s 150s 0.08 TreeTime.reroot: with method or node: least-squares 150s 150s 0.08 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 150s 150s 0.09 TreeTime.reroot: with method or node: least-squares 150s 150s 0.09 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 150s 150s 0.15 ###TreeTime.run: INITIAL ROUND 150s 150s 0.63 TreeTime.reroot: with method or node: least-squares 150s 150s 0.63 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 150s 150s 0.65 ###TreeTime.run: rerunning timetree after rerooting 150s 150s 1.15 ###TreeTime.run: ITERATION 1 out of 2 iterations 150s 150s 1.15 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 150s polytomies using the old 'greedy' mode. This is not well suited for large 150s polytomies. Stochastic resolution will become the default in future 150s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 150s keep using the greedy method in the future, run with `--greedy-resolve` 150s 150s 1.67 ###TreeTime.run: CONVERGED 150s 150s 3.15 ###TreeTime.run: FINAL ROUND - confidence estimation via marginal 150s reconstruction 150s 150s Inferred sequence evolution model (saved as 2024-11-15_treetime/sequence_evolution_model.txt): 150s Substitution rate (mu): 1.0 150s 150s Equilibrium frequencies (pi_i): 150s A: 0.3088 150s C: 0.1897 150s G: 0.2335 150s T: 0.2581 150s -: 0.0099 150s 150s Symmetrized rates from j->i (W_ij): 150s A C G T - 150s A 0 0.7003 3.0669 0.2651 0.9742 150s C 0.7003 0 0.3354 3.399 0.999 150s G 3.0669 0.3354 0 0.4258 0.9892 150s T 0.2651 3.399 0.4258 0 0.9848 150s - 0.9742 0.999 0.9892 0.9848 0 150s 150s Actual rates from j->i (Q_ij): 150s A C G T - 150s A 0 0.2163 0.9472 0.0819 0.3009 150s C 0.1328 0 0.0636 0.6448 0.1895 150s G 0.716 0.0783 0 0.0994 0.2309 150s T 0.0684 0.8772 0.1099 0 0.2541 150s - 0.0097 0.0099 0.0098 0.0098 0 150s 150s 150s Inferred sequence evolution model (saved as 2024-11-15_treetime/molecular_clock.txt): 150s Root-Tip-Regression: 150s --rate: 2.620e-03 +/- 3.96e-04 (one std-dev) 150s --chi^2: 8.56 150s --r^2: 0.98 150s 150s --- saved tree as 150s 2024-11-15_treetime/timetree.pdf 150s 150s --- root-to-tip plot saved to 150s 2024-11-15_treetime/root_to_tip_regression.pdf 150s 150s --- alignment including ancestral nodes saved as 150s 2024-11-15_treetime/ancestral_sequences.fasta 150s 150s --- saved divergence times in 150s 2024-11-15_treetime/dates.tsv 150s 150s --- tree saved in nexus format as 150s 2024-11-15_treetime/timetree.nexus 150s 150s --- tree saved in auspice json format as 150s 2024-11-15_treetime/auspice_tree.json 150s 150s --- divergence tree saved in nexus format as 150s 2024-11-15_treetime/divergence_tree.nexus 150s 150s timetree_inference ok 151s /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]` 151s weight_dict = {row[0]:row[1] for ri,row in tmp_weights.iterrows() if not np.isnan(row[1])} 152s Using column '#name' as taxon name. This needs to match the taxa in the tree! 152s Assigned discrete traits to 86 out of 86 taxa. 152s 152s 152s Completed mugration model inference of attribute 'country' for zika/zika.nwk 152s 152s Saved inferred mugration model as: 2024-11-15_mugration/GTR.txt 152s Saved annotated tree as: 2024-11-15_mugration/annotated_tree.nexus 152s ---Done! 152s 152s mugration ok 190s 190s Attempting to parse dates... 190s Using column 'strain' as name. This needs match the taxon names in the tree!! 190s Using column 'date' as date. 190s 190s 0.00 -TreeAnc: set-up 190s 190s 4.20 TreeTime.reroot: with method or node: least-squares 190s 190s 4.20 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 190s 190s 4.33 TreeTime.reroot: with method or node: least-squares 190s 190s 4.33 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 190s 190s 5.17 ###TreeTime.run: INITIAL ROUND 190s 190s 11.10 TreeTime.reroot: with method or node: least-squares 190s 190s 11.10 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 190s 190s 11.22 ###TreeTime.run: rerunning timetree after rerooting 190s 190s 17.53 ###TreeTime.run: ITERATION 1 out of 2 iterations 190s 190s 17.53 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 190s polytomies using the old 'greedy' mode. This is not well suited for large 190s polytomies. Stochastic resolution will become the default in future 190s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 190s keep using the greedy method in the future, run with `--greedy-resolve` 190s 190s 26.15 ###TreeTime.run: ITERATION 2 out of 2 iterations 190s 190s 34.08 TreeTime: the following tips have been marked as outliers. Their date 190s constraints were not used. Please remove them from the tree. Their dates 190s have been reset: 190s 190s 34.08 G22619, input date: [2011.0013698630137, 2011.9986301369863], apparent 190s date: 1985.96 190s 190s 34.08 G22625, input date: [2009.0013698630137, 2009.9986301369863], apparent 190s date: 2025.24 190s 190s 34.08 G22703, input date: [2004.0013661202186, 2004.9986338797814], apparent 190s date: 2027.50 190s 190s Inferred sequence evolution model (saved as 2024-11-15-0001_treetime/sequence_evolution_model.txt): 190s Substitution rate (mu): 1.0 190s 190s Equilibrium frequencies (pi_i): 190s A: 0.1669 190s C: 0.3286 190s G: 0.3273 190s T: 0.1669 190s -: 0.0103 190s 190s Symmetrized rates from j->i (W_ij): 190s A C G T - 190s A 0 0.7593 1.6498 0.312 35.8547 190s C 0.7593 0 0.3143 1.4117 35.7543 190s G 1.6498 0.3143 0 0.7444 49.3452 190s T 0.312 1.4117 0.7444 0 32.3622 190s - 35.8547 35.7543 49.3452 32.3622 0 190s 190s Actual rates from j->i (Q_ij): 190s A C G T - 190s A 0 0.1267 0.2754 0.0521 5.9845 190s C 0.2495 0 0.1033 0.4639 11.748 190s G 0.54 0.1029 0 0.2437 16.1518 190s T 0.0521 0.2356 0.1242 0 5.4006 190s - 0.3696 0.3686 0.5087 0.3336 0 190s 190s 190s Inferred sequence evolution model (saved as 2024-11-15-0001_treetime/molecular_clock.txt): 190s Root-Tip-Regression: 190s --rate: 1.000e-07 190s --r^2: 0.41 190s 190s --- saved tree as 190s 2024-11-15-0001_treetime/timetree.pdf 190s 190s --- root-to-tip plot saved to 190s 2024-11-15-0001_treetime/root_to_tip_regression.pdf 190s Sites that were constant except for ambiguous bases were made constant 190s by TreeTime. This happened 1343 times. These sites are now excluded 190s from the VCF. 190s 190s ***WARNING: vcf_utils.py 190s 52 sites were found that had no alternative bases. If this data has 190s been run through TreeTime and contains ambiguous bases, try calling 190s get_tree_dict with var_ambigs=True to see if this clears the error. 