0s autopkgtest [08:06:31]: starting date and time: 2024-11-13 08:06:31+0000 0s autopkgtest [08:06:31]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [08:06:31]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mvz89s23/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-15@lcy02-45.secgroup --name adt-plucky-amd64-augur-20241113-080630-juju-7f2275-prod-proposed-migration-environment-15-2a125556-6b92-4f99-9443-6ffb9765ae00 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 251s autopkgtest [08:10:42]: testbed dpkg architecture: amd64 251s autopkgtest [08:10:42]: testbed apt version: 2.9.8 251s autopkgtest [08:10:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 251s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 251s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 251s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 251s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 251s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [848 kB] 251s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 251s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 251s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 251s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 251s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 251s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 251s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 252s Fetched 2171 kB in 0s (6952 kB/s) 252s Reading package lists... 253s Reading package lists... 253s Building dependency tree... 253s Reading state information... 254s Calculating upgrade... 254s The following NEW packages will be installed: 254s python3.13-gdbm 254s The following packages will be upgraded: 254s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 254s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 254s Need to get 253 kB of archives. 254s After this operation, 147 kB of additional disk space will be used. 254s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 254s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 254s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 254s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 254s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 254s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 254s Fetched 253 kB in 0s (8415 kB/s) 254s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 254s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 254s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 254s Setting up python3-minimal (3.12.7-1) ... 255s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 255s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 255s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 255s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 255s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 255s Selecting previously unselected package python3.13-gdbm. 255s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 255s Unpacking python3.13-gdbm (3.13.0-2) ... 255s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 255s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 255s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 255s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 255s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 255s Setting up python3.13-gdbm (3.13.0-2) ... 255s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 255s Setting up python3 (3.12.7-1) ... 255s Setting up python3-gdbm:amd64 (3.12.7-1) ... 255s Processing triggers for man-db (2.12.1-3) ... 256s Processing triggers for libc-bin (2.40-1ubuntu3) ... 256s Reading package lists... 256s Building dependency tree... 256s Reading state information... 257s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 257s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 258s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 258s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 258s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 259s Reading package lists... 259s Reading package lists... 260s Building dependency tree... 260s Reading state information... 260s Calculating upgrade... 260s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 260s Reading package lists... 261s Building dependency tree... 261s Reading state information... 261s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 262s autopkgtest [08:10:53]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 262s autopkgtest [08:10:53]: @@@@@@@@@@@@@@@@@@@@ apt-source augur 263s Get:1 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (dsc) [2754 B] 263s Get:2 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (tar) [6802 kB] 263s Get:3 http://ftpmaster.internal/ubuntu plucky/universe augur 24.4.0-1 (diff) [16.5 kB] 263s gpgv: Signature made Wed May 22 16:59:51 2024 UTC 263s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 263s gpgv: issuer "emollier@debian.org" 263s gpgv: Can't check signature: No public key 263s dpkg-source: warning: cannot verify inline signature for ./augur_24.4.0-1.dsc: no acceptable signature found 263s autopkgtest [08:10:54]: testing package augur version 24.4.0-1 263s autopkgtest [08:10:54]: build not needed 264s autopkgtest [08:10:55]: test run-unit-test: preparing testbed 270s Reading package lists... 271s Building dependency tree... 271s Reading state information... 271s Starting pkgProblemResolver with broken count: 0 271s Starting 2 pkgProblemResolver with broken count: 0 271s Done 272s The following additional packages will be installed: 272s augur blt fasttree flake8 fontconfig-config fonts-dejavu-core 272s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libamd3 libblas3 libcairo2 272s libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 libdsdp-5.8t64 272s libfftw3-double3 libfontconfig1 libfontenc1 libgfortran5 libglpk40 libgomp1 272s libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 272s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 272s liblcms2-2 liblerc4 libltdl7 libopenjp2-7 libpixman-1-0 272s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 272s libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 libumfpack6 272s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 272s libxrender1 libxslt1.1 libxss1 mafft mypy pigz python-matplotlib-data 272s python3-all python3-appdirs python3-asttokens python3-bcbio-gff 272s python3-biopython python3-boto3 python3-botocore python3-brotli 272s python3-cairo python3-contourpy python3-cvxopt python3-cycler 272s python3-dateutil python3-decorator python3-dendropy python3-executing 272s python3-flake8 python3-fonttools python3-freetype python3-freezegun 272s python3-fs python3-importlib-metadata python3-iniconfig python3-ipdb 272s python3-ipython python3-isodate python3-jedi python3-jmespath 272s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 272s python3-matplotlib-inline python3-mccabe python3-mpmath python3-mypy 272s python3-mypy-extensions python3-networkx python3-numpy python3-packaging 272s python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil 272s python3-pil.imagetk python3-pluggy python3-prompt-toolkit python3-psutil 272s python3-ptyprocess python3-pure-eval python3-pycodestyle python3-pyfaidx 272s python3-pyfastx python3-pyflakes python3-pygtrie python3-pytest 272s python3-pytest-mock python3-reportlab python3-rlpycairo python3-s3transfer 272s python3-schedule python3-scipy python3-seaborn python3-six 272s python3-stack-data python3-sympy python3-tk python3-traitlets 272s python3-treetime python3-typeshed python3-tz python3-ufolib2 272s python3-unicodedata2 python3-wcwidth python3-xopen python3-zstandard 272s python3.12-tk python3.13 python3.13-minimal python3.13-tk raxml seqmagick 272s sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common 272s xfonts-encodings xfonts-utils xml-core 272s Suggested packages: 272s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre