6s autopkgtest [08:46:48]: starting date and time: 2024-11-13 08:46:48+0000 6s autopkgtest [08:46:48]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 6s autopkgtest [08:46:48]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.btt552ph/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade 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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-7.secgroup --name adt-plucky-arm64-augur-20241113-084632-juju-7f2275-prod-proposed-migration-environment-20-3aec0107-9333-449d-b0c0-8ad1046d505a --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 189s autopkgtest [08:49:51]: testbed dpkg architecture: arm64 189s autopkgtest [08:49:51]: testbed apt version: 2.9.8 189s autopkgtest [08:49:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 190s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 190s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 191s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 191s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 191s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 191s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 191s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 191s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 191s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 191s Fetched 1793 kB in 1s (1913 kB/s) 191s Reading package lists... 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 195s Calculating upgrade... 196s The following NEW packages will be installed: 196s python3.13-gdbm 196s The following packages will be upgraded: 196s libpython3-stdlib python3 python3-gdbm python3-minimal 196s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 196s Need to get 101 kB of archives. 196s After this operation, 141 kB of additional disk space will be used. 196s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 196s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 196s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 196s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 196s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 197s Fetched 101 kB in 0s (255 kB/s) 197s (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 ... 79924 files and directories currently installed.) 197s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 197s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 197s Setting up python3-minimal (3.12.7-1) ... 197s (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 ... 79924 files and directories currently installed.) 197s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 197s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 198s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 198s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 198s Selecting previously unselected package python3.13-gdbm. 198s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 198s Unpacking python3.13-gdbm (3.13.0-2) ... 198s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 198s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 198s Setting up python3.13-gdbm (3.13.0-2) ... 198s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 198s Setting up python3 (3.12.7-1) ... 198s Setting up python3-gdbm:arm64 (3.12.7-1) ... 198s Processing triggers for man-db (2.12.1-3) ... 199s Reading package lists... 199s Building dependency tree... 199s Reading state information... 201s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 201s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 201s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 202s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 202s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 203s Reading package lists... 203s Reading package lists... 203s Building dependency tree... 203s Reading state information... 204s Calculating upgrade... 204s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 204s Reading package lists... 205s Building dependency tree... 205s Reading state information... 205s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 208s autopkgtest [08:50:10]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 209s autopkgtest [08:50:11]: @@@@@@@@@@@@@@@@@@@@ apt-source augur 211s Get:1 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (dsc) [2754 B] 211s Get:2 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (tar) [6802 kB] 211s Get:3 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (diff) [16.5 kB] 211s gpgv: Signature made Wed May 22 16:59:51 2024 UTC 211s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 211s gpgv: issuer "emollier@debian.org" 211s gpgv: Can't check signature: No public key 211s dpkg-source: warning: cannot verify inline signature for ./augur_24.4.0-1.dsc: no acceptable signature found 211s autopkgtest [08:50:13]: testing package augur version 24.4.0-1 212s autopkgtest [08:50:14]: build not needed 213s autopkgtest [08:50:15]: test run-unit-test: preparing testbed 216s Reading package lists... 217s Building dependency tree... 217s Reading state information... 217s Starting pkgProblemResolver with broken count: 0 217s Starting 2 pkgProblemResolver with broken count: 0 217s Done 218s The following additional packages will be installed: 218s augur blt fasttree flake8 fontconfig-config fonts-dejavu-core 218s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libamd3 libblas3 libcairo2 218s libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 libdsdp-5.8t64 218s libfftw3-double3 libfontconfig1 libfontenc1 libgfortran5 libglpk40 libgomp1 218s libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 218s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 218s liblcms2-2 liblerc4 libltdl7 libopenjp2-7 libpixman-1-0 218s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 218s libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 libumfpack6 218s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 218s libxrender1 libxslt1.1 libxss1 mafft mypy pigz python-matplotlib-data 218s python3-all python3-appdirs python3-asttokens python3-bcbio-gff 218s python3-biopython python3-boto3 python3-botocore python3-brotli 218s python3-cairo python3-contourpy python3-cvxopt python3-cycler 218s python3-dateutil python3-decorator python3-dendropy python3-executing 218s python3-flake8 python3-fonttools python3-freetype python3-freezegun 218s python3-fs python3-importlib-metadata python3-iniconfig python3-ipdb 218s python3-ipython python3-isodate python3-jedi python3-jmespath 218s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 218s python3-matplotlib-inline python3-mccabe python3-mpmath python3-mypy 218s python3-mypy-extensions python3-networkx python3-numpy python3-packaging 218s python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil 218s python3-pil.imagetk python3-pluggy python3-prompt-toolkit python3-psutil 218s python3-ptyprocess python3-pure-eval python3-pycodestyle python3-pyfaidx 218s python3-pyfastx python3-pyflakes python3-pygtrie python3-pytest 218s python3-pytest-mock python3-reportlab python3-rlpycairo python3-s3transfer 218s python3-schedule python3-scipy python3-seaborn python3-six 218s python3-stack-data python3-sympy python3-tk python3-traitlets 218s python3-treetime python3-typeshed python3-tz python3-ufolib2 218s python3-unicodedata2 python3-wcwidth python3-xopen python3-zstandard 218s python3.12-tk python3.13 python3.13-minimal python3.13-tk raxml seqmagick 218s sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common 218s xfonts-encodings xfonts-utils xml-core 218s Suggested packages: 218s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre libfftw3-bin 218s libfftw3-dev libiodbc2-dev default-libmysqlclient-dev gsl-ref-psdoc 218s | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libjs-jquery-ui-docs 218s liblcms2-utils tcl8.6 tk8.6 mypy-doc bwa clustalo clustalw dialign dssp 218s emboss muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf 218s python3-rdflib python3-psycopg2 samtools t-coffee wise python-cvxopt-doc 218s python-cycler-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng 218s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 218s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 218s python3-gobject python3-pyqt5 python3-sip python3-tornado 218s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 218s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 