0s autopkgtest [00:04:51]: starting date and time: 2024-11-15 00:04:51+0000 0s autopkgtest [00:04:51]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [00:04:51]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r9co12_0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-biopython --apt-upgrade python-treetime --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-biopython/1.84+dfsg-4build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-21.secgroup --name adt-plucky-ppc64el-python-treetime-20241114-233130-juju-7f2275-prod-proposed-migration-environment-20-2f3eac4c-0a6e-4e49-b8da-a88bc620d91e --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -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/ 122s autopkgtest [00:06:53]: testbed dpkg architecture: ppc64el 122s autopkgtest [00:06:53]: testbed apt version: 2.9.8 122s autopkgtest [00:06:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 123s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 123s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1015 kB] 123s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.1 kB] 123s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 123s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [121 kB] 123s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [759 kB] 123s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8632 B] 124s Fetched 2100 kB in 1s (2192 kB/s) 124s Reading package lists... 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade... 126s The following packages will be upgraded: 126s bpfcc-tools bpftrace libbpfcc libcap-ng0 libgnutls30t64 libjson-glib-1.0-0 126s libjson-glib-1.0-common libnewt0.52 libutempter0 lxd-installer man-db 126s pastebinit python3-bpfcc python3-newt python3-systemd whiptail 127s 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Need to get 6045 kB of archives. 127s After this operation, 453 kB of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcap-ng0 ppc64el 0.8.5-3build1 [16.3 kB] 127s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 128s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 128s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 128s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 128s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el man-db ppc64el 2.13.0-1 [1361 kB] 128s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 128s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 128s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 128s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 128s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 128s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 128s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 128s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el lxd-installer all 9 [5084 B] 128s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el pastebinit all 1.7.1-1 [14.9 kB] 128s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-systemd ppc64el 235-1build5 [48.7 kB] 128s Preconfiguring packages ... 128s Fetched 6045 kB in 1s (7542 kB/s) 128s (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 ... 73767 files and directories currently installed.) 128s Preparing to unpack .../libcap-ng0_0.8.5-3build1_ppc64el.deb ... 128s Unpacking libcap-ng0:ppc64el (0.8.5-3build1) over (0.8.5-1) ... 128s Setting up libcap-ng0:ppc64el (0.8.5-3build1) ... 128s (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 ... 73767 files and directories currently installed.) 128s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 128s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 128s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 128s (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 ... 73767 files and directories currently installed.) 128s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 128s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 128s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 128s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 128s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 128s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 128s Preparing to unpack .../03-man-db_2.13.0-1_ppc64el.deb ... 128s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 128s Preparing to unpack .../04-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 128s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 128s Preparing to unpack .../05-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 128s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 128s Preparing to unpack .../06-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 128s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 128s Preparing to unpack .../07-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 128s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 128s Preparing to unpack .../08-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 128s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 128s Preparing to unpack .../09-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 128s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 129s Preparing to unpack .../10-libutempter0_1.2.1-4_ppc64el.deb ... 129s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 129s Preparing to unpack .../11-lxd-installer_9_all.deb ... 129s Unpacking lxd-installer (9) over (8) ... 129s Preparing to unpack .../12-pastebinit_1.7.1-1_all.deb ... 129s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 129s Preparing to unpack .../13-python3-systemd_235-1build5_ppc64el.deb ... 129s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 129s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 129s Setting up pastebinit (1.7.1-1) ... 129s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 129s Setting up man-db (2.13.0-1) ... 129s Updating database of manual pages ... 131s man-db.service is a disabled or a static unit not running, not starting it. 131s Setting up lxd-installer (9) ... 132s Setting up libutempter0:ppc64el (1.2.1-4) ... 132s Setting up whiptail (0.52.24-2ubuntu4) ... 132s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 132s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 132s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 132s Setting up python3-systemd (235-1build5) ... 132s Setting up bpftrace (0.21.2-2ubuntu2) ... 132s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 132s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 132s Processing triggers for libc-bin (2.40-1ubuntu3) ... 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 133s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 133s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 133s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 134s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Calculating upgrade... