0s autopkgtest [10:14:02]: starting date and time: 2024-11-13 10:14:02+0000
  0s autopkgtest [10:14:02]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [10:14:02]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kd7k2g90/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-bioframe --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-51.secgroup --name adt-plucky-arm64-python-bioframe-20241113-101402-juju-7f2275-prod-proposed-migration-environment-15-4449b231-1e22-4b16-81e8-19c4425fe8cc --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 84s autopkgtest [10:15:26]: testbed dpkg architecture: arm64
 84s autopkgtest [10:15:26]: testbed apt version: 2.9.8
 84s autopkgtest [10:15:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 86s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 86s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
 87s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 87s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
 87s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
 87s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB]
 87s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
 87s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB]
 87s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB]
 87s Fetched 1794 kB in 1s (2043 kB/s)
 87s Reading package lists...
 90s Reading package lists...
 91s Building dependency tree...
 91s Reading state information...
 91s Calculating upgrade...
 92s The following NEW packages will be installed:
 92s   python3.13-gdbm
 92s The following packages will be upgraded:
 92s   libpython3-stdlib python3 python3-gdbm python3-minimal
 92s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 92s Need to get 101 kB of archives.
 92s After this operation, 141 kB of additional disk space will be used.
 92s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB]
 93s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB]
 93s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB]
 93s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB]
 93s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B]
 93s Fetched 101 kB in 0s (281 kB/s)
 93s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 79924 files and directories currently installed.)
 93s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ...
 93s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 93s Setting up python3-minimal (3.12.7-1) ...
 94s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 79924 files and directories currently installed.)
 94s Preparing to unpack .../python3_3.12.7-1_arm64.deb ...
 94s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 94s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ...
 94s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 94s Selecting previously unselected package python3.13-gdbm.
 94s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ...
 94s Unpacking python3.13-gdbm (3.13.0-2) ...
 94s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ...
 94s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
 94s Setting up python3.13-gdbm (3.13.0-2) ...
 94s Setting up libpython3-stdlib:arm64 (3.12.7-1) ...
 94s Setting up python3 (3.12.7-1) ...
 94s Setting up python3-gdbm:arm64 (3.12.7-1) ...
 94s Processing triggers for man-db (2.12.1-3) ...
 95s Reading package lists...
 95s Building dependency tree...
 95s Reading state information...
 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 96s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 96s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 96s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 96s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 97s Reading package lists...
 97s Reading package lists...
 98s Building dependency tree...
 98s Reading state information...
 98s Calculating upgrade...
 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 99s Reading package lists...
 99s Building dependency tree...
 99s Reading state information...
100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
103s autopkgtest [10:15:45]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
103s autopkgtest [10:15:45]: @@@@@@@@@@@@@@@@@@@@ apt-source python-bioframe
105s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-bioframe 0.4.1-1 (dsc) [1611 B]
105s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-bioframe 0.4.1-1 (tar) [816 kB]
105s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-bioframe 0.4.1-1 (diff) [3464 B]
105s gpgv: Signature made Mon Jun 12 17:55:46 2023 UTC
105s gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
105s gpgv: Can't check signature: No public key
105s dpkg-source: warning: cannot verify inline signature for ./python-bioframe_0.4.1-1.dsc: no acceptable signature found
105s autopkgtest [10:15:47]: testing package python-bioframe version 0.4.1-1
106s autopkgtest [10:15:48]: build not needed
106s autopkgtest [10:15:48]: test run-unit-test: preparing testbed
109s Reading package lists...
109s Building dependency tree...
109s Reading state information...