218s python3-dev python-pandas-doc python3-statsmodels python-pexpect-doc 218s python-pil-doc python-pygtrie-doc python-pytest-mock-doc pdf-viewer 218s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 218s python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 218s python-traitlets-doc python-zstandard-doc python3.13-venv python3.13-doc 218s binfmt-support sgml-base-doc debhelper 218s Recommended packages: 218s iqtree javascript-common blast2 libwww-perl lynx ruby python-biopython-doc 218s ncbi-blast+ python3-bs4 python3-cssselect python3-html5lib python3-orjson 218s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 218s python3-tables python3-olefile pyflakes3 fonts-dejavu-extra g++ 218s | c++-compiler isympy-common tabix 218s The following NEW packages will be installed: 218s augur autopkgtest-satdep blt fasttree flake8 fontconfig-config 218s fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libamd3 218s libblas3 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 218s libdsdp-5.8t64 libfftw3-double3 libfontconfig1 libfontenc1 libgfortran5 218s libglpk40 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b 218s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 218s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libltdl7 libopenjp2-7 218s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 218s libraqm0 libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 218s libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 218s libxft2 libxrender1 libxslt1.1 libxss1 mafft mypy pigz 218s python-matplotlib-data python3-all python3-appdirs python3-asttokens 218s python3-bcbio-gff python3-biopython python3-boto3 python3-botocore 218s python3-brotli python3-cairo python3-contourpy python3-cvxopt python3-cycler 218s python3-dateutil python3-decorator python3-dendropy python3-executing 218s python3-flake8 python3-fonttools python3-freetype python3-freezegun 218s python3-fs python3-importlib-metadata python3-iniconfig python3-ipdb 218s python3-ipython python3-isodate python3-jedi python3-jmespath 218s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 218s python3-matplotlib-inline python3-mccabe python3-mpmath python3-mypy 218s python3-mypy-extensions python3-networkx python3-numpy python3-packaging 218s python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil 218s python3-pil.imagetk python3-pluggy python3-prompt-toolkit python3-psutil 218s python3-ptyprocess python3-pure-eval python3-pycodestyle python3-pyfaidx 218s python3-pyfastx python3-pyflakes python3-pygtrie python3-pytest 218s python3-pytest-mock python3-reportlab python3-rlpycairo python3-s3transfer 218s python3-schedule python3-scipy python3-seaborn python3-six 218s python3-stack-data python3-sympy python3-tk python3-traitlets 218s python3-treetime python3-typeshed python3-tz python3-ufolib2 218s python3-unicodedata2 python3-wcwidth python3-xopen python3-zstandard 218s python3.12-tk python3.13 python3.13-minimal python3.13-tk raxml seqmagick 218s sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common 218s xfonts-encodings xfonts-utils xml-core 218s 0 upgraded, 157 newly installed, 0 to remove and 0 not upgraded. 218s Need to get 122 MB/122 MB of archives. 218s After this operation, 618 MB of additional disk space will be used. 218s Get:1 /tmp/autopkgtest.88fRyY/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [752 B] 218s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 219s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 219s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 219s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 pigz arm64 2.8-1 [60.7 kB] 219s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 219s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 219s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 219s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 219s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 219s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 219s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 219s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 219s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 219s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 219s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 219s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 220s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 220s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 220s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 220s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 220s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 220s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 220s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 220s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 220s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 220s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 220s Get:28 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 220s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 220s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 220s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 220s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 220s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 220s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 220s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 220s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 220s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 220s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 220s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 220s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 220s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 220s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 220s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 220s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 220s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 220s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 220s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 220s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 220s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 220s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 220s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 220s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 220s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 220s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 220s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 220s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 220s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 220s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 220s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 220s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-bcbio-gff all 0.7.1-2 [33.9 kB] 220s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-2 [13.1 kB] 220s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd3 arm64 1:7.8.3+dfsg-2 [26.1 kB] 220s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcamd3 arm64 1:7.8.3+dfsg-2 [22.6 kB] 220s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 libccolamd3 arm64 1:7.8.3+dfsg-2 [25.5 kB] 220s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-2 [18.2 kB] 220s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcholmod5 arm64 1:7.8.3+dfsg-2 [614 kB] 220s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdsdp-5.8t64 arm64 5.8-10.1build1 [184 kB] 220s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu4 [392 kB] 220s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libltdl7 arm64 2.4.7-7build1 [40.4 kB] 220s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB] 220s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgslcblas0 arm64 2.8+dfsg-5 [87.3 kB] 220s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgsl28 arm64 2.8+dfsg-5 [983 kB] 220s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 libumfpack6 arm64 1:7.8.3+dfsg-2 [249 kB] 220s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cvxopt arm64 1.3.0+dfsg-1build7 [272 kB] 220s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-isodate all 0.6.1-3 [24.3 kB] 220s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 221s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 