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s autopkgtest [00:07:06]: rebooting testbed after setup commands that affected boot 139s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 165s autopkgtest [00:07:36]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 167s autopkgtest [00:07:38]: @@@@@@@@@@@@@@@@@@@@ apt-source python-treetime 170s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (dsc) [2611 B] 170s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [5117 kB] 170s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [1291 kB] 170s Get:4 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (diff) [8028 B] 170s gpgv: Signature made Sat Nov 9 21:31:47 2024 UTC 170s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 170s gpgv: issuer "emollier@debian.org" 170s gpgv: Can't check signature: No public key 170s dpkg-source: warning: cannot verify inline signature for ./python-treetime_0.11.4-1.dsc: no acceptable signature found 170s autopkgtest [00:07:41]: testing package python-treetime version 0.11.4-1 170s autopkgtest [00:07:41]: build not needed 172s autopkgtest [00:07:43]: test run-unit-test: preparing testbed 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 173s Starting pkgProblemResolver with broken count: 0 173s Starting 2 pkgProblemResolver with broken count: 0 173s Done 174s The following additional packages will be installed: 174s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 174s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 174s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 174s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 174s liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 174s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 174s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 174s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 174s python3-cairo python3-contourpy python3-cycler python3-dateutil 174s python3-decorator python3-fonttools python3-freetype python3-fs 174s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 174s python3-mpmath python3-numpy python3-packaging python3-pandas 174s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 174s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 174s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 174s python3.12-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 174s xfonts-encodings xfonts-utils xml-core 174s Suggested packages: 174s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 174s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 174s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 174s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 174s t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng 174s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 174s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 174s python3-gobject python3-pyqt5 python3-sip python3-tornado 174s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gcc 174s gfortran python-numpy-doc python3-dev python3-pytest python-pandas-doc 174s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 174s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc 174s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.13-tk 174s sgml-base-doc debhelper 174s Recommended packages: 174s javascript-common python-biopython-doc ncbi-blast+ python3-bs4 174s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 174s python3-odf python3-openpyxl python3-tables python3-olefile 174s fonts-dejavu-extra g++ | c++-compiler isympy-common 174s The following NEW packages will be installed: 174s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 174s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 174s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 174s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 174s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 174s libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 174s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 174s libxslt1.1 libxss1 python-matplotlib-data python3-appdirs python3-biopython 174s python3-brotli python3-cairo python3-contourpy python3-cycler 174s python3-dateutil python3-decorator python3-fonttools python3-freetype 174s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 174s python3-mpmath python3-numpy python3-packaging python3-pandas 174s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 174s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 174s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 174s python3.12-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 174s xfonts-encodings xfonts-utils xml-core 174s 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 174s Need to get 85.8 MB/85.8 MB of archives. 174s After this operation, 359 MB of additional disk space will be used. 174s Get:1 /tmp/autopkgtest.Qc05KN/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 174s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.15+dfsg-2 [1201 kB] 174s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 174s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 174s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 174s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 174s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 174s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 174s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 175s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB] 175s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB] 175s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 175s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 175s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 175s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.15-1 [942 kB] 175s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-7build1 [784 kB] 175s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el blt ppc64el 2.5.3+dfsg-7build1 [4840 B] 175s Get:19 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-lyx all 2.4.2.1-1 [171 kB] 175s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 175s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 175s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 175s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 175s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 175s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 175s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 175s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 175s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 175s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB] 175s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 175s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB] 175s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 175s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 175s Get:34 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 175s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 175s Get:36 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 175s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 175s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB] 175s Get:39 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6build1 [225 kB] 175s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB] 175s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB] 175s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 175s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB] 175s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 175s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 175s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 175s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu1 [191 kB] 175s Get:48 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-matplotlib-data all 3.8.3-3 [2928 kB] 175s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 175s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 175s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-tk