190s Alternative causes: - Not all sequences in your alignment are in the 190s tree (if you are running TreeTime via commandline this is most likely) 190s - In TreeTime, can be caused by overwriting variants in tips with 190s small branch lengths (debug) These are the positions affected 190s (numbering starts at 0): 190s 46593, 52473, 165918, 304891, 662240, 954864, 954865, 954866, 954867, 190s 963561, 1046706, 1145470, 1321893, 1468105, 1468106, 1512661, 1704463, 190s 1716723, 1743968, 1951837, 2129868, 2215816, 2274543, 2515984, 190s 2580886, 2626512, 2626513, 2626599, 2686156, 2736331, 2823901, 190s 2869282, 2894207, 2911378, 3047997, 3160385, 3314001, 3321447, 190s 3336505, 3461793, 3490408, 3618189, 3734466, 3764813, 3828626, 190s 3842630, 3894439, 3912292, 3913650, 3956227, 4149358, 4183687 190s 190s --- alignment including ancestral nodes saved as 190s 2024-11-15-0001_treetime/ancestral_sequences.vcf 190s 190s --- saved divergence times in 190s 2024-11-15-0001_treetime/dates.tsv 190s 190s --- tree saved in nexus format as 190s 2024-11-15-0001_treetime/timetree.nexus 190s 190s --- tree saved in auspice json format as 190s 2024-11-15-0001_treetime/auspice_tree.json 190s 190s --- divergence tree saved in nexus format as 190s 2024-11-15-0001_treetime/divergence_tree.nexus 190s 190s --- saved detected outliers as 2024-11-15-0001_treetime/outliers.tsv 190s timetree_inference on vcf data ok 275s 275s Attempting to parse dates... 275s Using column 'name' as name. This needs match the taxon names in the tree!! 275s Using column 'date' as date. 275s 275s 0.00 -TreeAnc: set-up 275s 275s 2.62 -WARNING: character U is unknown. Treating it as missing information 275s 275s 10.27 TreeTime.reroot: with method or node: least-squares 275s 275s 10.27 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 275s 275s 10.63 TreeTime.reroot: with method or node: least-squares 275s 275s 10.63 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 275s 275s 14.84 ###TreeTime.run: INITIAL ROUND 275s 275s 23.16 TreeTime.reroot: with method or node: least-squares 275s 275s 23.16 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 275s 275s 23.48 ###TreeTime.run: rerunning timetree after rerooting 275s 275s 34.10 ###TreeTime.run: ITERATION 1 out of 2 iterations 275s 275s 34.60 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 275s polytomies using the old 'greedy' mode. This is not well suited for large 275s polytomies. Stochastic resolution will become the default in future 275s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 275s keep using the greedy method in the future, run with `--greedy-resolve` 275s 275s 50.75 ###TreeTime.run: ITERATION 2 out of 2 iterations 275s 275s 79.98 TreeTime: the following tips have been marked as outliers. Their date 275s constraints were not used. Please remove them from the tree. Their dates 275s have been reset: 275s 275s 79.98 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.10 275s 275s 79.98 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.10 275s 275s 79.98 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.10 275s 275s 79.98 NZG_0381, input date: 2016.23, apparent date: 2015.10 275s 275s 79.98 NZG_0393, input date: 2016.24, apparent date: 2015.17 275s 275s 79.98 NZG_0358, input date: 2016.22, apparent date: 2015.17 275s 275s 79.98 NZG_0422, input date: 2016.25, apparent date: 2015.17 275s 275s 79.98 2607_C2_12855_EMLH, input date: 2015.28, apparent date: 2015.48 275s 275s 79.98 2607_C2_12916_EMLH, input date: 2015.32, apparent date: 2015.48 275s 275s 79.98 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.58 275s 275s 79.98 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.84 275s 275s 79.98 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.84 275s 275s 79.98 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.84 275s 275s 79.98 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2015.98 275s 275s 79.98 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.91 275s 275s 79.98 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.91 275s 275s 79.98 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.78 275s 275s 79.98 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.91 275s 275s 79.98 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2015.98 275s 275s 79.98 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2015.98 275s 275s Inferred sequence evolution model (saved as 2024-11-15-0002_treetime/sequence_evolution_model.txt): 275s Substitution rate (mu): 1.0 275s 275s Equilibrium frequencies (pi_i): 275s A: 0.3139 275s C: 0.2145 275s G: 0.1978 275s T: 0.2638 275s -: 0.01 275s 275s Symmetrized rates from j->i (W_ij): 275s A C G T - 275s A 0 0.3826 2.5279 0.2294 6.7953 275s C 0.3826 0 0.1691 3.5596 12.1794 275s G 2.5279 0.1691 0 0.3724 5.2952 275s T 0.2294 3.5596 0.3724 0 27.7425 275s - 6.7953 12.1794 5.2952 27.7425 0 275s 275s Actual rates from j->i (Q_ij): 275s A C G T - 275s A 0 0.1201 0.7935 0.072 2.1329 275s C 0.0821 0 0.0363 0.7635 2.6124 275s G 0.5001 0.0334 0 0.0737 1.0476 275s T 0.0605 0.9392 0.0983 0 7.3196 275s - 0.0676 0.1212 0.0527 0.2761 0 275s 275s 275s Inferred sequence evolution model (saved as 2024-11-15-0002_treetime/molecular_clock.txt): 275s Root-Tip-Regression: 275s --rate: 7.885e-04 275s --r^2: 0.80 275s 275s Inferred coalescent model 275s Skyline assuming 100.0 gen/year and approximate confidence bounds (+/- 2.000000 standard deviations of the LH) 275s date N_e lower upper 275s 2013.970 3.779e+01 1.550e+01 9.215e+01 275s 2014.067 6.339e+01 3.460e+01 1.161e+02 275s 2014.164 1.354e+02 8.250e+01 2.223e+02 275s 2014.261 1.434e+02 8.615e+01 2.388e+02 275s 2014.358 1.456e+02 9.660e+01 2.195e+02 275s 2014.454 3.232e+02 2.259e+02 4.623e+02 275s 2014.551 9.284e+02 6.292e+02 1.370e+03 275s 2014.648 1.085e+03 7.003e+02 1.681e+03 275s 2014.745 1.104e+03 7.162e+02 1.702e+03 275s 2014.842 9.915e+02 6.074e+02 1.618e+03 275s 2014.939 8.238e+02 5.130e+02 1.323e+03 275s 2015.035 3.155e+02 1.913e+02 5.201e+02 275s 2015.132 2.679e+02 1.773e+02 4.048e+02 275s 2015.229 2.758e+02 