0s autopkgtest [11:14:36]: starting date and time: 2024-11-13 11:14:36+0000 0s autopkgtest [11:14:36]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [11:14:36]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.954h1zhd/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 augur --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-18.secgroup --name adt-plucky-i386-augur-20241113-103527-juju-7f2275-prod-proposed-migration-environment-20-648ce6c4-8021-4b82-85e2-7096745d8ca0 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 1725s autopkgtest [11:43:21]: testbed dpkg architecture: amd64 1725s autopkgtest [11:43:21]: testbed apt version: 2.9.8 1725s autopkgtest [11:43:21]: test architecture: i386 1725s autopkgtest [11:43:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1727s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 1727s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 1727s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 1727s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 1727s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 1728s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 1728s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 1728s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 1728s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 1728s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 1728s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 1728s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 1728s Fetched 2175 kB in 2s (1435 kB/s) 1728s Reading package lists... 1730s Reading package lists... 1730s Building dependency tree... 1730s Reading state information... 1730s Calculating upgrade... 1731s The following NEW packages will be installed: 1731s python3.13-gdbm 1731s The following packages will be upgraded: 1731s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 1731s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1731s Need to get 253 kB of archives. 1731s After this operation, 147 kB of additional disk space will be used. 1731s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 1731s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 1731s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 1731s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 1731s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 1731s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 1732s Fetched 253 kB in 1s (275 kB/s) 1732s (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.) 1732s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 1732s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 1732s Setting up python3-minimal (3.12.7-1) ... 1732s (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.) 1732s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 1732s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 1732s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 1732s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 1732s Selecting previously unselected package python3.13-gdbm. 1732s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 1732s Unpacking python3.13-gdbm (3.13.0-2) ... 1732s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 1732s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 1732s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 1732s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 1732s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 1732s Setting up python3.13-gdbm (3.13.0-2) ... 1732s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 1732s Setting up python3 (3.12.7-1) ... 1732s Setting up python3-gdbm:amd64 (3.12.7-1) ... 1732s Processing triggers for man-db (2.12.1-3) ... 1733s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1733s Reading package lists... 1733s Building dependency tree... 1733s Reading state information... 1734s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1734s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 1734s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1734s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1734s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1735s Reading package lists... 1735s Reading package lists... 1735s Building dependency tree... 1735s Reading state information... 1735s Calculating upgrade... 1735s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1735s Reading package lists... 1735s Building dependency tree... 1735s Reading state information... 1736s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1738s autopkgtest [11:43:34]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 1739s autopkgtest [11:43:35]: @@@@@@@@@@@@@@@@@@@@ apt-source augur 1742s Get:1 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (dsc) [2754 B] 1742s Get:2 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (tar) [6802 kB] 1742s Get:3 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (diff) [16.5 kB] 1742s gpgv: Signature made Wed May 22 16:59:51 2024 UTC 1742s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 1742s gpgv: issuer "emollier@debian.org" 1742s gpgv: Can't check signature: No public key 1742s dpkg-source: warning: cannot verify inline signature for ./augur_24.4.0-1.dsc: no acceptable signature found 1742s autopkgtest [11:43:38]: testing package augur version 24.4.0-1 1742s autopkgtest [11:43:38]: build not needed 1744s autopkgtest [11:43:40]: test run-unit-test: preparing testbed 1746s Note, using file '/tmp/autopkgtest.Na5A3H/1-autopkgtest-satdep.dsc' to get the build dependencies 1746s Reading package lists... 1746s Building dependency tree... 1746s Reading state information... 1747s Starting pkgProblemResolver with broken count: 0 1747s Starting 2 pkgProblemResolver with broken count: 0 1747s Done 1747s The following NEW packages will be installed: 1747s augur blt build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu 1747s cpp-x86-64-linux-gnu fasttree flake8 fontconfig-config fonts-dejavu-core 1747s fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-14 1747s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 1747s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libamd3 libasan8 libblas3 1747s libcairo2 libcamd3 libcc1-0 libccolamd3 libcholmod5 libcolamd3 libdeflate0 1747s libdsdp-5.8t64 libfftw3-double3 libfontconfig1 libfontenc1 libgcc-14-dev 1747s libgfortran5 libglpk40 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 1747s libharfbuzz0b libhwasan0 libimagequant0 libisl23 libitm1 libjbig0 1747s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 1747s liblcms2-2 liblerc4 liblsan0 libltdl7 libmpc3 libopenjp2-7 libpixman-1-0 1747s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libquadmath0 1747s libraqm0 libsharpyuv0 libstdc++-14-dev libsuitesparseconfig7 libtcl8.6 1747s libtiff6 libtk8.6 libtsan2 libubsan1 libumfpack6 libwebp7 libwebpdemux2 1747s libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 1747s libxss1 mafft mypy pigz python-matplotlib-data python3-all python3-appdirs 1747s python3-asttokens python3-bcbio-gff python3-biopython python3-boto3 1747s python3-botocore python3-brotli python3-cairo python3-contourpy 1747s python3-cvxopt python3-cycler python3-dateutil python3-decorator 1747s python3-dendropy python3-executing python3-flake8 python3-fonttools 1747s python3-freetype python3-freezegun python3-fs python3-importlib-metadata 1747s python3-iniconfig python3-ipdb python3-ipython python3-isodate python3-jedi 1747s python3-jmespath python3-kiwisolver python3-lxml python3-lz4 1747s python3-matplotlib python3-matplotlib-inline python3-mccabe python3-mpmath 1747s python3-mypy python3-mypy-extensions python3-networkx python3-numpy 1747s python3-packaging python3-pandas python3-pandas-lib python3-parso 1747s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 1747s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 1747s python3-pycodestyle python3-pyfaidx python3-pyfastx python3-pyflakes 1747s python3-pygtrie python3-pytest python3-pytest-mock python3-reportlab 1747s python3-rlpycairo python3-s3transfer python3-schedule python3-scipy 1747s python3-seaborn python3-six python3-stack-data python3-sympy python3-tk 1747s python3-traitlets python3-treetime python3-typeshed python3-tz 1747s python3-ufolib2 python3-unicodedata2 python3-wcwidth python3-xopen 1747s python3-zstandard python3.12-tk python3.13 python3.13-minimal python3.13-tk 1747s raxml seqmagick sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib 1747s x11-common xfonts-encodings xfonts-utils xml-core 1748s 0 upgraded, 181 newly installed, 0 to remove and 0 not upgraded. 1748s Need to get 195 MB of archives. 