0s autopkgtest [10:25:09]: starting date and time: 2025-11-17 10:25:09+0000 0s autopkgtest [10:25:09]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [10:25:09]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6ebwqghc/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:mypy,src:python3-defaults --apt-upgrade augur --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=mypy/1.18.2-2ubuntu1 python3-defaults/3.13.7-2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-3.secgroup --name adt-resolute-i386-augur-20251117-102509-juju-7f2275-prod-proposed-migration-environment-20-9386a087-4b32-411a-971c-6d399473ca58 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-i386-augur-20251117-102509-juju-7f2275-prod-proposed-migration-environment-20-9386a087-4b32-411a-971c-6d399473ca58 from image adt/ubuntu-resolute-amd64-server-20251117.img (UUID 47cb9b95-dcf3-40f8-972d-d06b1b09ded2)... 94s autopkgtest [10:26:43]: testbed dpkg architecture: amd64 94s autopkgtest [10:26:43]: testbed apt version: 3.1.11 95s autopkgtest [10:26:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s autopkgtest [10:26:44]: testbed release detected to be: None 96s autopkgtest [10:26:45]: updating testbed package index (apt update) 96s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 96s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 96s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 96s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 96s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 96s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [881 kB] 97s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 97s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [80.3 kB] 97s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [158 kB] 97s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [118 kB] 97s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3128 B] 97s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3744 B] 97s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [64.6 kB] 97s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 97s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [614 kB] 97s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [282 kB] 97s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [22.2 kB] 97s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [13.4 kB] 97s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [6516 B] 97s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [680 B] 100s Fetched 2367 kB in 1s (2170 kB/s) 100s Reading package lists... 101s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 101s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 101s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 101s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 102s Reading package lists... 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Calculating upgrade... 102s The following packages will be upgraded: 102s libpython3-stdlib python3 python3-minimal usbutils 102s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 146 kB of archives. 102s After this operation, 0 B of additional disk space will be used. 102s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB] 103s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB] 103s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB] 103s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 usbutils amd64 1:019-1 [83.9 kB] 103s dpkg-preconfigure: unable to re-open stdin: No such file or directory 103s Fetched 146 kB in 0s (342 kB/s) 103s (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 ... 83372 files and directories currently installed.) 103s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ... 103s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 103s Setting up python3-minimal (3.13.7-2) ... 103s (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 ... 83372 files and directories currently installed.) 103s Preparing to unpack .../python3_3.13.7-2_amd64.deb ... 103s running python pre-rtupdate hooks for python3.13... 103s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 104s Preparing to unpack .../libpython3-stdlib_3.13.7-2_amd64.deb ... 104s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ... 104s Preparing to unpack .../usbutils_1%3a019-1_amd64.deb ... 104s Unpacking usbutils (1:019-1) over (1:018-2) ... 104s Setting up usbutils (1:019-1) ... 104s Setting up libpython3-stdlib:amd64 (3.13.7-2) ... 104s Setting up python3 (3.13.7-2) ... 104s running python rtupdate hooks for python3.13... 104s running python post-rtupdate hooks for python3.13... 104s Processing triggers for man-db (2.13.1-1) ... 105s autopkgtest [10:26:54]: upgrading testbed (apt dist-upgrade and autopurge) 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Solving dependencies... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s autopkgtest [10:26:58]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 109s autopkgtest [10:26:58]: @@@@@@@@@@@@@@@@@@@@ apt-source augur 111s Get:1 http://ftpmaster.internal/ubuntu resolute/universe augur 24.4.0-1 (dsc) [2754 B] 111s Get:2 http://ftpmaster.internal/ubuntu resolute/universe augur 24.4.0-1 (tar) [6802 kB] 111s Get:3 http://ftpmaster.internal/ubuntu resolute/universe augur 24.4.0-1 (diff) [16.5 kB] 111s gpgv: Signature made Wed May 22 16:59:51 2024 UTC 111s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 111s gpgv: issuer "emollier@debian.org" 111s gpgv: Can't check signature: No public key 111s dpkg-source: warning: cannot verify inline signature for ./augur_24.4.0-1.dsc: no acceptable signature found 112s autopkgtest [10:27:01]: testing package augur version 24.4.0-1 112s autopkgtest [10:27:01]: build not needed 114s autopkgtest [10:27:03]: test run-unit-test: preparing testbed 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Solving dependencies... 