ppc64el 3.12.7-3 [116 kB] 175s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tk ppc64el 3.12.6-1ubuntu1 [9806 B] 175s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pil.imagetk ppc64el 10.4.0-1ubuntu1 [9810 B] 175s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB] 175s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB] 175s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB] 175s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 175s Get:58 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 175s Get:59 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB] 175s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB] 175s Get:61 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 175s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4build1 [1745 kB] 175s Get:63 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-brotli ppc64el 1.1.0-2build2 [413 kB] 175s Get:64 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-contourpy ppc64el 1.3.0-2 [217 kB] 175s Get:65 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cycler all 0.12.1-1 [9716 B] 175s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-six all 1.16.0-7 [13.1 kB] 175s Get:67 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-2 [80.3 kB] 175s Get:68 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 175s Get:69 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB] 176s Get:70 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 176s Get:71 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mpmath all 1.3.0-1 [425 kB] 176s Get:72 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sympy all 1.13.3-1 [4228 kB] 176s Get:73 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB] 176s Get:74 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fs all 2.4.16-4 [91.3 kB] 176s Get:75 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.0-1 [1354 kB] 176s Get:76 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1build4 [27.8 kB] 176s Get:77 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-unicodedata2 ppc64el 15.1.0+ds-1build2 [361 kB] 176s Get:78 http://ftpmaster.internal/ubuntu plucky/universe ppc64el unicode-data all 15.1.0-1 [8878 kB] 176s Get:79 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fonttools ppc64el 4.46.0-1build2 [1473 kB] 176s Get:80 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-kiwisolver ppc64el 1.4.7-2build1 [72.9 kB] 176s Get:81 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 176s Get:82 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-matplotlib ppc64el 3.8.3-3 [4610 kB] 176s Get:83 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5 [4761 kB] 177s Get:84 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5 [3112 kB] 177s Get:85 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-treetime all 0.11.4-1 [941 kB] 177s Fetched 85.8 MB in 3s (29.6 MB/s) 177s Selecting previously unselected package sgml-base. 177s (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 ... 73774 files and directories currently installed.) 177s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 177s Unpacking sgml-base (1.31) ... 177s Selecting previously unselected package libtcl8.6:ppc64el. 177s Preparing to unpack .../01-libtcl8.6_8.6.15+dfsg-2_ppc64el.deb ... 177s Unpacking libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 177s Selecting previously unselected package fonts-dejavu-mono. 177s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 177s Unpacking fonts-dejavu-mono (2.37-8) ... 177s Selecting previously unselected package fonts-dejavu-core. 177s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 178s Unpacking fonts-dejavu-core (2.37-8) ... 178s Selecting previously unselected package libfontenc1:ppc64el. 178s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 178s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 178s Selecting previously unselected package x11-common. 178s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 178s Unpacking x11-common (1:7.7+23ubuntu3) ... 178s Selecting previously unselected package xfonts-encodings. 178s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 178s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 178s Selecting previously unselected package xfonts-utils. 178s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 178s Unpacking xfonts-utils (1:7.7+7) ... 178s Selecting previously unselected package fonts-urw-base35. 178s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 178s Unpacking fonts-urw-base35 (20200910-8) ... 178s Selecting previously unselected package fontconfig-config. 178s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ... 178s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 178s Selecting previously unselected package libfontconfig1:ppc64el. 178s Preparing to unpack .../10-libfontconfig1_2.15.0-1.1ubuntu2_ppc64el.deb ... 178s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 178s Selecting previously unselected package libxrender1:ppc64el. 178s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 178s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 178s Selecting previously unselected package libxft2:ppc64el. 178s Preparing to unpack .../12-libxft2_2.3.6-1build1_ppc64el.deb ... 178s Unpacking libxft2:ppc64el (2.3.6-1build1) ... 178s Selecting previously unselected package libxss1:ppc64el. 178s Preparing to unpack .../13-libxss1_1%3a1.2.3-1build3_ppc64el.deb ... 178s Unpacking libxss1:ppc64el (1:1.2.3-1build3) ... 178s Selecting previously unselected package libtk8.6:ppc64el. 178s Preparing to unpack .../14-libtk8.6_8.6.15-1_ppc64el.deb ... 178s Unpacking libtk8.6:ppc64el (8.6.15-1) ... 178s Selecting previously unselected package tk8.6-blt2.5. 178s Preparing to unpack .../15-tk8.6-blt2.5_2.5.3+dfsg-7build1_ppc64el.deb ... 178s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 178s Selecting previously unselected package blt. 178s Preparing to unpack .../16-blt_2.5.3+dfsg-7build1_ppc64el.deb ... 178s Unpacking blt (2.5.3+dfsg-7build1) ... 178s Selecting previously unselected package fonts-lyx. 178s Preparing to unpack .../17-fonts-lyx_2.4.2.1-1_all.deb ... 178s Unpacking fonts-lyx (2.4.2.1-1) ... 178s Selecting previously unselected package libblas3:ppc64el. 178s Preparing to unpack .../18-libblas3_3.12.0-3build2_ppc64el.deb ... 178s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 178s Selecting previously unselected package libpixman-1-0:ppc64el. 178s Preparing to unpack .../19-libpixman-1-0_0.44.0-3_ppc64el.deb ... 178s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 178s Selecting previously unselected package libxcb-render0:ppc64el. 178s Preparing to unpack .../20-libxcb-render0_1.17.0-2_ppc64el.deb ... 178s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 178s Selecting previously unselected package libxcb-shm0:ppc64el. 178s Preparing to unpack .../21-libxcb-shm0_1.17.0-2_ppc64el.deb ... 178s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 178s Selecting previously unselected package libcairo2:ppc64el. 178s Preparing to unpack .../22-libcairo2_1.18.2-2_ppc64el.deb ... 178s Unpacking libcairo2:ppc64el (1.18.2-2) ... 178s Selecting previously unselected package libdeflate0:ppc64el. 178s Preparing to unpack .../23-libdeflate0_1.22-1_ppc64el.deb ... 178s Unpacking libdeflate0:ppc64el (1.22-1) ... 