1748s After this operation, 850 MB of additional disk space will be used. 1748s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 1748s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 1749s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 1749s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 pigz amd64 2.8-1 [65.6 kB] 1749s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 1749s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 1749s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 1749s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 1750s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 1750s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 1750s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 1750s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 1750s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 1750s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 1750s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 1750s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 1750s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 1750s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 1750s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 1750s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 1750s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 1750s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 1750s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 1750s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 1750s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 1751s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 1751s Get:27 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 1751s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 1751s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 1751s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 1751s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 1751s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 1751s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 1751s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 1751s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 1751s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 1751s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 1751s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 1751s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 1751s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 1751s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 1751s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 1751s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 1751s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 1751s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 1751s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 1751s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 1751s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 1751s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 1751s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 1751s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 1751s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 1751s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 1751s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 1751s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 1751s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 1751s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 1751s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 1751s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bcbio-gff all 0.7.1-2 [33.9 kB] 1751s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-2 [13.4 kB] 1751s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd3 amd64 1:7.8.3+dfsg-2 [31.1 kB] 1751s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcamd3 amd64 1:7.8.3+dfsg-2 [27.6 kB] 1751s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccolamd3 amd64 1:7.8.3+dfsg-2 [27.5 kB] 1751s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-2 [19.5 kB] 1751s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcholmod5 amd64 1:7.8.3+dfsg-2 [876 kB] 1751s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdsdp-5.8t64 amd64 5.8-10.1build1 [199 kB] 1751s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu4 [839 kB] 1751s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.4.7-7build1 [40.3 kB] 1751s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglpk40 amd64 5.0-1build2 [369 kB] 1751s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgslcblas0 amd64 2.8+dfsg-5 [290 kB] 1751s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgsl28 amd64 2.8+dfsg-5 [1285 kB] 1751s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 libumfpack6 amd64 1:7.8.3+dfsg-2 [337 kB] 1751s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cvxopt amd64 1.3.0+dfsg-1build7 [279 kB] 1751s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-isodate all 0.6.1-3 [24.3 kB] 1751s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 1752s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 1752s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 1752s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 1752s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 1752s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 1752s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 1752s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 1752s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfastx amd64 2.1.0-2 [56.7 kB] 1752s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 1752s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 1752s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 1752s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 1752s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 1752s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 1752s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 1752s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 1752s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 1752s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 1752s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 1752s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 1752s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 1752s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 1752s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 1752s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 1752s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 1752s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 1753s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 1753s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 1753s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 1753s Get:105 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 1753s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 1753s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 1753s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 1753s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 1753s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 1754s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 1754s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-xopen all 1.7.0-2 [17.0 kB] 1754s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jmespath all 1.0.1-1 [21.3 kB] 1754s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-botocore all 1.34.46+repack-1ubuntu1 [6211 kB] 1754s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-s3transfer all 0.10.1-1ubuntu2 [54.3 kB] 1754s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-boto3 all 1.34.46+dfsg-1ubuntu1 [72.5 kB] 1754s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dendropy all 4.6.1-1 [278 kB] 1754s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-schedule all 1.2.2-1 [12.2 kB] 1754s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-seaborn all 0.13.2-4 [225 kB] 1754s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-zstandard amd64 0.23.0-2 [362 kB] 1754s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pygtrie all 2.2-2 [16.0 kB] 1754s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 seqmagick all 0.8.6-3 [38.6 kB] 1754s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 1754s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 1754s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 1754s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 1754s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 1754s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 1754s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pexpect all 4.9-2 [48.1 kB] 1754s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 1754s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 1754s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-asttokens