0s autopkgtest [11:23:46]: starting date and time: 2024-11-13 11:23:46+0000 0s autopkgtest [11:23:46]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [11:23:46]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hhxk0dur/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-treetime --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-39.secgroup --name adt-plucky-i386-python-treetime-20241113-112345-juju-7f2275-prod-proposed-migration-environment-15-b4d3766e-ea3c-458d-b255-8244a7556046 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 64s autopkgtest [11:24:50]: testbed dpkg architecture: amd64 64s autopkgtest [11:24:50]: testbed apt version: 2.9.8 64s autopkgtest [11:24:50]: test architecture: i386 64s autopkgtest [11:24:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 65s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 65s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 65s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 65s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 65s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 65s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 65s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 65s Fetched 2175 kB in 0s (5557 kB/s) 65s Reading package lists... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 68s The following NEW packages will be installed: 68s python3.13-gdbm 68s The following packages will be upgraded: 68s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 68s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 68s Need to get 253 kB of archives. 68s After this operation, 147 kB of additional disk space will be used. 68s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 68s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 68s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 68s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 68s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 68s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 68s Fetched 253 kB in 0s (6165 kB/s) 68s (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 ... 75541 files and directories currently installed.) 68s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 68s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 68s Setting up python3-minimal (3.12.7-1) ... 69s (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 ... 75541 files and directories currently installed.) 69s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 69s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 69s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 69s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 69s Selecting previously unselected package python3.13-gdbm. 69s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 69s Unpacking python3.13-gdbm (3.13.0-2) ... 69s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 69s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 69s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 69s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 69s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 69s Setting up python3.13-gdbm (3.13.0-2) ... 69s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 69s Setting up python3 (3.12.7-1) ... 69s Setting up python3-gdbm:amd64 (3.12.7-1) ... 69s Processing triggers for man-db (2.12.1-3) ... 70s Processing triggers for libc-bin (2.40-1ubuntu3) ... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 71s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 71s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 71s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 72s Reading package lists... 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 73s Calculating upgrade... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s autopkgtest [11:25:01]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 76s autopkgtest [11:25:02]: @@@@@@@@@@@@@@@@@@@@ apt-source python-treetime 77s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (dsc) [2611 B] 77s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [5117 kB] 77s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (tar) [1291 kB] 77s Get:4 http://ftpmaster.internal/ubuntu plucky/universe python-treetime 0.11.4-1 (diff) [8028 B] 77s gpgv: Signature made Sat Nov 9 21:31:47 2024 UTC 77s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 77s gpgv: issuer "emollier@debian.org" 77s gpgv: Can't check signature: No public key 77s dpkg-source: warning: cannot verify inline signature for ./python-treetime_0.11.4-1.dsc: no acceptable signature found 78s autopkgtest [11:25:04]: testing package python-treetime version 0.11.4-1 78s autopkgtest [11:25:04]: build not needed 79s autopkgtest [11:25:05]: test run-unit-test: preparing testbed 83s Note, using file '/tmp/autopkgtest.ryRc6R/1-autopkgtest-satdep.dsc' to get the build dependencies 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Starting pkgProblemResolver with broken count: 0 84s Starting 2 pkgProblemResolver with broken count: 0 84s Done 85s The following NEW packages will be installed: 85s blt build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 85s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 85s fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 85s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libblas3 85s libcairo2 libcc1-0 libdeflate0 libfontconfig1 libfontenc1 libgcc-14-dev 85s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libimagequant0 85s libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 85s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libmpc3 85s libopenjp2-7 libpixman-1-0 libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 85s libstdc++-14-dev libtcl8.6 libtiff6 libtk8.6 libtsan2 libubsan1 libwebp7 85s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 85s libxslt1.1 libxss1 python-matplotlib-data python3-appdirs python3-biopython 85s python3-brotli python3-cairo python3-contourpy python3-cycler 85s python3-dateutil python3-decorator python3-fonttools python3-freetype 85s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 85s python3-mpmath python3-numpy python3-packaging python3-pandas 85s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 85s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 85s python3-treetime python3-tz python3-ufolib2 python3-unicodedata2 85s python3.12-tk python3.13-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib 85s x11-common xfonts-encodings xfonts-utils xml-core 85s 0 upgraded, 110 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 150 MB of archives. 85s After this operation, 562 MB of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 85s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 85s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 85s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 85s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 85s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 85s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 85s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 85s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 85s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 85s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 85s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 85s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 85s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 85s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 85s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 85s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 85s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 85s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 85s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 85s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 85s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 85s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 85s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 85s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 85s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 85s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 85s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 85s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 85s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 85s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 85s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 85s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 85s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 85s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 85s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 85s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 85s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 85s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 85s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 85s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 85s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 85s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 85s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 85s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 85s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 85s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 85s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 85s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 85s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 85s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 85s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 85s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 85s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 85s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 85s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 85s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 85s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 85s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 85s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 85s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 85s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 85s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 85s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 85s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 85s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 85s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 85s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 85s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 85s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 85s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 85s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 85s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 85s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 85s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 85s Get:77 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 85s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 85s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 85s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 85s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 