109s Starting pkgProblemResolver with broken count: 0
109s Starting 2 pkgProblemResolver with broken count: 0
109s Done
110s The following additional packages will be installed:
110s   blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3
110s   libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3
110s   libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery
110s   libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7
110s   libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0
110s   libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3
110s   libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data python3-all
110s   python3-appdirs python3-bioframe python3-brotli python3-contourpy
110s   python3-cycler python3-dateutil python3-decorator python3-fonttools
110s   python3-fs python3-iniconfig python3-kiwisolver python3-lxml python3-lz4
110s   python3-matplotlib python3-mpmath python3-numpy python3-packaging
110s   python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk
110s   python3-pluggy python3-pytest python3-scipy python3-six python3-sympy
110s   python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk
110s   python3.13 python3.13-minimal python3.13-tk tk8.6-blt2.5 unicode-data
110s   x11-common
110s Suggested packages:
110s   blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc
110s   python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript
110s   gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc
110s   python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip
110s   python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc
110s   python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python-pandas-doc
110s   python3-statsmodels python-pil-doc python-scipy-doc texlive-fonts-extra
110s   python-sympy-doc tix python3-tk-dbg python3.13-venv python3.13-doc
110s   binfmt-support
110s Recommended packages:
110s   javascript-common python3-bs4 python3-cssselect python3-html5lib
110s   python3-bottleneck python3-numexpr python3-odf python3-openpyxl
110s   python3-tables python3-olefile g++ | c++-compiler isympy-common
110s The following NEW packages will be installed:
110s   autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono
110s   fonts-lyx libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1
110s   libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8
110s   libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4
110s   libopenjp2-7 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0
110s   libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2
110s   libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data
110s   python3-all python3-appdirs python3-bioframe python3-brotli
110s   python3-contourpy python3-cycler python3-dateutil python3-decorator
110s   python3-fonttools python3-fs python3-iniconfig python3-kiwisolver
110s   python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy
110s   python3-packaging python3-pandas python3-pandas-lib python3-pil
110s   python3-pil.imagetk python3-pluggy python3-pytest python3-scipy python3-six
110s   python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2
110s   python3.12-tk python3.13 python3.13-minimal python3.13-tk tk8.6-blt2.5
110s   unicode-data x11-common
110s 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded.
110s Need to get 69.1 MB/69.1 MB of archives.
110s After this operation, 304 MB of additional disk space will be used.
110s Get:1 /tmp/autopkgtest.Px9SGQ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B]
110s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB]
111s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB]
111s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB]
111s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
111s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
111s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
111s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
111s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
111s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
111s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
111s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
111s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB]
111s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB]
111s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B]
111s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB]
111s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB]
111s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB]
111s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB]
111s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB]
111s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
111s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB]
111s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
111s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB]
111s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
111s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
111s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
111s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB]
111s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB]
111s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB]
111s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB]
111s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB]
111s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB]
111s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB]
111s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB]
111s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
111s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB]
111s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
111s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB]
111s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB]
111s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB]
111s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB]
111s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB]
111s Get:44 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B]
111s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB]
111s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB]
111s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB]
111s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB]
111s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB]
111s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB]
111s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB]
111s Get:52 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.12.7-1 [9752 B]
112s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B]
112s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB]
112s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB]
112s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B]
112s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB]
112s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
112s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB]
113s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB]
113s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB]
113s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB]
113s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB]
113s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB]
113s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB]
113s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB]
113s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB]
113s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB]
113s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB]
113s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2 [50.4 kB]
113s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB]
113s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB]
113s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB]
113s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB]
113s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-bioframe all 0.4.1-1 [76.1 kB]
113s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B]
113s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB]
113s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB]
114s Fetched 69.1 MB in 3s (20.5 MB/s)
114s Selecting previously unselected package libpython3.13-minimal:arm64.
114s (Reading database ... 
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(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 79931 files and directories currently installed.)
114s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ...
114s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ...
114s Selecting previously unselected package python3.13-minimal.
114s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ...
114s Unpacking python3.13-minimal (3.13.0-2) ...
114s Selecting previously unselected package libtcl8.6:arm64.
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114s Selecting previously unselected package fonts-dejavu-mono.
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114s Selecting previously unselected package fonts-dejavu-core.
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114s Selecting previously unselected package fontconfig-config.
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115s Selecting previously unselected package libfontconfig1:arm64.
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115s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
115s Selecting previously unselected package libxrender1:arm64.
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115s Selecting previously unselected package libxft2:arm64.