221s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 221s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 221s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 221s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 221s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 221s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 221s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfastx arm64 2.1.0-2 [56.1 kB] 221s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 221s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 221s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 221s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 221s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 221s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 221s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 221s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 221s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 221s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 221s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 221s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 221s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 221s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 221s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 221s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 221s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 221s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 222s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB] 222s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 222s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 223s Get:106 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 223s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 224s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 225s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2 [50.4 kB] 225s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 225s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 225s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-treetime all 0.11.4-1 [941 kB] 226s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-xopen all 1.7.0-2 [17.0 kB] 226s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jmespath all 1.0.1-1 [21.3 kB] 226s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-botocore all 1.34.46+repack-1ubuntu1 [6211 kB] 227s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-s3transfer all 0.10.1-1ubuntu2 [54.3 kB] 227s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-boto3 all 1.34.46+dfsg-1ubuntu1 [72.5 kB] 227s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-dendropy all 4.6.1-1 [278 kB] 227s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-schedule all 1.2.2-1 [12.2 kB] 227s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-seaborn all 0.13.2-4 [225 kB] 227s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-zstandard arm64 0.23.0-2 [338 kB] 227s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pygtrie all 2.2-2 [16.0 kB] 227s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 seqmagick all 0.8.6-3 [38.6 kB] 227s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.3-1 [67.2 kB] 227s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 227s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 227s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 227s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 227s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 227s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-2 [48.1 kB] 227s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 227s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 227s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 2.4.1-2 [20.8 kB] 227s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.1.0-0.1 [24.4 kB] 227s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 227s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 227s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 228s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipdb all 0.13.13-2 [15.4 kB] 228s Get:139 http://ftpmaster.internal/ubuntu plucky/universe arm64 mafft arm64 7.505-1 [756 kB] 228s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 raxml arm64 8.2.13+dfsg-1 [999 kB] 228s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 228s Get:142 http://ftpmaster.internal/ubuntu plucky/universe arm64 vcftools arm64 0.1.16-3 [375 kB] 228s Get:143 http://ftpmaster.internal/ubuntu plucky/universe arm64 augur all 24.4.0-1 [238 kB] 228s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mccabe all 0.7.0-1 [8678 B] 228s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pycodestyle all 2.11.1-1 [29.9 kB] 228s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyflakes all 3.2.0-1 [52.8 kB] 228s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-flake8 all 7.1.1-1 [43.9 kB] 228s Get:148 http://ftpmaster.internal/ubuntu plucky/universe arm64 flake8 all 7.1.1-1 [6442 B] 228s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mypy-extensions all 1.0.0-1 [6148 B] 228s Get:150 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-psutil arm64 5.9.8-2build2 [196 kB] 228s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mypy arm64 1.13.0-1 [8230 kB] 230s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 mypy all 1.13.0-1 [24.9 kB] 230s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freezegun all 1.5.1-1.1 [15.9 kB] 230s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 230s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 230s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 230s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 231s Fetched 122 MB in 11s (10.6 MB/s) 231s Selecting previously unselected package libpython3.13-minimal:arm64. 231s (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 ... 79931 files and directories currently installed.) 231s Preparing to unpack .../000-libpython3.13-minimal_3.13.0-2_arm64.deb ... 231s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 231s Selecting previously unselected package python3.13-minimal. 231s Preparing to unpack .../001-python3.13-minimal_3.13.0-2_arm64.deb ... 231s Unpacking python3.13-minimal (3.13.0-2) ... 231s Selecting previously unselected package sgml-base. 231s Preparing to unpack .../002-sgml-base_1.31_all.deb ... 231s Unpacking sgml-base (1.31) ... 231s Selecting previously unselected package pigz. 231s Preparing to unpack .../003-pigz_2.8-1_arm64.deb ... 231s Unpacking pigz (2.8-1) ... 231s Selecting previously unselected package libblas3:arm64. 231s Preparing to unpack .../004-libblas3_3.12.0-3build2_arm64.deb ... 231s Unpacking libblas3:arm64 (3.12.0-3build2) ... 231s Selecting previously unselected package libgfortran5:arm64. 231s Preparing to unpack .../005-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 231s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 231s Selecting previously unselected package liblapack3:arm64. 231s Preparing to unpack .../006-liblapack3_3.12.0-3build2_arm64.deb ... 231s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 231s Selecting previously unselected package python3-numpy. 231s Preparing to unpack .../007-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 231s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 231s Selecting previously unselected package libtcl8.6:arm64. 231s Preparing to unpack .../008-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 231s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 232s Selecting previously unselected package fonts-dejavu-mono. 232s Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ... 232s Unpacking fonts-dejavu-mono (2.37-8) ... 232s Selecting previously unselected package fonts-dejavu-core. 232s Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ... 232s Unpacking fonts-dejavu-core (2.37-8) ... 232s Selecting previously unselected package libfontenc1:arm64. 232s Preparing to unpack .../011-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 232s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 232s Selecting previously unselected package x11-common. 232s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ... 232s Unpacking x11-common (1:7.7+23ubuntu3) ... 232s Selecting previously unselected package xfonts-encodings. 