all 2.4.1-2 [20.8 kB] 1754s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-executing all 2.1.0-0.1 [24.4 kB] 1754s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 1754s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 1754s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 1754s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipdb all 0.13.13-2 [15.4 kB] 1754s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 mafft amd64 7.505-1 [795 kB] 1754s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB] 1754s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 1754s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 vcftools amd64 0.1.16-3 [393 kB] 1754s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 augur all 24.4.0-1 [238 kB] 1754s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 1754s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 1754s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 1755s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 1755s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 1755s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 1755s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 1755s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 1755s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 1755s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 1755s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 1755s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 1755s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 1755s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 1755s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 1755s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 1757s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 1757s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 1757s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 1757s Get:162 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 1757s Get:163 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 1758s Get:164 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 1758s Get:165 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 1758s Get:166 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 1758s Get:167 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 1758s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mccabe all 0.7.0-1 [8678 B] 1758s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pycodestyle all 2.11.1-1 [29.9 kB] 1758s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyflakes all 3.2.0-1 [52.8 kB] 1758s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-flake8 all 7.1.1-1 [43.9 kB] 1758s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 flake8 all 7.1.1-1 [6442 B] 1758s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mypy-extensions all 1.0.0-1 [6148 B] 1758s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psutil amd64 5.9.8-2build2 [195 kB] 1758s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mypy amd64 1.13.0-1 [8679 kB] 1759s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 mypy all 1.13.0-1 [24.9 kB] 1759s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freezegun all 1.5.1-1.1 [15.9 kB] 1759s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 1759s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 1759s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 1759s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 1759s Fetched 195 MB in 11s (17.0 MB/s) 1760s Selecting previously unselected package libpython3.13-minimal:amd64. 1760s (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.) 1760s Preparing to unpack .../000-libpython3.13-minimal_3.13.0-2_amd64.deb ... 1760s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 1760s Selecting previously unselected package python3.13-minimal. 1760s Preparing to unpack .../001-python3.13-minimal_3.13.0-2_amd64.deb ... 1760s Unpacking python3.13-minimal (3.13.0-2) ... 1760s Selecting previously unselected package sgml-base. 1760s Preparing to unpack .../002-sgml-base_1.31_all.deb ... 1760s Unpacking sgml-base (1.31) ... 1760s Selecting previously unselected package pigz. 1760s Preparing to unpack .../003-pigz_2.8-1_amd64.deb ... 1760s Unpacking pigz (2.8-1) ... 1760s Selecting previously unselected package libblas3:amd64. 1760s Preparing to unpack .../004-libblas3_3.12.0-3build2_amd64.deb ... 1760s Unpacking libblas3:amd64 (3.12.0-3build2) ... 1760s Selecting previously unselected package libgfortran5:amd64. 1760s Preparing to unpack .../005-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 1760s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 1760s Selecting previously unselected package liblapack3:amd64. 1760s Preparing to unpack .../006-liblapack3_3.12.0-3build2_amd64.deb ... 1760s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 1760s Selecting previously unselected package python3-numpy. 1760s Preparing to unpack .../007-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 1760s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 1760s Selecting previously unselected package libtcl8.6:amd64. 1760s Preparing to unpack .../008-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 1760s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 1760s Selecting previously unselected package fonts-dejavu-mono. 1760s Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ... 1760s Unpacking fonts-dejavu-mono (2.37-8) ... 1760s Selecting previously unselected package fonts-dejavu-core. 1760s Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ... 1760s Unpacking fonts-dejavu-core (2.37-8) ... 1760s Selecting previously unselected package libfontenc1:amd64. 1760s Preparing to unpack .../011-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 1760s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 1760s Selecting previously unselected package x11-common. 1760s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ... 1760s Unpacking x11-common (1:7.7+23ubuntu3) ... 1760s Selecting previously unselected package xfonts-encodings. 1760s Preparing to unpack .../013-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 1760s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 1760s Selecting previously unselected package xfonts-utils. 1760s Preparing to unpack .../014-xfonts-utils_1%3a7.7+7_amd64.deb ... 1760s Unpacking xfonts-utils (1:7.7+7) ... 1760s Selecting previously unselected package fonts-urw-base35. 1760s Preparing to unpack .../015-fonts-urw-base35_20200910-8_all.deb ... 1760s Unpacking fonts-urw-base35 (20200910-8) ... 1761s Selecting previously unselected package fontconfig-config. 1761s Preparing to unpack .../016-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 1761s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 1761s Selecting previously unselected package libfontconfig1:amd64. 1761s Preparing to unpack .../017-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 1761s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 1761s Selecting previously unselected package libxrender1:amd64. 1761s Preparing to unpack .../018-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 1761s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 1761s Selecting previously unselected package libxft2:amd64. 1761s Preparing to unpack .../019-libxft2_2.3.6-1build1_amd64.deb ... 1761s Unpacking libxft2:amd64 (2.3.6-1build1) ... 1761s Selecting previously unselected package libxss1:amd64. 1761s Preparing to unpack .../020-libxss1_1%3a1.2.3-1build3_amd64.deb ... 1761s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 1761s Selecting previously unselected package libtk8.6:amd64. 1761s Preparing to unpack .../021-libtk8.6_8.6.15-1_amd64.deb ... 1761s Unpacking libtk8.6:amd64 (8.6.15-1) ... 1761s Selecting previously unselected package python3.12-tk. 1761s Preparing to unpack .../022-python3.12-tk_3.12.7-3_amd64.deb ... 1761s Unpacking python3.12-tk (3.12.7-3) ... 1761s Selecting previously unselected package python3.13-tk. 1761s Preparing to unpack .../023-python3.13-tk_3.13.0-2_amd64.deb ... 1761s Unpacking python3.13-tk (3.13.0-2) ... 1761s Selecting previously unselected package tk8.6-blt2.5. 1761s Preparing to unpack .../024-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 1761s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 1761s Selecting previously unselected package blt. 1761s Preparing to unpack .../025-blt_2.5.3+dfsg-7build1_amd64.deb ... 1761s Unpacking blt (2.5.3+dfsg-7build1) ... 1761s Selecting previously unselected package python3-tk:amd64. 1761s Preparing to unpack .../026-python3-tk_3.12.7-1_amd64.deb ... 1761s Unpacking python3-tk:amd64 (3.12.7-1) ... 