libfftw3-bin 272s libfftw3-dev libiodbc2-dev default-libmysqlclient-dev gsl-ref-psdoc 272s | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libjs-jquery-ui-docs 272s liblcms2-utils tcl8.6 tk8.6 mypy-doc bwa clustalo clustalw dialign dssp 272s emboss muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf 272s python3-rdflib python3-psycopg2 samtools t-coffee wise python-cvxopt-doc 272s python-cycler-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng 272s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 272s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 272s python3-gobject python3-pyqt5 python3-sip python3-tornado 272s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 272s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 272s python3-dev python-pandas-doc python3-statsmodels python-pexpect-doc 272s python-pil-doc python-pygtrie-doc python-pytest-mock-doc pdf-viewer 272s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 272s python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 272s python-traitlets-doc python-zstandard-doc python3.13-venv python3.13-doc 272s binfmt-support sgml-base-doc debhelper 272s Recommended packages: 272s iqtree javascript-common blast2 libwww-perl lynx ruby python-biopython-doc 272s ncbi-blast+ python3-bs4 python3-cssselect python3-html5lib python3-orjson 272s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 272s python3-tables python3-numba python3-olefile pyflakes3 fonts-dejavu-extra 272s g++ | c++-compiler isympy-common tabix 272s The following NEW packages will be installed: 272s augur autopkgtest-satdep blt fasttree flake8 fontconfig-config 272s fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 libamd3 272s libblas3 libcairo2 libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 272s libdsdp-5.8t64 libfftw3-double3 libfontconfig1 libfontenc1 libgfortran5 272s libglpk40 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b 272s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 272s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libltdl7 libopenjp2-7 272s libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 272s libraqm0 libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 272s libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 272s libxft2 libxrender1 libxslt1.1 libxss1 mafft mypy pigz 272s python-matplotlib-data python3-all python3-appdirs python3-asttokens 272s python3-bcbio-gff python3-biopython python3-boto3 python3-botocore 272s python3-brotli python3-cairo python3-contourpy python3-cvxopt python3-cycler 272s python3-dateutil python3-decorator python3-dendropy python3-executing 272s python3-flake8 python3-fonttools python3-freetype python3-freezegun 272s python3-fs python3-importlib-metadata python3-iniconfig python3-ipdb 272s python3-ipython python3-isodate python3-jedi python3-jmespath 272s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 272s python3-matplotlib-inline python3-mccabe python3-mpmath python3-mypy 272s python3-mypy-extensions python3-networkx python3-numpy python3-packaging 272s python3-pandas python3-pandas-lib python3-parso python3-pexpect python3-pil 272s python3-pil.imagetk python3-pluggy python3-prompt-toolkit python3-psutil 272s python3-ptyprocess python3-pure-eval python3-pycodestyle python3-pyfaidx 272s python3-pyfastx python3-pyflakes python3-pygtrie python3-pytest 272s python3-pytest-mock python3-reportlab python3-rlpycairo python3-s3transfer 272s python3-schedule python3-scipy python3-seaborn python3-six 272s python3-stack-data python3-sympy python3-tk python3-traitlets 272s python3-treetime python3-typeshed python3-tz python3-ufolib2 272s python3-unicodedata2 python3-wcwidth python3-xopen python3-zstandard 272s python3.12-tk python3.13 python3.13-minimal python3.13-tk raxml seqmagick 272s sgml-base tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common 272s xfonts-encodings xfonts-utils xml-core 272s 0 upgraded, 157 newly installed, 0 to remove and 0 not upgraded. 272s Need to get 130 MB/130 MB of archives. 272s After this operation, 628 MB of additional disk space will be used. 272s Get:1 /tmp/autopkgtest.InsqFC/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [756 B] 272s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 272s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 272s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 272s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 pigz amd64 2.8-1 [65.6 kB] 272s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 272s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 272s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 272s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 272s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 272s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 272s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 272s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 272s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 272s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 272s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 272s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 272s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 272s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 272s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 272s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 272s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 272s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 272s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 272s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 272s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 272s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 272s Get:28 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 272s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 272s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 272s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 272s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 272s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 272s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 272s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 272s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 272s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 272s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 272s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 272s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 272s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 272s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 272s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 272s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 272s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 272s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 272s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 272s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 272s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 272s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 272s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 272s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 272s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 272s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 272s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 272s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 272s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 272s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 272s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 272s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bcbio-gff all 0.7.1-2 [33.9 kB] 272s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-2 [13.4 kB] 272s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd3 amd64 1:7.8.3+dfsg-2 [31.1 kB] 272s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcamd3 