232s Preparing to unpack .../013-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 232s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 232s Selecting previously unselected package xfonts-utils. 232s Preparing to unpack .../014-xfonts-utils_1%3a7.7+7_arm64.deb ... 232s Unpacking xfonts-utils (1:7.7+7) ... 232s Selecting previously unselected package fonts-urw-base35. 232s Preparing to unpack .../015-fonts-urw-base35_20200910-8_all.deb ... 232s Unpacking fonts-urw-base35 (20200910-8) ... 232s Selecting previously unselected package fontconfig-config. 232s Preparing to unpack .../016-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 232s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 233s Selecting previously unselected package libfontconfig1:arm64. 233s Preparing to unpack .../017-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 233s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 233s Selecting previously unselected package libxrender1:arm64. 233s Preparing to unpack .../018-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 233s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 233s Selecting previously unselected package libxft2:arm64. 233s Preparing to unpack .../019-libxft2_2.3.6-1build1_arm64.deb ... 233s Unpacking libxft2:arm64 (2.3.6-1build1) ... 233s Selecting previously unselected package libxss1:arm64. 233s Preparing to unpack .../020-libxss1_1%3a1.2.3-1build3_arm64.deb ... 233s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 233s Selecting previously unselected package libtk8.6:arm64. 233s Preparing to unpack .../021-libtk8.6_8.6.15-1_arm64.deb ... 233s Unpacking libtk8.6:arm64 (8.6.15-1) ... 233s Selecting previously unselected package python3.12-tk. 233s Preparing to unpack .../022-python3.12-tk_3.12.7-3_arm64.deb ... 233s Unpacking python3.12-tk (3.12.7-3) ... 233s Selecting previously unselected package python3.13-tk. 233s Preparing to unpack .../023-python3.13-tk_3.13.0-2_arm64.deb ... 233s Unpacking python3.13-tk (3.13.0-2) ... 233s Selecting previously unselected package tk8.6-blt2.5. 233s Preparing to unpack .../024-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 233s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 233s Selecting previously unselected package blt. 233s Preparing to unpack .../025-blt_2.5.3+dfsg-7build1_arm64.deb ... 233s Unpacking blt (2.5.3+dfsg-7build1) ... 233s Selecting previously unselected package python3-tk:arm64. 233s Preparing to unpack .../026-python3-tk_3.12.7-1_arm64.deb ... 233s Unpacking python3-tk:arm64 (3.12.7-1) ... 233s Selecting previously unselected package python3-pil.imagetk:arm64. 233s Preparing to unpack .../027-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 233s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 233s Selecting previously unselected package libgomp1:arm64. 233s Preparing to unpack .../028-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 233s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 233s Selecting previously unselected package libimagequant0:arm64. 233s Preparing to unpack .../029-libimagequant0_2.18.0-1build1_arm64.deb ... 233s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 233s Selecting previously unselected package libjpeg-turbo8:arm64. 233s Preparing to unpack .../030-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 233s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 233s Selecting previously unselected package libjpeg8:arm64. 233s Preparing to unpack .../031-libjpeg8_8c-2ubuntu11_arm64.deb ... 233s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 233s Selecting previously unselected package liblcms2-2:arm64. 233s Preparing to unpack .../032-liblcms2-2_2.16-2_arm64.deb ... 233s Unpacking liblcms2-2:arm64 (2.16-2) ... 233s Selecting previously unselected package libopenjp2-7:arm64. 233s Preparing to unpack .../033-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 233s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 233s Selecting previously unselected package libgraphite2-3:arm64. 233s Preparing to unpack .../034-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 233s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 233s Selecting previously unselected package libharfbuzz0b:arm64. 233s Preparing to unpack .../035-libharfbuzz0b_10.0.1-1_arm64.deb ... 233s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 233s Selecting previously unselected package libraqm0:arm64. 233s Preparing to unpack .../036-libraqm0_0.10.1-1build1_arm64.deb ... 233s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 233s Selecting previously unselected package libdeflate0:arm64. 233s Preparing to unpack .../037-libdeflate0_1.22-1_arm64.deb ... 233s Unpacking libdeflate0:arm64 (1.22-1) ... 233s Selecting previously unselected package libjbig0:arm64. 233s Preparing to unpack .../038-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 233s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 233s Selecting previously unselected package liblerc4:arm64. 234s Preparing to unpack .../039-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 234s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 234s Selecting previously unselected package libsharpyuv0:arm64. 234s Preparing to unpack .../040-libsharpyuv0_1.4.0-0.1_arm64.deb ... 234s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 234s Selecting previously unselected package libwebp7:arm64. 234s Preparing to unpack .../041-libwebp7_1.4.0-0.1_arm64.deb ... 234s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 234s Selecting previously unselected package libtiff6:arm64. 234s Preparing to unpack .../042-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 234s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 234s Selecting previously unselected package libwebpdemux2:arm64. 234s Preparing to unpack .../043-libwebpdemux2_1.4.0-0.1_arm64.deb ... 234s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 234s Selecting previously unselected package libwebpmux3:arm64. 234s Preparing to unpack .../044-libwebpmux3_1.4.0-0.1_arm64.deb ... 234s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 234s Selecting previously unselected package python3-pil:arm64. 234s Preparing to unpack .../045-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 234s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 234s Selecting previously unselected package libpixman-1-0:arm64. 234s Preparing to unpack .../046-libpixman-1-0_0.44.0-3_arm64.deb ... 234s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 234s Selecting previously unselected package libxcb-render0:arm64. 234s Preparing to unpack .../047-libxcb-render0_1.17.0-2_arm64.deb ... 234s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 234s Selecting previously unselected package libxcb-shm0:arm64. 234s Preparing to unpack .../048-libxcb-shm0_1.17.0-2_arm64.deb ... 234s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 234s Selecting previously unselected package libcairo2:arm64. 234s Preparing to unpack .../049-libcairo2_1.18.2-2_arm64.deb ... 234s Unpacking libcairo2:arm64 (1.18.2-2) ... 234s Selecting previously unselected package python3-cairo. 234s Preparing to unpack .../050-python3-cairo_1.26.1-2_arm64.deb ... 234s Unpacking python3-cairo (1.26.1-2) ... 234s Selecting previously unselected package python3-freetype. 234s Preparing to unpack .../051-python3-freetype_2.5.1-1_all.deb ... 234s Unpacking python3-freetype (2.5.1-1) ... 234s Selecting previously unselected package python3-rlpycairo. 234s Preparing to unpack .../052-python3-rlpycairo_0.3.0-3_all.deb ... 234s Unpacking python3-rlpycairo (0.3.0-3) ... 234s Selecting previously unselected package python3-reportlab. 234s Preparing to unpack .../053-python3-reportlab_4.2.5-1_all.deb ... 234s Unpacking python3-reportlab (4.2.5-1) ... 234s Selecting previously unselected package xml-core. 234s Preparing to unpack .../054-xml-core_0.19_all.deb ... 234s Unpacking xml-core (0.19) ... 234s Selecting previously unselected package w3c-sgml-lib. 234s Preparing to unpack .../055-w3c-sgml-lib_1.3-3_all.deb ... 234s Unpacking w3c-sgml-lib (1.3-3) ... 234s Selecting previously unselected package python3-biopython. 234s Preparing to unpack .../056-python3-biopython_1.84+dfsg-4_arm64.deb ... 234s Unpacking python3-biopython (1.84+dfsg-4) ... 235s Selecting previously unselected package python3-six. 235s Preparing to unpack .../057-python3-six_1.16.0-7_all.deb ... 