1.735e+02 4.385e+02 275s 2015.326 1.805e+02 1.116e+02 2.921e+02 275s 2015.423 1.530e+02 1.005e+02 2.330e+02 275s 2015.520 1.091e+02 6.672e+01 1.785e+02 275s 2015.616 1.082e+02 6.706e+01 1.746e+02 275s 2015.713 3.511e+01 1.861e+01 6.624e+01 275s 2015.810 1.024e+01 4.143e+00 2.529e+01 275s 275s --- written skyline to 2024-11-15-0002_treetime/skyline.tsv 275s 275s --- saved tree as 275s 2024-11-15-0002_treetime/timetree.pdf 275s 275s --- root-to-tip plot saved to 275s 2024-11-15-0002_treetime/root_to_tip_regression.pdf 275s 275s --- alignment including ancestral nodes saved as 275s 2024-11-15-0002_treetime/ancestral_sequences.fasta 275s 275s --- saved divergence times in 275s 2024-11-15-0002_treetime/dates.tsv 275s 275s --- tree saved in nexus format as 275s 2024-11-15-0002_treetime/timetree.nexus 275s 275s --- tree saved in auspice json format as 275s 2024-11-15-0002_treetime/auspice_tree.json 275s 275s --- divergence tree saved in nexus format as 275s 2024-11-15-0002_treetime/divergence_tree.nexus 275s 275s --- saved detected outliers as 2024-11-15-0002_treetime/outliers.tsv 276s skyline approximation ok 300s 300s Attempting to parse dates... 300s Using column 'name' as name. This needs match the taxon names in the tree!! 300s Using column 'date' as date. 300s 300s 0.00 -TreeAnc: set-up 300s 300s 0.05 TreeTime.reroot: with method or node: least-squares 300s 300s 0.05 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 300s 300s 0.48 TreeTime.reroot: with method or node: least-squares 300s 300s 0.48 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 300s 300s 0.81 ###TreeTime.run: INITIAL ROUND 300s 300s 7.81 TreeTime.reroot: with method or node: least-squares 300s 300s 7.81 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 300s 300s 8.14 ###TreeTime.run: rerunning timetree after rerooting 300s 300s 15.54 ###TreeTime.run: ITERATION 1 out of 2 iterations 300s 300s 15.54 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 300s polytomies using the old 'greedy' mode. This is not well suited for large 300s polytomies. Stochastic resolution will become the default in future 300s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 300s keep using the greedy method in the future, run with `--greedy-resolve` 300s 300s 22.68 ###TreeTime.run: CONVERGED 300s 300s 22.68 TreeTime: the following tips have been marked as outliers. Their date 300s constraints were not used. Please remove them from the tree. Their dates 300s have been reset: 300s 300s 22.68 NZG_0393, input date: 2016.24, apparent date: 2015.26 300s 300s 22.68 NZG_0422, input date: 2016.25, apparent date: 2015.26 300s 300s 22.68 NZG_0358, input date: 2016.22, apparent date: 2015.26 300s 300s 22.68 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.19 300s 300s 22.68 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.19 300s 300s 22.68 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.19 300s 300s 22.68 NZG_0381, input date: 2016.23, apparent date: 2015.19 300s 300s 22.68 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.40 300s 300s 22.68 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.81 300s 300s 22.68 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.81 300s 300s 22.68 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2015.87 300s 300s 22.68 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2015.87 300s 300s 22.68 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.74 300s 300s 22.68 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.81 300s 300s 22.68 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.68 300s 300s 22.68 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.74 300s 300s 22.68 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.74 300s 300s 22.68 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2015.87 300s 300s Inferred sequence evolution model (saved as 2024-11-15-0003_treetime/sequence_evolution_model.txt): 300s Substitution rate (mu): 1.0 300s 300s Equilibrium frequencies (pi_i): 300s A: 0.2 300s C: 0.2 300s G: 0.2 300s T: 0.2 300s -: 0.2 300s 300s Symmetrized rates from j->i (W_ij): 300s A C G T - 300s A 0 1.25 1.25 1.25 1.25 300s C 1.25 0 1.25 1.25 1.25 300s G 1.25 1.25 0 1.25 1.25 300s T 1.25 1.25 1.25 0 1.25 300s - 1.25 1.25 1.25 1.25 0 300s 300s Actual rates from j->i (Q_ij): 300s A C G T - 300s A 0 0.25 0.25 0.25 0.25 300s C 0.25 0 0.25 0.25 0.25 300s G 0.25 0.25 0 0.25 0.25 300s T 0.25 0.25 0.25 0 0.25 300s - 0.25 0.25 0.25 0.25 0 300s 300s 300s Inferred sequence evolution model (saved as 2024-11-15-0003_treetime/molecular_clock.txt): 300s Root-Tip-Regression: 300s --rate: 8.047e-04 300s --r^2: 0.79 300s 300s --- saved tree as 300s 2024-11-15-0003_treetime/timetree.pdf 300s 300s --- root-to-tip plot saved to 300s 2024-11-15-0003_treetime/root_to_tip_regression.pdf 300s --- saved divergence times in 300s 2024-11-15-0003_treetime/dates.tsv 300s 300s --- tree saved in nexus format as 300s 2024-11-15-0003_treetime/timetree.nexus 300s 300s --- tree saved in auspice json format as 300s 2024-11-15-0003_treetime/auspice_tree.json 300s 300s --- divergence tree saved in nexus format as 300s 2024-11-15-0003_treetime/divergence_tree.nexus 300s 300s --- saved detected outliers as 2024-11-15-0003_treetime/outliers.tsv 301s sequence length only ok 301s All tests passed 301s autopkgtest [05:51:35]: test run-unit-test: -----------------------] 302s run-unit-test PASS 302s autopkgtest [05:51:36]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 302s autopkgtest [05:51:36]: test autodep8-python3: preparing testbed 357s autopkgtest [05:52:31]: testbed dpkg architecture: amd64 357s autopkgtest [05:52:31]: testbed apt version: 2.9.8 357s autopkgtest [05:52:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 358s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 358s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1055 kB] 358s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 358s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 358s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [97.2 kB] 358s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [131 kB] 358s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [198 kB] 358s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 358s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [818 kB] 358s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [299 kB] 358s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 358s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9128 B] 359s Fetched 2737 kB in 1s (3371 kB/s) 359s Reading package lists... 