1761s Selecting previously unselected package python3-pil.imagetk:amd64. 1761s Preparing to unpack .../027-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 1761s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 1761s Selecting previously unselected package libgomp1:amd64. 1761s Preparing to unpack .../028-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 1761s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 1761s Selecting previously unselected package libimagequant0:amd64. 1761s Preparing to unpack .../029-libimagequant0_2.18.0-1build1_amd64.deb ... 1761s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 1761s Selecting previously unselected package libjpeg-turbo8:amd64. 1761s Preparing to unpack .../030-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 1761s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 1761s Selecting previously unselected package libjpeg8:amd64. 1761s Preparing to unpack .../031-libjpeg8_8c-2ubuntu11_amd64.deb ... 1761s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 1761s Selecting previously unselected package liblcms2-2:amd64. 1761s Preparing to unpack .../032-liblcms2-2_2.16-2_amd64.deb ... 1761s Unpacking liblcms2-2:amd64 (2.16-2) ... 1761s Selecting previously unselected package libopenjp2-7:amd64. 1761s Preparing to unpack .../033-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 1761s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 1761s Selecting previously unselected package libgraphite2-3:amd64. 1761s Preparing to unpack .../034-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 1761s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 1761s Selecting previously unselected package libharfbuzz0b:amd64. 1761s Preparing to unpack .../035-libharfbuzz0b_10.0.1-1_amd64.deb ... 1761s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 1761s Selecting previously unselected package libraqm0:amd64. 1761s Preparing to unpack .../036-libraqm0_0.10.1-1build1_amd64.deb ... 1761s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 1761s Selecting previously unselected package libdeflate0:amd64. 1761s Preparing to unpack .../037-libdeflate0_1.22-1_amd64.deb ... 1761s Unpacking libdeflate0:amd64 (1.22-1) ... 1761s Selecting previously unselected package libjbig0:amd64. 1761s Preparing to unpack .../038-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 1761s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 1761s Selecting previously unselected package liblerc4:amd64. 1761s Preparing to unpack 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1761s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 1761s Selecting previously unselected package python3-pil:amd64. 1761s Preparing to unpack .../045-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 1761s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 1761s Selecting previously unselected package libpixman-1-0:amd64. 1761s Preparing to unpack .../046-libpixman-1-0_0.44.0-3_amd64.deb ... 1761s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 1761s Selecting previously unselected package libxcb-render0:amd64. 1761s Preparing to unpack .../047-libxcb-render0_1.17.0-2_amd64.deb ... 1761s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 1761s Selecting previously unselected package libxcb-shm0:amd64. 1761s Preparing to unpack .../048-libxcb-shm0_1.17.0-2_amd64.deb ... 1761s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 1761s Selecting previously unselected package libcairo2:amd64. 1761s Preparing to unpack .../049-libcairo2_1.18.2-2_amd64.deb ... 1761s Unpacking libcairo2:amd64 (1.18.2-2) ... 1762s Selecting previously unselected package python3-cairo. 1762s Preparing to unpack .../050-python3-cairo_1.26.1-2_amd64.deb ... 1762s Unpacking python3-cairo (1.26.1-2) ... 1762s Selecting previously unselected package python3-freetype. 1762s Preparing to unpack .../051-python3-freetype_2.5.1-1_all.deb ... 1762s Unpacking python3-freetype (2.5.1-1) ... 1762s Selecting previously unselected package python3-rlpycairo. 1762s Preparing to unpack .../052-python3-rlpycairo_0.3.0-3_all.deb ... 1762s Unpacking python3-rlpycairo (0.3.0-3) ... 1762s Selecting previously unselected package python3-reportlab. 1762s Preparing to unpack .../053-python3-reportlab_4.2.5-1_all.deb ... 1762s Unpacking python3-reportlab (4.2.5-1) ... 1762s Selecting previously unselected package xml-core. 1762s Preparing to unpack .../054-xml-core_0.19_all.deb ... 1762s Unpacking xml-core (0.19) ... 1762s Selecting previously unselected package w3c-sgml-lib. 1762s Preparing to unpack .../055-w3c-sgml-lib_1.3-3_all.deb ... 1762s Unpacking w3c-sgml-lib (1.3-3) ... 1762s Selecting previously unselected package python3-biopython. 1762s Preparing to unpack .../056-python3-biopython_1.84+dfsg-4_amd64.deb ... 1762s Unpacking python3-biopython (1.84+dfsg-4) ... 1762s Selecting previously unselected package python3-six. 1762s Preparing to unpack .../057-python3-six_1.16.0-7_all.deb ... 1762s Unpacking python3-six (1.16.0-7) ... 1762s Selecting previously unselected package python3-bcbio-gff. 1762s Preparing to unpack .../058-python3-bcbio-gff_0.7.1-2_all.deb ... 1762s Unpacking python3-bcbio-gff (0.7.1-2) ... 1762s Selecting previously unselected package libsuitesparseconfig7:amd64. 1762s Preparing to unpack .../059-libsuitesparseconfig7_1%3a7.8.3+dfsg-2_amd64.deb ... 1762s Unpacking libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-2) ... 1762s Selecting previously unselected package libamd3:amd64. 1762s Preparing to unpack .../060-libamd3_1%3a7.8.3+dfsg-2_amd64.deb ... 1762s Unpacking libamd3:amd64 (1:7.8.3+dfsg-2) 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unselected package libfftw3-double3:amd64. 1762s Preparing to unpack .../066-libfftw3-double3_3.3.10-1ubuntu4_amd64.deb ... 1762s Unpacking libfftw3-double3:amd64 (3.3.10-1ubuntu4) ... 1762s Selecting previously unselected package libltdl7:amd64. 1762s Preparing to unpack .../067-libltdl7_2.4.7-7build1_amd64.deb ... 1762s Unpacking libltdl7:amd64 (2.4.7-7build1) ... 1762s Selecting previously unselected package libglpk40:amd64. 1762s Preparing to unpack .../068-libglpk40_5.0-1build2_amd64.deb ... 1762s Unpacking libglpk40:amd64 (5.0-1build2) ... 1762s Selecting previously unselected package libgslcblas0:amd64. 1762s Preparing to unpack .../069-libgslcblas0_2.8+dfsg-5_amd64.deb ... 1762s Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... 1762s Selecting previously unselected package libgsl28:amd64. 1762s Preparing to unpack .../070-libgsl28_2.8+dfsg-5_amd64.deb ... 1762s Unpacking libgsl28:amd64 (2.8+dfsg-5) ... 1762s Selecting previously unselected package libumfpack6:amd64. 1762s Preparing to unpack .../071-libumfpack6_1%3a7.8.3+dfsg-2_amd64.deb ... 1762s Unpacking libumfpack6:amd64 (1:7.8.3+dfsg-2) ... 1762s Selecting previously unselected package python3-cvxopt. 1762s Preparing to unpack .../072-python3-cvxopt_1.3.0+dfsg-1build7_amd64.deb ... 1762s Unpacking python3-cvxopt (1.3.0+dfsg-1build7) ... 1762s Selecting previously unselected package python3-isodate. 1762s Preparing to unpack .../073-python3-isodate_0.6.1-3_all.deb ... 1762s Unpacking python3-isodate (0.6.1-3) ... 1762s Selecting previously unselected package python3-networkx. 1762s Preparing to unpack .../074-python3-networkx_3.2.1-4ubuntu1_all.deb ... 1762s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 1763s Selecting previously unselected package python3-packaging. 1763s Preparing to unpack .../075-python3-packaging_24.1-1_all.deb ... 1763s Unpacking python3-packaging (24.1-1) ... 1763s Selecting previously unselected package python3-dateutil. 1763s Preparing to unpack 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Selecting previously unselected package libjs-jquery-ui. 1764s Preparing to unpack .../087-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 1764s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 1764s Selecting previously unselected package fonts-lyx. 1764s Preparing to unpack .../088-fonts-lyx_2.4.2.1-1_all.deb ... 1764s Unpacking fonts-lyx (2.4.2.1-1) ... 1764s Selecting previously unselected package python-matplotlib-data. 1764s Preparing to unpack .../089-python-matplotlib-data_3.8.3-3_all.deb ... 1764s Unpacking python-matplotlib-data (3.8.3-3) ... 1764s Selecting previously unselected package python3-contourpy. 1764s Preparing to unpack .../090-python3-contourpy_1.3.0-2_amd64.deb ... 1764s Unpacking python3-contourpy (1.3.0-2) ... 1764s Selecting previously unselected package python3-cycler. 1764s Preparing to unpack .../091-python3-cycler_0.12.1-1_all.deb ... 1764s Unpacking python3-cycler (0.12.1-1) ... 1764s Selecting previously unselected package python3-brotli. 