235s Unpacking python3-six (1.16.0-7) ... 235s Selecting previously unselected package python3-bcbio-gff. 235s Preparing to unpack .../058-python3-bcbio-gff_0.7.1-2_all.deb ... 235s Unpacking python3-bcbio-gff (0.7.1-2) ... 235s Selecting previously unselected package libsuitesparseconfig7:arm64. 235s Preparing to unpack .../059-libsuitesparseconfig7_1%3a7.8.3+dfsg-2_arm64.deb ... 235s Unpacking libsuitesparseconfig7:arm64 (1:7.8.3+dfsg-2) ... 235s Selecting previously unselected package libamd3:arm64. 235s Preparing to unpack .../060-libamd3_1%3a7.8.3+dfsg-2_arm64.deb ... 235s Unpacking libamd3:arm64 (1:7.8.3+dfsg-2) ... 235s Selecting previously unselected package libcamd3:arm64. 235s Preparing to unpack .../061-libcamd3_1%3a7.8.3+dfsg-2_arm64.deb ... 235s Unpacking libcamd3:arm64 (1:7.8.3+dfsg-2) ... 235s Selecting previously unselected package libccolamd3:arm64. 235s Preparing to unpack .../062-libccolamd3_1%3a7.8.3+dfsg-2_arm64.deb ... 235s Unpacking libccolamd3:arm64 (1:7.8.3+dfsg-2) ... 235s Selecting previously unselected package libcolamd3:arm64. 235s Preparing to unpack .../063-libcolamd3_1%3a7.8.3+dfsg-2_arm64.deb ... 235s Unpacking libcolamd3:arm64 (1:7.8.3+dfsg-2) ... 235s Selecting previously unselected package libcholmod5:arm64. 235s Preparing to unpack .../064-libcholmod5_1%3a7.8.3+dfsg-2_arm64.deb ... 235s Unpacking libcholmod5:arm64 (1:7.8.3+dfsg-2) ... 235s Selecting previously unselected package libdsdp-5.8t64. 235s Preparing to unpack .../065-libdsdp-5.8t64_5.8-10.1build1_arm64.deb ... 235s Unpacking libdsdp-5.8t64 (5.8-10.1build1) ... 235s Selecting previously unselected package libfftw3-double3:arm64. 235s Preparing to unpack .../066-libfftw3-double3_3.3.10-1ubuntu4_arm64.deb ... 235s Unpacking libfftw3-double3:arm64 (3.3.10-1ubuntu4) ... 235s Selecting previously unselected package libltdl7:arm64. 235s Preparing to unpack .../067-libltdl7_2.4.7-7build1_arm64.deb ... 235s Unpacking libltdl7:arm64 (2.4.7-7build1) ... 235s Selecting previously unselected package libglpk40:arm64. 235s Preparing to unpack .../068-libglpk40_5.0-1build2_arm64.deb ... 235s Unpacking libglpk40:arm64 (5.0-1build2) ... 235s Selecting previously unselected package libgslcblas0:arm64. 235s Preparing to unpack .../069-libgslcblas0_2.8+dfsg-5_arm64.deb ... 235s Unpacking libgslcblas0:arm64 (2.8+dfsg-5) ... 235s Selecting previously unselected package libgsl28:arm64. 235s Preparing to unpack .../070-libgsl28_2.8+dfsg-5_arm64.deb ... 235s Unpacking libgsl28:arm64 (2.8+dfsg-5) ... 235s Selecting previously unselected package libumfpack6:arm64. 235s Preparing to unpack .../071-libumfpack6_1%3a7.8.3+dfsg-2_arm64.deb ... 235s Unpacking libumfpack6:arm64 (1:7.8.3+dfsg-2) ... 235s Selecting previously unselected package python3-cvxopt. 235s Preparing to unpack .../072-python3-cvxopt_1.3.0+dfsg-1build7_arm64.deb ... 235s Unpacking python3-cvxopt (1.3.0+dfsg-1build7) ... 235s Selecting previously unselected package python3-isodate. 235s Preparing to unpack .../073-python3-isodate_0.6.1-3_all.deb ... 235s Unpacking python3-isodate (0.6.1-3) ... 235s Selecting previously unselected package python3-networkx. 235s Preparing to unpack .../074-python3-networkx_3.2.1-4ubuntu1_all.deb ... 235s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 236s Selecting previously unselected package python3-packaging. 236s Preparing to unpack .../075-python3-packaging_24.1-1_all.deb ... 236s Unpacking python3-packaging (24.1-1) ... 236s Selecting previously unselected package python3-dateutil. 236s Preparing to unpack .../076-python3-dateutil_2.9.0-2_all.deb ... 236s Unpacking python3-dateutil (2.9.0-2) ... 236s Selecting previously unselected package python3-tz. 236s Preparing to unpack .../077-python3-tz_2024.1-2_all.deb ... 236s Unpacking python3-tz (2024.1-2) ... 236s Selecting previously unselected package python3-pandas-lib:arm64. 236s Preparing to unpack .../078-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 236s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 236s Selecting previously unselected package python3-pandas. 236s Preparing to unpack .../079-python3-pandas_2.2.3+dfsg-5_all.deb ... 236s Unpacking python3-pandas (2.2.3+dfsg-5) ... 236s Selecting previously unselected package python3-importlib-metadata. 236s Preparing to unpack .../080-python3-importlib-metadata_8.5.0-1_all.deb ... 236s Unpacking python3-importlib-metadata (8.5.0-1) ... 237s Selecting previously unselected package python3-pyfaidx. 237s Preparing to unpack .../081-python3-pyfaidx_0.8.1.3-1_all.deb ... 237s Unpacking python3-pyfaidx (0.8.1.3-1) ... 237s Selecting previously unselected package python3-pyfastx. 237s Preparing to unpack .../082-python3-pyfastx_2.1.0-2_arm64.deb ... 237s Unpacking python3-pyfastx (2.1.0-2) ... 237s Selecting previously unselected package python3-decorator. 237s Preparing to unpack .../083-python3-decorator_5.1.1-5_all.deb ... 237s Unpacking python3-decorator (5.1.1-5) ... 237s Selecting previously unselected package liblbfgsb0:arm64. 237s Preparing to unpack .../084-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 237s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 237s Selecting previously unselected package python3-scipy. 237s Preparing to unpack .../085-python3-scipy_1.13.1-5_arm64.deb ... 237s Unpacking python3-scipy (1.13.1-5) ... 237s Selecting previously unselected package libjs-jquery. 237s Preparing to unpack .../086-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 237s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 237s Selecting previously unselected package libjs-jquery-ui. 237s Preparing to unpack .../087-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 237s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 237s Selecting previously unselected package fonts-lyx. 237s Preparing to unpack .../088-fonts-lyx_2.4.2.1-1_all.deb ... 237s Unpacking fonts-lyx (2.4.2.1-1) ... 237s Selecting previously unselected package python-matplotlib-data. 237s Preparing to unpack .../089-python-matplotlib-data_3.8.3-3_all.deb ... 237s Unpacking python-matplotlib-data (3.8.3-3) ... 237s Selecting previously unselected package python3-contourpy. 237s Preparing to unpack .../090-python3-contourpy_1.3.0-2_arm64.deb ... 237s Unpacking python3-contourpy (1.3.0-2) ... 238s Selecting previously unselected package python3-cycler. 238s Preparing to unpack .../091-python3-cycler_0.12.1-1_all.deb ... 238s Unpacking python3-cycler (0.12.1-1) ... 238s Selecting previously unselected package python3-brotli. 238s Preparing to unpack .../092-python3-brotli_1.1.0-2build2_arm64.deb ... 238s Unpacking python3-brotli (1.1.0-2build2) ... 238s Selecting previously unselected package python3-ufolib2. 238s Preparing to unpack .../093-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 238s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 238s Selecting previously unselected package python3-mpmath. 238s Preparing to unpack .../094-python3-mpmath_1.3.0-1_all.deb ... 238s Unpacking python3-mpmath (1.3.0-1) ... 238s Selecting previously unselected package python3-sympy. 238s Preparing to unpack .../095-python3-sympy_1.13.3-1_all.deb ... 238s Unpacking python3-sympy (1.13.3-1) ... 238s Selecting previously unselected package python3-appdirs. 238s Preparing to unpack .../096-python3-appdirs_1.4.4-4_all.deb ... 238s Unpacking python3-appdirs (1.4.4-4) ... 238s Selecting previously unselected package python3-fs. 238s Preparing to unpack .../097-python3-fs_2.4.16-4_all.deb ... 238s Unpacking python3-fs (2.4.16-4) ... 238s Selecting previously unselected package libxslt1.1:arm64. 238s Preparing to unpack .../098-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 238s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 238s Selecting previously unselected package python3-lxml:arm64. 238s Preparing to unpack .../099-python3-lxml_5.3.0-1_arm64.deb ... 238s Unpacking python3-lxml:arm64 (5.3.0-1) ... 238s Selecting previously unselected package python3-lz4. 238s Preparing to unpack .../100-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 238s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 238s Selecting previously unselected package python3-unicodedata2. 238s Preparing to unpack .../101-python3-unicodedata2_15.1.0+ds-1build1_arm64.deb ... 