85s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 85s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 85s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 86s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 86s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 86s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 86s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 86s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 86s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 86s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 86s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 86s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 86s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 86s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 86s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 86s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 86s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 86s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 86s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 86s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 86s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 86s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 86s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 86s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 86s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 86s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 86s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 86s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 86s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 87s Fetched 150 MB in 1s (102 MB/s) 87s Selecting previously unselected package sgml-base. 87s (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 ... 75548 files and directories currently installed.) 87s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 87s Unpacking sgml-base (1.31) ... 87s Selecting previously unselected package libtcl8.6:amd64. 87s Preparing to unpack .../001-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 87s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 87s Selecting previously unselected package fonts-dejavu-mono. 87s Preparing to unpack .../002-fonts-dejavu-mono_2.37-8_all.deb ... 87s Unpacking fonts-dejavu-mono (2.37-8) ... 87s Selecting previously unselected package fonts-dejavu-core. 87s Preparing to unpack .../003-fonts-dejavu-core_2.37-8_all.deb ... 87s Unpacking fonts-dejavu-core (2.37-8) ... 87s Selecting previously unselected package libfontenc1:amd64. 87s Preparing to unpack .../004-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 87s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 87s Selecting previously unselected package x11-common. 87s Preparing to unpack .../005-x11-common_1%3a7.7+23ubuntu3_all.deb ... 87s Unpacking x11-common (1:7.7+23ubuntu3) ... 87s Selecting previously unselected package xfonts-encodings. 87s Preparing to unpack .../006-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 87s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 87s Selecting previously unselected package xfonts-utils. 87s Preparing to unpack .../007-xfonts-utils_1%3a7.7+7_amd64.deb ... 87s Unpacking xfonts-utils (1:7.7+7) ... 87s Selecting previously unselected package fonts-urw-base35. 87s Preparing to unpack .../008-fonts-urw-base35_20200910-8_all.deb ... 87s Unpacking fonts-urw-base35 (20200910-8) ... 87s Selecting previously unselected package fontconfig-config. 87s Preparing to unpack .../009-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 87s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 87s Selecting previously unselected package libfontconfig1:amd64. 87s Preparing to unpack .../010-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 88s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 88s Selecting previously unselected package libxrender1:amd64. 88s Preparing to unpack .../011-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 88s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 88s Selecting previously unselected package libxft2:amd64. 88s Preparing to unpack .../012-libxft2_2.3.6-1build1_amd64.deb ... 88s Unpacking libxft2:amd64 (2.3.6-1build1) ... 88s Selecting previously unselected package libxss1:amd64. 88s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_amd64.deb ... 88s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 88s Selecting previously unselected package libtk8.6:amd64. 88s Preparing to unpack .../014-libtk8.6_8.6.15-1_amd64.deb ... 88s Unpacking libtk8.6:amd64 (8.6.15-1) ... 88s Selecting previously unselected package tk8.6-blt2.5. 88s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 88s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 88s Selecting previously unselected package blt. 88s Preparing to unpack .../016-blt_2.5.3+dfsg-7build1_amd64.deb ... 88s Unpacking blt (2.5.3+dfsg-7build1) ... 88s Selecting previously unselected package libisl23:amd64. 88s Preparing to unpack .../017-libisl23_0.27-1_amd64.deb ... 88s Unpacking libisl23:amd64 (0.27-1) ... 88s Selecting previously unselected package libmpc3:amd64. 88s Preparing to unpack .../018-libmpc3_1.3.1-1build2_amd64.deb ... 88s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 88s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 88s Preparing to unpack .../019-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 88s Selecting previously unselected package cpp-14. 88s Preparing to unpack .../020-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 88s Selecting previously unselected package cpp-x86-64-linux-gnu. 88s Preparing to unpack .../021-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 88s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 88s Selecting previously unselected package cpp. 88s Preparing to unpack .../022-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 88s Unpacking cpp (4:14.1.0-2ubuntu1) ... 88s Selecting previously unselected package libcc1-0:amd64. 88s Preparing to unpack .../023-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 88s Selecting previously unselected package libgomp1:amd64. 88s Preparing to unpack .../024-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 88s Selecting previously unselected package libitm1:amd64. 88s Preparing to unpack .../025-libitm1_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 88s Selecting previously unselected package libasan8:amd64. 88s Preparing to unpack .../026-libasan8_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 88s Selecting previously unselected package liblsan0:amd64. 88s Preparing to unpack .../027-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 88s Selecting previously unselected package libtsan2:amd64. 88s Preparing to unpack .../028-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 89s Selecting previously unselected package libubsan1:amd64. 89s Preparing to unpack .../029-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 89s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 89s Selecting previously unselected package libhwasan0:amd64. 89s Preparing to unpack .../030-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 89s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 89s Selecting previously unselected package libquadmath0:amd64. 89s Preparing to unpack .../031-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 89s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 89s Selecting previously unselected package libgcc-14-dev:amd64. 89s Preparing to unpack .../032-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 89s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 89s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 89s Preparing to unpack .../033-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 89s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 89s Selecting previously unselected package gcc-14. 89s Preparing to unpack .../034-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 89s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 89s Selecting previously unselected package gcc-x86-64-linux-gnu. 89s Preparing to unpack .../035-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 89s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 89s Selecting previously unselected package gcc. 89s Preparing to unpack .../036-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 89s Unpacking gcc (4:14.1.0-2ubuntu1) ... 89s Selecting previously unselected package libstdc++-14-dev:amd64. 89s Preparing to unpack .../037-libstdc++-14-dev_14.2.0-8ubuntu1_amd64.deb ... 89s Unpacking libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 90s Selecting previously unselected package g++-14-x86-64-linux-gnu. 90s Preparing to unpack .../038-g++-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 90s Unpacking g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 90s Selecting previously unselected package g++-14. 90s Preparing to unpack .../039-g++-14_14.2.0-8ubuntu1_amd64.deb ... 90s Unpacking g++-14 (14.2.0-8ubuntu1) ... 90s Selecting previously unselected package g++-x86-64-linux-gnu. 90s Preparing to unpack .../040-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 90s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 90s Selecting previously unselected package g++. 90s Preparing to unpack .../041-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 90s Unpacking g++ (4:14.1.0-2ubuntu1) ... 90s Selecting previously unselected package build-essential. 90s Preparing to unpack .../042-build-essential_12.10ubuntu1_amd64.deb ... 90s Unpacking build-essential (12.10ubuntu1) ... 90s Selecting previously unselected package fonts-lyx. 90s Preparing to unpack .../043-fonts-lyx_2.4.2.1-1_all.deb ... 90s Unpacking fonts-lyx (2.4.2.1-1) ... 90s Selecting previously unselected package libblas3:amd64. 90s Preparing to unpack .../044-libblas3_3.12.0-3build2_amd64.deb ... 90s Unpacking libblas3:amd64 (3.12.0-3build2) ... 90s Selecting previously unselected package libpixman-1-0:amd64. 90s Preparing to unpack .../045-libpixman-1-0_0.44.0-3_amd64.deb ... 90s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 90s Selecting previously unselected package libxcb-render0:amd64. 90s Preparing to unpack .../046-libxcb-render0_1.17.0-2_amd64.deb ... 90s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 90s Selecting previously unselected package libxcb-shm0:amd64. 90s Preparing to unpack .../047-libxcb-shm0_1.17.0-2_amd64.deb ... 90s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 90s Selecting previously unselected package libcairo2:amd64. 90s Preparing to unpack .../048-libcairo2_1.18.2-2_amd64.deb ... 90s Unpacking libcairo2:amd64 (1.18.2-2) ... 90s Selecting previously unselected package libdeflate0:amd64. 90s Preparing to unpack .../049-libdeflate0_1.22-1_amd64.deb ... 90s Unpacking libdeflate0:amd64 (1.22-1) ... 90s Selecting previously unselected package libgfortran5:amd64. 90s Preparing to unpack .../050-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 90s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 90s Selecting previously unselected package libgraphite2-3:amd64. 