178s Selecting previously unselected package libgfortran5:ppc64el. 178s Preparing to unpack .../24-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 178s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package libgomp1:ppc64el. 178s Preparing to unpack .../25-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 178s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package libgraphite2-3:ppc64el. 178s Preparing to unpack .../26-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 178s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 178s Selecting previously unselected package libharfbuzz0b:ppc64el. 178s Preparing to unpack .../27-libharfbuzz0b_10.0.1-1_ppc64el.deb ... 178s Unpacking libharfbuzz0b:ppc64el (10.0.1-1) ... 178s Selecting previously unselected package libimagequant0:ppc64el. 178s Preparing to unpack .../28-libimagequant0_2.18.0-1build1_ppc64el.deb ... 178s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 178s Selecting previously unselected package libjpeg-turbo8:ppc64el. 178s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu2_ppc64el.deb ... 178s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 178s Selecting previously unselected package libjpeg8:ppc64el. 178s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 178s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 178s Selecting previously unselected package libjs-jquery. 178s Preparing to unpack .../31-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 178s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 178s Selecting previously unselected package libjs-jquery-ui. 178s Preparing to unpack .../32-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 178s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 178s Selecting previously unselected package liblapack3:ppc64el. 178s Preparing to unpack .../33-liblapack3_3.12.0-3build2_ppc64el.deb ... 178s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 178s Selecting previously unselected package liblbfgsb0:ppc64el. 178s Preparing to unpack .../34-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 178s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 178s Selecting previously unselected package liblcms2-2:ppc64el. 178s Preparing to unpack .../35-liblcms2-2_2.16-2_ppc64el.deb ... 178s Unpacking liblcms2-2:ppc64el (2.16-2) ... 178s Selecting previously unselected package liblerc4:ppc64el. 179s Preparing to unpack .../36-liblerc4_4.0.0+ds-4ubuntu2_ppc64el.deb ... 179s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 179s Selecting previously unselected package libqhull-r8.0:ppc64el. 179s Preparing to unpack .../37-libqhull-r8.0_2020.2-6build1_ppc64el.deb ... 179s Unpacking libqhull-r8.0:ppc64el (2020.2-6build1) ... 179s Selecting previously unselected package libraqm0:ppc64el. 179s Preparing to unpack .../38-libraqm0_0.10.1-1build1_ppc64el.deb ... 179s Unpacking libraqm0:ppc64el (0.10.1-1build1) ... 179s Selecting previously unselected package libsharpyuv0:ppc64el. 179s Preparing to unpack .../39-libsharpyuv0_1.4.0-0.1_ppc64el.deb ... 179s Unpacking libsharpyuv0:ppc64el (1.4.0-0.1) ... 179s Selecting previously unselected package libjbig0:ppc64el. 179s Preparing to unpack .../40-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 179s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 179s Selecting previously unselected package libwebp7:ppc64el. 179s Preparing to unpack .../41-libwebp7_1.4.0-0.1_ppc64el.deb ... 179s Unpacking libwebp7:ppc64el (1.4.0-0.1) ... 179s Selecting previously unselected package libtiff6:ppc64el. 179s Preparing to unpack .../42-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ... 179s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 179s Selecting previously unselected package libwebpdemux2:ppc64el. 179s Preparing to unpack .../43-libwebpdemux2_1.4.0-0.1_ppc64el.deb ... 179s Unpacking libwebpdemux2:ppc64el (1.4.0-0.1) ... 179s Selecting previously unselected package libwebpmux3:ppc64el. 179s Preparing to unpack .../44-libwebpmux3_1.4.0-0.1_ppc64el.deb ... 179s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ... 179s Selecting previously unselected package libxslt1.1:ppc64el. 179s Preparing to unpack .../45-libxslt1.1_1.1.39-0exp1ubuntu1_ppc64el.deb ... 179s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 179s Selecting previously unselected package python-matplotlib-data. 179s Preparing to unpack .../46-python-matplotlib-data_3.8.3-3_all.deb ... 179s Unpacking python-matplotlib-data (3.8.3-3) ... 179s Selecting previously unselected package python3-appdirs. 179s Preparing to unpack .../47-python3-appdirs_1.4.4-4_all.deb ... 179s Unpacking python3-appdirs (1.4.4-4) ... 179s Selecting previously unselected package python3-numpy. 179s Preparing to unpack .../48-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 179s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 179s Selecting previously unselected package python3.12-tk. 179s Preparing to unpack .../49-python3.12-tk_3.12.7-3_ppc64el.deb ... 179s Unpacking python3.12-tk (3.12.7-3) ... 179s Selecting previously unselected package python3-tk:ppc64el. 179s Preparing to unpack .../50-python3-tk_3.12.6-1ubuntu1_ppc64el.deb ... 179s Unpacking python3-tk:ppc64el (3.12.6-1ubuntu1) ... 179s Selecting previously unselected package python3-pil.imagetk:ppc64el. 179s Preparing to unpack .../51-python3-pil.imagetk_10.4.0-1ubuntu1_ppc64el.deb ... 179s Unpacking python3-pil.imagetk:ppc64el (10.4.0-1ubuntu1) ... 179s Selecting previously unselected package libopenjp2-7:ppc64el. 179s Preparing to unpack .../52-libopenjp2-7_2.5.0-2ubuntu1_ppc64el.deb ... 179s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 179s Selecting previously unselected package python3-pil:ppc64el. 179s Preparing to unpack .../53-python3-pil_10.4.0-1ubuntu1_ppc64el.deb ... 179s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu1) ... 179s Selecting previously unselected package python3-cairo. 179s Preparing to unpack .../54-python3-cairo_1.26.1-2_ppc64el.deb ... 179s Unpacking python3-cairo (1.26.1-2) ... 179s Selecting previously unselected package python3-freetype. 179s Preparing to unpack .../55-python3-freetype_2.5.1-1_all.deb ... 179s Unpacking python3-freetype (2.5.1-1) ... 179s Selecting previously unselected package python3-rlpycairo. 179s Preparing to unpack .../56-python3-rlpycairo_0.3.0-3_all.deb ... 179s Unpacking python3-rlpycairo (0.3.0-3) ... 179s Selecting previously unselected package python3-reportlab. 179s Preparing to unpack .../57-python3-reportlab_4.2.5-1_all.deb ... 179s Unpacking python3-reportlab (4.2.5-1) ... 179s Selecting previously unselected package xml-core. 179s Preparing to unpack .../58-xml-core_0.19_all.deb ... 179s Unpacking xml-core (0.19) ... 179s Selecting previously unselected package w3c-sgml-lib. 179s Preparing to unpack .../59-w3c-sgml-lib_1.3-3_all.deb ... 179s Unpacking w3c-sgml-lib (1.3-3) ... 179s Selecting previously unselected package python3-biopython. 179s Preparing to unpack .../60-python3-biopython_1.84+dfsg-4build1_ppc64el.deb ... 179s Unpacking python3-biopython (1.84+dfsg-4build1) ... 179s Selecting previously unselected package python3-brotli. 179s Preparing to unpack .../61-python3-brotli_1.1.0-2build2_ppc64el.deb ... 179s Unpacking python3-brotli (1.1.0-2build2) ... 179s Selecting previously unselected package python3-contourpy. 179s Preparing to unpack .../62-python3-contourpy_1.3.0-2_ppc64el.deb ... 