115s Preparing to unpack .../08-libxft2_2.3.6-1build1_arm64.deb ...
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115s Selecting previously unselected package x11-common.
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115s Selecting previously unselected package libxss1:arm64.
115s Preparing to unpack .../10-libxss1_1%3a1.2.3-1build3_arm64.deb ...
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115s Selecting previously unselected package libtk8.6:arm64.
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115s Selecting previously unselected package tk8.6-blt2.5.
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115s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
115s Selecting previously unselected package blt.
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115s Unpacking blt (2.5.3+dfsg-7build1) ...
115s Selecting previously unselected package fonts-lyx.
115s Preparing to unpack .../14-fonts-lyx_2.4.2.1-1_all.deb ...
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115s Selecting previously unselected package libblas3:arm64.
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115s Selecting previously unselected package libdeflate0:arm64.
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115s Selecting previously unselected package libgfortran5:arm64.
115s Preparing to unpack .../17-libgfortran5_14.2.0-8ubuntu1_arm64.deb ...
115s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ...
115s Selecting previously unselected package libgomp1:arm64.
115s Preparing to unpack .../18-libgomp1_14.2.0-8ubuntu1_arm64.deb ...
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115s Selecting previously unselected package libgraphite2-3:arm64.
115s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
115s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
115s Selecting previously unselected package libharfbuzz0b:arm64.
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115s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ...
115s Selecting previously unselected package libimagequant0:arm64.
115s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_arm64.deb ...
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115s Selecting previously unselected package libjpeg-turbo8:arm64.
115s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ...
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115s Selecting previously unselected package libjpeg8:arm64.
115s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_arm64.deb ...
115s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
115s Selecting previously unselected package libjs-jquery.
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115s Selecting previously unselected package libjs-jquery-ui.
115s Preparing to unpack .../25-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
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115s Selecting previously unselected package liblapack3:arm64.
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115s Unpacking liblapack3:arm64 (3.12.0-3build2) ...
115s Selecting previously unselected package liblbfgsb0:arm64.
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115s Selecting previously unselected package liblcms2-2:arm64.
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115s Selecting previously unselected package liblerc4:arm64.
115s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ...
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115s Selecting previously unselected package libpython3.13-stdlib:arm64.
115s Preparing to unpack .../30-libpython3.13-stdlib_3.13.0-2_arm64.deb ...
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116s Selecting previously unselected package libqhull-r8.0:arm64.
116s Preparing to unpack .../31-libqhull-r8.0_2020.2-6build1_arm64.deb ...
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116s Selecting previously unselected package libraqm0:arm64.
116s Preparing to unpack .../32-libraqm0_0.10.1-1build1_arm64.deb ...
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116s Selecting previously unselected package libsharpyuv0:arm64.
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116s Selecting previously unselected package libjbig0:arm64.
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116s Selecting previously unselected package libwebp7:arm64.
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116s Selecting previously unselected package libtiff6:arm64.
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116s Selecting previously unselected package libwebpdemux2:arm64.
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116s Selecting previously unselected package libwebpmux3:arm64.
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116s Selecting previously unselected package libxslt1.1:arm64.
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116s Selecting previously unselected package python-matplotlib-data.
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116s Selecting previously unselected package python3.13.
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116s Selecting previously unselected package python3-all.
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116s Selecting previously unselected package python3-appdirs.
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116s Selecting previously unselected package python3-six.
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116s Unpacking python3-six (1.16.0-7) ...
116s Selecting previously unselected package python3-dateutil.
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116s Selecting previously unselected package libopenjp2-7:arm64.
116s Preparing to unpack .../46-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ...
116s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ...
116s Selecting previously unselected package python3-pil:arm64.
116s Preparing to unpack .../47-python3-pil_10.4.0-1ubuntu1_arm64.deb ...
116s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ...
116s Selecting previously unselected package python3.12-tk.
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116s Selecting previously unselected package python3.13-tk.
116s Preparing to unpack .../49-python3.13-tk_3.13.0-2_arm64.deb ...
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116s Selecting previously unselected package python3-tk:arm64.