90s Preparing to unpack .../051-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 90s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 90s Selecting previously unselected package libharfbuzz0b:amd64. 90s Preparing to unpack .../052-libharfbuzz0b_10.0.1-1_amd64.deb ... 90s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 90s Selecting previously unselected package libimagequant0:amd64. 90s Preparing to unpack .../053-libimagequant0_2.18.0-1build1_amd64.deb ... 90s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 90s Selecting previously unselected package libjpeg-turbo8:amd64. 90s Preparing to unpack .../054-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 90s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 90s Selecting previously unselected package libjpeg8:amd64. 90s Preparing to unpack .../055-libjpeg8_8c-2ubuntu11_amd64.deb ... 90s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 90s Selecting previously unselected package libjs-jquery. 90s Preparing to unpack .../056-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 90s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 90s Selecting previously unselected package libjs-jquery-ui. 90s Preparing to unpack .../057-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 90s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 90s Selecting previously unselected package liblapack3:amd64. 90s Preparing to unpack .../058-liblapack3_3.12.0-3build2_amd64.deb ... 90s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 91s Selecting previously unselected package liblbfgsb0:amd64. 91s Preparing to unpack .../059-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 91s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 91s Selecting previously unselected package liblcms2-2:amd64. 91s Preparing to unpack .../060-liblcms2-2_2.16-2_amd64.deb ... 91s Unpacking liblcms2-2:amd64 (2.16-2) ... 91s Selecting previously unselected package liblerc4:amd64. 91s Preparing to unpack .../061-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 91s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 91s Selecting previously unselected package libqhull-r8.0:amd64. 91s Preparing to unpack .../062-libqhull-r8.0_2020.2-6build1_amd64.deb ... 91s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 91s Selecting previously unselected package libraqm0:amd64. 91s Preparing to unpack .../063-libraqm0_0.10.1-1build1_amd64.deb ... 91s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 91s Selecting previously unselected package libsharpyuv0:amd64. 91s Preparing to unpack .../064-libsharpyuv0_1.4.0-0.1_amd64.deb ... 91s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 91s Selecting previously unselected package libjbig0:amd64. 91s Preparing to unpack .../065-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 91s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 91s Selecting previously unselected package libwebp7:amd64. 91s Preparing to unpack .../066-libwebp7_1.4.0-0.1_amd64.deb ... 91s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 91s Selecting previously unselected package libtiff6:amd64. 91s Preparing to unpack .../067-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 91s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 91s Selecting previously unselected package libwebpdemux2:amd64. 91s Preparing to unpack .../068-libwebpdemux2_1.4.0-0.1_amd64.deb ... 91s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 91s Selecting previously unselected package libwebpmux3:amd64. 91s Preparing to unpack .../069-libwebpmux3_1.4.0-0.1_amd64.deb ... 91s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 91s Selecting previously unselected package libxslt1.1:amd64. 91s Preparing to unpack .../070-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 91s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 91s Selecting previously unselected package python-matplotlib-data. 91s Preparing to unpack .../071-python-matplotlib-data_3.8.3-3_all.deb ... 91s Unpacking python-matplotlib-data (3.8.3-3) ... 91s Selecting previously unselected package python3-appdirs. 91s Preparing to unpack .../072-python3-appdirs_1.4.4-4_all.deb ... 91s Unpacking python3-appdirs (1.4.4-4) ... 91s Selecting previously unselected package python3-numpy. 91s Preparing to unpack .../073-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 91s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 91s Selecting previously unselected package python3.12-tk. 91s Preparing to unpack .../074-python3.12-tk_3.12.7-3_amd64.deb ... 91s Unpacking python3.12-tk (3.12.7-3) ... 91s Selecting previously unselected package python3.13-tk. 91s Preparing to unpack .../075-python3.13-tk_3.13.0-2_amd64.deb ... 91s Unpacking python3.13-tk (3.13.0-2) ... 91s Selecting previously unselected package python3-tk:amd64. 91s Preparing to unpack .../076-python3-tk_3.12.7-1_amd64.deb ... 91s Unpacking python3-tk:amd64 (3.12.7-1) ... 92s Selecting previously unselected package python3-pil.imagetk:amd64. 92s Preparing to unpack .../077-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 92s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 92s Selecting previously unselected package libopenjp2-7:amd64. 92s Preparing to unpack .../078-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 92s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 92s Selecting previously unselected package python3-pil:amd64. 92s Preparing to unpack .../079-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 92s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 92s Selecting previously unselected package python3-cairo. 92s Preparing to unpack .../080-python3-cairo_1.26.1-2_amd64.deb ... 92s Unpacking python3-cairo (1.26.1-2) ... 92s Selecting previously unselected package python3-freetype. 92s Preparing to unpack .../081-python3-freetype_2.5.1-1_all.deb ... 92s Unpacking python3-freetype (2.5.1-1) ... 92s Selecting previously unselected package python3-rlpycairo. 92s Preparing to unpack .../082-python3-rlpycairo_0.3.0-3_all.deb ... 92s Unpacking python3-rlpycairo (0.3.0-3) ... 92s Selecting previously unselected package python3-reportlab. 92s Preparing to unpack .../083-python3-reportlab_4.2.5-1_all.deb ... 92s Unpacking python3-reportlab (4.2.5-1) ... 92s Selecting previously unselected package xml-core. 92s Preparing to unpack .../084-xml-core_0.19_all.deb ... 92s Unpacking xml-core (0.19) ... 92s Selecting previously unselected package w3c-sgml-lib. 92s Preparing to unpack .../085-w3c-sgml-lib_1.3-3_all.deb ... 92s Unpacking w3c-sgml-lib (1.3-3) ... 92s Selecting previously unselected package python3-biopython. 92s Preparing to unpack .../086-python3-biopython_1.84+dfsg-4_amd64.deb ... 92s Unpacking python3-biopython (1.84+dfsg-4) ... 92s Selecting previously unselected package python3-brotli. 92s Preparing to unpack .../087-python3-brotli_1.1.0-2build2_amd64.deb ... 92s Unpacking python3-brotli (1.1.0-2build2) ... 92s Selecting previously unselected package python3-contourpy. 92s Preparing to unpack .../088-python3-contourpy_1.3.0-2_amd64.deb ... 92s Unpacking python3-contourpy (1.3.0-2) ... 92s Selecting previously 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114s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 114s Setting up python3-rlpycairo (0.3.0-3) ... 114s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 114s Setting up python3-reportlab (4.2.5-1) ... 115s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 115s Setting up g++-14 (14.2.0-8ubuntu1) ... 115s Setting up gcc (4:14.1.0-2ubuntu1) ... 115s Setting up g++ (4:14.1.0-2ubuntu1) ... 115s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 115s Setting up build-essential (12.10ubuntu1) ... 115s Setting up python3-fonttools (4.46.0-1build2) ... 116s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 116s Setting up python3-matplotlib (3.8.3-3) ... 117s Processing triggers for libc-bin (2.40-1ubuntu3) ... 117s Processing triggers for man-db (2.12.1-3) ... 118s Processing triggers for sgml-base (1.31) ... 118s Setting up w3c-sgml-lib (1.3-3) ... 145s Setting up python3-biopython (1.84+dfsg-4) ... 146s Setting up python3-treetime (0.11.4-1) ... 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 149s The following NEW packages will be installed: 149s autopkgtest-satdep 149s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 149s Need to get 0 B/696 B of archives. 149s After this operation, 0 B of additional disk space will be used. 149s Get:1 /tmp/autopkgtest.ryRc6R/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 150s Selecting previously unselected package autopkgtest-satdep. 150s (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 ... 87560 files and directories currently installed.) 150s Preparing to unpack .../2-autopkgtest-satdep.deb ... 150s Unpacking autopkgtest-satdep (0) ... 150s Setting up autopkgtest-satdep (0) ... 151s (Reading database ... 87560 files and directories currently installed.) 151s Removing autopkgtest-satdep (0) ... 152s autopkgtest [11:26:18]: test run-unit-test: [----------------------- 153s 153s 0.00 -TreeAnc: set-up 153s read alignment from file h3n2_na/h3n2_na_20.fasta with 19 sequences of length 1407 153s read tree from file h3n2_na/h3n2_na_20.nwk with 19 leaves 153s 153s inferring ancestral sequences... 153s ...done. 153s 153s The TOTAL tree length is 1.311e-01 and 183 mutations were observed. 153s Of these 183 mutations, 153s - 148 occur 1 times 153s - 16 occur 2 times 153s - 1 occur 3 times 153s 153s Of the 1407 positions in the genome, 153s - 1237 were hit 0 times (expected 1235.40) 153s - 124 were hit 1 times (expected 160.68) 153s - 25 were hit 2 times (expected 10.45) 153s - 3 were hit 3 times (expected 0.45) 153s 153s log-likelihood difference to Poisson distribution with same mean: -1.226e+01 153s 153s 153s The ten most homoplasic mutations are: 153s mut multiplicity 153s G27A 3 153s A88G 2 153s A267G 2 153s G451R 2 153s G629A 2 153s C763T 2 153s G780A 2 153s C825T 2 153s C891A 2 153s C906T 2 153s homoplasy_scanning ok 153s 153s 0.00 -TreeAnc: set-up 153s 153s Inferred sequence evolution model (saved as 2024-11-13_ancestral/sequence_evolution_model.txt): 153s Substitution rate (mu): 1.0 153s 153s Equilibrium frequencies (pi_i): 153s A: 0.3062 153s C: 0.1925 153s G: 0.2336 153s T: 0.2577 153s -: 0.01 153s 153s Symmetrized rates from j->i (W_ij): 153s A C G T - 153s A 0 0.8311 2.7926 0.4496 1.0287 153s C 0.8311 0 0.577 2.8797 1.0535 153s G 2.7926 0.577 0 0.612 1.0437 153s T 0.4496 2.8797 0.612 0 1.0394 153s - 1.0287 1.0535 1.0437 1.0394 0 153s 153s Actual rates from j->i (Q_ij): 153s A C G T - 153s A 0 0.2545 0.8551 0.1377 0.315 153s C 0.16 0 0.1111 0.5543 0.2028 153s G 0.6523 0.1348 0 0.143 0.2438 153s T 0.1159 0.7421 0.1577 0 0.2678 153s - 0.0103 0.0106 0.0105 0.0104 0 153s 153s 153s --- alignment including ancestral nodes saved as 153s 2024-11-13_ancestral/ancestral_sequences.fasta 153s 153s --- tree saved in nexus format as 153s 2024-11-13_ancestral/annotated_tree.nexus 153s 153s --- tree saved in auspice json format as 153s 2024-11-13_ancestral/auspice_tree.json 153s 154s ancestral_reconstruction ok 155s 155s 0.00 -TreeAnc: set-up 155s 155s Attempting to parse dates... 