1764s Preparing to unpack .../092-python3-brotli_1.1.0-2build2_amd64.deb ... 1764s Unpacking python3-brotli (1.1.0-2build2) ... 1764s Selecting previously unselected package python3-ufolib2. 1764s Preparing to unpack .../093-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 1764s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 1764s Selecting previously unselected package python3-mpmath. 1764s Preparing to unpack .../094-python3-mpmath_1.3.0-1_all.deb ... 1765s Unpacking python3-mpmath (1.3.0-1) ... 1765s Selecting previously unselected package python3-sympy. 1765s Preparing to unpack .../095-python3-sympy_1.13.3-1_all.deb ... 1765s Unpacking python3-sympy (1.13.3-1) ... 1765s Selecting previously unselected package python3-appdirs. 1765s Preparing to unpack .../096-python3-appdirs_1.4.4-4_all.deb ... 1765s Unpacking python3-appdirs (1.4.4-4) ... 1765s Selecting previously unselected package python3-fs. 1765s Preparing to unpack .../097-python3-fs_2.4.16-4_all.deb ... 1765s Unpacking python3-fs (2.4.16-4) ... 1765s Selecting previously unselected package libxslt1.1:amd64. 1765s Preparing to unpack .../098-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 1765s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 1765s Selecting previously unselected package python3-lxml:amd64. 1765s Preparing to unpack .../099-python3-lxml_5.3.0-1_amd64.deb ... 1765s Unpacking python3-lxml:amd64 (5.3.0-1) ... 1765s Selecting previously unselected package python3-lz4. 1765s Preparing to unpack .../100-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 1765s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 1765s Selecting previously unselected package python3-unicodedata2. 1765s Preparing to unpack .../101-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 1765s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 1765s Selecting previously unselected package libpython3.13-stdlib:amd64. 1765s Preparing to unpack .../102-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 1765s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) 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.../108-libqhull-r8.0_2020.2-6build1_amd64.deb ... 1766s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 1766s Selecting previously unselected package python3-matplotlib. 1766s Preparing to unpack .../109-python3-matplotlib_3.8.3-3_amd64.deb ... 1766s Unpacking python3-matplotlib (3.8.3-3) ... 1766s Selecting previously unselected package python3-treetime. 1766s Preparing to unpack .../110-python3-treetime_0.11.4-1_all.deb ... 1766s Unpacking python3-treetime (0.11.4-1) ... 1766s Selecting previously unselected package python3-xopen. 1766s Preparing to unpack .../111-python3-xopen_1.7.0-2_all.deb ... 1766s Unpacking python3-xopen (1.7.0-2) ... 1766s Selecting previously unselected package python3-jmespath. 1766s Preparing to unpack .../112-python3-jmespath_1.0.1-1_all.deb ... 1766s Unpacking python3-jmespath (1.0.1-1) ... 1766s Selecting previously unselected package python3-botocore. 1766s Preparing to unpack .../113-python3-botocore_1.34.46+repack-1ubuntu1_all.deb ... 1766s Unpacking python3-botocore (1.34.46+repack-1ubuntu1) ... 1766s Selecting previously unselected package python3-s3transfer. 1766s Preparing to unpack .../114-python3-s3transfer_0.10.1-1ubuntu2_all.deb ... 1766s Unpacking python3-s3transfer (0.10.1-1ubuntu2) ... 1767s Selecting previously unselected package python3-boto3. 1767s Preparing to unpack .../115-python3-boto3_1.34.46+dfsg-1ubuntu1_all.deb ... 1767s Unpacking python3-boto3 (1.34.46+dfsg-1ubuntu1) ... 1767s Selecting previously unselected package python3-dendropy. 1767s Preparing to unpack .../116-python3-dendropy_4.6.1-1_all.deb ... 1767s Unpacking python3-dendropy (4.6.1-1) ... 1767s Selecting previously unselected package python3-schedule. 1767s Preparing to unpack .../117-python3-schedule_1.2.2-1_all.deb ... 1767s Unpacking python3-schedule (1.2.2-1) ... 1767s Selecting previously unselected package python3-seaborn. 1767s Preparing to unpack .../118-python3-seaborn_0.13.2-4_all.deb ... 1767s Unpacking python3-seaborn 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.../129-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 1768s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 1768s Selecting previously unselected package python3-prompt-toolkit. 1768s Preparing to unpack .../130-python3-prompt-toolkit_3.0.48-1_all.deb ... 1768s Unpacking python3-prompt-toolkit (3.0.48-1) ... 1768s Selecting previously unselected package python3-asttokens. 1768s Preparing to unpack .../131-python3-asttokens_2.4.1-2_all.deb ... 1768s Unpacking python3-asttokens (2.4.1-2) ... 1768s Selecting previously unselected package python3-executing. 1768s Preparing to unpack .../132-python3-executing_2.1.0-0.1_all.deb ... 1768s Unpacking python3-executing (2.1.0-0.1) ... 1768s Selecting previously unselected package python3-pure-eval. 1768s Preparing to unpack .../133-python3-pure-eval_0.2.3-1_all.deb ... 1768s Unpacking python3-pure-eval (0.2.3-1) ... 1768s Selecting previously unselected package python3-stack-data. 1768s Preparing to unpack .../134-python3-stack-data_0.6.3-1_all.deb 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unselected package cpp-x86-64-linux-gnu. 1768s Preparing to unpack .../146-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 1768s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 1769s Selecting previously unselected package cpp. 1769s Preparing to unpack .../147-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 1769s Unpacking cpp (4:14.1.0-2ubuntu1) ... 1769s Selecting previously unselected package libcc1-0:amd64. 1769s Preparing to unpack .../148-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 1769s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 1769s Selecting previously unselected package libitm1:amd64. 1769s Preparing to unpack .../149-libitm1_14.2.0-8ubuntu1_amd64.deb ... 1769s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 1769s Selecting previously unselected package libasan8:amd64. 1769s Preparing to unpack .../150-libasan8_14.2.0-8ubuntu1_amd64.deb ... 1769s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 1769s Selecting previously unselected package liblsan0:amd64. 1769s Preparing to unpack .../151-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 1769s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 1769s Selecting previously unselected package libtsan2:amd64. 1769s Preparing to unpack .../152-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 1769s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 1769s Selecting previously unselected package libubsan1:amd64. 1769s Preparing to unpack .../153-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 1769s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 1769s Selecting previously unselected package libhwasan0:amd64. 1769s Preparing to unpack .../154-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 1769s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 1769s Selecting previously unselected package libquadmath0:amd64. 1769s Preparing to unpack .../155-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 1769s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 1769s Selecting previously unselected package libgcc-14-dev:amd64. 1769s Preparing to unpack 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.../166-build-essential_12.10ubuntu1_amd64.deb ... 1770s Unpacking build-essential (12.10ubuntu1) ... 1770s Selecting previously unselected package python3-mccabe. 1770s Preparing to unpack .../167-python3-mccabe_0.7.0-1_all.deb ... 1770s Unpacking python3-mccabe (0.7.0-1) ... 1770s Selecting previously unselected package python3-pycodestyle. 1770s Preparing to unpack .../168-python3-pycodestyle_2.11.1-1_all.deb ... 1770s Unpacking python3-pycodestyle (2.11.1-1) ... 1770s Selecting previously unselected package python3-pyflakes. 1770s Preparing to unpack .../169-python3-pyflakes_3.2.0-1_all.deb ... 1770s Unpacking python3-pyflakes (3.2.0-1) ... 1770s Selecting previously unselected package python3-flake8. 1770s Preparing to unpack .../170-python3-flake8_7.1.1-1_all.deb ... 1770s Unpacking python3-flake8 (7.1.1-1) ... 1770s Selecting previously unselected package flake8. 1770s Preparing to unpack .../171-flake8_7.1.1-1_all.deb ... 1770s Unpacking flake8 (7.1.1-1) ... 1770s Selecting previously unselected package python3-mypy-extensions. 1770s Preparing to unpack .../172-python3-mypy-extensions_1.0.0-1_all.deb ... 1770s Unpacking python3-mypy-extensions (1.0.0-1) ... 1770s Selecting previously unselected package python3-psutil. 1770s Preparing to unpack .../173-python3-psutil_5.9.8-2build2_amd64.deb ... 