114s The following NEW packages will be installed: 114s augur blt fasttree flake8 fontconfig-config fonts-dejavu-core 114s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libamd3 libblas3 libcairo2 114s libcamd3 libccolamd3 libcholmod5 libcolamd3 libdeflate0 libdsdp-5.8t64 114s libfftw3-double3 libfontconfig1 libfontenc1 libgfortran5 libglpk40 libgomp1 114s libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libimagequant0 libjbig0 114s libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 libltdl7 libopenjp2-7 114s libpixman-1-0 libpython3.14-minimal libpython3.14-stdlib libqhull-r8.0 114s libraqm0 libsharpyuv0 libsuitesparseconfig7 libtcl8.6 libtiff6 libtk8.6 114s libumfpack6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 114s libxft2 libxrender1 libxslt1.1 libxss1 libzopfli1 mafft mypy pigz 114s python-matplotlib-data python3-all python3-asttokens python3-bcbio-gff 114s python3-biopython python3-brotli python3-cairo python3-charset-normalizer 114s python3-contourpy python3-cvxopt python3-cycler python3-decorator 114s python3-dendropy python3-executing python3-flake8 python3-fonttools 114s python3-freetype python3-freezegun python3-fs python3-iniconfig python3-ipdb 114s python3-ipython python3-isodate python3-jedi python3-kiwisolver python3-lxml 114s python3-lz4 python3-matplotlib python3-matplotlib-inline python3-mccabe 114s python3-mpmath python3-mypy python3-mypy-extensions python3-networkx 114s python3-numpy python3-numpy-dev python3-pandas python3-pandas-lib 114s python3-parso python3-pathspec python3-pil python3-pil.imagetk 114s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 114s python3-pure-eval python3-pycodestyle python3-pyfaidx python3-pyfastx 114s python3-pyflakes python3-pygtrie python3-pytest python3-pytest-mock 114s python3-pytz python3-reportlab python3-rlpycairo python3-schedule 114s python3-scipy python3-seaborn python3-stack-data python3-sympy python3-tk 114s python3-traitlets python3-treetime python3-typeshed python3-ufolib2 114s python3-wcwidth python3-xopen python3-zopfli python3-zstandard python3.13-tk 114s python3.14 python3.14-minimal python3.14-tk raxml seqmagick sgml-base 114s tk8.6-blt2.5 unicode-data vcftools w3c-sgml-lib x11-common xfonts-encodings 114s xfonts-utils xml-core 115s 0 upgraded, 147 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 153 MB of archives. 115s After this operation, 693 MB of additional disk space will be used. 115s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 115s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 115s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-7ubuntu1 [939 kB] 115s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 115s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 116s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.0-4 [906 kB] 116s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.0-4 [2559 kB] 116s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 pigz amd64 2.8-1 [65.6 kB] 116s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.3-1 [174 kB] 116s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 116s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 116s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 116s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 116s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 116s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 116s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 116s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 116s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 116s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 116s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 116s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 116s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 116s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 116s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-tk amd64 3.14.0-4 [108 kB] 116s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] 116s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 116s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 116s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.9-1 [8946 B] 116s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 11.3.0-1ubuntu2 [9804 B] 116s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-7ubuntu1 [151 kB] 116s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 116s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 116s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 116s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.17-1 [170 kB] 116s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 116s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 116s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 116s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 116s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 116s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 116s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 116s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 116s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 116s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 116s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 116s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 116s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu2 [504 kB] 116s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 116s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 116s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 116s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 116s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2build1 [140 kB] 116s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-2 [92.2 kB] 116s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-4 [9332 B] 116s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.4-2 [1147 kB] 116s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 116s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 116s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 117s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.85+dfsg-4 [1719 kB] 117s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-bcbio-gff all 0.7.1-2 [33.9 kB] 117s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libsuitesparseconfig7 amd64 1:7.11.0+dfsg-2 [21.9 kB] 117s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd3 amd64 1:7.11.0+dfsg-2 [35.8 kB] 117s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcamd3 amd64 1:7.11.0+dfsg-2 [32.2 kB] 117s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 libccolamd3 amd64 1:7.11.0+dfsg-2 [34.5 kB] 117s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolamd3 amd64 1:7.11.0+dfsg-2 [27.4 kB] 117s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcholmod5 amd64 1:7.11.0+dfsg-2 [717 kB] 117s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 libdsdp-5.8t64 amd64 5.8-11 [201 kB] 117s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libfftw3-double3 amd64 3.3.10-2fakesync1build2 [860 kB] 117s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libltdl7 amd64 2.5.4-7 [43.3 kB] 117s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 libglpk40 amd64 5.0-2 [380 kB] 117s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgslcblas0 amd64 2.8+dfsg-5.1ubuntu1 [133 kB] 117s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgsl28 amd64 2.8+dfsg-5.1ubuntu1 [1104 kB] 117s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 libumfpack6 amd64 1:7.11.0+dfsg-2 [298 kB] 117s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cvxopt amd64 1.3.2+dfsg-2 [302 kB] 117s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-isodate all 0.7.2-2 [18.8 kB] 117s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 