amd64 1:7.8.3+dfsg-2 [27.6 kB] 272s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccolamd3 amd64 1:7.8.3+dfsg-2 [27.5 kB] 272s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-2 [19.5 kB] 272s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcholmod5 amd64 1:7.8.3+dfsg-2 [876 kB] 272s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 libdsdp-5.8t64 amd64 5.8-10.1build1 [199 kB] 272s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu4 [839 kB] 272s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.4.7-7build1 [40.3 kB] 272s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglpk40 amd64 5.0-1build2 [369 kB] 272s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgslcblas0 amd64 2.8+dfsg-5 [290 kB] 272s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgsl28 amd64 2.8+dfsg-5 [1285 kB] 272s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 libumfpack6 amd64 1:7.8.3+dfsg-2 [337 kB] 272s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cvxopt amd64 1.3.0+dfsg-1build7 [279 kB] 272s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-isodate all 0.6.1-3 [24.3 kB] 272s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 272s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 272s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 272s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 272s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 273s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 273s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 273s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 273s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfastx amd64 2.1.0-2 [56.7 kB] 273s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 273s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 273s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 273s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 273s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 273s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 273s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 273s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 273s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 273s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 273s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 273s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 273s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 273s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 273s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 273s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 273s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 273s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 273s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 273s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 273s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 273s Get:106 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 273s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 273s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 273s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 273s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 273s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 273s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 273s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-xopen all 1.7.0-2 [17.0 kB] 273s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jmespath all 1.0.1-1 [21.3 kB] 273s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-botocore all 1.34.46+repack-1ubuntu1 [6211 kB] 273s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-s3transfer all 0.10.1-1ubuntu2 [54.3 kB] 273s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-boto3 all 1.34.46+dfsg-1ubuntu1 [72.5 kB] 273s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-dendropy all 4.6.1-1 [278 kB] 273s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-schedule all 1.2.2-1 [12.2 kB] 273s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-seaborn all 0.13.2-4 [225 kB] 273s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-zstandard amd64 0.23.0-2 [362 kB] 273s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pygtrie all 2.2-2 [16.0 kB] 273s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 seqmagick all 0.8.6-3 [38.6 kB] 273s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 273s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 273s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 273s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 273s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 273s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 273s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pexpect all 4.9-2 [48.1 kB] 273s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 273s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 273s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-asttokens all 2.4.1-2 [20.8 kB] 273s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-executing all 2.1.0-0.1 [24.4 kB] 273s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 273s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 273s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 273s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipdb all 0.13.13-2 [15.4 kB] 273s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 mafft amd64 7.505-1 [795 kB] 273s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB] 273s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 273s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 vcftools amd64 0.1.16-3 [393 kB] 273s Get:143 http://ftpmaster.internal/ubuntu plucky/universe amd64 augur all 24.4.0-1 [238 kB] 273s Get:144 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mccabe all 0.7.0-1 [8678 B] 273s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pycodestyle all 2.11.1-1 [29.9 kB] 273s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyflakes all 3.2.0-1 [52.8 kB] 273s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-flake8 all 7.1.1-1 [43.9 kB] 273s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 flake8 all 7.1.1-1 [6442 B] 273s Get:149 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mypy-extensions all 1.0.0-1 [6148 B] 273s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psutil amd64 5.9.8-2build2 [195 kB] 273s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mypy amd64 1.13.0-1 [8679 kB] 273s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 mypy all 1.13.0-1 [24.9 kB] 273s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freezegun all 1.5.1-1.1 [15.9 kB] 273s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 273s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 273s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 273s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-mock all 3.14.0-2 [11.7 kB] 274s Fetched 130 MB in 2s (78.3 MB/s) 274s Selecting previously unselected package libpython3.13-minimal:amd64. 274s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75548 files and directories currently installed.) 274s Preparing to unpack .../000-libpython3.13-minimal_3.13.0-2_amd64.deb ... 274s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 274s Selecting previously unselected package python3.13-minimal. 274s Preparing to unpack .../001-python3.13-minimal_3.13.0-2_amd64.deb ... 274s Unpacking python3.13-minimal (3.13.0-2) ... 274s Selecting previously unselected package sgml-base. 274s Preparing to unpack .../002-sgml-base_1.31_all.deb ... 274s Unpacking sgml-base (1.31) ... 274s Selecting previously unselected package pigz. 274s Preparing to unpack .../003-pigz_2.8-1_amd64.deb ... 274s Unpacking pigz (2.8-1) ... 274s Selecting previously unselected package libblas3:amd64. 274s Preparing to unpack .../004-libblas3_3.12.0-3build2_amd64.deb ... 274s Unpacking libblas3:amd64 (3.12.0-3build2) ... 