238s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 238s Selecting previously unselected package libpython3.13-stdlib:arm64. 238s Preparing to unpack .../102-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 238s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 239s Selecting previously unselected package python3.13. 239s Preparing to unpack .../103-python3.13_3.13.0-2_arm64.deb ... 239s Unpacking python3.13 (3.13.0-2) ... 239s Selecting previously unselected package python3-all. 239s Preparing to unpack .../104-python3-all_3.12.7-1_arm64.deb ... 239s Unpacking python3-all (3.12.7-1) ... 239s Selecting previously unselected package unicode-data. 239s Preparing to unpack .../105-unicode-data_15.1.0-1_all.deb ... 239s Unpacking unicode-data (15.1.0-1) ... 239s Selecting previously unselected package python3-fonttools. 239s Preparing to unpack .../106-python3-fonttools_4.46.0-1build2_arm64.deb ... 239s Unpacking python3-fonttools (4.46.0-1build2) ... 239s Selecting previously unselected package python3-kiwisolver. 239s Preparing to unpack .../107-python3-kiwisolver_1.4.7-2_arm64.deb ... 239s Unpacking python3-kiwisolver (1.4.7-2) ... 239s Selecting previously unselected package libqhull-r8.0:arm64. 239s Preparing to unpack .../108-libqhull-r8.0_2020.2-6build1_arm64.deb ... 239s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 239s Selecting previously unselected package python3-matplotlib. 239s Preparing to unpack .../109-python3-matplotlib_3.8.3-3_arm64.deb ... 239s Unpacking python3-matplotlib (3.8.3-3) ... 239s Selecting previously unselected package python3-treetime. 239s Preparing to unpack .../110-python3-treetime_0.11.4-1_all.deb ... 239s Unpacking python3-treetime (0.11.4-1) ... 239s Selecting previously unselected package python3-xopen. 239s Preparing to unpack .../111-python3-xopen_1.7.0-2_all.deb ... 239s Unpacking python3-xopen (1.7.0-2) ... 239s Selecting previously unselected package python3-jmespath. 239s Preparing to unpack .../112-python3-jmespath_1.0.1-1_all.deb ... 239s Unpacking python3-jmespath (1.0.1-1) ... 240s Selecting previously unselected package python3-botocore. 240s Preparing to unpack .../113-python3-botocore_1.34.46+repack-1ubuntu1_all.deb ... 240s Unpacking python3-botocore (1.34.46+repack-1ubuntu1) ... 240s Selecting previously unselected package python3-s3transfer. 240s Preparing to unpack .../114-python3-s3transfer_0.10.1-1ubuntu2_all.deb ... 240s Unpacking python3-s3transfer (0.10.1-1ubuntu2) ... 240s Selecting previously unselected package python3-boto3. 240s Preparing to unpack .../115-python3-boto3_1.34.46+dfsg-1ubuntu1_all.deb ... 240s Unpacking python3-boto3 (1.34.46+dfsg-1ubuntu1) ... 240s Selecting previously unselected package python3-dendropy. 240s Preparing to unpack .../116-python3-dendropy_4.6.1-1_all.deb ... 240s Unpacking python3-dendropy (4.6.1-1) ... 240s Selecting previously unselected package python3-schedule. 240s Preparing to unpack .../117-python3-schedule_1.2.2-1_all.deb ... 240s Unpacking python3-schedule (1.2.2-1) ... 240s Selecting previously unselected package python3-seaborn. 240s Preparing to unpack .../118-python3-seaborn_0.13.2-4_all.deb ... 240s Unpacking python3-seaborn (0.13.2-4) ... 240s Selecting previously unselected package python3-zstandard. 240s Preparing to unpack .../119-python3-zstandard_0.23.0-2_arm64.deb ... 240s Unpacking python3-zstandard (0.23.0-2) ... 240s Selecting previously unselected package python3-pygtrie. 241s Preparing to unpack .../120-python3-pygtrie_2.2-2_all.deb ... 241s Unpacking python3-pygtrie (2.2-2) ... 241s Selecting previously unselected package seqmagick. 241s Preparing to unpack .../121-seqmagick_0.8.6-3_all.deb ... 241s Unpacking seqmagick (0.8.6-3) ... 241s Selecting previously unselected package python3-parso. 241s Preparing to unpack .../122-python3-parso_0.8.3-1_all.deb ... 241s Unpacking python3-parso (0.8.3-1) ... 241s Selecting previously unselected package python3-typeshed. 241s Preparing to unpack .../123-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 241s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 241s Selecting previously unselected package python3-jedi. 241s Preparing to unpack .../124-python3-jedi_0.19.1+ds1-1_all.deb ... 241s Unpacking python3-jedi (0.19.1+ds1-1) ... 242s Selecting previously unselected package python3-traitlets. 242s Preparing to unpack .../125-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 242s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 242s Selecting previously unselected package python3-matplotlib-inline. 242s Preparing to unpack .../126-python3-matplotlib-inline_0.1.6-2_all.deb ... 242s Unpacking python3-matplotlib-inline (0.1.6-2) ... 242s Selecting previously unselected package python3-ptyprocess. 242s Preparing to unpack .../127-python3-ptyprocess_0.7.0-6_all.deb ... 242s Unpacking python3-ptyprocess (0.7.0-6) ... 242s Selecting previously unselected package python3-pexpect. 242s Preparing to unpack .../128-python3-pexpect_4.9-2_all.deb ... 242s Unpacking python3-pexpect (4.9-2) ... 242s Selecting previously unselected package python3-wcwidth. 242s Preparing to unpack .../129-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 242s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 242s Selecting previously unselected package python3-prompt-toolkit. 242s Preparing to unpack .../130-python3-prompt-toolkit_3.0.48-1_all.deb ... 242s Unpacking python3-prompt-toolkit (3.0.48-1) ... 242s Selecting previously unselected package python3-asttokens. 242s Preparing to unpack .../131-python3-asttokens_2.4.1-2_all.deb ... 242s Unpacking python3-asttokens (2.4.1-2) ... 242s Selecting previously unselected package python3-executing. 242s Preparing to unpack .../132-python3-executing_2.1.0-0.1_all.deb ... 242s Unpacking python3-executing (2.1.0-0.1) ... 242s Selecting previously unselected package python3-pure-eval. 242s Preparing to unpack .../133-python3-pure-eval_0.2.3-1_all.deb ... 242s Unpacking python3-pure-eval (0.2.3-1) ... 242s Selecting previously unselected package python3-stack-data. 242s Preparing to unpack .../134-python3-stack-data_0.6.3-1_all.deb ... 242s Unpacking python3-stack-data (0.6.3-1) ... 242s Selecting previously unselected package python3-ipython. 242s Preparing to unpack .../135-python3-ipython_8.20.0-1ubuntu1_all.deb ... 242s Unpacking python3-ipython (8.20.0-1ubuntu1) ... 242s Selecting previously unselected package python3-ipdb. 242s Preparing to unpack .../136-python3-ipdb_0.13.13-2_all.deb ... 242s Unpacking python3-ipdb (0.13.13-2) ... 242s Selecting previously unselected package mafft. 242s Preparing to unpack .../137-mafft_7.505-1_arm64.deb ... 242s Unpacking mafft (7.505-1) ... 242s Selecting previously unselected package raxml. 242s Preparing to unpack .../138-raxml_8.2.13+dfsg-1_arm64.deb ... 242s Unpacking raxml (8.2.13+dfsg-1) ... 242s Selecting previously unselected package fasttree. 242s Preparing to unpack .../139-fasttree_2.1.11-2_arm64.deb ... 242s Unpacking fasttree (2.1.11-2) ... 242s Selecting previously unselected package vcftools. 243s Preparing to unpack .../140-vcftools_0.1.16-3_arm64.deb ... 243s Unpacking vcftools (0.1.16-3) ... 243s Selecting previously unselected package augur. 243s Preparing to unpack .../141-augur_24.4.0-1_all.deb ... 243s Unpacking augur (24.4.0-1) ... 243s Selecting previously unselected package python3-mccabe. 243s Preparing to unpack .../142-python3-mccabe_0.7.0-1_all.deb ... 243s Unpacking python3-mccabe (0.7.0-1) ... 243s Selecting previously unselected package python3-pycodestyle. 243s Preparing to unpack .../143-python3-pycodestyle_2.11.1-1_all.deb ... 243s Unpacking python3-pycodestyle (2.11.1-1) ... 243s Selecting previously unselected package python3-pyflakes. 243s Preparing to unpack .../144-python3-pyflakes_3.2.0-1_all.deb ... 243s Unpacking python3-pyflakes (3.2.0-1) ... 243s Selecting previously unselected package python3-flake8. 243s Preparing to unpack .../145-python3-flake8_7.1.1-1_all.deb ... 243s Unpacking python3-flake8 (7.1.1-1) ... 243s Selecting previously unselected package flake8. 243s Preparing to unpack .../146-flake8_7.1.1-1_all.deb ... 243s Unpacking flake8 (7.1.1-1) ... 243s Selecting previously unselected package python3-mypy-extensions. 243s Preparing to unpack .../147-python3-mypy-extensions_1.0.0-1_all.deb ... 