361s Reading package lists... 361s Building dependency tree... 361s Reading state information... 361s Calculating upgrade... 361s The following packages will be upgraded: 361s firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0 361s libexpat1 lxd-installer man-db pastebinit python3-systemd xfsprogs 361s 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 361s Need to get 13.6 MB of archives. 361s After this operation, 477 kB of additional disk space will be used. 361s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 362s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB] 362s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB] 362s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB] 362s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB] 362s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB] 362s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB] 362s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB] 362s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B] 362s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 362s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB] 362s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB] 362s Preconfiguring packages ... 363s Fetched 13.6 MB in 1s (13.3 MB/s) 363s (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.) 363s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 363s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 363s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ... 363s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ... 363s Setting up libcap-ng0:amd64 (0.8.5-3build1) ... 363s (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 ... 75568 files and directories currently installed.) 363s Preparing to unpack .../0-libexpat1_2.6.4-1_amd64.deb ... 363s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ... 363s Preparing to unpack .../1-man-db_2.13.0-1_amd64.deb ... 363s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 363s Preparing to unpack .../2-grub2-common_2.12-5ubuntu7_amd64.deb ... 363s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 363s Preparing to unpack .../3-grub-pc_2.12-5ubuntu7_amd64.deb ... 363s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 363s Preparing to unpack .../4-grub-pc-bin_2.12-5ubuntu7_amd64.deb ... 363s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 363s Preparing to unpack .../5-grub-common_2.12-5ubuntu7_amd64.deb ... 363s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ... 363s Preparing to unpack .../6-lxd-installer_9_all.deb ... 363s Unpacking lxd-installer (9) over (8) ... 364s Preparing to unpack .../7-pastebinit_1.7.1-1_all.deb ... 364s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 364s Preparing to unpack .../8-python3-systemd_235-1build5_amd64.deb ... 364s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 364s Preparing to unpack .../9-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ... 364s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 364s Setting up libexpat1:amd64 (2.6.4-1) ... 364s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 364s Setting up pastebinit (1.7.1-1) ... 364s Setting up man-db (2.13.0-1) ... 364s Updating database of manual pages ... 366s man-db.service is a disabled or a static unit not running, not starting it. 366s Setting up grub-common (2.12-5ubuntu7) ... 366s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 366s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 366s update-initramfs: deferring update (trigger activated) 367s Setting up lxd-installer (9) ... 367s Setting up python3-systemd (235-1build5) ... 367s Setting up grub2-common (2.12-5ubuntu7) ... 367s Setting up grub-pc-bin (2.12-5ubuntu7) ... 367s Setting up grub-pc (2.12-5ubuntu7) ... 368s Installing for i386-pc platform. 368s Installation finished. No error reported. 368s Sourcing file `/etc/default/grub' 368s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 368s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 368s Generating grub configuration file ... 368s Found linux image: /boot/vmlinuz-6.11.0-8-generic 368s Found initrd image: /boot/initrd.img-6.11.0-8-generic 369s Warning: os-prober will not be executed to detect other bootable partitions. 369s Systems on them will not be added to the GRUB boot configuration. 369s Check GRUB_DISABLE_OS_PROBER documentation entry. 369s Adding boot menu entry for UEFI Firmware Settings ... 369s done 369s Processing triggers for libc-bin (2.40-1ubuntu3) ... 369s Processing triggers for install-info (7.1.1-1) ... 369s Processing triggers for initramfs-tools (0.142ubuntu34) ... 369s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 369s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 376s Reading package lists... 377s Building dependency tree... 377s Reading state information... 377s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 377s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 377s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 377s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 377s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 378s Reading package lists... 378s Reading package lists... 378s Building dependency tree... 378s Reading state information... 378s Calculating upgrade... 379s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 379s Reading package lists... 379s Building dependency tree... 379s Reading state information... 379s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 379s autopkgtest [05:52:53]: rebooting testbed after setup commands that affected boot 399s Reading package lists... 399s Building dependency tree... 399s Reading state information... 