1770s Unpacking python3-psutil (5.9.8-2build2) ... 1770s Selecting previously unselected package python3-mypy. 1770s Preparing to unpack .../174-python3-mypy_1.13.0-1_amd64.deb ... 1770s Unpacking python3-mypy (1.13.0-1) ... 1771s Selecting previously unselected package mypy. 1771s Preparing to unpack .../175-mypy_1.13.0-1_all.deb ... 1771s Unpacking mypy (1.13.0-1) ... 1771s Selecting previously unselected package python3-freezegun. 1771s Preparing to unpack .../176-python3-freezegun_1.5.1-1.1_all.deb ... 1771s Unpacking python3-freezegun (1.5.1-1.1) ... 1771s Selecting previously unselected package python3-iniconfig. 1771s Preparing to unpack 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Setting up python3-pure-eval (0.2.3-1) ... 1771s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 1771s Setting up python3-importlib-metadata (8.5.0-1) ... 1771s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 1771s Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... 1771s Setting up python3-parso (0.8.3-1) ... 1772s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 1772s Setting up libxcb-render0:amd64 (1.17.0-2) ... 1772s Setting up mafft (7.505-1) ... 1772s Setting up python3-asttokens (2.4.1-2) ... 1772s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 1772s Setting up fonts-lyx (2.4.2.1-1) ... 1772s Setting up python3-mypy-extensions (1.0.0-1) ... 1772s Setting up python3-pyflakes (3.2.0-1) ... 1772s Setting up x11-common (1:7.7+23ubuntu3) ... 1773s Setting up libdeflate0:amd64 (1.22-1) ... 1773s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 1773s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 1773s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 1773s Setting up python3-freetype (2.5.1-1) ... 1773s Setting up python3-networkx (3.2.1-4ubuntu1) ... 1775s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 1775s Setting up python3-psutil (5.9.8-2build2) ... 1775s Setting up python3-tz (2024.1-2) ... 1776s Setting up unicode-data (15.1.0-1) ... 1776s Setting up python3-six (1.16.0-7) ... 1776s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 1776s Setting up python3-isodate (0.6.1-3) ... 1776s Setting up python3-decorator (5.1.1-5) ... 1776s Setting up python3-pycodestyle (2.11.1-1) ... 1776s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 1776s Setting up python3-pygtrie (2.2-2) ... 1777s Setting up libblas3:amd64 (3.12.0-3build2) ... 1777s 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 1777s Setting up python3-zstandard (0.23.0-2) ... 1777s Setting up python3-packaging (24.1-1) ... 1777s Setting up python3-wcwidth 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up python3-pluggy (1.5.0-1) ... 1780s Setting up libwebp7:amd64 (1.4.0-0.1) ... 1780s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 1780s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 1780s Setting up pigz (2.8-1) ... 1780s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 1780s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 1780s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 1780s Setting up libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-2) ... 1780s Setting up mypy (1.13.0-1) ... 1780s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 1780s Setting up python3.13-minimal (3.13.0-2) ... 1781s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 1781s Setting up python3-dateutil (2.9.0-2) ... 1781s Setting up fasttree (2.1.11-2) ... 1781s Setting up python3-mccabe (0.7.0-1) ... 1781s Setting up sgml-base (1.31) ... 1781s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 1781s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 1781s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1782s Setting up python3-mpmath (1.3.0-1) ... 1782s Setting up libisl23:amd64 (0.27-1) ... 1782s Setting up libgsl28:amd64 (2.8+dfsg-5) ... 1782s Setting up python-matplotlib-data (3.8.3-3) ... 1782s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 1782s Setting up python3-dendropy (4.6.1-1) ... 1783s Setting up python3-appdirs (1.4.4-4) ... 1783s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 1783s Setting up python3-stack-data (0.6.3-1) ... 1783s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 1783s Setting up python3-freezegun (1.5.1-1.1) ... 1783s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 1783s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 1783s Setting up raxml (8.2.13+dfsg-1) ... 1783s Setting up python3-ptyprocess (0.7.0-6) ... 1783s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 1783s Setting up python3-prompt-toolkit (3.0.48-1) ... 1784s Setting up python3-pyfaidx (0.8.1.3-1) ... 1784s Setting up python3-sympy (1.13.3-1) ... 1794s Setting up liblapack3:amd64 (3.12.0-3build2) ... 1794s 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 1794s Setting up libamd3:amd64 (1:7.8.3+dfsg-2) ... 1794s Setting up python3-jedi (0.19.1+ds1-1) ... 1794s Setting up libcolamd3:amd64 (1:7.8.3+dfsg-2) ... 1794s Setting up python3.13 (3.13.0-2) ... 1795s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 1795s Setting up python3-pytest (8.3.3-1) ... 1795s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 1795s Setting up python3-pyfastx (2.1.0-2) ... 1795s Setting up python3-all (3.12.7-1) ... 1795s Setting up xfonts-utils (1:7.7+7) ... 1795s Setting up libcamd3:amd64 (1:7.8.3+dfsg-2) ... 1795s Setting up python3-matplotlib-inline (0.1.6-2) ... 1796s Setting up python3-flake8 (7.1.1-1) ... 1796s Setting up python3-fs (2.4.16-4) ... 1796s Setting up python3-xopen (1.7.0-2) ... 1796s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 1796s Setting up libglpk40:amd64 (5.0-1build2) ... 1796s Setting up python3-pexpect (4.9-2) ... 1796s Setting up libraqm0:amd64 (0.10.1-1build1) ... 1796s Setting up python3-botocore (1.34.46+repack-1ubuntu1) ... 1797s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 1797s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 1800s Setting up cpp-14 (14.2.0-8ubuntu1) ... 1800s Setting up libccolamd3:amd64 (1:7.8.3+dfsg-2) ... 1800s Setting up python3-pytest-mock (3.14.0-2) ... 1800s Setting up python3-lxml:amd64 (5.3.0-1) ... 1800s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 1800s Setting up xml-core (0.19) ... 1800s Setting up libdsdp-5.8t64 (5.8-10.1build1) ... 1800s Setting up python3-contourpy (1.3.0-2) ... 1800s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 1800s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 1800s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 1800s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 1800s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 1800s Setting up libcholmod5:amd64 (1:7.8.3+dfsg-2) ... 1800s Setting up libxft2:amd64 (2.3.6-1build1) ... 1801s Setting up python3-scipy (1.13.1-5) ... 1805s Setting up libtk8.6:amd64 (8.6.15-1) ... 1805s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 1805s Setting up python3-s3transfer (0.10.1-1ubuntu2) ... 1805s Setting up python3.12-tk (3.12.7-3) ... 1805s Setting up flake8 (7.1.1-1) ... 1805s Setting up fonts-urw-base35 (20200910-8) ... 1806s Setting up libcairo2:amd64 (1.18.2-2) ... 1806s Setting up python3.13-tk (3.13.0-2) ... 1806s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 1806s Setting up python3-pandas (2.2.3+dfsg-5) ... 1813s Setting up python3-ipython (8.20.0-1ubuntu1) ... 1814s Setting up python3-boto3 (1.34.46+dfsg-1ubuntu1) ... 1814s Setting up libumfpack6:amd64 (1:7.8.3+dfsg-2) ... 1814s Setting up cpp (4:14.1.0-2ubuntu1) ... 1814s Setting up python3-ipdb (0.13.13-2) ... 1814s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 1815s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 1815s Setting up python3-cairo (1.26.1-2) ... 1815s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 1815s Setting up python3-cvxopt (1.3.0+dfsg-1build7) ... 1815s Setting up blt (2.5.3+dfsg-7build1) ... 1815s Setting up python3-tk:amd64 (3.12.7-1) ... 1815s Setting up gcc-14 (14.2.0-8ubuntu1) ... 1815s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 1815s Setting up python3-rlpycairo (0.3.0-3) ... 1815s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 1815s Setting up python3-reportlab (4.2.5-1) ... 1816s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 1816s Setting up g++-14 (14.2.0-8ubuntu1) ... 1816s Setting up gcc (4:14.1.0-2ubuntu1) ... 1816s Setting up g++ (4:14.1.0-2ubuntu1) ... 1816s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1816s Setting up build-essential (12.10ubuntu1) ... 1816s Setting up python3-fonttools (4.46.0-1build2) ... 1818s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 1818s Setting up python3-matplotlib (3.8.3-3) ... 1820s Setting up python3-seaborn (0.13.2-4) ... 