179s Unpacking python3-contourpy (1.3.0-2) ... 179s Selecting previously unselected package python3-cycler. 179s Preparing to unpack .../63-python3-cycler_0.12.1-1_all.deb ... 179s Unpacking python3-cycler (0.12.1-1) ... 179s Selecting previously unselected package python3-six. 179s Preparing to unpack .../64-python3-six_1.16.0-7_all.deb ... 179s Unpacking python3-six (1.16.0-7) ... 179s Selecting previously unselected package python3-dateutil. 179s Preparing to unpack .../65-python3-dateutil_2.9.0-2_all.deb 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up python3-fonttools (4.46.0-1build2) ... 206s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 206s Setting up python3-matplotlib (3.8.3-3) ... 208s Processing triggers for libc-bin (2.40-1ubuntu3) ... 208s Processing triggers for man-db (2.13.0-1) ... 209s Processing triggers for sgml-base (1.31) ... 209s Setting up w3c-sgml-lib (1.3-3) ... 240s Setting up python3-biopython (1.84+dfsg-4build1) ... 241s Setting up python3-treetime (0.11.4-1) ... 241s Setting up autopkgtest-satdep (0) ... 244s (Reading database ... 84520 files and directories currently installed.) 244s Removing autopkgtest-satdep (0) ... 245s autopkgtest [00:08:56]: test run-unit-test: [----------------------- 246s 246s 0.00 -TreeAnc: set-up 246s read alignment from file h3n2_na/h3n2_na_20.fasta with 19 sequences of length 1407 246s read tree from file h3n2_na/h3n2_na_20.nwk with 19 leaves 246s 246s inferring ancestral sequences... 246s ...done. 246s 246s The TOTAL tree length is 1.311e-01 and 183 mutations were observed. 246s Of these 183 mutations, 246s - 148 occur 1 times 246s - 16 occur 2 times 246s - 1 occur 3 times 246s 246s Of the 1407 positions in the genome, 246s - 1237 were hit 0 times (expected 1235.40) 246s - 124 were hit 1 times (expected 160.68) 246s - 25 were hit 2 times (expected 10.45) 246s - 3 were hit 3 times (expected 0.45) 246s 246s log-likelihood difference to Poisson distribution with same mean: -1.226e+01 246s 246s 246s The ten most homoplasic mutations are: 246s mut multiplicity 246s G27A 3 246s A88G 2 246s A267G 2 246s G451R 2 246s G629A 2 246s C763T 2 246s G780A 2 246s C825T 2 246s C891A 2 246s C906T 2 247s homoplasy_scanning ok 247s 247s 0.00 -TreeAnc: set-up 247s 247s Inferred sequence evolution model (saved as 2024-11-15_ancestral/sequence_evolution_model.txt): 247s Substitution rate (mu): 1.0 247s 247s Equilibrium frequencies (pi_i): 247s A: 0.3062 247s C: 0.1925 247s G: 0.2336 247s T: 0.2577 247s -: 0.01 247s 247s Symmetrized rates from j->i (W_ij): 247s A C G T - 247s A 0 0.8311 2.7926 0.4496 1.0287 247s C 0.8311 0 0.577 2.8797 1.0535 247s G 2.7926 0.577 0 0.612 1.0437 247s T 0.4496 2.8797 0.612 0 1.0394 247s - 1.0287 1.0535 1.0437 1.0394 0 247s 247s Actual rates from j->i (Q_ij): 247s A C G T - 247s A 0 0.2545 0.8551 0.1377 0.315 247s C 0.16 0 0.1111 0.5543 0.2028 247s G 0.6523 0.1348 0 0.143 0.2438 247s T 0.1159 0.7421 0.1577 0 0.2678 247s - 0.0103 0.0106 0.0105 0.0104 0 247s 247s 247s --- alignment including ancestral nodes saved as 247s 2024-11-15_ancestral/ancestral_sequences.fasta 247s 247s --- tree saved in nexus format as 247s 2024-11-15_ancestral/annotated_tree.nexus 247s 247s --- tree saved in auspice json format as 247s 2024-11-15_ancestral/auspice_tree.json 247s 247s ancestral_reconstruction ok 250s 250s 0.00 -TreeAnc: set-up 250s 250s Attempting to parse dates... 250s Using column 'name' as name. This needs match the taxon names in the tree!! 250s Using column 'date' as date. 250s 250s 0.01 TreeTime.reroot: with method or node: least-squares 250s 250s 0.01 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 250s 250s 0.04 TreeTime.reroot: with method or node: least-squares 250s 250s 0.04 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 250s 250s 0.07 TreeTime.reroot: with method or node: least-squares 250s 250s 0.07 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 250s 250s Root-Tip-Regression: 250s --rate: 2.826e-03 250s --r^2: 0.98 250s 250s The R^2 value indicates the fraction of variation inroot-to-tip 250s distance explained by the sampling times.Higher values corresponds 250s more clock-like behavior (max 1.0). 250s 250s The rate is the slope of the best fit of the date tothe root-to-tip 250s distance and provides an estimate ofthe substitution rate. The rate 250s needs to be positive!Negative rates suggest an inappropriate root. 250s 250s 250s The estimated rate and tree correspond to a root date: 250s 250s --- root-date: 1996.75 250s 250s 250s --- new tree written to 250s 2024-11-15_clock/rerooted.newick 250s 250s --- wrote dates and root-to-tip distances to 250s 2024-11-15_clock/rtt.csv 250s 250s --- root-to-tip plot saved to 250s 2024-11-15_clock/root_to_tip_regression.pdf 250s temporal_signal ok 258s 258s Attempting to parse dates... 258s Using column 'name' as name. This needs match the taxon names in the tree!! 258s Using column 'date' as date. 258s 258s 0.00 -TreeAnc: set-up 258s 258s 0.15 TreeTime.reroot: with method or node: least-squares 258s 258s 0.15 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 258s 258s 0.19 TreeTime.reroot: with method or node: least-squares 258s 258s 0.19 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 258s 258s 0.35 ###TreeTime.run: INITIAL ROUND 258s 258s 1.31 TreeTime.reroot: with method or node: least-squares 258s 258s 1.31 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 258s 258s 1.35 ###TreeTime.run: rerunning timetree after rerooting 258s 258s 2.28 ###TreeTime.run: ITERATION 1 out of 2 iterations 258s 258s 2.28 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 258s polytomies using the old 'greedy' mode. This is not well suited for large 258s polytomies. Stochastic resolution will become the default in future 258s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 258s keep using the greedy method in the future, run with `--greedy-resolve` 258s 258s 3.20 ###TreeTime.run: CONVERGED 258s 258s 5.83 ###TreeTime.run: FINAL ROUND - confidence estimation via marginal 258s reconstruction 258s 258s Inferred sequence evolution model (saved as 2024-11-15_treetime/sequence_evolution_model.txt): 258s Substitution rate (mu): 1.0 258s 258s Equilibrium frequencies (pi_i): 258s A: 0.3088 258s C: 0.1897 258s G: 0.2335 258s T: 0.2581 258s -: 0.0099 258s 258s Symmetrized rates from j->i (W_ij): 258s A C G T - 258s A 0 0.7003 3.0669 0.2651 0.9742 258s C 0.7003 0 0.3354 3.399 0.999 258s G 3.0669 0.3354 0 0.4258 0.9892 258s T 0.2651 3.399 0.4258 0 0.9848 258s - 0.9742 0.999 0.9892 0.9848 0 258s 258s Actual rates from j->i (Q_ij): 258s A C G T - 258s A 0 0.2163 0.9472 0.0819 0.3009 258s C 0.1328 0 0.0636 0.6448 0.1895 258s G 0.716 0.0783 0 0.0994 0.2309 258s T 0.0684 0.8772 0.1099 0 0.2541 258s - 0.0097 0.0099 0.0098 0.0098 0 258s 258s 258s Inferred sequence evolution model (saved as 2024-11-15_treetime/molecular_clock.txt): 258s Root-Tip-Regression: 258s --rate: 2.537e-03 +/- 3.96e-04 (one std-dev) 258s --chi^2: 15.23 258s --r^2: 0.96 258s 258s --- saved tree as 258s 2024-11-15_treetime/timetree.pdf 258s 258s --- root-to-tip plot saved to 258s 2024-11-15_treetime/root_to_tip_regression.pdf 258s 258s --- alignment including ancestral nodes saved as 258s 2024-11-15_treetime/ancestral_sequences.fasta 258s 258s --- saved divergence times in 258s 2024-11-15_treetime/dates.tsv 258s 258s --- tree saved in nexus format as 258s 2024-11-15_treetime/timetree.nexus 258s 258s --- tree saved in auspice json format as 258s 2024-11-15_treetime/auspice_tree.json 258s 258s --- divergence tree saved in nexus format as 258s 2024-11-15_treetime/divergence_tree.nexus 258s 258s timetree_inference ok 259s /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]` 259s weight_dict = {row[0]:row[1] for ri,row in tmp_weights.iterrows() if not np.isnan(row[1])} 260s Using column '#name' as taxon name. This needs to match the taxa in the tree! 260s Assigned discrete traits to 86 out of 86 taxa. 260s 260s 260s Completed mugration model inference of attribute 'country' for zika/zika.nwk 260s 260s Saved inferred mugration model as: 2024-11-15_mugration/GTR.txt 260s Saved annotated tree as: 2024-11-15_mugration/annotated_tree.nexus 260s ---Done! 260s 260s mugration ok 332s 332s Attempting to parse dates... 