155s Using column 'name' as name. This needs match the taxon names in the tree!! 155s Using column 'date' as date. 155s 155s 0.00 TreeTime.reroot: with method or node: least-squares 155s 155s 0.00 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 155s 155s 0.03 TreeTime.reroot: with method or node: least-squares 155s 155s 0.03 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 155s 155s 0.05 TreeTime.reroot: with method or node: least-squares 155s 155s 0.05 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 155s 155s Root-Tip-Regression: 155s --rate: 2.826e-03 155s --r^2: 0.98 155s 155s The R^2 value indicates the fraction of variation inroot-to-tip 155s distance explained by the sampling times.Higher values corresponds 155s more clock-like behavior (max 1.0). 155s 155s The rate is the slope of the best fit of the date tothe root-to-tip 155s distance and provides an estimate ofthe substitution rate. The rate 155s needs to be positive!Negative rates suggest an inappropriate root. 155s 155s 155s The estimated rate and tree correspond to a root date: 155s 155s --- root-date: 1996.75 155s 155s 155s --- new tree written to 155s 2024-11-13_clock/rerooted.newick 155s 155s --- wrote dates and root-to-tip distances to 155s 2024-11-13_clock/rtt.csv 155s 155s --- root-to-tip plot saved to 155s 2024-11-13_clock/root_to_tip_regression.pdf 155s temporal_signal ok 161s 161s Attempting to parse dates... 161s Using column 'name' as name. This needs match the taxon names in the tree!! 161s Using column 'date' as date. 161s 161s 0.00 -TreeAnc: set-up 161s 161s 0.10 TreeTime.reroot: with method or node: least-squares 161s 161s 0.10 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 161s 161s 0.12 TreeTime.reroot: with method or node: least-squares 161s 161s 0.12 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 161s 161s 0.19 ###TreeTime.run: INITIAL ROUND 161s 161s 0.80 TreeTime.reroot: with method or node: least-squares 161s 161s 0.80 TreeTime.reroot: rerooting will account for covariance and shared ancestry. 161s 161s 0.82 ###TreeTime.run: rerunning timetree after rerooting 161s 161s 1.49 ###TreeTime.run: ITERATION 1 out of 2 iterations 161s 161s 1.49 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 161s polytomies using the old 'greedy' mode. This is not well suited for large 161s polytomies. Stochastic resolution will become the default in future 161s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 161s keep using the greedy method in the future, run with `--greedy-resolve` 161s 161s 2.15 ###TreeTime.run: CONVERGED 161s 161s 4.19 ###TreeTime.run: FINAL ROUND - confidence estimation via marginal 161s reconstruction 161s 161s Inferred sequence evolution model (saved as 2024-11-13_treetime/sequence_evolution_model.txt): 161s Substitution rate (mu): 1.0 161s 161s Equilibrium frequencies (pi_i): 161s A: 0.3088 161s C: 0.1897 161s G: 0.2335 161s T: 0.2581 161s -: 0.0099 161s 161s Symmetrized rates from j->i (W_ij): 161s A C G T - 161s A 0 0.7003 3.0669 0.2651 0.9742 161s C 0.7003 0 0.3354 3.399 0.999 161s G 3.0669 0.3354 0 0.4258 0.9892 161s T 0.2651 3.399 0.4258 0 0.9848 161s - 0.9742 0.999 0.9892 0.9848 0 161s 161s Actual rates from j->i (Q_ij): 161s A C G T - 161s A 0 0.2163 0.9472 0.0819 0.3009 161s C 0.1328 0 0.0636 0.6448 0.1895 161s G 0.716 0.0783 0 0.0994 0.2309 161s T 0.0684 0.8772 0.1099 0 0.2541 161s - 0.0097 0.0099 0.0098 0.0098 0 161s 161s 161s Inferred sequence evolution model (saved as 2024-11-13_treetime/molecular_clock.txt): 161s Root-Tip-Regression: 161s --rate: 2.653e-03 +/- 3.99e-04 (one std-dev) 161s --chi^2: 8.12 161s --r^2: 0.98 161s 161s --- saved tree as 161s 2024-11-13_treetime/timetree.pdf 161s 161s --- root-to-tip plot saved to 161s 2024-11-13_treetime/root_to_tip_regression.pdf 161s 161s --- alignment including ancestral nodes saved as 161s 2024-11-13_treetime/ancestral_sequences.fasta 161s 161s --- saved divergence times in 161s 2024-11-13_treetime/dates.tsv 161s 161s --- tree saved in nexus format as 161s 2024-11-13_treetime/timetree.nexus 161s 161s --- tree saved in auspice json format as 161s 2024-11-13_treetime/auspice_tree.json 161s 161s --- divergence tree saved in nexus format as 161s 2024-11-13_treetime/divergence_tree.nexus 161s 162s timetree_inference ok 162s /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]` 162s weight_dict = {row[0]:row[1] for ri,row in tmp_weights.iterrows() if not np.isnan(row[1])} 163s Using column '#name' as taxon name. This needs to match the taxa in the tree! 163s Assigned discrete traits to 86 out of 86 taxa. 163s 163s 163s Completed mugration model inference of attribute 'country' for zika/zika.nwk 163s 163s Saved inferred mugration model as: 2024-11-13_mugration/GTR.txt 163s Saved annotated tree as: 2024-11-13_mugration/annotated_tree.nexus 163s ---Done! 163s 163s mugration ok 214s 214s Attempting to parse dates... 214s Using column 'strain' as name. This needs match the taxon names in the tree!! 214s Using column 'date' as date. 214s 214s 0.00 -TreeAnc: set-up 214s 214s 5.57 TreeTime.reroot: with method or node: least-squares 214s 214s 5.57 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 214s 214s 5.76 TreeTime.reroot: with method or node: least-squares 214s 214s 5.76 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 214s 214s 6.85 ###TreeTime.run: INITIAL ROUND 214s 214s 14.93 TreeTime.reroot: with method or node: least-squares 214s 214s 14.93 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 214s 214s 15.11 ###TreeTime.run: rerunning timetree after rerooting 214s 214s 23.75 ###TreeTime.run: ITERATION 1 out of 2 iterations 214s 214s 23.75 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 214s polytomies using the old 'greedy' mode. This is not well suited for large 214s polytomies. Stochastic resolution will become the default in future 214s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 214s keep using the greedy method in the future, run with `--greedy-resolve` 214s 214s 34.91 ###TreeTime.run: ITERATION 2 out of 2 iterations 214s 214s 45.22 TreeTime: the following tips have been marked as outliers. Their date 214s constraints were not used. Please remove them from the tree. Their dates 214s have been reset: 214s 214s 45.22 G22703, input date: [2004.0013661202186, 2004.9986338797814], apparent 214s date: 2012.13 214s 214s Inferred sequence evolution model (saved as 2024-11-13-0001_treetime/sequence_evolution_model.txt): 214s Substitution rate (mu): 1.0 214s 214s Equilibrium frequencies (pi_i): 214s A: 0.1669 214s C: 0.3286 214s G: 0.3273 214s T: 0.1669 214s -: 0.0103 214s 214s Symmetrized rates from j->i (W_ij): 214s A C G T - 214s A 0 0.76 1.6604 0.3123 35.6093 214s C 0.76 0 0.3147 1.4131 35.7158 214s G 1.6604 0.3147 0 0.7451 49.2461 214s T 0.3123 1.4131 0.7451 0 31.973 214s - 35.6093 35.7158 49.2461 31.973 0 214s 214s Actual rates from j->i (Q_ij): 214s A C G T - 214s A 0 0.1269 0.2771 0.0521 5.9436 214s C 0.2497 0 0.1034 0.4643 11.7354 214s G 0.5435 0.103 0 0.2439 16.1194 214s T 0.0521 0.2358 0.1243 0 5.3356 214s - 0.3671 0.3682 0.5077 0.3296 0 214s 214s 214s Inferred sequence evolution model (saved as 2024-11-13-0001_treetime/molecular_clock.txt): 214s Root-Tip-Regression: 214s --rate: 1.000e-07 214s --r^2: 0.36 214s 214s --- saved tree as 214s 2024-11-13-0001_treetime/timetree.pdf 214s 214s --- root-to-tip plot saved to 214s 2024-11-13-0001_treetime/root_to_tip_regression.pdf 214s Sites that were constant except for ambiguous bases were made constant 214s by TreeTime. This happened 1343 times. These sites are now excluded 214s from the VCF. 214s 214s ***WARNING: vcf_utils.py 214s 52 sites were found that had no alternative bases. If this data has 214s been run through TreeTime and contains ambiguous bases, try calling 214s get_tree_dict with var_ambigs=True to see if this clears the error. 214s Alternative causes: - Not all sequences in your alignment are in the 214s tree (if you are running TreeTime via commandline this is most likely) 214s - In TreeTime, can be caused by overwriting variants in tips with 214s small branch lengths (debug) These are the positions affected 214s (numbering starts at 0): 214s 46593, 52473, 165918, 304891, 662240, 954864, 954865, 954866, 954867, 214s 963561, 1046706, 1145470, 1321893, 1468105, 1468106, 1512661, 1704463, 214s 1716723, 1743968, 1951837, 2129868, 2215816, 2274543, 2515984, 214s 2580886, 2626512, 2626513, 2626599, 2686156, 2736331, 2823901, 214s 2869282, 2894207, 2911378, 3047997, 3160385, 3314001, 3321447, 214s 3336505, 3461793, 3490408, 3618189, 3734466, 3764813, 3828626, 214s 3842630, 3894439, 3912292, 3913650, 3956227, 4149358, 4183687 214s 214s --- alignment including ancestral nodes saved as 214s 2024-11-13-0001_treetime/ancestral_sequences.vcf 214s 214s --- saved divergence times in 214s 2024-11-13-0001_treetime/dates.tsv 214s 214s --- tree saved in nexus format as 214s 2024-11-13-0001_treetime/timetree.nexus 214s 214s --- tree saved in auspice json format as 214s 2024-11-13-0001_treetime/auspice_tree.json 214s 214s --- divergence tree saved in nexus format as 214s 2024-11-13-0001_treetime/divergence_tree.nexus 214s 214s --- saved detected outliers as 2024-11-13-0001_treetime/outliers.tsv 215s timetree_inference on vcf data ok 330s 330s Attempting to parse dates... 330s Using column 'name' as name. This needs match the taxon names in the tree!! 330s Using column 'date' as date. 330s 330s 0.00 -TreeAnc: set-up 330s 330s 3.91 -WARNING: character U is unknown. Treating it as missing information 330s 330s 14.17 TreeTime.reroot: with method or node: least-squares 330s 330s 14.17 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 330s 330s 14.63 TreeTime.reroot: with method or node: least-squares 330s 330s 14.64 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 330s 330s 21.17 ###TreeTime.run: INITIAL ROUND 330s 330s 31.61 TreeTime.reroot: with method or node: least-squares 330s 330s 31.61 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 330s 330s 32.04 ###TreeTime.run: rerunning timetree after rerooting 330s 330s 45.74 ###TreeTime.run: ITERATION 1 out of 2 iterations 330s 330s 46.47 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 330s polytomies using the old 'greedy' mode. This is not well suited for large 330s polytomies. Stochastic resolution will become the default in future 330s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 330s keep using the greedy method in the future, run with `--greedy-resolve` 330s 330s 68.11 ###TreeTime.run: ITERATION 2 out of 2 iterations 330s 330s 108.95 TreeTime: the following tips have been marked as outliers. Their date 330s constraints were not used. Please remove them from the tree. Their dates 330s have been reset: 330s 330s 108.95 NZG_0393, input date: 2016.24, apparent date: 2015.16 330s 330s 108.95 NZG_0422, input date: 2016.25, apparent date: 2015.16 330s 330s 108.95 NZG_0358, input date: 2016.22, apparent date: 2015.16 330s 330s 108.95 NZG_0381, input date: 2016.23, apparent date: 2015.11 330s 330s 108.95 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.11 