117s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB] 117s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-1ubuntu1 [7668 kB] 117s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 117s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyfaidx all 0.8.1.3-2 [29.7 kB] 117s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyfastx amd64 2.2.0-1build2 [64.5 kB] 117s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 117s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.15.3-1ubuntu1 [20.3 MB] 118s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-2 [171 kB] 118s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.7+dfsg1-1 [2930 kB] 118s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.1-2 [255 kB] 118s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-2 [9850 B] 118s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build6 [340 kB] 118s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.3.7-1 [16.9 kB] 118s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-9ubuntu1 [91.5 kB] 118s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.3 [172 kB] 118s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.2-1 [2333 kB] 118s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.4+dfsg-3 [27.5 kB] 118s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-2 [423 kB] 118s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.14.0-2 [4306 kB] 118s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 118s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.0-4 [2397 kB] 118s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.0-4 [805 kB] 118s Get:99 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.13.7-2 [890 B] 118s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 118s Get:101 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.4.0-1 [11.1 kB] 118s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 16.0.0-1 [9513 kB] 120s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-2build1 [1731 kB] 120s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.10~rc0-1 [65.5 kB] 120s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-7 [197 kB] 120s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.7+dfsg1-1 [17.2 MB] 122s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-treetime all 0.11.4-1 [941 kB] 122s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-xopen all 1.7.0-3 [17.2 kB] 122s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-dendropy all 4.6.1-2 [278 kB] 122s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-schedule all 1.2.2-1 [12.2 kB] 122s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-seaborn all 0.13.2-5 [225 kB] 122s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zstandard amd64 0.25.0-1 [409 kB] 122s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pygtrie all 2.2-3 [16.3 kB] 122s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 seqmagick all 0.8.6-3 [38.6 kB] 122s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-parso all 0.8.5-1 [68.0 kB] 122s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-typeshed all 0.0~git20241223.ea91db2-4 [1554 kB] 122s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 122s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 122s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib-inline all 0.1.7-1 [9186 B] 122s Get:120 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 122s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-prompt-toolkit all 3.0.52-1 [258 kB] 122s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-asttokens all 3.0.0-2 [20.5 kB] 122s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-executing all 2.2.0-0.2 [25.0 kB] 122s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 122s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 122s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ipython all 8.35.0-2 [575 kB] 122s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ipdb all 0.13.13-3 [15.4 kB] 122s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 mafft amd64 7.525-1 [841 kB] 122s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 raxml amd64 8.2.13+dfsg-2 [1670 kB] 122s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 122s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 vcftools amd64 0.1.17-1 [421 kB] 122s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 augur all 24.4.0-1 [238 kB] 122s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mccabe all 0.7.0-1 [8678 B] 122s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pycodestyle all 2.12.1-2 [30.2 kB] 122s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyflakes all 3.2.0-3 [53.0 kB] 122s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-flake8 all 7.1.1-3 [44.0 kB] 122s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 flake8 all 7.1.1-3 [6438 B] 122s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mypy-extensions all 1.1.0-1 [6716 B] 122s Get:139 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pathspec all 0.12.1-1 [24.5 kB] 122s Get:140 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-psutil amd64 7.1.0-1ubuntu1 [191 kB] 122s Get:141 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 python3-mypy amd64 1.18.2-2ubuntu1 [17.6 MB] 123s Get:142 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 mypy all 1.18.2-2ubuntu1 [26.3 kB] 123s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freezegun all 1.5.1-1.2 [15.9 kB] 123s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-1 [6840 B] 123s Get:145 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 123s Get:146 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 8.3.5-2 [252 kB] 123s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest-mock all 3.15.1-1 [11.9 kB] 123s Fetched 153 MB in 9s (17.9 MB/s) 123s Selecting previously unselected package python3-numpy-dev:amd64. 123s (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 ... 83372 files and directories currently installed.) 123s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 123s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 123s Selecting previously unselected package libblas3:amd64. 123s Preparing to unpack .../001-libblas3_3.12.1-7_amd64.deb ... 123s Unpacking libblas3:amd64 (3.12.1-7) ... 123s Selecting previously unselected package libgfortran5:amd64. 123s Preparing to unpack .../002-libgfortran5_15.2.0-7ubuntu1_amd64.deb ... 123s Unpacking libgfortran5:amd64 (15.2.0-7ubuntu1) ... 123s Selecting previously unselected package liblapack3:amd64. 123s Preparing to unpack .../003-liblapack3_3.12.1-7_amd64.deb ... 123s Unpacking liblapack3:amd64 (3.12.1-7) ... 123s Selecting previously unselected package python3-numpy. 124s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 124s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 124s Selecting previously unselected package libpython3.14-minimal:amd64. 