274s Selecting previously unselected package libgfortran5:amd64. 274s Preparing to unpack .../005-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 274s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 274s Selecting previously unselected package liblapack3:amd64. 274s Preparing to unpack .../006-liblapack3_3.12.0-3build2_amd64.deb ... 274s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 274s Selecting previously unselected package python3-numpy. 274s Preparing to unpack .../007-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 274s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 275s Selecting previously unselected package libtcl8.6:amd64. 275s Preparing to unpack .../008-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 275s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 275s Selecting previously unselected package fonts-dejavu-mono. 275s Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ... 275s Unpacking fonts-dejavu-mono (2.37-8) ... 275s Selecting previously unselected package fonts-dejavu-core. 275s Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ... 275s Unpacking fonts-dejavu-core (2.37-8) ... 275s Selecting previously unselected package libfontenc1:amd64. 275s Preparing to unpack .../011-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 275s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 275s Selecting previously unselected package x11-common. 275s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ... 275s Unpacking x11-common (1:7.7+23ubuntu3) ... 275s Selecting previously unselected package xfonts-encodings. 275s Preparing to unpack .../013-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 275s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 275s Selecting previously unselected package xfonts-utils. 275s Preparing to unpack .../014-xfonts-utils_1%3a7.7+7_amd64.deb ... 275s Unpacking xfonts-utils (1:7.7+7) ... 275s Selecting previously unselected package fonts-urw-base35. 275s Preparing to unpack .../015-fonts-urw-base35_20200910-8_all.deb ... 275s Unpacking fonts-urw-base35 (20200910-8) ... 275s Selecting previously unselected package fontconfig-config. 275s Preparing to unpack .../016-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 275s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 275s Selecting previously unselected package libfontconfig1:amd64. 275s Preparing to unpack .../017-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 275s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 275s Selecting previously unselected package libxrender1:amd64. 275s Preparing to unpack .../018-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 275s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 275s Selecting previously unselected package libxft2:amd64. 275s Preparing to unpack .../019-libxft2_2.3.6-1build1_amd64.deb ... 275s Unpacking libxft2:amd64 (2.3.6-1build1) ... 275s Selecting previously unselected package libxss1:amd64. 275s Preparing to unpack .../020-libxss1_1%3a1.2.3-1build3_amd64.deb ... 275s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 275s Selecting previously unselected package libtk8.6:amd64. 275s Preparing to unpack .../021-libtk8.6_8.6.15-1_amd64.deb ... 275s Unpacking libtk8.6:amd64 (8.6.15-1) ... 276s Selecting previously unselected package python3.12-tk. 276s Preparing to unpack .../022-python3.12-tk_3.12.7-3_amd64.deb ... 276s Unpacking python3.12-tk (3.12.7-3) ... 276s Selecting previously unselected package python3.13-tk. 276s Preparing to unpack .../023-python3.13-tk_3.13.0-2_amd64.deb ... 276s Unpacking python3.13-tk (3.13.0-2) ... 276s Selecting previously unselected package tk8.6-blt2.5. 276s Preparing to unpack .../024-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 276s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 276s Selecting previously unselected package blt. 276s Preparing to unpack .../025-blt_2.5.3+dfsg-7build1_amd64.deb ... 276s Unpacking blt (2.5.3+dfsg-7build1) ... 276s Selecting previously unselected package python3-tk:amd64. 276s Preparing to unpack .../026-python3-tk_3.12.7-1_amd64.deb ... 276s Unpacking python3-tk:amd64 (3.12.7-1) ... 276s Selecting previously unselected package python3-pil.imagetk:amd64. 276s Preparing to unpack .../027-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 276s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 276s Selecting previously unselected package libgomp1:amd64. 276s Preparing to unpack .../028-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 276s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 276s Selecting previously unselected package libimagequant0:amd64. 276s Preparing to unpack .../029-libimagequant0_2.18.0-1build1_amd64.deb ... 276s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 276s Selecting previously unselected package libjpeg-turbo8:amd64. 276s Preparing to unpack .../030-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 276s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 276s Selecting previously unselected package libjpeg8:amd64. 276s Preparing to unpack .../031-libjpeg8_8c-2ubuntu11_amd64.deb ... 276s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 276s Selecting previously unselected package liblcms2-2:amd64. 276s Preparing to unpack .../032-liblcms2-2_2.16-2_amd64.deb ... 276s Unpacking liblcms2-2:amd64 (2.16-2) ... 276s Selecting previously unselected package libopenjp2-7:amd64. 276s Preparing to unpack .../033-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 276s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 276s Selecting previously unselected package libgraphite2-3:amd64. 276s Preparing to unpack .../034-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 276s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 276s Selecting previously unselected package libharfbuzz0b:amd64. 276s Preparing to unpack .../035-libharfbuzz0b_10.0.1-1_amd64.deb ... 276s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 276s Selecting previously unselected package libraqm0:amd64. 276s Preparing to unpack .../036-libraqm0_0.10.1-1build1_amd64.deb ... 276s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 276s Selecting previously unselected package libdeflate0:amd64. 276s Preparing to unpack .../037-libdeflate0_1.22-1_amd64.deb ... 276s Unpacking libdeflate0:amd64 (1.22-1) ... 276s Selecting previously unselected package libjbig0:amd64. 276s Preparing to unpack .../038-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 276s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 276s Selecting previously unselected package liblerc4:amd64. 276s Preparing to unpack .../039-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 276s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 276s Selecting previously unselected package libsharpyuv0:amd64. 276s Preparing to unpack .../040-libsharpyuv0_1.4.0-0.1_amd64.deb ... 276s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 276s Selecting previously unselected package libwebp7:amd64. 276s Preparing to unpack .../041-libwebp7_1.4.0-0.1_amd64.deb ... 276s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 276s Selecting previously unselected package libtiff6:amd64. 276s Preparing to unpack .../042-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 276s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 276s Selecting previously unselected package libwebpdemux2:amd64. 276s Preparing to unpack .../043-libwebpdemux2_1.4.0-0.1_amd64.deb ... 276s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 276s Selecting previously unselected package libwebpmux3:amd64. 276s Preparing to unpack .../044-libwebpmux3_1.4.0-0.1_amd64.deb ... 276s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 276s Selecting previously unselected package python3-pil:amd64. 276s Preparing to unpack .../045-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 276s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 276s Selecting previously unselected package libpixman-1-0:amd64. 