330s 330s 108.95 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.11 330s 330s 108.95 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.11 330s 330s 108.95 2607_C2_12916_EMLH, input date: 2015.32, apparent date: 2015.49 330s 330s 108.95 2607_C2_12855_EMLH, input date: 2015.28, apparent date: 2015.49 330s 330s 108.95 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.59 330s 330s 108.95 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.87 330s 330s 108.95 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.87 330s 330s 108.95 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.87 330s 330s 108.95 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2016.00 330s 330s 108.95 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.94 330s 330s 108.95 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.94 330s 330s 108.95 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.80 330s 330s 108.95 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.94 330s 330s 108.95 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2016.00 330s 330s 108.95 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2016.00 330s 330s Inferred sequence evolution model (saved as 2024-11-13-0002_treetime/sequence_evolution_model.txt): 330s Substitution rate (mu): 1.0 330s 330s Equilibrium frequencies (pi_i): 330s A: 0.3139 330s C: 0.2144 330s G: 0.1979 330s T: 0.2638 330s -: 0.01 330s 330s Symmetrized rates from j->i (W_ij): 330s A C G T - 330s A 0 0.3826 2.5275 0.2294 6.7953 330s C 0.3826 0 0.1691 3.5602 12.1803 330s G 2.5275 0.1691 0 0.3724 5.2949 330s T 0.2294 3.5602 0.3724 0 27.7427 330s - 6.7953 12.1803 5.2949 27.7427 0 330s 330s Actual rates from j->i (Q_ij): 330s A C G T - 330s A 0 0.1201 0.7933 0.072 2.1329 330s C 0.0821 0 0.0363 0.7634 2.6119 330s G 0.5002 0.0335 0 0.0737 1.0478 330s T 0.0605 0.9393 0.0982 0 7.3197 330s - 0.0676 0.1212 0.0527 0.2761 0 330s 330s 330s Inferred sequence evolution model (saved as 2024-11-13-0002_treetime/molecular_clock.txt): 330s Root-Tip-Regression: 330s --rate: 7.885e-04 330s --r^2: 0.80 330s 330s Inferred coalescent model 330s Skyline assuming 100.0 gen/year and approximate confidence bounds (+/- 2.000000 standard deviations of the LH) 330s date N_e lower upper 330s 2014.122 2.632e+01 1.151e+01 6.020e+01 330s 2014.211 6.037e+01 4.019e+01 9.069e+01 330s 2014.300 8.570e+01 4.997e+01 1.470e+02 330s 2014.389 1.035e+02 7.037e+01 1.523e+02 330s 2014.478 3.637e+02 2.528e+02 5.233e+02 330s 2014.567 4.629e+02 3.110e+02 6.891e+02 330s 2014.655 9.009e+02 6.139e+02 1.322e+03 330s 2014.744 2.273e+03 1.447e+03 3.570e+03 330s 2014.833 1.365e+03 8.078e+02 2.306e+03 330s 2014.922 9.529e+02 5.749e+02 1.580e+03 330s 2015.011 5.982e+02 3.668e+02 9.754e+02 330s 2015.099 5.753e+02 3.639e+02 9.096e+02 330s 2015.188 4.231e+02 2.665e+02 6.720e+02 330s 2015.277 3.015e+02 1.858e+02 4.893e+02 330s 2015.366 2.892e+02 1.849e+02 4.523e+02 330s 2015.455 1.595e+02 9.811e+01 2.593e+02 330s 2015.544 1.225e+02 7.098e+01 2.113e+02 330s 2015.632 1.458e+02 8.694e+01 2.446e+02 330s 2015.721 7.790e+01 4.112e+01 1.476e+02 330s 2015.810 2.331e+01 8.752e+00 6.207e+01 330s 330s --- written skyline to 2024-11-13-0002_treetime/skyline.tsv 330s 330s --- saved tree as 330s 2024-11-13-0002_treetime/timetree.pdf 330s 330s --- root-to-tip plot saved to 330s 2024-11-13-0002_treetime/root_to_tip_regression.pdf 330s 330s --- alignment including ancestral nodes saved as 330s 2024-11-13-0002_treetime/ancestral_sequences.fasta 330s 330s --- saved divergence times in 330s 2024-11-13-0002_treetime/dates.tsv 330s 330s --- tree saved in nexus format as 330s 2024-11-13-0002_treetime/timetree.nexus 330s 330s --- tree saved in auspice json format as 330s 2024-11-13-0002_treetime/auspice_tree.json 330s 330s --- divergence tree saved in nexus format as 330s 2024-11-13-0002_treetime/divergence_tree.nexus 330s 330s --- saved detected outliers as 2024-11-13-0002_treetime/outliers.tsv 330s skyline approximation ok 362s 362s Attempting to parse dates... 362s Using column 'name' as name. This needs match the taxon names in the tree!! 362s Using column 'date' as date. 362s 362s 0.00 -TreeAnc: set-up 362s 362s 0.07 TreeTime.reroot: with method or node: least-squares 362s 362s 0.07 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 362s 362s 0.69 TreeTime.reroot: with method or node: least-squares 362s 362s 0.69 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 362s 362s 1.14 ###TreeTime.run: INITIAL ROUND 362s 362s 10.39 TreeTime.reroot: with method or node: least-squares 362s 362s 10.39 TreeTime.reroot: rerooting will ignore covariance and shared ancestry. 362s 362s 10.83 ###TreeTime.run: rerunning timetree after rerooting 362s 362s 19.83 ###TreeTime.run: ITERATION 1 out of 2 iterations 362s 362s 19.83 DEPRECATION WARNING. TreeTime.resolve_polytomies: You are resolving 362s polytomies using the old 'greedy' mode. This is not well suited for large 362s polytomies. Stochastic resolution will become the default in future 362s versions. To switch now, rerun with the flag `--stochastic-resolve`. To 362s keep using the greedy method in the future, run with `--greedy-resolve` 362s 362s 28.83 ###TreeTime.run: CONVERGED 362s 362s 28.83 TreeTime: the following tips have been marked as outliers. Their date 362s constraints were not used. Please remove them from the tree. Their dates 362s have been reset: 362s 362s 28.83 NZG_0393, input date: 2016.24, apparent date: 2015.26 362s 362s 28.83 NZG_0422, input date: 2016.25, apparent date: 2015.26 362s 362s 28.83 NZG_0358, input date: 2016.22, apparent date: 2015.26 362s 362s 28.83 EM_NG_2016_029366, input date: 2016.21, apparent date: 2015.19 362s 362s 28.83 EM_NG_2016_029364, input date: 2016.21, apparent date: 2015.19 362s 362s 28.83 EM_NG_2016_029417, input date: 2016.22, apparent date: 2015.19 362s 362s 28.83 NZG_0381, input date: 2016.23, apparent date: 2015.19 362s 362s 28.83 1708_C1_13031_EMLH, input date: 2015.38, apparent date: 2015.40 362s 362s 28.83 1507_C1_18660_EMLH, input date: 2015.52, apparent date: 2015.81 362s 362s 28.83 2208_C2_18642R_EMLH, input date: 2015.51, apparent date: 2015.81 362s 362s 28.83 1507_C1_18636_EMLH, input date: 2015.51, apparent date: 2015.87 362s 362s 28.83 2208_C2_18687R_EMLH, input date: 2015.53, apparent date: 2015.87 362s 362s 28.83 1507_C1_18650_EMLH, input date: 2015.52, apparent date: 2015.74 362s 362s 28.83 1507_C1_13268_EMLH, input date: 2015.47, apparent date: 2015.81 362s 362s 28.83 1507_C1_18647_EMLH, input date: 2015.52, apparent date: 2015.68 362s 362s 28.83 0208_C1_MK10173, input date: 2015.58, apparent date: 2015.74 362s 362s 28.83 1507_C1_18706_EMLH, input date: 2015.53, apparent date: 2015.74 362s 362s 28.83 2208_C2_18659R_EMLH, input date: 2015.52, apparent date: 2015.87 362s 362s Inferred sequence evolution model (saved as 2024-11-13-0003_treetime/sequence_evolution_model.txt): 362s Substitution rate (mu): 1.0 362s 362s Equilibrium frequencies (pi_i): 362s A: 0.2 362s C: 0.2 362s G: 0.2 362s T: 0.2 362s -: 0.2 362s 362s Symmetrized rates from j->i (W_ij): 362s A C G T - 362s A 0 1.25 1.25 1.25 1.25 362s C 1.25 0 1.25 1.25 1.25 362s G 1.25 1.25 0 1.25 1.25 362s T 1.25 1.25 1.25 0 1.25 362s - 1.25 1.25 1.25 1.25 0 362s 362s Actual rates from j->i (Q_ij): 362s A C G T - 362s A 0 0.25 0.25 0.25 0.25 362s C 0.25 0 0.25 0.25 0.25 362s G 0.25 0.25 0 0.25 0.25 362s T 0.25 0.25 0.25 0 0.25 362s - 0.25 0.25 0.25 0.25 0 362s 362s 362s Inferred sequence evolution model (saved as 2024-11-13-0003_treetime/molecular_clock.txt): 362s Root-Tip-Regression: 362s --rate: 8.047e-04 362s --r^2: 0.79 362s 362s --- saved tree as 362s 2024-11-13-0003_treetime/timetree.pdf 362s 362s --- root-to-tip plot saved to 362s 2024-11-13-0003_treetime/root_to_tip_regression.pdf 362s --- saved divergence times in 362s 2024-11-13-0003_treetime/dates.tsv 362s 362s --- tree saved in nexus format as 362s 2024-11-13-0003_treetime/timetree.nexus 362s 362s --- tree saved in auspice json format as 362s 2024-11-13-0003_treetime/auspice_tree.json 362s 362s --- divergence tree saved in nexus format as 362s 2024-11-13-0003_treetime/divergence_tree.nexus 362s 362s --- saved detected outliers as 2024-11-13-0003_treetime/outliers.tsv 362s sequence length only ok 362s All tests passed 362s autopkgtest [11:29:48]: test run-unit-test: -----------------------] 363s autopkgtest [11:29:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 363s run-unit-test PASS 363s autopkgtest [11:29:49]: test autodep8-python3: preparing testbed 438s autopkgtest [11:31:04]: testbed dpkg architecture: amd64 439s autopkgtest [11:31:05]: testbed apt version: 2.9.8 439s autopkgtest [11:31:05]: test architecture: i386 439s autopkgtest [11:31:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 441s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 441s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 441s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 441s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 441s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 441s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 441s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 441s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 441s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 441s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 441s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 441s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 441s Fetched 2175 kB in 0s (6853 kB/s) 441s Reading package lists... 446s Reading package lists... 447s Building dependency tree... 447s Reading state information... 447s Calculating upgrade... 447s The following NEW packages will be installed: 447s python3.13-gdbm 447s The following packages will be upgraded: 447s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 447s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 447s Need to get 253 kB of archives. 447s After this operation, 147 kB of additional disk space will be used. 447s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 447s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 447s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 447s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 447s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 447s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 448s Fetched 253 kB in 0s (5136 kB/s) 448s (Reading database ... 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http://ftpmaster.internal/ubuntu plucky-updates InRelease 458s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 459s Reading package lists... 459s Reading package lists... 459s Building dependency tree... 459s Reading state information... 460s Calculating upgrade... 460s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 460s Reading package lists... 460s Building dependency tree... 460s Reading state information... 461s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 522s Note, using file '/tmp/autopkgtest.ryRc6R/3-autopkgtest-satdep.dsc' to get the build dependencies 522s Reading package lists... 523s Building dependency tree... 523s Reading state information... 