116s Preparing to unpack .../50-python3-tk_3.12.7-1_arm64.deb ...
116s Unpacking python3-tk:arm64 (3.12.7-1) ...
116s Selecting previously unselected package python3-pil.imagetk:arm64.
116s Preparing to unpack .../51-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ...
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116s Selecting previously unselected package python3-numpy.
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116s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
117s Selecting previously unselected package python3-contourpy.
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117s Selecting previously unselected package python3-brotli.
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119s Unpacking autopkgtest-satdep (0) ...
119s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
119s Setting up liblcms2-2:arm64 (2.16-2) ...
119s Setting up python3-iniconfig (1.1.1-2) ...
119s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ...
119s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ...
119s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
119s Setting up python3-lz4 (4.0.2+dfsg-1build4) ...
119s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ...
119s Setting up fonts-lyx (2.4.2.1-1) ...
119s Setting up x11-common (1:7.7+23ubuntu3) ...
120s Setting up libdeflate0:arm64 (1.22-1) ...
120s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ...
120s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ...
120s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
120s Setting up python3-tz (2024.1-2) ...
120s Setting up unicode-data (15.1.0-1) ...
120s Setting up python3-six (1.16.0-7) ...
120s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ...
120s Setting up python3-decorator (5.1.1-5) ...
120s Setting up libblas3:arm64 (3.12.0-3build2) ...
120s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
120s Setting up python3-packaging (24.1-1) ...
121s Setting up python3-brotli (1.1.0-2build2) ...
121s Setting up python3-cycler (0.12.1-1) ...
121s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
121s Setting up fonts-dejavu-mono (2.37-8) ...
121s Setting up python3-kiwisolver (1.4.7-2) ...
121s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ...
121s Setting up fonts-dejavu-core (2.37-8) ...
121s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
121s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ...
121s Setting up python3-pluggy (1.5.0-1) ...
122s Setting up libwebp7:arm64 (1.4.0-0.1) ...
122s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ...
122s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ...
122s Setting up python3.13-minimal (3.13.0-2) ...
122s Setting up libharfbuzz0b:arm64 (10.0.1-1) ...
122s Setting up python3-dateutil (2.9.0-2) ...
123s Setting up libxss1:arm64 (1:1.2.3-1build3) ...
123s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
123s Setting up python3-mpmath (1.3.0-1) ...
124s Setting up python-matplotlib-data (3.8.3-3) ...
124s Setting up libwebpmux3:arm64 (1.4.0-0.1) ...
124s Setting up python3-appdirs (1.4.4-4) ...
124s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ...
124s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
124s Setting up python3-sympy (1.13.3-1) ...
139s Setting up liblapack3:arm64 (3.12.0-3build2) ...
139s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
139s Setting up python3.13 (3.13.0-2) ...
140s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
140s Setting up python3-pytest (8.3.3-1) ...
141s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ...
141s Setting up python3-all (3.12.7-1) ...
141s Setting up python3-fs (2.4.16-4) ...
141s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
141s Setting up libraqm0:arm64 (0.10.1-1build1) ...
141s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
145s Setting up python3-lxml:arm64 (5.3.0-1) ...
145s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
145s Setting up python3-contourpy (1.3.0-2) ...
145s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
145s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
145s Setting up libxft2:arm64 (2.3.6-1build1) ...
145s Setting up python3-scipy (1.13.1-5) ...
153s Setting up libtk8.6:arm64 (8.6.15-1) ...
153s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ...
153s Setting up python3.12-tk (3.12.7-3) ...
153s Setting up python3.13-tk (3.13.0-2) ...
153s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ...
154s Setting up python3-pandas (2.2.3+dfsg-5) ...
165s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
165s Setting up blt (2.5.3+dfsg-7build1) ...
165s Setting up python3-tk:arm64 (3.12.7-1) ...
165s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ...
165s Setting up python3-fonttools (4.46.0-1build2) ...
167s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ...
167s Setting up python3-matplotlib (3.8.3-3) ...
170s Setting up python3-bioframe (0.4.1-1) ...
170s Setting up autopkgtest-satdep (0) ...