276s Preparing to unpack .../046-libpixman-1-0_0.44.0-3_amd64.deb ... 276s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 276s Selecting previously unselected package libxcb-render0:amd64. 276s Preparing to unpack .../047-libxcb-render0_1.17.0-2_amd64.deb ... 276s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 276s Selecting previously unselected package libxcb-shm0:amd64. 276s Preparing to unpack .../048-libxcb-shm0_1.17.0-2_amd64.deb ... 276s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 276s Selecting previously unselected package libcairo2:amd64. 276s Preparing to unpack .../049-libcairo2_1.18.2-2_amd64.deb ... 276s Unpacking libcairo2:amd64 (1.18.2-2) ... 276s Selecting previously unselected package python3-cairo. 276s Preparing to unpack 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python3-biopython. 277s Preparing to unpack .../056-python3-biopython_1.84+dfsg-4_amd64.deb ... 277s Unpacking python3-biopython (1.84+dfsg-4) ... 277s Selecting previously unselected package python3-six. 277s Preparing to unpack .../057-python3-six_1.16.0-7_all.deb ... 277s Unpacking python3-six (1.16.0-7) ... 277s Selecting previously unselected package python3-bcbio-gff. 277s Preparing to unpack .../058-python3-bcbio-gff_0.7.1-2_all.deb ... 277s Unpacking python3-bcbio-gff (0.7.1-2) ... 277s Selecting previously unselected package libsuitesparseconfig7:amd64. 277s Preparing to unpack .../059-libsuitesparseconfig7_1%3a7.8.3+dfsg-2_amd64.deb ... 277s Unpacking libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-2) ... 277s Selecting previously unselected package libamd3:amd64. 277s Preparing to unpack .../060-libamd3_1%3a7.8.3+dfsg-2_amd64.deb ... 277s Unpacking libamd3:amd64 (1:7.8.3+dfsg-2) ... 277s Selecting previously unselected package libcamd3:amd64. 277s Preparing to unpack .../061-libcamd3_1%3a7.8.3+dfsg-2_amd64.deb ... 277s Unpacking libcamd3:amd64 (1:7.8.3+dfsg-2) ... 277s Selecting previously unselected package libccolamd3:amd64. 277s Preparing to unpack .../062-libccolamd3_1%3a7.8.3+dfsg-2_amd64.deb ... 277s Unpacking libccolamd3:amd64 (1:7.8.3+dfsg-2) ... 277s Selecting previously unselected package libcolamd3:amd64. 277s Preparing to unpack .../063-libcolamd3_1%3a7.8.3+dfsg-2_amd64.deb ... 277s Unpacking libcolamd3:amd64 (1:7.8.3+dfsg-2) ... 277s Selecting previously unselected package libcholmod5:amd64. 277s Preparing to unpack .../064-libcholmod5_1%3a7.8.3+dfsg-2_amd64.deb ... 277s Unpacking libcholmod5:amd64 (1:7.8.3+dfsg-2) ... 277s Selecting previously unselected package libdsdp-5.8t64. 277s Preparing to unpack .../065-libdsdp-5.8t64_5.8-10.1build1_amd64.deb ... 277s Unpacking libdsdp-5.8t64 (5.8-10.1build1) ... 277s Selecting previously unselected package libfftw3-double3:amd64. 277s Preparing to unpack .../066-libfftw3-double3_3.3.10-1ubuntu4_amd64.deb ... 277s Unpacking libfftw3-double3:amd64 (3.3.10-1ubuntu4) ... 277s Selecting previously unselected package libltdl7:amd64. 277s Preparing to unpack .../067-libltdl7_2.4.7-7build1_amd64.deb ... 277s Unpacking libltdl7:amd64 (2.4.7-7build1) ... 277s Selecting previously unselected package libglpk40:amd64. 277s Preparing to unpack .../068-libglpk40_5.0-1build2_amd64.deb ... 277s Unpacking libglpk40:amd64 (5.0-1build2) ... 277s Selecting previously unselected package libgslcblas0:amd64. 277s Preparing to unpack .../069-libgslcblas0_2.8+dfsg-5_amd64.deb ... 277s Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... 277s Selecting previously unselected package libgsl28:amd64. 277s Preparing to unpack .../070-libgsl28_2.8+dfsg-5_amd64.deb ... 277s Unpacking libgsl28:amd64 (2.8+dfsg-5) ... 277s Selecting previously unselected package libumfpack6:amd64. 277s Preparing to unpack .../071-libumfpack6_1%3a7.8.3+dfsg-2_amd64.deb ... 277s Unpacking libumfpack6:amd64 (1:7.8.3+dfsg-2) ... 277s Selecting previously unselected package python3-cvxopt. 277s Preparing to unpack .../072-python3-cvxopt_1.3.0+dfsg-1build7_amd64.deb ... 277s Unpacking python3-cvxopt (1.3.0+dfsg-1build7) ... 277s Selecting previously unselected package python3-isodate. 277s Preparing to unpack .../073-python3-isodate_0.6.1-3_all.deb ... 277s Unpacking python3-isodate (0.6.1-3) ... 277s Selecting previously unselected package python3-networkx. 277s Preparing to unpack .../074-python3-networkx_3.2.1-4ubuntu1_all.deb ... 277s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 278s Selecting previously unselected package python3-packaging. 278s Preparing to unpack .../075-python3-packaging_24.1-1_all.deb ... 278s Unpacking python3-packaging (24.1-1) ... 278s Selecting previously unselected package python3-dateutil. 278s Preparing to unpack .../076-python3-dateutil_2.9.0-2_all.deb ... 278s Unpacking python3-dateutil (2.9.0-2) ... 278s Selecting previously unselected package python3-tz. 278s Preparing to unpack .../077-python3-tz_2024.1-2_all.deb ... 278s Unpacking python3-tz (2024.1-2) ... 278s Selecting previously unselected package python3-pandas-lib:amd64. 278s Preparing to unpack .../078-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ... 278s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 278s Selecting previously unselected package python3-pandas. 278s Preparing to unpack .../079-python3-pandas_2.2.3+dfsg-5_all.deb ... 278s Unpacking python3-pandas (2.2.3+dfsg-5) ... 279s Selecting previously unselected package python3-importlib-metadata. 279s Preparing to unpack .../080-python3-importlib-metadata_8.5.0-1_all.deb ... 279s Unpacking python3-importlib-metadata (8.5.0-1) ... 279s Selecting previously unselected package python3-pyfaidx. 279s Preparing to unpack .../081-python3-pyfaidx_0.8.1.3-1_all.deb ... 279s Unpacking python3-pyfaidx (0.8.1.3-1) ... 279s Selecting previously unselected package python3-pyfastx. 279s Preparing to unpack .../082-python3-pyfastx_2.1.0-2_amd64.deb ... 279s Unpacking python3-pyfastx (2.1.0-2) ... 279s Selecting previously unselected package python3-decorator. 279s Preparing to unpack .../083-python3-decorator_5.1.1-5_all.deb ... 279s Unpacking python3-decorator (5.1.1-5) ... 279s Selecting previously unselected package liblbfgsb0:amd64. 279s Preparing to unpack .../084-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 279s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 279s Selecting previously unselected package python3-scipy. 279s Preparing to unpack .../085-python3-scipy_1.13.1-5_amd64.deb ... 279s Unpacking python3-scipy (1.13.1-5) ... 279s Selecting previously unselected package libjs-jquery. 279s Preparing to unpack .../086-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 279s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 279s Selecting previously unselected package libjs-jquery-ui. 279s Preparing to unpack .../087-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 279s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 279s Selecting previously unselected package fonts-lyx. 279s Preparing to unpack .../088-fonts-lyx_2.4.2.1-1_all.deb ... 279s Unpacking fonts-lyx (2.4.2.1-1) ... 279s Selecting previously unselected package python-matplotlib-data. 279s Preparing to unpack .../089-python-matplotlib-data_3.8.3-3_all.deb ... 279s Unpacking python-matplotlib-data (3.8.3-3) ... 279s Selecting previously unselected package python3-contourpy. 279s Preparing to unpack .../090-python3-contourpy_1.3.0-2_amd64.deb ... 279s Unpacking python3-contourpy (1.3.0-2) ... 280s Selecting previously unselected package python3-cycler. 280s Preparing to unpack .../091-python3-cycler_0.12.1-1_all.deb ... 280s Unpacking python3-cycler (0.12.1-1) ... 280s Selecting previously unselected package python3-brotli. 280s Preparing to unpack .../092-python3-brotli_1.1.0-2build2_amd64.deb ... 280s Unpacking python3-brotli (1.1.0-2build2) ... 