400s Starting pkgProblemResolver with broken count: 0 400s Starting 2 pkgProblemResolver with broken count: 0 400s Done 400s The following additional packages will be installed: 400s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 400s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 400s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 400s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 400s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 400s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 400s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 400s python-matplotlib-data python3-all python3-appdirs python3-biopython 400s python3-brotli python3-cairo python3-contourpy python3-cycler 400s python3-dateutil python3-decorator python3-fonttools python3-freetype 400s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 400s python3-mpmath python3-numpy python3-packaging python3-pandas 400s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 400s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 400s python3-treetime python3-tz python3-ufolib2 python3.12-tk sgml-base 400s tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 400s xfonts-utils xml-core 400s Suggested packages: 400s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 400s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 400s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 400s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 400s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 400s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 400s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 400s python3-gobject python3-pyqt5 python3-sip python3-tornado 400s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 400s gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 400s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 400s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 400s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-tk 400s sgml-base-doc debhelper 400s Recommended packages: 400s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 400s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 400s python3-odf python3-openpyxl python3-tables python3-numba python3-olefile 400s fonts-dejavu-extra g++ | c++-compiler isympy-common 400s The following NEW packages will be installed: 400s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 400s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 400s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 400s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 400s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 400s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 400s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 400s libxslt1.1 libxss1 python-matplotlib-data python3-all python3-appdirs 400s python3-biopython python3-brotli python3-cairo python3-contourpy 400s python3-cycler python3-dateutil python3-decorator python3-fonttools 400s python3-freetype python3-fs python3-kiwisolver python3-lxml python3-lz4 400s python3-matplotlib python3-mpmath python3-numpy python3-packaging 400s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 400s python3-reportlab python3-rlpycairo python3-scipy python3-six python3-sympy 400s python3-tk python3-treetime python3-tz python3-ufolib2 python3.12-tk 400s sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 400s xfonts-utils xml-core 400s 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 400s Need to get 84.4 MB/84.4 MB of archives. 400s After this operation, 339 MB of additional disk space will be used. 400s Get:1 /tmp/autopkgtest.sHJI2r/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 400s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 400s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 401s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 401s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 401s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 401s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 401s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 401s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 401s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 401s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 401s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 401s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 401s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 401s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 401s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 401s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 401s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 401s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 401s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 401s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 401s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 401s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 401s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 401s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 401s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 401s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 401s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 401s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 401s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 402s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 402s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 402s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 402s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 402s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 402s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 402s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 402s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 402s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 402s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 402s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 402s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 402s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 402s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 402s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 402s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 402s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 402s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 402s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 402s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 402s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 