1820s Processing triggers for systemd (256.5-2ubuntu4) ... 1820s Processing triggers for man-db (2.12.1-3) ... 1822s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1822s Processing triggers for sgml-base (1.31) ... 1822s Setting up w3c-sgml-lib (1.3-3) ... 1844s Setting up python3-biopython (1.84+dfsg-4) ... 1845s Setting up python3-treetime (0.11.4-1) ... 1846s Setting up seqmagick (0.8.6-3) ... 1846s Setting up python3-bcbio-gff (0.7.1-2) ... 1846s Setting up augur (24.4.0-1) ... 1852s Reading package lists... 1852s Building dependency tree... 1852s Reading state information... 1852s Starting pkgProblemResolver with broken count: 0 1852s Starting 2 pkgProblemResolver with broken count: 0 1852s Done 1852s The following NEW packages will be installed: 1852s autopkgtest-satdep 1852s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1852s Need to get 0 B/696 B of archives. 1852s After this operation, 0 B of additional disk space will be used. 1852s Get:1 /tmp/autopkgtest.Na5A3H/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 1852s Selecting previously unselected package autopkgtest-satdep. 1853s (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 ... 104282 files and directories currently installed.) 1853s Preparing to unpack .../2-autopkgtest-satdep.deb ... 1853s Unpacking autopkgtest-satdep (0) ... 1853s Setting up autopkgtest-satdep (0) ... 1854s (Reading database ... 104282 files and directories currently installed.) 1854s Removing autopkgtest-satdep (0) ... 1855s autopkgtest [11:45:31]: test run-unit-test: [----------------------- 1855s ============================= test session starts ============================== 1855s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 1855s cachedir: .pytest_cache 1855s rootdir: /tmp/autopkgtest.Na5A3H/build.ICA/src 1855s plugins: mock-3.14.0, typeguard-4.4.1 1857s collecting ... collected 2 items / 26 errors 1857s 1857s ==================================== ERRORS ==================================== 1857s _____________ ERROR collecting tests/dates/test_ambiguous_date.py ______________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/dates/test_ambiguous_date.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/dates/test_ambiguous_date.py:3: in 1857s from augur.dates import ambiguous_date 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s __________________ ERROR collecting tests/dates/test_dates.py __________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/dates/test_dates.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/dates/test_dates.py:4: in 1857s from augur import dates 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s _____________ ERROR collecting tests/filter/test_relative_dates.py _____________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/filter/test_relative_dates.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/filter/test_relative_dates.py:12: in 1857s from augur.filter import register_arguments 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s _______________ ERROR collecting tests/filter/test_subsample.py ________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/filter/test_subsample.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/filter/test_subsample.py:2: in 1857s import pandas as pd 1857s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 1857s raise ImportError( 1857s E ImportError: Unable to import required dependencies: 1857s E numpy: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s ____________________ ERROR collecting tests/io/test_file.py ____________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/io/test_file.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/io/test_file.py:2: in 1857s import augur.io.file 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s __________________ ERROR collecting tests/io/test_metadata.py __________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/io/test_metadata.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/io/test_metadata.py:6: in 1857s from augur.errors import AugurError 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s _________________ ERROR collecting tests/io/test_sequences.py __________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/io/test_sequences.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/io/test_sequences.py:2: in 1857s from Bio import SeqIO 1857s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 1857s from Bio.SeqIO import TwoBitIO 1857s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 1857s raise MissingPythonDependencyError( 1857s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1857s ____________ ERROR collecting tests/io/test_shell_command_runner.py ____________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/io/test_shell_command_runner.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/io/test_shell_command_runner.py:5: in 1857s from augur.io.shell_command_runner import ShellCommandRunner 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s __________________ ERROR collecting tests/io/test_strains.py ___________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/io/test_strains.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/io/test_strains.py:3: in 1857s from augur.io.strains import read_strains 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s ____________________ ERROR collecting tests/io/test_vcf.py _____________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/io/test_vcf.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/io/test_vcf.py:2: in 1857s import augur.io.vcf 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s _____________________ ERROR collecting tests/test_align.py _____________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_align.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_align.py:10: in 1857s from Bio import SeqIO 1857s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 1857s from Bio.SeqIO import TwoBitIO 1857s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 1857s raise MissingPythonDependencyError( 1857s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1857s ___________________ ERROR collecting tests/test_ancestral.py ___________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_ancestral.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_ancestral.py:1: in 1857s from augur.ancestral import run_ancestral 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s ____________________ ERROR collecting tests/test_clades.py _____________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_clades.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_clades.py:4: in 1857s from augur.clades import read_in_clade_definitions 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s __________________ ERROR collecting tests/test_frequencies.py __________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_frequencies.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_frequencies.py:6: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s _____________________ ERROR collecting tests/test_mask.py ______________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_mask.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_mask.py:11: in 1857s from Bio import SeqIO 1857s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 1857s from Bio.SeqIO import TwoBitIO 1857s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 1857s raise MissingPythonDependencyError( 1857s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1857s _____________________ ERROR collecting tests/test_parse.py _____________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_parse.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_parse.py:1: in 1857s import Bio.SeqIO 1857s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 1857s from Bio.SeqIO import TwoBitIO 1857s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 1857s raise MissingPythonDependencyError( 1857s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 1857s ____________________ ERROR collecting tests/test_schemas.py ____________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_schemas.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_schemas.py:2: in 1857s import jsonschema.validators 1857s /usr/lib/python3/dist-packages/jsonschema/__init__.py:13: in 1857s from jsonschema._format import FormatChecker 1857s /usr/lib/python3/dist-packages/jsonschema/_format.py:11: in 1857s from jsonschema.exceptions import FormatError 1857s /usr/lib/python3/dist-packages/jsonschema/exceptions.py:15: in 1857s from referencing.exceptions import Unresolvable as _Unresolvable 1857s /usr/lib/python3/dist-packages/referencing/__init__.py:5: in 1857s from referencing._core import Anchor, Registry, Resource, Specification 1857s /usr/lib/python3/dist-packages/referencing/_core.py:9: in 1857s from rpds import HashTrieMap, HashTrieSet, List 1857s /usr/lib/python3/dist-packages/rpds/__init__.py:1: in 1857s from .rpds import * 1857s E ModuleNotFoundError: No module named 'rpds.rpds' 1857s _________________ ERROR collecting tests/test_titer_models.py __________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_titer_models.