332s Using column 'strain' as name. This needs match the taxon names in the tree!! 332s Using column 'date' as date. 332s 332s 0.00 -TreeAnc: set-up 332s 332s 7.32 TreeTime.reroot: with method or node: least-squares 332s 332s 7.32 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 332s 332s 7.59 TreeTime.reroot: with method or node: least-squares 332s 332s 7.59 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 332s 332s 9.09 ###TreeTime.run: INITIAL ROUND 332s 332s 20.09 TreeTime.reroot: with method or node: least-squares 332s 332s 20.09 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 332s 332s 20.34 ###TreeTime.run: rerunning timetree after rerooting 332s 332s 32.16 ###TreeTime.run: ITERATION 1 out of 2 iterations 332s 332s 32.16 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 332s polytomies using the old 'greedy' mode. This is not well suited for large 332s polytomies. Stochastic resolution will become the default in future 332s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 332s keep using the greedy method in the future, run with `--greedy-resolve` 332s 332s 48.32 ###TreeTime.run: ITERATION 2 out of 2 iterations 332s 332s 62.93 TreeTime: the following tips have been marked as outliers. Their date 332s constraints were not used. Please remove them from the tree. Their dates 332s have been reset: 332s 332s 62.93 G22619, input date: [2011.0013698630137, 2011.9986301369863], apparent 332s date: 1984.70 332s 332s 62.93 G22703, input date: [2004.0013661202186, 2004.9986338797814], apparent 332s date: 2012.13 332s 332s Inferred sequence evolution model (saved as 2024-11-15-0001_treetime/sequence_evolution_model.txt): 332s Substitution rate (mu): 1.0 332s 332s Equilibrium frequencies (pi_i): 332s A: 0.1669 332s C: 0.3286 332s G: 0.3273 332s T: 0.1669 332s -: 0.0103 332s 332s Symmetrized rates from j->i (W_ij): 332s A C G T - 332s A 0 0.7489 1.6555 0.3287 35.5042 332s C 0.7489 0 0.3183 1.4089 35.6836 332s G 1.6555 0.3183 0 0.7519 49.1742 332s T 0.3287 1.4089 0.7519 0 32.1584 332s - 35.5042 35.6836 49.1742 32.1584 0 332s 332s Actual rates from j->i (Q_ij): 332s A C G T - 332s A 0 0.125 0.2763 0.0549 5.9261 332s C 0.2461 0 0.1046 0.4629 11.7248 332s G 0.5419 0.1042 0 0.2461 16.0959 332s T 0.0549 0.2351 0.1255 0 5.3666 332s - 0.366 0.3679 0.507 0.3315 0 332s 332s 332s Inferred sequence evolution model (saved as 2024-11-15-0001_treetime/molecular_clock.txt): 332s Root-Tip-Regression: 332s --rate: 1.000e-07 332s --r^2: 0.45 332s 332s --- saved tree as 332s 2024-11-15-0001_treetime/timetree.pdf 332s 332s --- root-to-tip plot saved to 332s 2024-11-15-0001_treetime/root_to_tip_regression.pdf 332s Sites that were constant except for ambiguous bases were made constant 332s by TreeTime. This happened 1343 times. These sites are now excluded 332s from the VCF. 332s 332s ***WARNING: vcf_utils.py 332s 52 sites were found that had no alternative bases. If this data has 332s been run through TreeTime and contains ambiguous bases, try calling 332s get_tree_dict with var_ambigs=True to see if this clears the error. 332s Alternative causes: - Not all sequences in your alignment are in the 332s tree (if you are running TreeTime via commandline this is most likely) 332s - In TreeTime, can be caused by overwriting variants in tips with 332s small branch lengths (debug) These are the positions affected 332s (numbering starts at 0): 332s 46593, 52473, 165918, 304891, 662240, 954864, 954865, 954866, 954867, 332s 963561, 1046706, 1145470, 1321893, 1468105, 1468106, 1512661, 1704463, 332s 1716723, 1743968, 1951837, 2129868, 2215816, 2274543, 2515984, 332s 2580886, 2626512, 2626513, 2626599, 2686156, 2736331, 2823901, 332s 2869282, 2894207, 2911378, 3047997, 3160385, 3314001, 3321447, 332s 3336505, 3461793, 3490408, 3618189, 3734466, 3764813, 3828626, 332s 3842630, 3894439, 3912292, 3913650, 3956227, 4149358, 4183687 332s 332s --- alignment including ancestral nodes saved as 332s 2024-11-15-0001_treetime/ancestral_sequences.vcf 332s 332s --- saved divergence times in 332s 2024-11-15-0001_treetime/dates.tsv 332s 332s --- tree saved in nexus format as 332s 2024-11-15-0001_treetime/timetree.nexus 332s 332s --- tree saved in auspice json format as 332s 2024-11-15-0001_treetime/auspice_tree.json 332s 332s --- divergence tree saved in nexus format as 332s 2024-11-15-0001_treetime/divergence_tree.nexus 332s 332s --- saved detected outliers as 2024-11-15-0001_treetime/outliers.tsv 332s timetree_inference on vcf data ok 486s 486s Attempting to parse dates... 486s Using column 'name' as name. This needs match the taxon names in the tree!! 486s Using column 'date' as date. 486s 486s 0.00 -TreeAnc: set-up 486s 486s 4.53 -WARNING: character U is unknown. Treating it as missing information 486s 486s 17.45 TreeTime.reroot: with method or node: least-squares 486s 486s 17.45 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 486s 486s 18.14 TreeTime.reroot: with method or node: least-squares 486s 486s 18.14 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 486s 486s 26.39 ###TreeTime.run: INITIAL ROUND 486s 486s 40.88 TreeTime.reroot: with method or node: least-squares 486s 486s 40.88 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 486s 486s 41.49 ###TreeTime.run: rerunning timetree after rerooting 486s 486s 59.82 ###TreeTime.run: ITERATION 1 out of 2 iterations 486s 486s 60.96 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 486s polytomies using the old 'greedy' mode. This is not well suited for large 486s polytomies. Stochastic resolution will become the default in future 486s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 486s keep using the greedy method in the future, run with `--greedy-resolve` 486s 486s 89.90 ###TreeTime.run: ITERATION 2 out of 2 iterations 486s 486s 147.09 TreeTime: the following tips have been marked as outliers. Their date 486s constraints were not used. Please remove them from the tree. Their dates 486s have been reset: 486s 486s 147.09 NZG_0393, input date: 2016.24, apparent date: 2015.24 486s 486s 147.09 NZG_0422, input date: 2016.25, apparent date: 2015.24 486s 486s 147.09 NZG_0358, input date: 2016.22, apparent date: 2015.24 486s 486s 147.09 NZG_0381, input date: 2016.23, apparent date: 2015.19 486s 486s 147.09 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.19 486s 486s 147.09 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.19 486s 486s 147.09 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.19 486s 486s 147.09 2607_C2_12916_EMLH, input