170s Processing triggers for libc-bin (2.40-1ubuntu3) ...
171s Processing triggers for systemd (256.5-2ubuntu4) ...
171s Processing triggers for man-db (2.12.1-3) ...
176s (Reading database ... 89596 files and directories currently installed.)
176s Removing autopkgtest-satdep (0) ...
176s autopkgtest [10:16:58]: test run-unit-test: [-----------------------
177s ============================= test session starts ==============================
177s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13
177s cachedir: .pytest_cache
177s rootdir: /tmp/autopkgtest.Px9SGQ/autopkgtest_tmp
177s plugins: typeguard-4.4.1
178s collecting ... collected 0 items / 8 errors
178s 
178s ==================================== ERRORS ====================================
178s __________________ ERROR collecting tests/test_core_checks.py __________________
178s ImportError while importing test module '/tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_core_checks.py'.
178s Hint: make sure your test modules/packages have valid Python names.
178s Traceback:
178s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
178s     return _bootstrap._gcd_import(name[level:], package, level)
178s tests/test_core_checks.py:3: in <module>
178s     import pandas as pd
178s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in <module>
178s     raise ImportError(
178s E   ImportError: Unable to import required dependencies:
178s E   numpy: Error importing numpy: you should not try to import numpy from
178s E           its source directory; please exit the numpy source tree, and relaunch
178s E           your python interpreter from there.
178s _______________ ERROR collecting tests/test_core_construction.py _______________
178s ImportError while importing test module '/tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_core_construction.py'.
178s Hint: make sure your test modules/packages have valid Python names.
178s Traceback:
178s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
178s     return _bootstrap._gcd_import(name[level:], package, level)
178s tests/test_core_construction.py:3: in <module>
178s     import pandas as pd
178s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in <module>
178s     raise ImportError(
178s E   ImportError: Unable to import required dependencies:
178s E   numpy: Error importing numpy: you should not try to import numpy from
178s E           its source directory; please exit the numpy source tree, and relaunch
178s E           your python interpreter from there.
178s __________________ ERROR collecting tests/test_core_specs.py ___________________
178s ImportError while importing test module '/tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_core_specs.py'.
178s Hint: make sure your test modules/packages have valid Python names.
178s Traceback:
178s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
178s     return _bootstrap._gcd_import(name[level:], package, level)
178s tests/test_core_specs.py:3: in <module>
178s     import pandas as pd
178s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in <module>
178s     raise ImportError(
178s E   ImportError: Unable to import required dependencies:
178s E   numpy: Error importing numpy: you should not try to import numpy from
178s E           its source directory; please exit the numpy source tree, and relaunch
178s E           your python interpreter from there.
178s ________________ ERROR collecting tests/test_core_stringops.py _________________
178s ImportError while importing test module '/tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_core_stringops.py'.
178s Hint: make sure your test modules/packages have valid Python names.
178s Traceback:
178s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
178s     return _bootstrap._gcd_import(name[level:], package, level)
178s tests/test_core_stringops.py:1: in <module>
178s     import pandas as pd
178s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in <module>
178s     raise ImportError(
178s E   ImportError: Unable to import required dependencies:
178s E   numpy: Error importing numpy: you should not try to import numpy from
178s E           its source directory; please exit the numpy source tree, and relaunch
178s E           your python interpreter from there.
178s ____________________ ERROR collecting tests/test_extras.py _____________________
178s ImportError while importing test module '/tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_extras.py'.
178s Hint: make sure your test modules/packages have valid Python names.
178s Traceback:
178s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
178s     return _bootstrap._gcd_import(name[level:], package, level)
178s tests/test_extras.py:4: in <module>
178s     import pandas as pd
178s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in <module>
178s     raise ImportError(
178s E   ImportError: Unable to import required dependencies:
178s E   numpy: Error importing numpy: you should not try to import numpy from
178s E           its source directory; please exit the numpy source tree, and relaunch
178s E           your python interpreter from there.
178s ______________________ ERROR collecting tests/test_io.py _______________________
178s ImportError while importing test module '/tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_io.py'.