523s Starting pkgProblemResolver with broken count: 0 523s Starting 2 pkgProblemResolver with broken count: 0 523s Done 524s The following NEW packages will be installed: 524s blt build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 524s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 524s fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 524s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libblas3 524s libcairo2 libcc1-0 libdeflate0 libfontconfig1 libfontenc1 libgcc-14-dev 524s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libimagequant0 524s libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 524s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 libmpc3 524s libopenjp2-7 libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib 524s libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 libstdc++-14-dev libtcl8.6 524s libtiff6 libtk8.6 libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 524s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 524s python-matplotlib-data python3-all python3-appdirs python3-biopython 524s python3-brotli python3-cairo python3-contourpy python3-cycler 524s python3-dateutil python3-decorator python3-fonttools python3-freetype 524s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 524s python3-mpmath python3-numpy python3-packaging python3-pandas 524s python3-pandas-lib python3-pil python3-pil.imagetk python3-reportlab 524s python3-rlpycairo python3-scipy python3-six python3-sympy python3-tk 524s python3-treetime python3-tz python3-ufolib2 python3.12-tk python3.13 524s python3.13-minimal python3.13-tk sgml-base tk8.6-blt2.5 unicode-data 524s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 524s 0 upgraded, 114 newly installed, 0 to remove and 0 not upgraded. 524s Need to get 156 MB of archives. 524s After this operation, 583 MB of additional disk space will be used. 524s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 524s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 524s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 524s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 524s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 524s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 524s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 524s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 524s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 524s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 524s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 524s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 524s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 524s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 524s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 524s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 524s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 524s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 524s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 524s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 524s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 524s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 524s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 524s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 524s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 524s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 524s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 524s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 524s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 524s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 524s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 524s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 524s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 524s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 524s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 524s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 524s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 524s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 524s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 524s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 524s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 524s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 524s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 524s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 524s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 524s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 524s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 524s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 524s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 524s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 524s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 524s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 524s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 524s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 524s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 524s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 524s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 524s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 524s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 524s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 524s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 524s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 524s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 524s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 524s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 524s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 524s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 524s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 524s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 524s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 524s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 524s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 524s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 524s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 524s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 524s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 524s Get:77 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 524s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 524s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 524s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 524s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 524s Get:82 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 524s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 524s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 524s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 524s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 524s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 524s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 524s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 524s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 524s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 524s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 524s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 524s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 524s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 524s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 524s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 524s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 524s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 525s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 525s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 525s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 525s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 525s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 525s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 525s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 525s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 525s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 525s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 525s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 525s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 525s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 525s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 525s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 525s Fetched 156 MB in 1s (110 MB/s) 525s Selecting previously unselected package libpython3.13-minimal:amd64. 526s (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 ... 75548 files and directories currently installed.) 526s Preparing to unpack .../000-libpython3.13-minimal_3.13.0-2_amd64.deb ... 526s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 526s Selecting previously unselected package python3.13-minimal. 526s Preparing to unpack .../001-python3.13-minimal_3.13.0-2_amd64.deb ... 526s Unpacking python3.13-minimal (3.13.0-2) ... 526s Selecting previously unselected package sgml-base. 526s Preparing to unpack .../002-sgml-base_1.31_all.deb ... 526s Unpacking sgml-base (1.31) ... 526s Selecting previously unselected package libtcl8.6:amd64. 526s Preparing to unpack .../003-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 526s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 526s Selecting previously unselected package fonts-dejavu-mono. 526s Preparing to unpack .../004-fonts-dejavu-mono_2.37-8_all.deb ... 526s Unpacking fonts-dejavu-mono (2.37-8) ... 526s Selecting previously unselected package fonts-dejavu-core. 526s Preparing to unpack .../005-fonts-dejavu-core_2.37-8_all.deb ... 526s Unpacking fonts-dejavu-core (2.37-8) ... 526s Selecting previously unselected package libfontenc1:amd64. 526s Preparing to unpack .../006-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 526s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 526s Selecting previously unselected package x11-common. 526s Preparing to unpack .../007-x11-common_1%3a7.7+23ubuntu3_all.deb ... 526s Unpacking x11-common (1:7.7+23ubuntu3) ... 526s Selecting previously unselected package xfonts-encodings. 526s Preparing to unpack .../008-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 526s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 526s Selecting previously unselected package xfonts-utils. 526s Preparing to unpack .../009-xfonts-utils_1%3a7.7+7_amd64.deb ... 526s Unpacking xfonts-utils (1:7.7+7) ... 526s Selecting previously unselected package fonts-urw-base35. 526s Preparing to unpack .../010-fonts-urw-base35_20200910-8_all.deb ... 526s Unpacking fonts-urw-base35 (20200910-8) ... 526s Selecting previously unselected package fontconfig-config. 526s Preparing to unpack .../011-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 527s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 527s Selecting previously unselected package libfontconfig1:amd64. 527s Preparing to unpack .../012-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 527s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 527s Selecting previously unselected package libxrender1:amd64. 