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_titer_models.py:2: in 1857s from augur.titer_model import TiterCollection 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s ___________________ ERROR collecting tests/test_translate.py ___________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_translate.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_translate.py:13: in 1857s from augur import translate 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s _____________________ ERROR collecting tests/test_utils.py _____________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_utils.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_utils.py:2: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s ___________________ ERROR collecting tests/test_validate.py ____________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_validate.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_validate.py:4: in 1857s from augur.validate import ( 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s ________________ ERROR collecting tests/test_validate_export.py ________________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/test_validate_export.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/test_validate_export.py:1: in 1857s import Bio.Phylo 1857s /usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in 1857s from Bio.Phylo._io import convert 1857s /usr/lib/python3/dist-packages/Bio/Phylo/_io.py:19: in 1857s from Bio.Phylo import PhyloXMLIO 1857s /usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in 1857s from Bio.Phylo import PhyloXML as PX 1857s /usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:23: in 1857s from Bio.Align import Alignment 1857s /usr/lib/python3/dist-packages/Bio/Align/__init__.py:32: in 1857s raise MissingPythonDependencyError( 1857s E Bio.MissingPythonDependencyError: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 1857s ___________ ERROR collecting tests/util_support/test_color_parser.py ___________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/util_support/test_color_parser.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/util_support/test_color_parser.py:1: in 1857s from augur.util_support.color_parser import ColorParser 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s ____________ ERROR collecting tests/util_support/test_node_data.py _____________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/util_support/test_node_data.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/util_support/test_node_data.py:1: in 1857s from augur.util_support.node_data import DuplicatedNonDictAttributeError 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s __________ ERROR collecting tests/util_support/test_node_data_file.py __________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/util_support/test_node_data_file.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/util_support/test_node_data_file.py:3: in 1857s from augur.__version__ import __version__ 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s _________ ERROR collecting tests/util_support/test_node_data_reader.py _________ 1857s ImportError while importing test module '/tmp/autopkgtest.Na5A3H/build.ICA/src/tests/util_support/test_node_data_reader.py'. 1857s Hint: make sure your test modules/packages have valid Python names. 1857s Traceback: 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 1857s from . import multiarray 1857s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 1857s from . import overrides 1857s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 1857s from numpy.core._multiarray_umath import ( 1857s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 1857s 1857s During handling of the above exception, another exception occurred: 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 1857s from numpy.__config__ import show as show_config 1857s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 1857s from numpy.core._multiarray_umath import ( 1857s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 1857s raise ImportError(msg) 1857s E ImportError: 1857s E 1857s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 1857s E 1857s E Importing the numpy C-extensions failed. This error can happen for 1857s E many reasons, often due to issues with your setup or how NumPy was 1857s E installed. 1857s E 1857s E We have compiled some common reasons and troubleshooting tips at: 1857s E 1857s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 1857s E 1857s E Please note and check the following: 1857s E 1857s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 1857s E * The NumPy version is: "1.26.4" 1857s E 1857s E and make sure that they are the versions you expect. 1857s E Please carefully study the documentation linked above for further help. 1857s E 1857s E Original error was: No module named 'numpy.core._multiarray_umath' 1857s 1857s The above exception was the direct cause of the following exception: 1857s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1857s return _bootstrap._gcd_import(name[level:], package, level) 1857s tests/util_support/test_node_data_reader.py:1: in 1857s from augur.util_support.node_data_reader import NodeDataReader 1857s augur/__init__.py:12: in 1857s from treetime import TreeTimeError, TreeTimeUnknownError 1857s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 1857s from .treeanc import TreeAnc 1857s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 1857s import numpy as np 1857s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 1857s raise ImportError(msg) from e 1857s E ImportError: Error importing numpy: you should not try to import numpy from 1857s E its source directory; please exit the numpy source tree, and relaunch 1857s E your python interpreter from there. 1857s =============================== warnings summary =============================== 1857s ../../../../usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2131 1857s /usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2131: BiopythonWarning: Import of C module failed (cannot import name 'cnexus' from 'Bio.Nexus' (/usr/lib/python3/dist-packages/Bio/Nexus/__init__.py)). Falling back to slow Python implementation 1857s warnings.warn( 1857s 1857s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1857s =========================== short test summary info ============================ 1857s ERROR tests/dates/test_ambiguous_date.py 1857s ERROR tests/dates/test_dates.py 1857s ERROR tests/filter/test_relative_dates.py 1857s ERROR tests/filter/test_subsample.py 1857s ERROR tests/io/test_file.py 1857s ERROR tests/io/test_metadata.py 1857s ERROR tests/io/test_sequences.py 1857s ERROR tests/io/test_shell_command_runner.py 1857s ERROR tests/io/test_strains.py 1857s ERROR tests/io/test_vcf.py 1857s ERROR tests/test_align.py 1857s ERROR tests/test_ancestral.py 1857s ERROR tests/test_clades.py 1857s ERROR tests/test_frequencies.py 1857s ERROR tests/test_mask.py 1857s ERROR tests/test_parse.py 1857s ERROR tests/test_schemas.py 1857s ERROR tests/test_titer_models.py 1857s ERROR tests/test_translate.py 1857s ERROR tests/test_utils.py 1857s ERROR tests/test_validate.py 1857s ERROR tests/test_validate_export.py 1857s ERROR tests/util_support/test_color_parser.py 1857s ERROR tests/util_support/test_node_data.py 1857s ERROR tests/util_support/test_node_data_file.py 1857s ERROR tests/util_support/test_node_data_reader.py 1857s !!!!!!!!!!!!!!!!!!! Interrupted: 26 errors during collection !!!!!!!!!!!!!!!!!!! 1857s ======================== 1 warning, 26 errors in 1.37s ========================= 1857s autopkgtest [11:45:33]: test run-unit-test: -----------------------] 1858s autopkgtest [11:45:34]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1858s run-unit-test FAIL non-zero exit status 2 1858s autopkgtest [11:45:34]: @@@@@@@@@@@@@@@@@@@@ summary 1858s run-unit-test FAIL non-zero exit status 2 2131s nova [W] Skipping flock for amd64 2131s Creating nova instance adt-plucky-i386-augur-20241113-103527-juju-7f2275-prod-proposed-migration-environment-20-648ce6c4-8021-4b82-85e2-7096745d8ca0 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)... 2131s nova [W] nova quota exceeded (attempt #0) 2131s nova [W] nova quota exceeded (attempt #1)