402s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 402s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.6-1ubuntu1 [9806 B] 402s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 402s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 402s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 402s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 402s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 402s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 402s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 402s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 402s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 402s Get:63 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB] 402s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 402s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 402s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 402s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 402s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 402s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 402s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 403s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 403s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 403s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 403s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 403s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 403s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 403s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 403s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 404s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 404s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 404s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 404s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 404s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 404s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 404s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 405s Fetched 84.4 MB in 4s (20.4 MB/s) 405s Selecting previously unselected package sgml-base. 405s (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 ... 75575 files and directories currently installed.) 405s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 405s Unpacking sgml-base (1.31) ... 405s Selecting previously unselected package libtcl8.6:amd64. 405s Preparing to unpack .../01-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 405s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 405s Selecting previously unselected package fonts-dejavu-mono. 405s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 405s Unpacking fonts-dejavu-mono (2.37-8) ... 405s Selecting previously unselected package fonts-dejavu-core. 405s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 405s Unpacking fonts-dejavu-core (2.37-8) ... 405s Selecting previously unselected package libfontenc1:amd64. 405s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 405s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 405s Selecting previously unselected package x11-common. 405s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 405s Unpacking x11-common (1:7.7+23ubuntu3) ... 405s Selecting previously unselected package xfonts-encodings. 405s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 405s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 405s Selecting previously unselected package xfonts-utils. 405s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_amd64.deb ... 405s Unpacking xfonts-utils (1:7.7+7) ... 405s Selecting previously unselected package fonts-urw-base35. 405s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 405s Unpacking fonts-urw-base35 (20200910-8) ... 405s Selecting previously unselected package fontconfig-config. 405s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 405s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 405s Selecting previously unselected package libfontconfig1:amd64. 406s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 406s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 406s Selecting previously unselected package libxrender1:amd64. 406s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 406s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 406s Selecting previously unselected package libxft2:amd64. 406s Preparing to unpack .../12-libxft2_2.3.6-1build1_amd64.deb ... 406s Unpacking libxft2:amd64 (2.3.6-1build1) ... 406s Selecting previously unselected package libxss1:amd64. 406s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_amd64.deb ... 406s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 406s Selecting previously unselected package libtk8.6:amd64. 406s Preparing to unpack .../14-libtk8.6_8.6.15-1_amd64.deb ... 406s Unpacking libtk8.6:amd64 (8.6.15-1) ... 406s Selecting previously unselected package tk8.6-blt2.5. 406s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 406s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 406s Selecting previously unselected package blt. 406s Preparing to unpack .../16-blt_2.5.3+dfsg-7build1_amd64.deb ... 406s Unpacking blt (2.5.3+dfsg-7build1) ... 406s Selecting previously unselected package fonts-lyx. 406s Preparing to unpack .../17-fonts-lyx_2.4.2.1-1_all.deb ... 406s Unpacking fonts-lyx (2.4.2.1-1) ... 406s Selecting previously unselected package libblas3:amd64. 406s Preparing to unpack .../18-libblas3_3.12.0-3build2_amd64.deb ... 406s Unpacking libblas3:amd64 (3.12.0-3build2) ... 406s Selecting previously unselected package libpixman-1-0:amd64. 406s Preparing to unpack .../19-libpixman-1-0_0.44.0-3_amd64.deb ... 406s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 406s Selecting previously unselected package libxcb-render0:amd64. 406s Preparing to unpack .../20-libxcb-render0_1.17.0-2_amd64.deb ... 406s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 406s Selecting previously unselected package libxcb-shm0:amd64. 406s Preparing to unpack .../21-libxcb-shm0_1.17.0-2_amd64.deb ... 406s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 406s Selecting previously unselected package libcairo2:amd64. 406s Preparing to unpack .../22-libcairo2_1.18.2-2_amd64.deb ... 406s Unpacking libcairo2:amd64 (1.18.2-2) ... 