178s Hint: make sure your test modules/packages have valid Python names.
178s Traceback:
178s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
178s     return _bootstrap._gcd_import(name[level:], package, level)
178s tests/test_io.py:3: in <module>
178s     import pandas as pd
178s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in <module>
178s     raise ImportError(
178s E   ImportError: Unable to import required dependencies:
178s E   numpy: Error importing numpy: you should not try to import numpy from
178s E           its source directory; please exit the numpy source tree, and relaunch
178s E           your python interpreter from there.
178s ______________________ ERROR collecting tests/test_ops.py ______________________
178s ImportError while importing test module '/tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_ops.py'.
178s Hint: make sure your test modules/packages have valid Python names.
178s Traceback:
178s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
178s     return _bootstrap._gcd_import(name[level:], package, level)
178s tests/test_ops.py:3: in <module>
178s     import pandas as pd
178s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in <module>
178s     raise ImportError(
178s E   ImportError: Unable to import required dependencies:
178s E   numpy: Error importing numpy: you should not try to import numpy from
178s E           its source directory; please exit the numpy source tree, and relaunch
178s E           your python interpreter from there.
178s __________________ ERROR collecting tests/test_ops_select.py ___________________
178s ImportError while importing test module '/tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_ops_select.py'.
178s Hint: make sure your test modules/packages have valid Python names.
178s Traceback:
178s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
178s     return _bootstrap._gcd_import(name[level:], package, level)
178s tests/test_ops_select.py:1: in <module>
178s     import pandas as pd
178s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in <module>
178s     raise ImportError(
178s E   ImportError: Unable to import required dependencies:
178s E   numpy: Error importing numpy: you should not try to import numpy from
178s E           its source directory; please exit the numpy source tree, and relaunch
178s E           your python interpreter from there.
178s =============================== warnings summary ===============================
178s tests/test_io.py:23
178s   /tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_io.py:23: SyntaxWarning: invalid escape sequence '\s'
178s     assert bioframe.read_table(StringIO(d), schema="bed3", sep="\s+").shape == (3, 3)
178s 
178s tests/test_io.py:24
178s   /tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_io.py:24: SyntaxWarning: invalid escape sequence '\s'
178s     assert bioframe.read_table(StringIO(d), schema="bed6", sep="\s+").shape == (3, 6)
178s 
178s tests/test_io.py:25
178s   /tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_io.py:25: SyntaxWarning: invalid escape sequence '\s'
178s     assert bioframe.read_table(StringIO(d), schema="bed12", sep="\s+").shape == (3, 12)
178s 
178s tests/test_io.py:33
178s   /tmp/autopkgtest.Px9SGQ/autopkgtest_tmp/tests/test_io.py:33: SyntaxWarning: invalid escape sequence '\s'
178s     StringIO(d), schema="bedpe", sep="\s+", schema_is_strict=True
178s 
178s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
178s =========================== short test summary info ============================
178s ERROR tests/test_core_checks.py
178s ERROR tests/test_core_construction.py
178s ERROR tests/test_core_specs.py
178s ERROR tests/test_core_stringops.py
178s ERROR tests/test_extras.py
178s ERROR tests/test_io.py
178s ERROR tests/test_ops.py
178s ERROR tests/test_ops_select.py
178s !!!!!!!!!!!!!!!!!!! Interrupted: 8 errors during collection !!!!!!!!!!!!!!!!!!!!
178s ======================== 4 warnings, 8 errors in 0.63s =========================
178s autopkgtest [10:17:00]: test run-unit-test: -----------------------]
178s autopkgtest [10:17:00]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
178s run-unit-test        FAIL non-zero exit status 2
179s autopkgtest [10:17:01]: @@@@@@@@@@@@@@@@@@@@ summary
179s run-unit-test        FAIL non-zero exit status 2
192s nova [W] Skipping flock in bos03-arm64
192s Creating nova instance adt-plucky-arm64-python-bioframe-20241113-101402-juju-7f2275-prod-proposed-migration-environment-15-4449b231-1e22-4b16-81e8-19c4425fe8cc from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...