280s Selecting previously unselected package python3-ufolib2. 280s Preparing to unpack .../093-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 280s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 280s Selecting previously unselected package python3-mpmath. 280s Preparing to unpack .../094-python3-mpmath_1.3.0-1_all.deb ... 280s Unpacking python3-mpmath (1.3.0-1) ... 280s Selecting previously unselected package python3-sympy. 280s Preparing to unpack .../095-python3-sympy_1.13.3-1_all.deb ... 280s Unpacking python3-sympy (1.13.3-1) ... 280s Selecting previously unselected package python3-appdirs. 280s Preparing to unpack .../096-python3-appdirs_1.4.4-4_all.deb ... 280s Unpacking python3-appdirs (1.4.4-4) ... 280s Selecting previously unselected package python3-fs. 280s Preparing to unpack .../097-python3-fs_2.4.16-4_all.deb ... 280s Unpacking python3-fs (2.4.16-4) ... 280s Selecting previously unselected package libxslt1.1:amd64. 280s Preparing to unpack .../098-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 280s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 280s Selecting previously unselected package python3-lxml:amd64. 280s Preparing to unpack .../099-python3-lxml_5.3.0-1_amd64.deb ... 280s Unpacking python3-lxml:amd64 (5.3.0-1) ... 280s Selecting previously unselected package python3-lz4. 280s Preparing to unpack .../100-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 280s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 280s Selecting previously unselected package python3-unicodedata2. 280s Preparing to unpack .../101-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 280s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 280s Selecting previously unselected package libpython3.13-stdlib:amd64. 280s Preparing to unpack .../102-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 280s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 280s Selecting previously unselected package python3.13. 280s Preparing to unpack .../103-python3.13_3.13.0-2_amd64.deb ... 280s Unpacking python3.13 (3.13.0-2) ... 280s Selecting previously unselected package python3-all. 280s Preparing to unpack .../104-python3-all_3.12.7-1_amd64.deb ... 280s Unpacking python3-all (3.12.7-1) ... 280s Selecting previously unselected package unicode-data. 281s Preparing to unpack .../105-unicode-data_15.1.0-1_all.deb ... 281s Unpacking unicode-data (15.1.0-1) ... 281s Selecting previously unselected package python3-fonttools. 281s Preparing to unpack .../106-python3-fonttools_4.46.0-1build2_amd64.deb ... 281s Unpacking python3-fonttools (4.46.0-1build2) ... 281s Selecting previously unselected package python3-kiwisolver. 281s Preparing to unpack .../107-python3-kiwisolver_1.4.7-2_amd64.deb ... 281s Unpacking python3-kiwisolver (1.4.7-2) ... 281s Selecting previously unselected package libqhull-r8.0:amd64. 281s Preparing to unpack .../108-libqhull-r8.0_2020.2-6build1_amd64.deb ... 281s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 281s Selecting previously unselected package python3-matplotlib. 281s Preparing to unpack .../109-python3-matplotlib_3.8.3-3_amd64.deb ... 281s Unpacking python3-matplotlib (3.8.3-3) ... 281s Selecting previously unselected package python3-treetime. 281s Preparing to unpack .../110-python3-treetime_0.11.4-1_all.deb ... 281s Unpacking python3-treetime (0.11.4-1) ... 281s Selecting previously unselected package python3-xopen. 281s Preparing to unpack .../111-python3-xopen_1.7.0-2_all.deb ... 281s Unpacking python3-xopen (1.7.0-2) ... 281s Selecting previously unselected package python3-jmespath. 281s Preparing to unpack .../112-python3-jmespath_1.0.1-1_all.deb ... 281s Unpacking python3-jmespath (1.0.1-1) ... 281s Selecting previously unselected package python3-botocore. 281s Preparing to unpack .../113-python3-botocore_1.34.46+repack-1ubuntu1_all.deb ... 281s Unpacking python3-botocore (1.34.46+repack-1ubuntu1) ... 282s Selecting previously unselected package python3-s3transfer. 282s Preparing to unpack .../114-python3-s3transfer_0.10.1-1ubuntu2_all.deb ... 282s Unpacking python3-s3transfer (0.10.1-1ubuntu2) ... 282s Selecting previously unselected package python3-boto3. 282s Preparing to unpack .../115-python3-boto3_1.34.46+dfsg-1ubuntu1_all.deb ... 282s Unpacking python3-boto3 (1.34.46+dfsg-1ubuntu1) ... 282s Selecting previously unselected package python3-dendropy. 282s Preparing to unpack .../116-python3-dendropy_4.6.1-1_all.deb ... 282s Unpacking python3-dendropy (4.6.1-1) ... 282s Selecting previously unselected package python3-schedule. 282s Preparing to unpack .../117-python3-schedule_1.2.2-1_all.deb ... 282s Unpacking python3-schedule (1.2.2-1) ... 282s Selecting previously unselected package python3-seaborn. 282s Preparing to unpack .../118-python3-seaborn_0.13.2-4_all.deb ... 282s Unpacking python3-seaborn (0.13.2-4) ... 282s Selecting previously unselected package python3-zstandard. 282s Preparing to unpack .../119-python3-zstandard_0.23.0-2_amd64.deb ... 282s Unpacking python3-zstandard (0.23.0-2) ... 282s Selecting previously unselected package python3-pygtrie. 282s Preparing to unpack .../120-python3-pygtrie_2.2-2_all.deb ... 282s Unpacking python3-pygtrie (2.2-2) ... 282s Selecting previously unselected package seqmagick. 282s Preparing to unpack .../121-seqmagick_0.8.6-3_all.deb ... 282s Unpacking seqmagick (0.8.6-3) ... 282s Selecting previously unselected package python3-parso. 282s Preparing to unpack .../122-python3-parso_0.8.3-1_all.deb ... 282s Unpacking python3-parso (0.8.3-1) ... 282s Selecting previously unselected package python3-typeshed. 282s Preparing to unpack .../123-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 282s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 283s Selecting previously unselected package python3-jedi. 283s Preparing to unpack .../124-python3-jedi_0.19.1+ds1-1_all.deb ... 283s Unpacking python3-jedi (0.19.1+ds1-1) ... 283s Selecting previously unselected package python3-traitlets. 283s Preparing to unpack .../125-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 283s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 283s Selecting previously unselected package python3-matplotlib-inline. 283s Preparing to unpack .../126-python3-matplotlib-inline_0.1.6-2_all.deb ... 283s Unpacking python3-matplotlib-inline (0.1.6-2) ... 283s Selecting previously unselected package python3-ptyprocess. 283s Preparing to unpack .../127-python3-ptyprocess_0.7.0-6_all.deb ... 283s Unpacking python3-ptyprocess (0.7.0-6) ... 283s Selecting previously unselected package python3-pexpect. 283s Preparing to unpack .../128-python3-pexpect_4.9-2_all.deb ... 283s Unpacking python3-pexpect (4.9-2) ... 283s Selecting previously unselected package python3-wcwidth. 283s Preparing to unpack .../129-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 283s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 283s Selecting previously unselected package python3-prompt-toolkit. 283s Preparing to unpack .../130-python3-prompt-toolkit_3.0.48-1_all.deb ... 283s Unpacking python3-prompt-toolkit (3.0.48-1) ... 283s Selecting previously unselected package python3-asttokens. 283s Preparing to unpack .../131-python3-asttokens_2.4.1-2_all.deb ... 283s Unpacking python3-asttokens (2.4.1-2) ... 283s Selecting previously unselected package python3-executing. 283s Preparing to unpack .../132-python3-executing_2.1.0-0.1_all.deb ... 283s Unpacking python3-executing (2.1.0-0.1) ... 284s Selecting previously unselected package python3-pure-eval. 284s Preparing to unpack .../133-python3-pure-eval_0.2.3-1_all.deb ... 284s Unpacking python3-pure-eval (0.2.3-1) ... 284s Selecting previously unselected package python3-stack-data. 284s Preparing to unpack .../134-python3-stack-data_0.6.3-1_all.deb ... 284s Unpacking python3-stack-data (0.6.3-1) ... 284s Selecting previously unselected package python3-ipython. 