406s Selecting previously unselected package libdeflate0:amd64. 406s Preparing to unpack .../23-libdeflate0_1.22-1_amd64.deb ... 406s Unpacking libdeflate0:amd64 (1.22-1) ... 406s Selecting previously unselected package libgfortran5:amd64. 406s Preparing to unpack .../24-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 406s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 406s Selecting previously unselected package libgomp1:amd64. 406s Preparing to unpack .../25-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 406s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 406s Selecting previously unselected package libgraphite2-3:amd64. 406s Preparing to unpack .../26-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 406s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 406s Selecting previously unselected package libharfbuzz0b:amd64. 406s Preparing to unpack .../27-libharfbuzz0b_10.0.1-1_amd64.deb ... 406s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 406s Selecting previously unselected package libimagequant0:amd64. 406s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_amd64.deb ... 406s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 406s Selecting previously unselected package libjpeg-turbo8:amd64. 406s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 406s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 406s Selecting previously unselected package libjpeg8:amd64. 406s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_amd64.deb ... 406s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 406s Selecting previously unselected package libjs-jquery. 406s Preparing to unpack .../31-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 406s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 406s Selecting previously unselected package libjs-jquery-ui. 406s Preparing to unpack .../32-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 406s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 406s Selecting previously unselected package liblapack3:amd64. 406s Preparing to unpack .../33-liblapack3_3.12.0-3build2_amd64.deb ... 406s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 406s Selecting previously unselected package liblbfgsb0:amd64. 406s Preparing to unpack .../34-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 406s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 406s Selecting previously unselected package liblcms2-2:amd64. 406s Preparing to unpack .../35-liblcms2-2_2.16-2_amd64.deb ... 406s Unpacking liblcms2-2:amd64 (2.16-2) ... 406s Selecting previously unselected package liblerc4:amd64. 406s Preparing to unpack .../36-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 406s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 406s Selecting previously unselected package libqhull-r8.0:amd64. 406s Preparing to unpack .../37-libqhull-r8.0_2020.2-6build1_amd64.deb ... 406s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 406s Selecting previously unselected package libraqm0:amd64. 406s Preparing to unpack .../38-libraqm0_0.10.1-1build1_amd64.deb ... 406s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 406s Selecting previously unselected package libsharpyuv0:amd64. 406s Preparing to unpack .../39-libsharpyuv0_1.4.0-0.1_amd64.deb ... 406s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 406s Selecting previously unselected package libjbig0:amd64. 406s Preparing to unpack .../40-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 406s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 406s Selecting previously unselected package libwebp7:amd64. 406s Preparing to unpack .../41-libwebp7_1.4.0-0.1_amd64.deb ... 406s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 406s Selecting previously unselected package libtiff6:amd64. 406s Preparing to unpack .../42-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 406s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 406s Selecting previously unselected package libwebpdemux2:amd64. 406s Preparing to unpack .../43-libwebpdemux2_1.4.0-0.1_amd64.deb ... 406s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 406s Selecting previously unselected package libwebpmux3:amd64. 406s Preparing to unpack .../44-libwebpmux3_1.4.0-0.1_amd64.deb ... 406s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 406s Selecting previously unselected package libxslt1.1:amd64. 406s Preparing to unpack .../45-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 406s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 406s Selecting previously unselected package python-matplotlib-data. 406s Preparing to unpack .../46-python-matplotlib-data_3.8.3-3_all.deb ... 406s Unpacking python-matplotlib-data (3.8.3-3) ... 407s Selecting previously unselected package python3-all. 407s Preparing to unpack .../47-python3-all_3.12.6-0ubuntu1_amd64.deb ... 407s Unpacking python3-all (3.12.6-0ubuntu1) ... 407s Selecting previously unselected package python3-appdirs. 407s Preparing to unpack .../48-python3-appdirs_1.4.4-4_all.deb ... 407s Unpacking python3-appdirs (1.4.4-4) ... 407s Selecting previously unselected package python3-numpy. 407s Preparing to unpack .../49-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 407s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 407s Selecting previously unselected package python3.12-tk. 407s Preparing to unpack .../50-python3.12-tk_3.12.7-3_amd64.deb ... 407s Unpacking python3.12-tk (3.12.7-3) ... 407s Selecting previously unselected package python3-tk:amd64. 407s Preparing to unpack .../51-python3-tk_3.12.6-1ubuntu1_amd64.deb ... 407s Unpacking python3-tk:amd64 (3.12.6-1ubuntu1) ... 407s Selecting previously unselected package python3-pil.imagetk:amd64. 407s Preparing to unpack .../52-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 407s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 407s Selecting previously unselected package libopenjp2-7:amd64. 407s Preparing to unpack .../53-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 407s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 407s Selecting previously unselected package python3-pil:amd64. 407s Preparing to unpack .../54-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 407s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 407s Selecting previously unselected package python3-cairo. 