124s Preparing to unpack .../005-libpython3.14-minimal_3.14.0-4_amd64.deb ... 124s Unpacking libpython3.14-minimal:amd64 (3.14.0-4) ... 124s Selecting previously unselected package python3.14-minimal. 124s Preparing to unpack .../006-python3.14-minimal_3.14.0-4_amd64.deb ... 124s Unpacking python3.14-minimal (3.14.0-4) ... 124s Selecting previously unselected package pigz. 124s Preparing to unpack .../007-pigz_2.8-1_amd64.deb ... 124s Unpacking pigz (2.8-1) ... 124s Selecting previously unselected package python3-charset-normalizer. 124s Preparing to unpack .../008-python3-charset-normalizer_3.4.3-1_amd64.deb ... 124s Unpacking python3-charset-normalizer (3.4.3-1) ... 124s Selecting previously unselected package libtcl8.6:amd64. 124s Preparing to unpack .../009-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 124s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 124s Selecting previously unselected package fonts-dejavu-mono. 124s Preparing to unpack .../010-fonts-dejavu-mono_2.37-8_all.deb ... 124s Unpacking fonts-dejavu-mono (2.37-8) ... 124s Selecting previously unselected package fonts-dejavu-core. 124s Preparing to unpack .../011-fonts-dejavu-core_2.37-8_all.deb ... 124s Unpacking fonts-dejavu-core (2.37-8) ... 124s Selecting previously unselected package libfontenc1:amd64. 124s Preparing to unpack .../012-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 124s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 124s Selecting previously unselected package x11-common. 124s Preparing to unpack .../013-x11-common_1%3a7.7+24ubuntu1_all.deb ... 124s Unpacking x11-common (1:7.7+24ubuntu1) ... 124s Selecting previously unselected package xfonts-encodings. 124s Preparing to unpack .../014-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 124s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 124s Selecting previously unselected package xfonts-utils. 124s Preparing to unpack .../015-xfonts-utils_1%3a7.7+7_amd64.deb ... 124s Unpacking xfonts-utils (1:7.7+7) ... 124s Selecting previously unselected package fonts-urw-base35. 124s Preparing to unpack .../016-fonts-urw-base35_20200910-8_all.deb ... 124s Unpacking fonts-urw-base35 (20200910-8) ... 124s Selecting previously unselected package fontconfig-config. 124s Preparing to unpack .../017-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 124s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 124s Selecting previously unselected package libfontconfig1:amd64. 124s Preparing to unpack .../018-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 124s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 124s Selecting previously unselected package libxrender1:amd64. 124s Preparing to unpack .../019-libxrender1_1%3a0.9.12-1_amd64.deb ... 124s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 124s Selecting previously unselected package libxft2:amd64. 124s Preparing to unpack .../020-libxft2_2.3.6-1build1_amd64.deb ... 124s Unpacking libxft2:amd64 (2.3.6-1build1) ... 124s Selecting previously unselected package libxss1:amd64. 124s Preparing to unpack .../021-libxss1_1%3a1.2.3-1build3_amd64.deb ... 124s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 124s Selecting previously unselected package libtk8.6:amd64. 124s Preparing to unpack .../022-libtk8.6_8.6.17-1_amd64.deb ... 124s Unpacking libtk8.6:amd64 (8.6.17-1) ... 124s Selecting previously unselected package python3.14-tk. 124s Preparing to unpack .../023-python3.14-tk_3.14.0-4_amd64.deb ... 124s Unpacking python3.14-tk (3.14.0-4) ... 124s Selecting previously unselected package python3.13-tk. 124s Preparing to unpack .../024-python3.13-tk_3.13.9-1_amd64.deb ... 124s Unpacking python3.13-tk (3.13.9-1) ... 124s Selecting previously unselected package tk8.6-blt2.5. 124s Preparing to unpack .../025-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 124s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 124s Selecting previously unselected package blt. 124s Preparing to unpack .../026-blt_2.5.3+dfsg-8_amd64.deb ... 124s Unpacking blt (2.5.3+dfsg-8) ... 125s Selecting previously unselected package python3-tk:amd64. 125s Preparing to unpack .../027-python3-tk_3.13.9-1_amd64.deb ... 125s Unpacking python3-tk:amd64 (3.13.9-1) ... 125s Selecting previously unselected package python3-pil.imagetk:amd64. 125s Preparing to unpack .../028-python3-pil.imagetk_11.3.0-1ubuntu2_amd64.deb ... 125s Unpacking python3-pil.imagetk:amd64 (11.3.0-1ubuntu2) ... 125s Selecting previously unselected package libgomp1:amd64. 125s Preparing to unpack .../029-libgomp1_15.2.0-7ubuntu1_amd64.deb ... 125s Unpacking libgomp1:amd64 (15.2.0-7ubuntu1) ... 125s Selecting previously unselected package libimagequant0:amd64. 125s Preparing to unpack .../030-libimagequant0_2.18.0-1build1_amd64.deb ... 125s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 125s Selecting previously unselected package libjpeg-turbo8:amd64. 125s Preparing to unpack .../031-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 125s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 125s Selecting previously unselected package libjpeg8:amd64. 125s Preparing to unpack .../032-libjpeg8_8c-2ubuntu11_amd64.deb ... 125s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 125s Selecting previously unselected package liblcms2-2:amd64. 125s Preparing to unpack .../033-liblcms2-2_2.17-1_amd64.deb ... 125s Unpacking liblcms2-2:amd64 (2.17-1) ... 125s Selecting previously unselected package libopenjp2-7:amd64. 125s Preparing to unpack .../034-libopenjp2-7_2.5.3-2.1_amd64.deb ... 125s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 125s Selecting previously unselected package libgraphite2-3:amd64. 125s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 125s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 125s Selecting previously unselected package libharfbuzz0b:amd64. 125s Preparing to unpack .../036-libharfbuzz0b_12.1.0-1_amd64.deb ... 125s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 125s Selecting previously unselected package libraqm0:amd64. 125s Preparing to unpack .../037-libraqm0_0.10.3-1_amd64.deb ... 125s Unpacking libraqm0:amd64 (0.10.3-1) ... 125s Selecting previously unselected package libdeflate0:amd64. 125s Preparing to unpack .../038-libdeflate0_1.23-2_amd64.deb ... 125s Unpacking libdeflate0:amd64 (1.23-2) ... 125s Selecting previously unselected package libjbig0:amd64. 125s Preparing to unpack .../039-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 125s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 125s Selecting previously unselected package liblerc4:amd64. 125s Preparing to unpack .../040-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 125s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 125s Selecting previously unselected package libsharpyuv0:amd64. 