284s Preparing to unpack .../135-python3-ipython_8.20.0-1ubuntu1_all.deb ... 284s Unpacking 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376s Setting up augur (24.4.0-1) ... 377s Setting up autopkgtest-satdep (0) ... 381s (Reading database ... 103025 files and directories currently installed.) 381s Removing autopkgtest-satdep (0) ... 382s autopkgtest [08:12:53]: test run-unit-test: [----------------------- 382s ============================= test session starts ============================== 382s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 382s cachedir: .pytest_cache 382s rootdir: /tmp/autopkgtest.InsqFC/build.cbZ/src 382s plugins: mock-3.14.0, typeguard-4.4.1 384s collecting ... collected 2 items / 26 errors 384s 384s ==================================== ERRORS ==================================== 384s _____________ ERROR collecting tests/dates/test_ambiguous_date.py ______________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/dates/test_ambiguous_date.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/dates/test_ambiguous_date.py:3: in 384s from augur.dates import ambiguous_date 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s __________________ ERROR collecting tests/dates/test_dates.py __________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/dates/test_dates.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/dates/test_dates.py:4: in 384s from augur import dates 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s _____________ ERROR collecting tests/filter/test_relative_dates.py _____________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/filter/test_relative_dates.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/filter/test_relative_dates.py:12: in 384s from augur.filter import register_arguments 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s _______________ ERROR collecting tests/filter/test_subsample.py ________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/filter/test_subsample.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/filter/test_subsample.py:2: in 384s import pandas as pd 384s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 384s raise ImportError( 384s E ImportError: Unable to import required dependencies: 384s E numpy: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s ____________________ ERROR collecting tests/io/test_file.py ____________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/io/test_file.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/io/test_file.py:2: in 384s import augur.io.file 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s __________________ ERROR collecting tests/io/test_metadata.py __________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/io/test_metadata.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/io/test_metadata.py:6: in 384s from augur.errors import AugurError 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s _________________ ERROR collecting tests/io/test_sequences.py __________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/io/test_sequences.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/io/test_sequences.py:2: in 384s from Bio import SeqIO 384s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 384s from Bio.SeqIO import TwoBitIO 384s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 384s raise MissingPythonDependencyError( 384s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 384s ____________ ERROR collecting tests/io/test_shell_command_runner.py ____________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/io/test_shell_command_runner.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/io/test_shell_command_runner.py:5: in 384s from augur.io.shell_command_runner import ShellCommandRunner 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s __________________ ERROR collecting tests/io/test_strains.py ___________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/io/test_strains.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/io/test_strains.py:3: in 384s from augur.io.strains import read_strains 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s ____________________ ERROR collecting tests/io/test_vcf.py _____________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/io/test_vcf.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/io/test_vcf.py:2: in 384s import augur.io.vcf 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s _____________________ ERROR collecting tests/test_align.py _____________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_align.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_align.py:10: in 384s from Bio import SeqIO 384s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 384s from Bio.SeqIO import TwoBitIO 384s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 384s raise MissingPythonDependencyError( 384s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 384s ___________________ ERROR collecting tests/test_ancestral.py ___________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_ancestral.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_ancestral.py:1: in 384s from augur.ancestral import run_ancestral 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s ____________________ ERROR collecting tests/test_clades.py _____________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_clades.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_clades.py:4: in 384s from augur.clades import read_in_clade_definitions 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s __________________ ERROR collecting tests/test_frequencies.py __________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_frequencies.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_frequencies.py:6: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s _____________________ ERROR collecting tests/test_mask.py ______________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_mask.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_mask.py:11: in 384s from Bio import SeqIO 384s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 384s from Bio.SeqIO import TwoBitIO 384s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 384s raise MissingPythonDependencyError( 384s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 384s _____________________ ERROR collecting tests/test_parse.py _____________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_parse.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_parse.py:1: in 384s import Bio.SeqIO 384s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 384s from Bio.SeqIO import TwoBitIO 384s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 384s raise MissingPythonDependencyError( 384s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 384s ____________________ ERROR collecting tests/test_schemas.py ____________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_schemas.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_schemas.py:2: in 384s import jsonschema.validators 384s /usr/lib/python3/dist-packages/jsonschema/__init__.py:13: in 384s from jsonschema._format import FormatChecker 384s /usr/lib/python3/dist-packages/jsonschema/_format.py:11: in 384s from jsonschema.exceptions import FormatError 384s /usr/lib/python3/dist-packages/jsonschema/exceptions.py:15: in 384s from referencing.exceptions import Unresolvable as _Unresolvable 384s /usr/lib/python3/dist-packages/referencing/__init__.py:5: in 384s from referencing._core import Anchor, Registry, Resource, Specification 384s /usr/lib/python3/dist-packages/referencing/_core.py:9: in 384s from rpds import HashTrieMap, HashTrieSet, List 384s /usr/lib/python3/dist-packages/rpds/__init__.py:1: in 384s from .rpds import * 384s E ModuleNotFoundError: No module named 'rpds.rpds' 384s _________________ ERROR collecting tests/test_titer_models.py __________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_titer_models.