date: 2015.32, apparent date: 2015.49 486s 486s 147.09 2607_C2_12855_EMLH, input date: 2015.28, apparent date: 2015.49 486s 486s 147.09 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.59 486s 486s 147.09 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.87 486s 486s 147.09 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.87 486s 486s 147.09 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.87 486s 486s 147.09 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2016.00 486s 486s 147.09 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.94 486s 486s 147.09 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.94 486s 486s 147.09 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.80 486s 486s 147.09 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.94 486s 486s 147.09 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2016.00 486s 486s 147.09 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2016.00 486s 486s Inferred sequence evolution model (saved as 2024-11-15-0002_treetime/sequence_evolution_model.txt): 486s Substitution rate (mu): 1.0 486s 486s Equilibrium frequencies (pi_i): 486s A: 0.3139 486s C: 0.2144 486s G: 0.1979 486s T: 0.2638 486s -: 0.01 486s 486s Symmetrized rates from j->i (W_ij): 486s A C G T - 486s A 0 0.3826 2.5275 0.2294 6.7953 486s C 0.3826 0 0.1691 3.5602 12.1803 486s G 2.5275 0.1691 0 0.3724 5.2949 486s T 0.2294 3.5602 0.3724 0 27.7427 486s - 6.7953 12.1803 5.2949 27.7427 0 486s 486s Actual rates from j->i (Q_ij): 486s A C G T - 486s A 0 0.1201 0.7933 0.072 2.1329 486s C 0.0821 0 0.0363 0.7634 2.6119 486s G 0.5002 0.0335 0 0.0737 1.0478 486s T 0.0605 0.9393 0.0982 0 7.3197 486s - 0.0676 0.1212 0.0527 0.2761 0 486s 486s 486s Inferred sequence evolution model (saved as 2024-11-15-0002_treetime/molecular_clock.txt): 486s Root-Tip-Regression: 486s --rate: 7.885e-04 486s --r^2: 0.80 486s 486s Inferred coalescent model 486s Skyline assuming 100.0 gen/year and approximate confidence bounds (+/- 2.000000 standard deviations of the LH) 486s date N_e lower upper 486s 2014.106 2.820e+01 1.185e+01 6.713e+01 486s 2014.196 6.351e+01 4.047e+01 9.968e+01 486s 2014.286 1.264e+02 7.563e+01 2.113e+02 486s 2014.375 7.353e+01 4.522e+01 1.196e+02 486s 2014.465 3.294e+02 2.314e+02 4.688e+02 486s 2014.555 4.778e+02 3.216e+02 7.100e+02 486s 2014.644 7.642e+02 5.223e+02 1.118e+03 486s 2014.734 2.282e+03 1.457e+03 3.573e+03 486s 2014.824 1.369e+03 7.951e+02 2.357e+03 486s 2014.913 1.050e+03 6.313e+02 1.748e+03 486s 2015.003 5.486e+02 3.337e+02 9.019e+02 486s 2015.093 5.848e+02 3.697e+02 9.250e+02 486s 2015.182 4.218e+02 2.638e+02 6.743e+02 486s 2015.272 3.187e+02 1.961e+02 5.180e+02 486s 2015.362 2.701e+02 1.719e+02 4.245e+02 486s 2015.451 1.673e+02 1.035e+02 2.704e+02 486s 2015.541 1.240e+02 7.169e+01 2.144e+02 486s 2015.631 1.467e+02 8.773e+01 2.452e+02 486s 2015.720 7.833e+01 4.141e+01 1.482e+02 486s 2015.810 2.347e+01 8.810e+00 6.252e+01 486s 486s --- written skyline to 2024-11-15-0002_treetime/skyline.tsv 486s 486s --- saved tree as 486s 2024-11-15-0002_treetime/timetree.pdf 486s 486s --- root-to-tip plot saved to 486s 2024-11-15-0002_treetime/root_to_tip_regression.pdf 486s 486s --- alignment including ancestral nodes saved as 486s 2024-11-15-0002_treetime/ancestral_sequences.fasta 486s 486s --- saved divergence times in 486s 2024-11-15-0002_treetime/dates.tsv 486s 486s --- tree saved in nexus format as 486s 2024-11-15-0002_treetime/timetree.nexus 486s 486s --- tree saved in auspice json format as 486s 2024-11-15-0002_treetime/auspice_tree.json 486s 486s --- divergence tree saved in nexus format as 486s 2024-11-15-0002_treetime/divergence_tree.nexus 486s 486s --- saved detected outliers as 2024-11-15-0002_treetime/outliers.tsv 486s skyline approximation ok 527s 527s Attempting to parse dates... 527s Using column 'name' as name. This needs match the taxon names in the tree!! 527s Using column 'date' as date. 527s 527s 0.00 -TreeAnc: set-up 527s 527s 0.10 TreeTime.reroot: with method or node: least-squares 527s 527s 0.10 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 527s 527s 0.95 TreeTime.reroot: with method or node: least-squares 527s 527s 0.95 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 527s 527s 1.58 ###TreeTime.run: INITIAL ROUND 527s 527s 13.55 TreeTime.reroot: with method or node: least-squares 527s 527s 13.56 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 527s 527s 14.18 ###TreeTime.run: rerunning timetree after rerooting 527s 527s 26.12 ###TreeTime.run: ITERATION 1 out of 2 iterations 527s 527s 26.12 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 527s polytomies using the old 'greedy' mode. This is not well suited for large 527s polytomies. Stochastic resolution will become the default in future 527s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 527s keep using the greedy method in the future, run with `--greedy-resolve` 527s 527s 38.11 ###TreeTime.run: CONVERGED 527s 527s 38.12 TreeTime: the following tips have been marked as outliers. Their date 527s constraints were not used. Please remove them from the tree. Their dates 527s have been reset: 527s 527s 38.12 NZG_0393, input date: 2016.24, apparent date: 2015.26 527s 527s 38.12 NZG_0422, input date: 2016.25, apparent date: 2015.26 527s 527s 38.12 NZG_0358, input date: 2016.22, apparent date: 2015.26 527s 527s 38.12 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.19 527s 527s 38.12 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.19 527s 527s 38.12 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.19 527s 527s 38.12 NZG_0381, input date: 2016.23, apparent date: 2015.19 527s 527s 38.12 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.40 527s 527s 38.12 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.81 527s 527s 38.12 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.81 527s 527s 38.12 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2015.87 527s 527s 38.12 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2015.87 527s 527s 38.12 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.74 527s 527s 38.12 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.81 527s 527s 38.12 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.68 527s 527s 38.12 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.74 527s 527s 38.12 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.74 527s 527s 38.12 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2015.87 527s 527s Inferred sequence evolution model (saved as 2024-11-15-0003_treetime/sequence_evolution_model.txt): 527s Substitution rate (mu): 1.0 527s 527s Equilibrium frequencies (pi_i): 527s A: 0.2 527s C: 0.2 527s G: 0.2 527s T: 0.2 527s -: 0.2 527s 527s Symmetrized rates from j->i (W_ij): 527s A C G T - 527s A 0 1.25 1.25 1.25 1.25 527s C 1.25 0 1.25 1.25 1.25 527s G 1.25 1.25 0 1.25 1.25 527s T 1.25 1.25 1.25 0 1.25 527s - 1.25 1.25 1.25 1.25 0 527s 527s Actual rates from j->i (Q_ij): 527s A C G T - 527s A 0 0.25 0.25 0.25 0.25 527s C 0.25 0 0.25 0.25 0.25 527s G 0.25 0.25 0 0.25 0.25 527s T 0.25 0.25 0.25 0 0.25 527s - 0.25 0.25 0.25 0.25 0 527s 527s 527s Inferred sequence evolution model (saved as 2024-11-15-0003_treetime/molecular_clock.txt): 527s Root-Tip-Regression: 527s --rate: 8.047e-04 527s --r^2: 0.79 527s 527s --- saved tree as 527s 2024-11-15-0003_treetime/timetree.pdf 527s 527s --- root-to-tip plot saved