125s Preparing to unpack .../041-libsharpyuv0_1.5.0-0.1_amd64.deb ... 125s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 125s Selecting previously unselected package libwebp7:amd64. 125s Preparing to unpack .../042-libwebp7_1.5.0-0.1_amd64.deb ... 125s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 125s Selecting previously unselected package libtiff6:amd64. 125s Preparing to unpack .../043-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 125s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 125s Selecting previously unselected package libwebpdemux2:amd64. 125s Preparing to unpack .../044-libwebpdemux2_1.5.0-0.1_amd64.deb ... 125s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 125s Selecting previously unselected package libwebpmux3:amd64. 125s Preparing to unpack .../045-libwebpmux3_1.5.0-0.1_amd64.deb ... 125s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 125s Selecting previously unselected package python3-pil:amd64. 125s Preparing to unpack .../046-python3-pil_11.3.0-1ubuntu2_amd64.deb ... 125s Unpacking python3-pil:amd64 (11.3.0-1ubuntu2) ... 125s Selecting previously unselected package libpixman-1-0:amd64. 125s Preparing to unpack .../047-libpixman-1-0_0.46.4-1_amd64.deb ... 125s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 125s Selecting previously unselected package libxcb-render0:amd64. 125s Preparing to unpack .../048-libxcb-render0_1.17.0-2build1_amd64.deb ... 125s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 125s Selecting previously unselected package libxcb-shm0:amd64. 125s Preparing to unpack .../049-libxcb-shm0_1.17.0-2build1_amd64.deb ... 125s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 125s Selecting previously unselected package libcairo2:amd64. 125s Preparing to unpack .../050-libcairo2_1.18.4-1build1_amd64.deb ... 125s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 125s Selecting previously unselected package python3-cairo. 125s Preparing to unpack .../051-python3-cairo_1.27.0-2build1_amd64.deb ... 125s Unpacking python3-cairo (1.27.0-2build1) ... 125s Selecting previously unselected package python3-freetype. 125s Preparing to unpack .../052-python3-freetype_2.5.1-2_all.deb ... 125s Unpacking python3-freetype (2.5.1-2) ... 125s Selecting previously unselected package python3-rlpycairo. 125s Preparing to unpack .../053-python3-rlpycairo_0.3.0-4_all.deb ... 125s Unpacking python3-rlpycairo (0.3.0-4) ... 125s Selecting previously unselected package python3-reportlab. 125s Preparing to unpack .../054-python3-reportlab_4.4.4-2_all.deb ... 125s Unpacking python3-reportlab (4.4.4-2) ... 125s Selecting previously unselected package sgml-base. 125s Preparing to unpack .../055-sgml-base_1.31+nmu1_all.deb ... 125s Unpacking sgml-base (1.31+nmu1) ... 125s Selecting previously unselected package xml-core. 125s Preparing to unpack .../056-xml-core_0.19_all.deb ... 125s Unpacking xml-core (0.19) ... 125s Selecting previously unselected package w3c-sgml-lib. 125s Preparing to unpack .../057-w3c-sgml-lib_1.3-3_all.deb ... 125s Unpacking w3c-sgml-lib (1.3-3) ... 125s Selecting previously unselected package python3-biopython. 125s Preparing to unpack .../058-python3-biopython_1.85+dfsg-4_amd64.deb ... 125s Unpacking python3-biopython (1.85+dfsg-4) ... 125s Selecting previously unselected package python3-bcbio-gff. 125s Preparing to unpack .../059-python3-bcbio-gff_0.7.1-2_all.deb ... 125s Unpacking python3-bcbio-gff (0.7.1-2) ... 125s Selecting previously unselected package libsuitesparseconfig7:amd64. 125s Preparing to unpack .../060-libsuitesparseconfig7_1%3a7.11.0+dfsg-2_amd64.deb ... 125s Unpacking libsuitesparseconfig7:amd64 (1:7.11.0+dfsg-2) ... 125s Selecting previously unselected package libamd3:amd64. 125s Preparing to unpack .../061-libamd3_1%3a7.11.0+dfsg-2_amd64.deb ... 125s Unpacking libamd3:amd64 (1:7.11.0+dfsg-2) ... 125s Selecting previously unselected package libcamd3:amd64. 125s Preparing to unpack .../062-libcamd3_1%3a7.11.0+dfsg-2_amd64.deb ... 125s Unpacking libcamd3:amd64 (1:7.11.0+dfsg-2) ... 125s Selecting previously unselected package libccolamd3:amd64. 125s Preparing to unpack .../063-libccolamd3_1%3a7.11.0+dfsg-2_amd64.deb ... 125s Unpacking libccolamd3:amd64 (1:7.11.0+dfsg-2) ... 125s Selecting previously unselected package libcolamd3:amd64. 125s Preparing to unpack .../064-libcolamd3_1%3a7.11.0+dfsg-2_amd64.deb ... 125s Unpacking libcolamd3:amd64 (1:7.11.0+dfsg-2) ... 125s Selecting previously unselected package libcholmod5:amd64. 125s Preparing to unpack .../065-libcholmod5_1%3a7.11.0+dfsg-2_amd64.deb ... 125s Unpacking libcholmod5:amd64 (1:7.11.0+dfsg-2) ... 125s Selecting previously unselected package libdsdp-5.8t64. 125s Preparing to unpack .../066-libdsdp-5.8t64_5.8-11_amd64.deb ... 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python3-iniconfig. 129s Preparing to unpack .../143-python3-iniconfig_2.1.0-1_all.deb ... 129s Unpacking python3-iniconfig (2.1.0-1) ... 129s Selecting previously unselected package python3-pluggy. 129s Preparing to unpack .../144-python3-pluggy_1.6.0-1_all.deb ... 129s Unpacking python3-pluggy (1.6.0-1) ... 129s Selecting previously unselected package python3-pytest. 129s Preparing to unpack .../145-python3-pytest_8.3.5-2_all.deb ... 129s Unpacking python3-pytest (8.3.5-2) ... 129s Selecting previously unselected package python3-pytest-mock. 129s Preparing to unpack .../146-python3-pytest-mock_3.15.1-1_all.deb ... 129s Unpacking python3-pytest-mock (3.15.1-1) ... 129s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 129s Setting up python3-schedule (1.2.2-1) ... 130s Setting up python3-pyfaidx (0.8.1.3-2) ... 130s Setting up liblcms2-2:amd64 (2.17-1) ... 130s Setting up python3-iniconfig (2.1.0-1) ... 130s Setting up libpixman-1-0:amd64 (0.46.4-1) ... 130s Setting up vcftools 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(2025.2-4) ... 132s Setting up libxcb-shm0:amd64 (1.17.0-2build1) ... 132s Setting up libgomp1:amd64 (15.2.0-7ubuntu1) ... 132s Setting up python3-freetype (2.5.1-2) ... 132s Setting up python3-networkx (3.2.1-4ubuntu1) ... 134s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 134s Setting up python3-platformdirs (4.3.7-1) ... 134s Setting up python3-psutil (7.1.0-1ubuntu1) ... 134s Setting up python3-fs (2.4.16-9ubuntu1) ... 135s Setting up unicode-data (16.0.0-1) ... 135s Setting up python3-isodate (0.7.2-2) ... 135s Setting up python3-decorator (5.2.1-2) ... 135s Setting up python3-pycodestyle (2.12.1-2) ... 135s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 135s Setting up python3-pygtrie (2.2-3) ... 135s Setting up libblas3:amd64 (3.12.1-7) ... 135s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 135s Setting up python3-zstandard (0.25.0-1) ... 