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_titer_models.py:2: in 384s from augur.titer_model import TiterCollection 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s ___________________ ERROR collecting tests/test_translate.py ___________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_translate.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_translate.py:13: in 384s from augur import translate 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s _____________________ ERROR collecting tests/test_utils.py _____________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_utils.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_utils.py:2: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s ___________________ ERROR collecting tests/test_validate.py ____________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_validate.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_validate.py:4: in 384s from augur.validate import ( 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s ________________ ERROR collecting tests/test_validate_export.py ________________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/test_validate_export.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/test_validate_export.py:1: in 384s import Bio.Phylo 384s /usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in 384s from Bio.Phylo._io import convert 384s /usr/lib/python3/dist-packages/Bio/Phylo/_io.py:19: in 384s from Bio.Phylo import PhyloXMLIO 384s /usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in 384s from Bio.Phylo import PhyloXML as PX 384s /usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:23: in 384s from Bio.Align import Alignment 384s /usr/lib/python3/dist-packages/Bio/Align/__init__.py:32: in 384s raise MissingPythonDependencyError( 384s E Bio.MissingPythonDependencyError: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 384s ___________ ERROR collecting tests/util_support/test_color_parser.py ___________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/util_support/test_color_parser.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/util_support/test_color_parser.py:1: in 384s from augur.util_support.color_parser import ColorParser 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s ____________ ERROR collecting tests/util_support/test_node_data.py _____________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/util_support/test_node_data.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/util_support/test_node_data.py:1: in 384s from augur.util_support.node_data import DuplicatedNonDictAttributeError 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s __________ ERROR collecting tests/util_support/test_node_data_file.py __________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/util_support/test_node_data_file.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/util_support/test_node_data_file.py:3: in 384s from augur.__version__ import __version__ 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s _________ ERROR collecting tests/util_support/test_node_data_reader.py _________ 384s ImportError while importing test module '/tmp/autopkgtest.InsqFC/build.cbZ/src/tests/util_support/test_node_data_reader.py'. 384s Hint: make sure your test modules/packages have valid Python names. 384s Traceback: 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 384s from . import multiarray 384s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 384s from . import overrides 384s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 384s from numpy.core._multiarray_umath import ( 384s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 384s 384s During handling of the above exception, another exception occurred: 384s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 384s from numpy.__config__ import show as show_config 384s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 384s from numpy.core._multiarray_umath import ( 384s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 384s raise ImportError(msg) 384s E ImportError: 384s E 384s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 384s E 384s E Importing the numpy C-extensions failed. This error can happen for 384s E many reasons, often due to issues with your setup or how NumPy was 384s E installed. 384s E 384s E We have compiled some common reasons and troubleshooting tips at: 384s E 384s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 384s E 384s E Please note and check the following: 384s E 384s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 384s E * The NumPy version is: "1.26.4" 384s E 384s E and make sure that they are the versions you expect. 384s E Please carefully study the documentation linked above for further help. 384s E 384s E Original error was: No module named 'numpy.core._multiarray_umath' 384s 384s The above exception was the direct cause of the following exception: 384s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 384s return _bootstrap._gcd_import(name[level:], package, level) 384s tests/util_support/test_node_data_reader.py:1: in 384s from augur.util_support.node_data_reader import NodeDataReader 384s augur/__init__.py:12: in 384s from treetime import TreeTimeError, TreeTimeUnknownError 384s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 384s from .treeanc import TreeAnc 384s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 384s import numpy as np 384s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 384s raise ImportError(msg) from e 384s E ImportError: Error importing numpy: you should not try to import numpy from 384s E its source directory; please exit the numpy source tree, and relaunch 384s E your python interpreter from there. 384s =============================== warnings summary =============================== 384s ../../../../usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2131 384s /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 384s warnings.warn( 384s 384s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 384s =========================== short test summary info ============================ 384s ERROR tests/dates/test_ambiguous_date.py 384s ERROR tests/dates/test_dates.py 384s ERROR tests/filter/test_relative_dates.py 384s ERROR tests/filter/test_subsample.py 384s ERROR tests/io/test_file.py 384s ERROR tests/io/test_metadata.py 384s ERROR tests/io/test_sequences.py 384s ERROR tests/io/test_shell_command_runner.py 384s ERROR tests/io/test_strains.py 384s ERROR tests/io/test_vcf.py 384s ERROR tests/test_align.py 384s ERROR tests/test_ancestral.py 384s ERROR tests/test_clades.py 384s ERROR tests/test_frequencies.py 384s ERROR tests/test_mask.py 384s ERROR tests/test_parse.py 384s ERROR tests/test_schemas.py 384s ERROR tests/test_titer_models.py 384s ERROR tests/test_translate.py 384s ERROR tests/test_utils.py 384s ERROR tests/test_validate.py 384s ERROR tests/test_validate_export.py 384s ERROR tests/util_support/test_color_parser.py 384s ERROR tests/util_support/test_node_data.py 384s ERROR tests/util_support/test_node_data_file.py 384s ERROR tests/util_support/test_node_data_reader.py 384s !!!!!!!!!!!!!!!!!!! Interrupted: 26 errors during collection !!!!!!!!!!!!!!!!!!! 384s ======================== 1 warning, 26 errors in 1.85s ========================= 384s autopkgtest [08:12:55]: test run-unit-test: -----------------------] 384s autopkgtest [08:12:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 384s run-unit-test FAIL non-zero exit status 2 385s autopkgtest [08:12:56]: @@@@@@@@@@@@@@@@@@@@ summary 385s run-unit-test FAIL non-zero exit status 2 395s nova [W] Skipping flock for amd64 395s Creating nova instance adt-plucky-amd64-augur-20241113-080630-juju-7f2275-prod-proposed-migration-environment-15-2a125556-6b92-4f99-9443-6ffb9765ae00 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...