to 527s 2024-11-15-0003_treetime/root_to_tip_regression.pdf 527s --- saved divergence times in 527s 2024-11-15-0003_treetime/dates.tsv 527s 527s --- tree saved in nexus format as 527s 2024-11-15-0003_treetime/timetree.nexus 527s 527s --- tree saved in auspice json format as 527s 2024-11-15-0003_treetime/auspice_tree.json 527s 527s --- divergence tree saved in nexus format as 527s 2024-11-15-0003_treetime/divergence_tree.nexus 527s 527s --- saved detected outliers as 2024-11-15-0003_treetime/outliers.tsv 527s sequence length only ok 527s All tests passed 528s autopkgtest [00:13:39]: test run-unit-test: -----------------------] 528s run-unit-test PASS 528s autopkgtest [00:13:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 529s autopkgtest [00:13:40]: test autodep8-python3: preparing testbed 608s autopkgtest [00:14:59]: testbed dpkg architecture: ppc64el 608s autopkgtest [00:14:59]: testbed apt version: 2.9.8 608s autopkgtest [00:14:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 610s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 610s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 610s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 610s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1015 kB] 610s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.1 kB] 610s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [121 kB] 610s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [759 kB] 610s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8632 B] 611s Fetched 2100 kB in 1s (2235 kB/s) 611s Reading package lists... 616s Reading package lists... 616s Building dependency tree... 616s Reading state information... 616s Calculating upgrade... 616s The following packages will be upgraded: 616s bpfcc-tools bpftrace libbpfcc libcap-ng0 libgnutls30t64 libjson-glib-1.0-0 616s libjson-glib-1.0-common libnewt0.52 libutempter0 lxd-installer man-db 616s pastebinit python3-bpfcc python3-newt python3-systemd whiptail 616s 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 616s Need to get 6045 kB of archives. 616s After this operation, 453 kB of additional disk space will be used. 616s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcap-ng0 ppc64el 0.8.5-3build1 [16.3 kB] 617s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 660s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 661s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 663s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 663s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el man-db ppc64el 2.13.0-1 [1361 kB] 715s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 717s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 717s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 718s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 719s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 719s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 719s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 719s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el lxd-installer all 9 [5084 B] 719s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el pastebinit all 1.7.1-1 [14.9 kB] 719s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-systemd ppc64el 235-1build5 [48.7 kB] 720s Preconfiguring packages ... 720s Fetched 6045 kB in 1min 44s (58.2 kB/s) 720s (Reading database ... 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whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 720s Preparing to unpack .../03-man-db_2.13.0-1_ppc64el.deb ... 720s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 720s Preparing to unpack .../04-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 720s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 720s Preparing to unpack .../05-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 720s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 720s Preparing to unpack .../06-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 720s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 720s Preparing to unpack .../07-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 720s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 721s Preparing to unpack .../08-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 721s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 721s Preparing to unpack .../09-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 721s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 721s Preparing to unpack .../10-libutempter0_1.2.1-4_ppc64el.deb ... 721s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 721s Preparing to unpack .../11-lxd-installer_9_all.deb ... 721s Unpacking lxd-installer (9) over (8) ... 721s Preparing to unpack .../12-pastebinit_1.7.1-1_all.deb ... 721s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 721s Preparing to unpack .../13-python3-systemd_235-1build5_ppc64el.deb ... 721s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 721s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 721s Setting up pastebinit (1.7.1-1) ... 721s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 721s Setting up man-db (2.13.0-1) ... 721s Updating database of manual pages ... 723s man-db.service is a disabled or a static unit not running, not starting it. 723s Setting up lxd-installer (9) ... 724s Setting up libutempter0:ppc64el (1.2.1-4) ... 724s Setting up whiptail (0.52.24-2ubuntu4) ... 724s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 724s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 724s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 724s Setting up python3-systemd (235-1build5) ... 724s Setting up bpftrace (0.21.2-2ubuntu2) ... 724s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 724s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 724s Processing triggers for libc-bin (2.40-1ubuntu3) ... 724s Reading package lists... 724s Building dependency tree... 724s Reading state information... 725s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 726s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 726s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 726s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 727s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 727s Reading package lists... 728s Reading package lists... 728s Building dependency tree... 728s Reading state information... 728s Calculating upgrade... 728s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 728s Reading package lists... 728s Building dependency tree... 728s Reading state information... 728s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 729s autopkgtest [00:17:00]: rebooting testbed after setup commands that affected boot 739s nova [W] Using flock in prodstack6-ppc64el 739s Creating nova instance adt-plucky-ppc64el-python-treetime-20241114-233130-juju-7f2275-prod-proposed-migration-environment-20-2f3eac4c-0a6e-4e49-b8da-a88bc620d91e from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)... 739s nova [W] Using flock in prodstack6-ppc64el 739s Creating nova instance adt-plucky-ppc64el-python-treetime-20241114-233130-juju-7f2275-prod-proposed-migration-environment-20-2f3eac4c-0a6e-4e49-b8da-a88bc620d91e from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)... 739s : failure: Failed to create /var/tmp/autopkgtest-run-wrapper 739s autopkgtest [00:17:10]: ERROR: testbed failure: unexpected eof from the testbed