243s Unpacking python3-mypy-extensions (1.0.0-1) ... 243s Selecting previously unselected package python3-psutil. 243s Preparing to unpack .../148-python3-psutil_5.9.8-2build2_arm64.deb ... 243s Unpacking python3-psutil (5.9.8-2build2) ... 243s Selecting previously unselected package python3-mypy. 243s Preparing to unpack .../149-python3-mypy_1.13.0-1_arm64.deb ... 243s Unpacking python3-mypy (1.13.0-1) ... 243s Selecting previously unselected package mypy. 243s Preparing to unpack .../150-mypy_1.13.0-1_all.deb ... 243s Unpacking mypy (1.13.0-1) ... 243s Selecting previously unselected package python3-freezegun. 243s Preparing to unpack .../151-python3-freezegun_1.5.1-1.1_all.deb ... 243s Unpacking python3-freezegun (1.5.1-1.1) ... 243s Selecting previously unselected package python3-iniconfig. 244s Preparing to unpack .../152-python3-iniconfig_1.1.1-2_all.deb ... 244s Unpacking python3-iniconfig (1.1.1-2) ... 244s Selecting previously unselected package python3-pluggy. 244s Preparing to 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347s Setting up augur (24.4.0-1) ... 347s Setting up autopkgtest-satdep (0) ... 354s (Reading database ... 107404 files and directories currently installed.) 354s Removing autopkgtest-satdep (0) ... 355s autopkgtest [08:52:37]: test run-unit-test: [----------------------- 356s ============================= test session starts ============================== 356s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 356s cachedir: .pytest_cache 356s rootdir: /tmp/autopkgtest.88fRyY/build.Pe2/src 356s plugins: mock-3.14.0, typeguard-4.4.1 358s collecting ... collected 2 items / 26 errors 358s 358s ==================================== ERRORS ==================================== 358s _____________ ERROR collecting tests/dates/test_ambiguous_date.py ______________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/dates/test_ambiguous_date.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/dates/test_ambiguous_date.py:3: in 358s from augur.dates import ambiguous_date 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s __________________ ERROR collecting tests/dates/test_dates.py __________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/dates/test_dates.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/dates/test_dates.py:4: in 358s from augur import dates 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s _____________ ERROR collecting tests/filter/test_relative_dates.py _____________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/filter/test_relative_dates.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/filter/test_relative_dates.py:12: in 358s from augur.filter import register_arguments 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s _______________ ERROR collecting tests/filter/test_subsample.py ________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/filter/test_subsample.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/filter/test_subsample.py:2: in 358s import pandas as pd 358s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 358s raise ImportError( 358s E ImportError: Unable to import required dependencies: 358s E numpy: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s ____________________ ERROR collecting tests/io/test_file.py ____________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/io/test_file.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/io/test_file.py:2: in 358s import augur.io.file 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s __________________ ERROR collecting tests/io/test_metadata.py __________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/io/test_metadata.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/io/test_metadata.py:6: in 358s from augur.errors import AugurError 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s _________________ ERROR collecting tests/io/test_sequences.py __________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/io/test_sequences.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/io/test_sequences.py:2: in 358s from Bio import SeqIO 358s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 358s from Bio.SeqIO import TwoBitIO 358s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 358s raise MissingPythonDependencyError( 358s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 358s ____________ ERROR collecting tests/io/test_shell_command_runner.py ____________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/io/test_shell_command_runner.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/io/test_shell_command_runner.py:5: in 358s from augur.io.shell_command_runner import ShellCommandRunner 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s __________________ ERROR collecting tests/io/test_strains.py ___________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/io/test_strains.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/io/test_strains.py:3: in 358s from augur.io.strains import read_strains 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s ____________________ ERROR collecting tests/io/test_vcf.py _____________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/io/test_vcf.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/io/test_vcf.py:2: in 358s import augur.io.vcf 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s _____________________ ERROR collecting tests/test_align.py _____________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_align.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_align.py:10: in 358s from Bio import SeqIO 358s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 358s from Bio.SeqIO import TwoBitIO 358s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 358s raise MissingPythonDependencyError( 358s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 358s ___________________ ERROR collecting tests/test_ancestral.py ___________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_ancestral.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_ancestral.py:1: in 358s from augur.ancestral import run_ancestral 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s ____________________ ERROR collecting tests/test_clades.py _____________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_clades.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_clades.py:4: in 358s from augur.clades import read_in_clade_definitions 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s __________________ ERROR collecting tests/test_frequencies.py __________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_frequencies.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_frequencies.py:6: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s _____________________ ERROR collecting tests/test_mask.py ______________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_mask.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_mask.py:11: in 358s from Bio import SeqIO 358s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 358s from Bio.SeqIO import TwoBitIO 358s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 358s raise MissingPythonDependencyError( 358s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 358s _____________________ ERROR collecting tests/test_parse.py _____________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_parse.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_parse.py:1: in 358s import Bio.SeqIO 358s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 358s from Bio.SeqIO import TwoBitIO 358s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 358s raise MissingPythonDependencyError( 358s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 358s ____________________ ERROR collecting tests/test_schemas.py ____________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_schemas.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_schemas.py:2: in 358s import jsonschema.validators 358s /usr/lib/python3/dist-packages/jsonschema/__init__.py:13: in 358s from jsonschema._format import FormatChecker 358s /usr/lib/python3/dist-packages/jsonschema/_format.py:11: in 358s from jsonschema.exceptions import FormatError 358s /usr/lib/python3/dist-packages/jsonschema/exceptions.py:15: in 358s from referencing.exceptions import Unresolvable as _Unresolvable 358s /usr/lib/python3/dist-packages/referencing/__init__.py:5: in 358s from referencing._core import Anchor, Registry, Resource, Specification 358s /usr/lib/python3/dist-packages/referencing/_core.py:9: in 358s from rpds import HashTrieMap, HashTrieSet, List 358s /usr/lib/python3/dist-packages/rpds/__init__.py:1: in 358s from .rpds import * 358s E ModuleNotFoundError: No module named 'rpds.rpds' 358s _________________ ERROR collecting tests/test_titer_models.py __________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_titer_models.