136s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 136s Setting up libzopfli1 (1.0.3-3) ... 136s Setting up python3-typeshed (0.0~git20241223.ea91db2-4) ... 136s Setting up python3-executing (2.2.0-0.2) ... 136s Setting up python3-brotli (1.1.0-2build6) ... 136s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 136s Setting up python3-cycler (0.12.1-2) ... 136s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 136s Setting up fonts-dejavu-mono (2.37-8) ... 136s Setting up python3-kiwisolver (1.4.10~rc0-1) ... 137s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 137s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 137s Setting up fonts-dejavu-core (2.37-8) ... 137s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 137s Setting up libltdl7:amd64 (2.5.4-7) ... 137s Setting up libfftw3-double3:amd64 (3.3.10-2fakesync1build2) ... 137s Setting up libgfortran5:amd64 (15.2.0-7ubuntu1) ... 137s Setting up python3-pluggy (1.6.0-1) ... 137s Setting up libwebp7:amd64 (1.5.0-0.1) ... 137s Setting up pigz (2.8-1) ... 137s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 137s Setting up libxslt1.1:amd64 (1.1.43-0.3) ... 137s Setting up libsuitesparseconfig7:amd64 (1:7.11.0+dfsg-2) ... 137s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 137s Setting up libharfbuzz0b:amd64 (12.1.0-1) ... 137s Setting up fasttree (2.1.11-2) ... 137s Setting up python3-mccabe (0.7.0-1) ... 137s Setting up sgml-base (1.31+nmu1) ... 137s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 137s Setting up python3-mpmath (1.3.0-2) ... 138s Setting up libgsl28:amd64 (2.8+dfsg-5.1ubuntu1) ... 138s Setting up python-matplotlib-data (3.10.7+dfsg1-1) ... 138s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 138s Setting up python3-pathspec (0.12.1-1) ... 138s Setting up python3-dendropy (4.6.1-2) ... 139s Setting up python3-stack-data (0.6.3-1) ... 139s Setting up python3.14-minimal (3.14.0-4) ... 140s Setting up python3-freezegun (1.5.1-1.2) ... 140s Setting up raxml (8.2.13+dfsg-2) ... 140s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 140s Setting up python3-prompt-toolkit (3.0.52-1) ... 140s Setting up python3-sympy (1.14.0-2) ... 150s /usr/lib/python3/dist-packages/sympy/testing/runtests.py:283: SyntaxWarning: 'return' in a 'finally' block 150s return p.returncode 150s Setting up liblapack3:amd64 (3.12.1-7) ... 150s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 150s Setting up libamd3:amd64 (1:7.11.0+dfsg-2) ... 150s Setting up python3-jedi (0.19.1+ds1-1) ... 151s Setting up libcolamd3:amd64 (1:7.11.0+dfsg-2) ... 151s Setting up libpython3.14-stdlib:amd64 (3.14.0-4) ... 151s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 151s Setting up python3-pytest (8.3.5-2) ... 151s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 151s Setting up xfonts-utils (1:7.7+7) ... 151s Setting up libcamd3:amd64 (1:7.11.0+dfsg-2) ... 151s Setting up python3-zopfli (0.4.0-1) ... 151s Setting up python3-matplotlib-inline (0.1.7-1) ... 152s Setting up python3-flake8 (7.1.1-3) ... 152s Setting up python3-xopen (1.7.0-3) ... 152s Setting up libglpk40:amd64 (5.0-2) ... 152s Setting up python3-ipython (8.35.0-2) ... 152s /usr/lib/python3/dist-packages/IPython/core/interactiveshell.py:3141: SyntaxWarning: 'return' in a 'finally' block 152s return result 153s Setting up libraqm0:amd64 (0.10.3-1) ... 153s Setting up python3-mypy (1.18.2-2ubuntu1) ... 155s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 158s Setting up libccolamd3:amd64 (1:7.11.0+dfsg-2) ... 158s Setting up python3-pytest-mock (3.15.1-1) ... 158s Setting up python3-lxml:amd64 (6.0.2-1) ... 158s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 158s Setting up xml-core (0.19) ... 158s Setting up mypy (1.18.2-2ubuntu1) ... 158s Setting up libdsdp-5.8t64 (5.8-11) ... 158s Setting up python3-contourpy (1.3.1-2) ... 158s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 158s Setting up python3-ipdb (0.13.13-3) ... 159s Setting up python3.14 (3.14.0-4) ... 159s Setting up libcholmod5:amd64 (1:7.11.0+dfsg-2) ... 159s Setting up libxft2:amd64 (2.3.6-1build1) ... 159s Setting up python3-scipy (1.15.3-1ubuntu1) ... 163s /usr/lib/python3/dist-packages/scipy/optimize/_optimize.py:921: SyntaxWarning: 'break' in a 'finally' block 163s break 165s Setting up libtk8.6:amd64 (8.6.17-1) ... 165s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ... 165s Setting up python3-all (3.13.7-2) ... 165s Setting up flake8 (7.1.1-3) ... 165s Setting up fonts-urw-base35 (20200910-8) ... 165s Setting up libcairo2:amd64 (1.18.4-1build1) ... 165s Setting up python3.13-tk (3.13.9-1) ... 165s Setting up python3-pil:amd64 (11.3.0-1ubuntu2) ... 166s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 174s Setting up libumfpack6:amd64 (1:7.11.0+dfsg-2) ... 174s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 174s Setting up python3.14-tk (3.14.0-4) ... 174s Setting up python3-cairo (1.27.0-2build1) ... 174s Setting up python3-cvxopt (1.3.2+dfsg-2) ... 174s Setting up blt (2.5.3+dfsg-8) ... 174s Setting up python3-tk:amd64 (3.13.9-1) ... 174s Setting up python3-pil.imagetk:amd64 (11.3.0-1ubuntu2) ... 174s Setting up python3-rlpycairo (0.3.0-4) ... 174s Setting up python3-reportlab (4.4.4-2) ... 176s Setting up python3-fonttools (4.57.0-2build1) ... 177s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 177s Setting up python3-matplotlib (3.10.7+dfsg1-1) ... 180s Setting up python3-seaborn (0.13.2-5) ... 180s Processing triggers for libc-bin (2.42-2ubuntu2) ... 180s Processing triggers for systemd (257.9-0ubuntu2) ... 180s Processing triggers for man-db (2.13.1-1) ... 181s Processing triggers for sgml-base (1.31+nmu1) ... 181s Setting up w3c-sgml-lib (1.3-3) ... 204s Setting up python3-biopython (1.85+dfsg-4) ... 205s Setting up python3-treetime (0.11.4-1) ... 206s Setting up seqmagick (0.8.6-3) ... 206s Setting up python3-bcbio-gff (0.7.1-2) ... 206s Setting up augur (24.4.0-1) ... 207s autopkgtest [10:28:36]: test environment configured for cross building 207s autopkgtest [10:28:36]: test run-unit-test: [----------------------- 208s ============================= test session starts ============================== 208s platform linux -- Python 3.14.0, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3.14 208s cachedir: .pytest_cache 208s rootdir: /tmp/autopkgtest.So2qMq/build.3S5/src 208s plugins: mock-3.15.1, typeguard-4.4.2 210s collecting ... collected 12 items / 25 errors 210s 210s ==================================== ERRORS ==================================== 210s _____________ ERROR collecting tests/dates/test_ambiguous_date.py ______________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/dates/test_ambiguous_date.