527s Preparing to unpack .../013-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 527s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 527s Selecting previously unselected package libxft2:amd64. 527s Preparing to unpack .../014-libxft2_2.3.6-1build1_amd64.deb ... 527s Unpacking libxft2:amd64 (2.3.6-1build1) ... 527s Selecting previously unselected package libxss1:amd64. 527s Preparing to unpack .../015-libxss1_1%3a1.2.3-1build3_amd64.deb ... 527s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 527s Selecting previously unselected package libtk8.6:amd64. 527s Preparing to unpack .../016-libtk8.6_8.6.15-1_amd64.deb ... 527s Unpacking libtk8.6:amd64 (8.6.15-1) ... 527s Selecting previously unselected package tk8.6-blt2.5. 527s Preparing to unpack .../017-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 527s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 527s Selecting previously unselected package blt. 527s Preparing to unpack .../018-blt_2.5.3+dfsg-7build1_amd64.deb ... 527s Unpacking blt (2.5.3+dfsg-7build1) ... 527s Selecting previously unselected package libisl23:amd64. 527s Preparing to unpack .../019-libisl23_0.27-1_amd64.deb ... 527s Unpacking libisl23:amd64 (0.27-1) ... 527s Selecting previously unselected package libmpc3:amd64. 527s Preparing to unpack .../020-libmpc3_1.3.1-1build2_amd64.deb ... 527s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 527s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 527s Preparing to unpack .../021-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 527s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 527s Selecting previously unselected package cpp-14. 527s Preparing to unpack .../022-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 527s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 527s Selecting previously unselected package cpp-x86-64-linux-gnu. 527s Preparing to unpack .../023-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 527s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 527s Selecting previously unselected package cpp. 527s Preparing to unpack .../024-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 527s Unpacking cpp (4:14.1.0-2ubuntu1) ... 527s Selecting previously unselected package libcc1-0:amd64. 527s Preparing to unpack .../025-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 527s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 527s Selecting previously unselected package libgomp1:amd64. 527s Preparing to unpack .../026-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 527s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 527s Selecting previously unselected package libitm1:amd64. 527s Preparing to unpack .../027-libitm1_14.2.0-8ubuntu1_amd64.deb ... 527s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 527s Selecting previously unselected package libasan8:amd64. 527s Preparing to unpack .../028-libasan8_14.2.0-8ubuntu1_amd64.deb ... 527s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 527s Selecting previously unselected package liblsan0:amd64. 527s Preparing to unpack .../029-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 527s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 527s Selecting previously unselected package libtsan2:amd64. 527s Preparing to unpack .../030-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 527s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 528s Selecting previously unselected package libubsan1:amd64. 528s Preparing to unpack .../031-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 528s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 528s Selecting previously unselected package libhwasan0:amd64. 528s Preparing to unpack .../032-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 528s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 528s Selecting previously unselected package libquadmath0:amd64. 528s Preparing to unpack .../033-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 528s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 528s Selecting previously unselected package libgcc-14-dev:amd64. 528s Preparing to unpack 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.../044-build-essential_12.10ubuntu1_amd64.deb ... 529s Unpacking build-essential (12.10ubuntu1) ... 529s Selecting previously unselected package fonts-lyx. 529s Preparing to unpack .../045-fonts-lyx_2.4.2.1-1_all.deb ... 529s Unpacking fonts-lyx (2.4.2.1-1) ... 529s Selecting previously unselected package libblas3:amd64. 529s Preparing to unpack .../046-libblas3_3.12.0-3build2_amd64.deb ... 529s Unpacking libblas3:amd64 (3.12.0-3build2) ... 529s Selecting previously unselected package libpixman-1-0:amd64. 529s Preparing to unpack .../047-libpixman-1-0_0.44.0-3_amd64.deb ... 529s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 529s Selecting previously unselected package libxcb-render0:amd64. 529s Preparing to unpack .../048-libxcb-render0_1.17.0-2_amd64.deb ... 529s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 529s Selecting previously unselected package libxcb-shm0:amd64. 529s Preparing to unpack .../049-libxcb-shm0_1.17.0-2_amd64.deb ... 529s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 529s Selecting previously unselected package libcairo2:amd64. 529s Preparing to unpack .../050-libcairo2_1.18.2-2_amd64.deb ... 529s Unpacking libcairo2:amd64 (1.18.2-2) ... 529s Selecting previously unselected package libdeflate0:amd64. 529s Preparing to unpack .../051-libdeflate0_1.22-1_amd64.deb ... 529s Unpacking libdeflate0:amd64 (1.22-1) ... 529s Selecting previously unselected package libgfortran5:amd64. 529s Preparing to unpack .../052-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 529s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 529s Selecting previously unselected package libgraphite2-3:amd64. 529s Preparing to unpack .../053-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 529s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 529s Selecting previously unselected package libharfbuzz0b:amd64. 529s Preparing to unpack .../054-libharfbuzz0b_10.0.1-1_amd64.deb ... 529s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 529s Selecting previously unselected package libimagequant0:amd64. 529s Preparing to unpack .../055-libimagequant0_2.18.0-1build1_amd64.deb ... 529s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 530s Selecting previously unselected package libjpeg-turbo8:amd64. 530s Preparing to unpack .../056-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 530s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 530s Selecting previously unselected package libjpeg8:amd64. 530s Preparing to unpack .../057-libjpeg8_8c-2ubuntu11_amd64.deb ... 530s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 530s Selecting previously unselected package libjs-jquery. 530s Preparing to unpack .../058-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 530s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 530s Selecting previously unselected package libjs-jquery-ui. 530s Preparing to unpack .../059-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 530s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 530s Selecting previously unselected package liblapack3:amd64. 530s Preparing to unpack .../060-liblapack3_3.12.0-3build2_amd64.deb ... 530s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 530s Selecting previously unselected package liblbfgsb0:amd64. 530s Preparing to unpack .../061-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 530s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 530s Selecting previously unselected package liblcms2-2:amd64. 530s Preparing to unpack .../062-liblcms2-2_2.16-2_amd64.deb ... 530s Unpacking liblcms2-2:amd64 (2.16-2) ... 530s Selecting previously unselected package liblerc4:amd64. 530s Preparing to unpack .../063-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 530s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 530s Selecting previously unselected package libpython3.13-stdlib:amd64. 530s Preparing to unpack .../064-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 530s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 530s Selecting previously unselected package libqhull-r8.0:amd64. 530s Preparing to unpack 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libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 530s Selecting previously unselected package libwebpdemux2:amd64. 530s Preparing to unpack .../071-libwebpdemux2_1.4.0-0.1_amd64.deb ... 530s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 530s Selecting previously unselected package libwebpmux3:amd64. 530s Preparing to unpack .../072-libwebpmux3_1.4.0-0.1_amd64.deb ... 530s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 530s Selecting previously unselected package libxslt1.1:amd64. 530s Preparing to unpack .../073-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 530s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 530s Selecting previously unselected package python-matplotlib-data. 530s Preparing to unpack .../074-python-matplotlib-data_3.8.3-3_all.deb ... 530s Unpacking python-matplotlib-data (3.8.3-3) ... 530s Selecting previously unselected package python3.13. 530s Preparing to unpack .../075-python3.13_3.13.0-2_amd64.deb ... 530s Unpacking python3.13 (3.13.0-2) ... 530s Selecting previously unselected package python3-all. 530s Preparing to unpack .../076-python3-all_3.12.7-1_amd64.deb ... 530s Unpacking python3-all (3.12.7-1) ... 530s Selecting previously unselected package python3-appdirs. 530s Preparing to unpack .../077-python3-appdirs_1.4.4-4_all.deb ... 530s Unpacking python3-appdirs (1.4.4-4) ... 530s Selecting previously unselected package python3-numpy. 530s Preparing to unpack .../078-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 530s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 531s Selecting previously unselected package python3.12-tk. 531s Preparing to unpack .../079-python3.12-tk_3.12.7-3_amd64.deb ... 531s Unpacking python3.12-tk (3.12.7-3) ... 531s Selecting previously unselected package python3.13-tk. 531s Preparing to unpack .../080-python3.13-tk_3.13.0-2_amd64.deb ... 531s Unpacking python3.13-tk (3.13.0-2) ... 531s Selecting previously unselected package python3-tk:amd64. 531s Preparing to unpack .../081-python3-tk_3.12.7-1_amd64.deb ... 531s Unpacking python3-tk:amd64 (3.12.7-1) ... 531s Selecting previously unselected package python3-pil.imagetk:amd64. 531s Preparing to unpack .../082-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 531s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 531s Selecting previously unselected package libopenjp2-7:amd64. 531s Preparing to unpack .../083-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 531s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 531s Selecting previously unselected package python3-pil:amd64. 531s Preparing to unpack .../084-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 531s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 531s Selecting previously unselected package python3-cairo. 