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_titer_models.py:2: in 358s from augur.titer_model import TiterCollection 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s ___________________ ERROR collecting tests/test_translate.py ___________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_translate.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_translate.py:13: in 358s from augur import translate 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s _____________________ ERROR collecting tests/test_utils.py _____________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_utils.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_utils.py:2: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s ___________________ ERROR collecting tests/test_validate.py ____________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_validate.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_validate.py:4: in 358s from augur.validate import ( 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s ________________ ERROR collecting tests/test_validate_export.py ________________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/test_validate_export.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/test_validate_export.py:1: in 358s import Bio.Phylo 358s /usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in 358s from Bio.Phylo._io import convert 358s /usr/lib/python3/dist-packages/Bio/Phylo/_io.py:19: in 358s from Bio.Phylo import PhyloXMLIO 358s /usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in 358s from Bio.Phylo import PhyloXML as PX 358s /usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:23: in 358s from Bio.Align import Alignment 358s /usr/lib/python3/dist-packages/Bio/Align/__init__.py:32: in 358s raise MissingPythonDependencyError( 358s E Bio.MissingPythonDependencyError: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 358s ___________ ERROR collecting tests/util_support/test_color_parser.py ___________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/util_support/test_color_parser.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/util_support/test_color_parser.py:1: in 358s from augur.util_support.color_parser import ColorParser 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s ____________ ERROR collecting tests/util_support/test_node_data.py _____________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/util_support/test_node_data.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/util_support/test_node_data.py:1: in 358s from augur.util_support.node_data import DuplicatedNonDictAttributeError 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s __________ ERROR collecting tests/util_support/test_node_data_file.py __________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/util_support/test_node_data_file.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/util_support/test_node_data_file.py:3: in 358s from augur.__version__ import __version__ 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s _________ ERROR collecting tests/util_support/test_node_data_reader.py _________ 358s ImportError while importing test module '/tmp/autopkgtest.88fRyY/build.Pe2/src/tests/util_support/test_node_data_reader.py'. 358s Hint: make sure your test modules/packages have valid Python names. 358s Traceback: 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 358s from . import multiarray 358s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 358s from . import overrides 358s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 358s from numpy.core._multiarray_umath import ( 358s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 358s 358s During handling of the above exception, another exception occurred: 358s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 358s from numpy.__config__ import show as show_config 358s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 358s from numpy.core._multiarray_umath import ( 358s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 358s raise ImportError(msg) 358s E ImportError: 358s E 358s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 358s E 358s E Importing the numpy C-extensions failed. This error can happen for 358s E many reasons, often due to issues with your setup or how NumPy was 358s E installed. 358s E 358s E We have compiled some common reasons and troubleshooting tips at: 358s E 358s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 358s E 358s E Please note and check the following: 358s E 358s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 358s E * The NumPy version is: "1.26.4" 358s E 358s E and make sure that they are the versions you expect. 358s E Please carefully study the documentation linked above for further help. 358s E 358s E Original error was: No module named 'numpy.core._multiarray_umath' 358s 358s The above exception was the direct cause of the following exception: 358s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 358s return _bootstrap._gcd_import(name[level:], package, level) 358s tests/util_support/test_node_data_reader.py:1: in 358s from augur.util_support.node_data_reader import NodeDataReader 358s augur/__init__.py:12: in 358s from treetime import TreeTimeError, TreeTimeUnknownError 358s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 358s from .treeanc import TreeAnc 358s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 358s import numpy as np 358s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 358s raise ImportError(msg) from e 358s E ImportError: Error importing numpy: you should not try to import numpy from 358s E its source directory; please exit the numpy source tree, and relaunch 358s E your python interpreter from there. 358s =============================== warnings summary =============================== 358s ../../../../usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2131 358s /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 358s warnings.warn( 358s 358s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 358s =========================== short test summary info ============================ 358s ERROR tests/dates/test_ambiguous_date.py 358s ERROR tests/dates/test_dates.py 358s ERROR tests/filter/test_relative_dates.py 358s ERROR tests/filter/test_subsample.py 358s ERROR tests/io/test_file.py 358s ERROR tests/io/test_metadata.py 358s ERROR tests/io/test_sequences.py 358s ERROR tests/io/test_shell_command_runner.py 358s ERROR tests/io/test_strains.py 358s ERROR tests/io/test_vcf.py 358s ERROR tests/test_align.py 358s ERROR tests/test_ancestral.py 358s ERROR tests/test_clades.py 358s ERROR tests/test_frequencies.py 358s ERROR tests/test_mask.py 358s ERROR tests/test_parse.py 358s ERROR tests/test_schemas.py 358s ERROR tests/test_titer_models.py 358s ERROR tests/test_translate.py 358s ERROR tests/test_utils.py 358s ERROR tests/test_validate.py 358s ERROR tests/test_validate_export.py 358s ERROR tests/util_support/test_color_parser.py 358s ERROR tests/util_support/test_node_data.py 358s ERROR tests/util_support/test_node_data_file.py 358s ERROR tests/util_support/test_node_data_reader.py 358s !!!!!!!!!!!!!!!!!!! Interrupted: 26 errors during collection !!!!!!!!!!!!!!!!!!! 358s ======================== 1 warning, 26 errors in 2.33s ========================= 359s autopkgtest [08:52:41]: test run-unit-test: -----------------------] 359s run-unit-test FAIL non-zero exit status 2 359s autopkgtest [08:52:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 359s autopkgtest [08:52:41]: @@@@@@@@@@@@@@@@@@@@ summary 359s run-unit-test FAIL non-zero exit status 2 385s nova [W] Skipping flock in bos03-arm64 385s Creating nova instance adt-plucky-arm64-augur-20241113-084632-juju-7f2275-prod-proposed-migration-environment-20-3aec0107-9333-449d-b0c0-8ad1046d505a from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...