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/dates/test_ambiguous_date.py:3: in 210s from augur.dates import ambiguous_date 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s __________________ ERROR collecting tests/dates/test_dates.py __________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/dates/test_dates.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/dates/test_dates.py:4: in 210s from augur import dates 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s _____________ ERROR collecting tests/filter/test_relative_dates.py _____________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/filter/test_relative_dates.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/filter/test_relative_dates.py:12: in 210s from augur.filter import register_arguments 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s _______________ ERROR collecting tests/filter/test_subsample.py ________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/filter/test_subsample.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/filter/test_subsample.py:2: in 210s import pandas as pd 210s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 210s raise ImportError( 210s E ImportError: Unable to import required dependencies: 210s E numpy: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s ____________________ ERROR collecting tests/io/test_file.py ____________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/io/test_file.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/io/test_file.py:2: in 210s import augur.io.file 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s __________________ ERROR collecting tests/io/test_metadata.py __________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/io/test_metadata.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/io/test_metadata.py:6: in 210s from augur.errors import AugurError 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s _________________ ERROR collecting tests/io/test_sequences.py __________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/io/test_sequences.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/io/test_sequences.py:2: in 210s from Bio import SeqIO 210s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 210s from Bio.SeqIO import TwoBitIO 210s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 210s raise MissingPythonDependencyError( 210s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 210s ____________ ERROR collecting tests/io/test_shell_command_runner.py ____________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/io/test_shell_command_runner.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/io/test_shell_command_runner.py:5: in 210s from augur.io.shell_command_runner import ShellCommandRunner 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s __________________ ERROR collecting tests/io/test_strains.py ___________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/io/test_strains.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/io/test_strains.py:3: in 210s from augur.io.strains import read_strains 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s ____________________ ERROR collecting tests/io/test_vcf.py _____________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/io/test_vcf.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/io/test_vcf.py:2: in 210s import augur.io.vcf 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s _____________________ ERROR collecting tests/test_align.py _____________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_align.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_align.py:10: in 210s from Bio import SeqIO 210s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 210s from Bio.SeqIO import TwoBitIO 210s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 210s raise MissingPythonDependencyError( 210s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 210s ___________________ ERROR collecting tests/test_ancestral.py ___________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_ancestral.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_ancestral.py:1: in 210s from augur.ancestral import run_ancestral 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s ____________________ ERROR collecting tests/test_clades.py _____________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_clades.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_clades.py:4: in 210s from augur.clades import read_in_clade_definitions 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s __________________ ERROR collecting tests/test_frequencies.py __________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_frequencies.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_frequencies.py:6: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s _____________________ ERROR collecting tests/test_mask.py ______________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_mask.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_mask.py:11: in 210s from Bio import SeqIO 210s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 210s from Bio.SeqIO import TwoBitIO 210s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 210s raise MissingPythonDependencyError( 210s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 210s _____________________ ERROR collecting tests/test_parse.py _____________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_parse.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_parse.py:1: in 210s import Bio.SeqIO 210s /usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:401: in 210s from Bio.SeqIO import TwoBitIO 210s /usr/lib/python3/dist-packages/Bio/SeqIO/TwoBitIO.py:80: in 210s raise MissingPythonDependencyError( 210s E Bio.MissingPythonDependencyError: Install NumPy if you want to use Bio.SeqIO with TwoBit files.See http://www.numpy.org/ 210s _________________ ERROR collecting tests/test_titer_models.py __________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_titer_models.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_titer_models.py:2: in 210s from augur.titer_model import TiterCollection 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s ___________________ ERROR collecting tests/test_translate.py ___________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_translate.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_translate.py:13: in 210s from augur import translate 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s _____________________ ERROR collecting tests/test_utils.py _____________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_utils.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_utils.py:2: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s ___________________ ERROR collecting tests/test_validate.py ____________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_validate.