531s Preparing to unpack .../085-python3-cairo_1.26.1-2_amd64.deb ... 531s Unpacking python3-cairo (1.26.1-2) ... 531s Selecting previously unselected package python3-freetype. 531s Preparing to unpack .../086-python3-freetype_2.5.1-1_all.deb 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unpack .../092-python3-brotli_1.1.0-2build2_amd64.deb ... 531s Unpacking python3-brotli (1.1.0-2build2) ... 531s Selecting previously unselected package python3-contourpy. 531s Preparing to unpack .../093-python3-contourpy_1.3.0-2_amd64.deb ... 531s Unpacking python3-contourpy (1.3.0-2) ... 531s Selecting previously unselected package python3-cycler. 531s Preparing to unpack .../094-python3-cycler_0.12.1-1_all.deb ... 531s Unpacking python3-cycler (0.12.1-1) ... 531s Selecting previously unselected package python3-six. 531s Preparing to unpack .../095-python3-six_1.16.0-7_all.deb ... 531s Unpacking python3-six (1.16.0-7) ... 531s Selecting previously unselected package python3-dateutil. 531s Preparing to unpack .../096-python3-dateutil_2.9.0-2_all.deb ... 531s Unpacking python3-dateutil (2.9.0-2) ... 531s Selecting previously unselected package python3-decorator. 531s Preparing to unpack .../097-python3-decorator_5.1.1-5_all.deb ... 531s Unpacking python3-decorator (5.1.1-5) ... 531s 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(2.16-2) ... 534s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 534s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 534s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 534s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 534s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 534s Setting up libxcb-render0:amd64 (1.17.0-2) ... 534s Setting up fonts-lyx (2.4.2.1-1) ... 534s Setting up x11-common (1:7.7+23ubuntu3) ... 534s Setting up libdeflate0:amd64 (1.22-1) ... 534s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 534s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 534s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 534s Setting up python3-freetype (2.5.1-1) ... 534s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 534s Setting up python3-tz (2024.1-2) ... 535s Setting up unicode-data (15.1.0-1) ... 535s Setting up python3-six (1.16.0-7) ... 535s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 535s Setting up python3-decorator (5.1.1-5) ... 535s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 535s Setting up libblas3:amd64 (3.12.0-3build2) ... 535s 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 535s Setting up python3-packaging (24.1-1) ... 535s Setting up python3-brotli (1.1.0-2build2) ... 535s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 535s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ... 535s Setting up python3-cycler (0.12.1-1) ... 536s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 536s Setting up fonts-dejavu-mono (2.37-8) ... 536s Setting up python3-kiwisolver (1.4.7-2) ... 536s Setting up libmpc3:amd64 (1.3.1-1build2) ... 536s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 536s Setting up fonts-dejavu-core (2.37-8) ... 536s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 536s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 536s Setting up libwebp7:amd64 (1.4.0-0.1) ... 536s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 536s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 536s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 536s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 536s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 536s Setting up python3.13-minimal (3.13.0-2) ... 537s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 537s Setting up python3-dateutil (2.9.0-2) ... 537s Setting up sgml-base (1.31) ... 537s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 537s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 537s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 537s Setting up python3-mpmath (1.3.0-1) ... 538s Setting up libisl23:amd64 (0.27-1) ... 538s Setting up python-matplotlib-data (3.8.3-3) ... 538s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 538s Setting up python3-appdirs (1.4.4-4) ... 538s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 538s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 538s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 538s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 538s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 538s Setting up python3-sympy (1.13.3-1) ... 550s Setting up liblapack3:amd64 (3.12.0-3build2) ... 550s 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 550s Setting up python3.13 (3.13.0-2) ... 551s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 551s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 551s Setting up python3-all (3.12.7-1) ... 551s Setting up xfonts-utils (1:7.7+7) ... 551s Setting up python3-fs (2.4.16-4) ... 552s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 552s Setting up libraqm0:amd64 (0.10.1-1build1) ... 552s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 552s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 555s Setting up cpp-14 (14.2.0-8ubuntu1) ... 555s Setting up python3-lxml:amd64 (5.3.0-1) ... 556s Setting up 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gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 573s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 573s Setting up python3-cairo (1.26.1-2) ... 573s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 573s Setting up blt (2.5.3+dfsg-7build1) ... 573s Setting up python3-tk:amd64 (3.12.7-1) ... 574s Setting up gcc-14 (14.2.0-8ubuntu1) ... 574s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 574s Setting up python3-rlpycairo (0.3.0-3) ... 574s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 574s Setting up python3-reportlab (4.2.5-1) ... 575s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 575s Setting up g++-14 (14.2.0-8ubuntu1) ... 575s Setting up gcc (4:14.1.0-2ubuntu1) ... 575s Setting up g++ (4:14.1.0-2ubuntu1) ... 575s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 575s Setting up build-essential (12.10ubuntu1) ... 575s Setting up python3-fonttools (4.46.0-1build2) ... 577s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 577s Setting up python3-matplotlib (3.8.3-3) ... 580s Processing triggers for libc-bin (2.40-1ubuntu3) ... 580s Processing triggers for systemd (256.5-2ubuntu4) ... 580s Processing triggers for man-db (2.12.1-3) ... 581s Processing triggers for sgml-base (1.31) ... 581s Setting up w3c-sgml-lib (1.3-3) ... 610s Setting up python3-biopython (1.84+dfsg-4) ... 612s Setting up python3-treetime (0.11.4-1) ... 616s Reading package lists... 616s Building dependency tree... 616s Reading state information... 616s Starting pkgProblemResolver with broken count: 0 616s Starting 2 pkgProblemResolver with broken count: 0 616s Done 617s The following NEW packages will be installed: 617s autopkgtest-satdep 617s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 617s Need to get 0 B/696 B of archives. 617s After this operation, 0 B of additional disk space will be used. 617s Get:1 /tmp/autopkgtest.ryRc6R/4-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 617s Selecting previously unselected package autopkgtest-satdep. 617s (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 ... 88285 files and directories currently installed.) 617s Preparing to unpack .../4-autopkgtest-satdep.deb ... 617s Unpacking autopkgtest-satdep (0) ... 617s Setting up autopkgtest-satdep (0) ... 618s autopkgtest: WARNING: package python3-treetime:i386 is not installed though it should be 619s (Reading database ... 88285 files and directories currently installed.) 619s Removing autopkgtest-satdep (0) ... 620s autopkgtest [11:34:06]: 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 620s autopkgtest [11:34:06]: test autodep8-python3: [----------------------- 620s Testing with python3.13: 620s Traceback (most recent call last): 620s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 620s from . import multiarray 620s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 620s from . import overrides 620s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 620s from numpy.core._multiarray_umath import ( 620s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 620s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 620s 620s During handling of the above exception, another exception occurred: 620s 620s Traceback (most recent call last): 620s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 620s from numpy.__config__ import show as show_config 620s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 620s from numpy.core._multiarray_umath import ( 620s ...<3 lines>... 620s ) 620s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 620s raise ImportError(msg) 620s ImportError: 620s 620s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 620s 620s Importing the numpy C-extensions failed. This error can happen for 620s many reasons, often due to issues with your setup or how NumPy was 620s installed. 620s 620s We have compiled some common reasons and troubleshooting tips at: 620s 620s https://numpy.org/devdocs/user/troubleshooting-importerror.html 620s 620s Please note and check the following: 620s 620s * The Python version is: Python3.13 from "/usr/bin/python3.13" 620s * The NumPy version is: "1.26.4" 620s 620s and make sure that they are the versions you expect. 620s Please carefully study the documentation linked above for further help. 620s 620s Original error was: No module named 'numpy.core._multiarray_umath' 620s 620s 620s The above exception was the direct cause of the following exception: 620s 620s Traceback (most recent call last): 620s File "", line 1, in 620s import treetime; print(treetime) 620s ^^^^^^^^^^^^^^^ 620s File "/usr/lib/python3/dist-packages/treetime/__init__.py", line 38, in 620s from .treeanc import TreeAnc 620s File "/usr/lib/python3/dist-packages/treetime/treeanc.py", line 3, in 620s import numpy as np 620s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 620s raise ImportError(msg) from e 620s ImportError: Error importing numpy: you should not try to import numpy from 620s its source directory; please exit the numpy source tree, and relaunch 620s your python interpreter from there. 621s autopkgtest [11:34:07]: test autodep8-python3: -----------------------] 621s autopkgtest [11:34:07]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 621s autodep8-python3 FAIL non-zero exit status 1 622s autopkgtest [11:34:08]: @@@@@@@@@@@@@@@@@@@@ summary 622s run-unit-test PASS 622s autodep8-python3 FAIL non-zero exit status 1 631s nova [W] Skipping flock for amd64 632s Creating nova instance adt-plucky-i386-python-treetime-20241113-112345-juju-7f2275-prod-proposed-migration-environment-15-b4d3766e-ea3c-458d-b255-8244a7556046 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)... 632s nova [W] Skipping flock for amd64 632s Creating nova instance adt-plucky-i386-python-treetime-20241113-112345-juju-7f2275-prod-proposed-migration-environment-15-b4d3766e-ea3c-458d-b255-8244a7556046 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...