407s Preparing to unpack .../55-python3-cairo_1.26.1-2_amd64.deb ... 407s Unpacking python3-cairo (1.26.1-2) ... 407s Selecting previously unselected package python3-freetype. 407s Preparing to unpack .../56-python3-freetype_2.5.1-1_all.deb ... 407s Unpacking python3-freetype (2.5.1-1) ... 407s Selecting previously unselected package python3-rlpycairo. 407s Preparing to unpack .../57-python3-rlpycairo_0.3.0-3_all.deb ... 407s Unpacking python3-rlpycairo (0.3.0-3) ... 407s Selecting previously unselected package python3-reportlab. 407s Preparing to unpack .../58-python3-reportlab_4.2.5-1_all.deb ... 407s Unpacking python3-reportlab (4.2.5-1) ... 407s Selecting previously unselected package xml-core. 407s Preparing to unpack .../59-xml-core_0.19_all.deb ... 407s Unpacking xml-core (0.19) ... 407s Selecting previously unselected package w3c-sgml-lib. 407s Preparing to unpack .../60-w3c-sgml-lib_1.3-3_all.deb ... 407s Unpacking w3c-sgml-lib (1.3-3) ... 407s Selecting previously unselected package python3-biopython. 407s Preparing to unpack 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410s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 410s Setting up python3-freetype (2.5.1-1) ... 410s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 410s Setting up python3-tz (2024.1-2) ... 410s Setting up unicode-data (15.1.0-1) ... 410s Setting up python3-six (1.16.0-7) ... 410s Setting up python3-decorator (5.1.1-5) ... 410s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 410s Setting up libblas3:amd64 (3.12.0-3build2) ... 410s 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 410s Setting up python3-packaging (24.1-1) ... 410s Setting up python3-brotli (1.1.0-2build2) ... 410s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 410s Setting up python3-cycler (0.12.1-1) ... 410s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 410s Setting up fonts-dejavu-mono (2.37-8) ... 410s Setting up python3-kiwisolver (1.4.7-2build1) ... 410s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 410s Setting up fonts-dejavu-core (2.37-8) ... 410s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 410s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 410s Setting up libwebp7:amd64 (1.4.0-0.1) ... 410s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 410s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 410s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 410s Setting up python3-dateutil (2.9.0-2) ... 411s Setting up sgml-base (1.31) ... 411s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 411s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 411s Setting up python3-mpmath (1.3.0-1) ... 411s Setting up python-matplotlib-data (3.8.3-3) ... 411s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 411s Setting up python3-appdirs (1.4.4-4) ... 411s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 411s Setting up python3-sympy (1.13.3-1) ... 416s Setting up liblapack3:amd64 (3.12.0-3build2) ... 416s 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 416s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 416s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 416s Setting up xfonts-utils (1:7.7+7) ... 416s Setting up python3-fs (2.4.16-4) ... 416s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 416s Setting up libraqm0:amd64 (0.10.1-1build1) ... 416s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 418s Setting up python3-lxml:amd64 (5.3.0-1) ... 418s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 418s Setting up xml-core (0.19) ... 418s Setting up python3-contourpy (1.3.0-2) ... 418s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 418s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 418s Setting up libxft2:amd64 (2.3.6-1build1) ... 418s Setting up python3-scipy (1.13.1-5) ... 421s Setting up libtk8.6:amd64 (8.6.15-1) ... 421s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 421s Setting up python3.12-tk (3.12.7-3) ... 421s Setting up fonts-urw-base35 (20200910-8) ... 421s Setting up libcairo2:amd64 (1.18.2-2) ... 421s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 421s Setting up python3-pandas (2.2.3+dfsg-5) ... 425s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 425s Setting up python3-cairo (1.26.1-2) ... 425s Setting up blt (2.5.3+dfsg-7build1) ... 425s Setting up python3-tk:amd64 (3.12.6-1ubuntu1) ... 425s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 425s Setting up python3-rlpycairo (0.3.0-3) ... 425s Setting up python3-reportlab (4.2.5-1) ... 426s Setting up python3-fonttools (4.46.0-1build2) ... 426s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 427s Setting up python3-matplotlib (3.8.3-3) ... 428s Processing triggers for libc-bin (2.40-1ubuntu3) ... 428s Processing triggers for man-db (2.13.0-1) ... 429s Processing triggers for sgml-base (1.31) ... 429s Setting up w3c-sgml-lib (1.3-3) ... 451s Setting up python3-biopython (1.84+dfsg-4build1) ... 452s Setting up python3-treetime (0.11.4-1) ... 452s Setting up autopkgtest-satdep (0) ... 455s (Reading database ... 86312 files and directories currently installed.) 455s Removing autopkgtest-satdep (0) ... 458s autopkgtest [05:54:12]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import treetime; print(treetime)" ; done 458s autopkgtest [05:54:12]: test autodep8-python3: [----------------------- 458s Testing with python3.12: 459s 459s autopkgtest [05:54:13]: test autodep8-python3: -----------------------] 460s autopkgtest [05:54:14]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 460s autodep8-python3 PASS (superficial) 460s autopkgtest [05:54:14]: @@@@@@@@@@@@@@@@@@@@ summary 460s run-unit-test PASS 460s autodep8-python3 PASS (superficial) 472s nova [W] Skipping flock for amd64 472s Creating nova instance adt-plucky-amd64-python-treetime-20241115-054633-juju-7f2275-prod-proposed-migration-environment-15-4c363df1-bacf-4c45-bff9-8271454996c5 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)... 472s nova [W] Skipping flock for amd64 472s Creating nova instance adt-plucky-amd64-python-treetime-20241115-054633-juju-7f2275-prod-proposed-migration-environment-15-4c363df1-bacf-4c45-bff9-8271454996c5 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...