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_validate.py:4: in 210s from augur.validate import ( 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s ________________ ERROR collecting tests/test_validate_export.py ________________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/test_validate_export.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/test_validate_export.py:1: in 210s import Bio.Phylo 210s /usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in 210s from Bio.Phylo._io import convert 210s /usr/lib/python3/dist-packages/Bio/Phylo/_io.py:19: in 210s from Bio.Phylo import PhyloXMLIO 210s /usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in 210s from Bio.Phylo import PhyloXML as PX 210s /usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:23: in 210s from Bio.Align import Alignment 210s /usr/lib/python3/dist-packages/Bio/Align/__init__.py:32: in 210s raise MissingPythonDependencyError( 210s E Bio.MissingPythonDependencyError: Please install NumPy if you want to use Bio.Align. See http://www.numpy.org/ 210s ___________ ERROR collecting tests/util_support/test_color_parser.py ___________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/util_support/test_color_parser.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/util_support/test_color_parser.py:1: in 210s from augur.util_support.color_parser import ColorParser 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s ____________ ERROR collecting tests/util_support/test_node_data.py _____________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/util_support/test_node_data.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/util_support/test_node_data.py:1: in 210s from augur.util_support.node_data import DuplicatedNonDictAttributeError 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s __________ ERROR collecting tests/util_support/test_node_data_file.py __________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/util_support/test_node_data_file.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/util_support/test_node_data_file.py:3: in 210s from augur.__version__ import __version__ 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s _________ ERROR collecting tests/util_support/test_node_data_reader.py _________ 210s ImportError while importing test module '/tmp/autopkgtest.So2qMq/build.3S5/src/tests/util_support/test_node_data_reader.py'. 210s Hint: make sure your test modules/packages have valid Python names. 210s Traceback: 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 210s from . import multiarray 210s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 210s from . import overrides 210s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 210s from numpy._core._multiarray_umath import ( 210s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 210s 210s During handling of the above exception, another exception occurred: 210s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 210s from numpy.__config__ import show_config 210s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 210s from numpy._core._multiarray_umath import ( 210s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 210s raise ImportError(msg) 210s E ImportError: 210s E 210s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 210s E 210s E Importing the numpy C-extensions failed. This error can happen for 210s E many reasons, often due to issues with your setup or how NumPy was 210s E installed. 210s E 210s E We have compiled some common reasons and troubleshooting tips at: 210s E 210s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 210s E 210s E Please note and check the following: 210s E 210s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 210s E * The NumPy version is: "2.2.4" 210s E 210s E and make sure that they are the versions you expect. 210s E Please carefully study the documentation linked above for further help. 210s E 210s E Original error was: No module named 'numpy._core._multiarray_umath' 210s 210s The above exception was the direct cause of the following exception: 210s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 210s return _bootstrap._gcd_import(name[level:], package, level) 210s tests/util_support/test_node_data_reader.py:1: in 210s from augur.util_support.node_data_reader import NodeDataReader 210s augur/__init__.py:12: in 210s from treetime import TreeTimeError, TreeTimeUnknownError 210s /usr/lib/python3/dist-packages/treetime/__init__.py:38: in 210s from .treeanc import TreeAnc 210s /usr/lib/python3/dist-packages/treetime/treeanc.py:3: in 210s import numpy as np 210s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 210s raise ImportError(msg) from e 210s E ImportError: Error importing numpy: you should not try to import numpy from 210s E its source directory; please exit the numpy source tree, and relaunch 210s E your python interpreter from there. 210s =============================== warnings summary =============================== 210s ../../../../usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2108 210s /usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:2108: 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 210s warnings.warn( 210s 210s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 210s =========================== short test summary info ============================ 210s ERROR tests/dates/test_ambiguous_date.py 210s ERROR tests/dates/test_dates.py 210s ERROR tests/filter/test_relative_dates.py 210s ERROR tests/filter/test_subsample.py 210s ERROR tests/io/test_file.py 210s ERROR tests/io/test_metadata.py 210s ERROR tests/io/test_sequences.py 210s ERROR tests/io/test_shell_command_runner.py 210s ERROR tests/io/test_strains.py 210s ERROR tests/io/test_vcf.py 210s ERROR tests/test_align.py 210s ERROR tests/test_ancestral.py 210s ERROR tests/test_clades.py 210s ERROR tests/test_frequencies.py 210s ERROR tests/test_mask.py 210s ERROR tests/test_parse.py 210s ERROR tests/test_titer_models.py 210s ERROR tests/test_translate.py 210s ERROR tests/test_utils.py 210s ERROR tests/test_validate.py 210s ERROR tests/test_validate_export.py 210s ERROR tests/util_support/test_color_parser.py 210s ERROR tests/util_support/test_node_data.py 210s ERROR tests/util_support/test_node_data_file.py 210s ERROR tests/util_support/test_node_data_reader.py 210s !!!!!!!!!!!!!!!!!!! Interrupted: 25 errors during collection !!!!!!!!!!!!!!!!!!! 210s ======================== 1 warning, 25 errors in 1.66s ========================= 210s autopkgtest [10:28:39]: test run-unit-test: -----------------------] 211s run-unit-test FAIL non-zero exit status 2 211s autopkgtest [10:28:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 211s autopkgtest [10:28:40]: @@@@@@@@@@@@@@@@@@@@ summary 211s run-unit-test FAIL non-zero exit status 2