0s autopkgtest [10:39:10]: starting date and time: 2024-11-13 10:39:10+0000 0s autopkgtest [10:39:10]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [10:39:10]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.74aeuh3c/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-8.secgroup --name adt-plucky-amd64-python-bioframe-20241113-103910-juju-7f2275-prod-proposed-migration-environment-15-8b3b138b-62f1-42f1-923e-afad2b260e8e --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 1492s autopkgtest [11:04:02]: testbed dpkg architecture: amd64 1492s autopkgtest [11:04:02]: testbed apt version: 2.9.8 1492s autopkgtest [11:04:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1493s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 1493s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 1493s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 1493s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 1493s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 1493s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 1493s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 1493s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 1493s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 1494s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 1494s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 1494s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 1494s Fetched 2175 kB in 1s (2622 kB/s) 1494s Reading package lists... 1497s Reading package lists... 1497s Building dependency tree... 1497s Reading state information... 1497s Calculating upgrade... 1497s The following NEW packages will be installed: 1497s python3.13-gdbm 1497s The following packages will be upgraded: 1497s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 1498s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1498s Need to get 253 kB of archives. 1498s After this operation, 147 kB of additional disk space will be used. 1498s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 1498s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 1498s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 1498s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 1498s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 1498s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 1499s Fetched 253 kB in 1s (263 kB/s) 1499s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 1499s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 1499s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 1499s Setting up python3-minimal (3.12.7-1) ... 1499s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 1499s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 1499s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 1499s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 1499s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 1499s Selecting previously unselected package python3.13-gdbm. 1499s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 1499s Unpacking python3.13-gdbm (3.13.0-2) ... 1499s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 1499s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 1499s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 1499s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 1499s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 1499s Setting up python3.13-gdbm (3.13.0-2) ... 1499s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 1499s Setting up python3 (3.12.7-1) ... 1499s Setting up python3-gdbm:amd64 (3.12.7-1) ... 1499s Processing triggers for man-db (2.12.1-3) ... 1500s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1500s Reading package lists... 1500s Building dependency tree... 1500s Reading state information... 1500s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1502s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 1502s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1502s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1502s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1503s Reading package lists... 1503s Reading package lists... 1503s Building dependency tree... 1503s Reading state information... 1503s Calculating upgrade... 1503s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1503s Reading package lists... 1504s Building dependency tree... 1504s Reading state information... 1504s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1508s autopkgtest [11:04:18]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 1508s autopkgtest [11:04:18]: @@@@@@@@@@@@@@@@@@@@ apt-source python-bioframe 1511s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-bioframe 0.4.1-1 (dsc) [1611 B] 1511s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-bioframe 0.4.1-1 (tar) [816 kB] 1511s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-bioframe 0.4.1-1 (diff) [3464 B] 1511s gpgv: Signature made Mon Jun 12 17:55:46 2023 UTC 1511s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 1511s gpgv: Can't check signature: No public key 1511s dpkg-source: warning: cannot verify inline signature for ./python-bioframe_0.4.1-1.dsc: no acceptable signature found 1511s autopkgtest [11:04:21]: testing package python-bioframe version 0.4.1-1 1511s autopkgtest [11:04:21]: build not needed 1512s autopkgtest [11:04:22]: test run-unit-test: preparing testbed 1516s Reading package lists... 1517s Building dependency tree... 1517s Reading state information... 1517s Starting pkgProblemResolver with broken count: 0 1517s Starting 2 pkgProblemResolver with broken count: 0 1517s Done 1517s The following additional packages will be installed: 1517s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 1517s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 1517s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 1517s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 1517s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 1517s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 1517s libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data python3-all 1517s python3-appdirs python3-bioframe python3-brotli python3-contourpy 1517s python3-cycler python3-dateutil python3-decorator python3-fonttools 1517s python3-fs python3-iniconfig python3-kiwisolver python3-lxml python3-lz4 1517s python3-matplotlib python3-mpmath python3-numpy python3-packaging 1517s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 1517s python3-pluggy python3-pytest python3-scipy python3-six python3-sympy 1517s python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk 1517s python3.13 python3.13-minimal python3.13-tk tk8.6-blt2.5 unicode-data 1517s x11-common 1517s Suggested packages: 1517s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 1517s python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript 1517s gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc 1517s python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip 1517s python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc 1517s python3-gmpy2 gcc gfortran python-numpy-doc python3-dev python-pandas-doc 1517s python3-statsmodels python-pil-doc python-scipy-doc texlive-fonts-extra 1517s python-sympy-doc tix python3-tk-dbg python3.13-venv python3.13-doc 1517s binfmt-support 1517s Recommended packages: 1517s javascript-common python3-bs4 python3-cssselect python3-html5lib 1517s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 1517s python3-tables python3-numba python3-olefile g++ | c++-compiler 1517s isympy-common 1517s The following NEW packages will be installed: 1517s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 1517s fonts-lyx libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 1517s libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 1517s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 1517s libopenjp2-7 libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 1517s libraqm0 libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 1517s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 1517s python3-all python3-appdirs python3-bioframe python3-brotli 1517s python3-contourpy python3-cycler python3-dateutil python3-decorator 1517s python3-fonttools python3-fs python3-iniconfig python3-kiwisolver 1517s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy 1517s python3-packaging python3-pandas python3-pandas-lib python3-pil 1517s python3-pil.imagetk python3-pluggy python3-pytest python3-scipy python3-six 1517s python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2 1517s python3.12-tk python3.13 python3.13-minimal python3.13-tk tk8.6-blt2.5 1517s unicode-data x11-common 1517s 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. 1517s Need to get 74.1 MB/74.1 MB of archives. 1517s After this operation, 321 MB of additional disk space will be used. 1517s Get:1 /tmp/autopkgtest.QOBEE0/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 1517s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 1518s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 1518s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 1518s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 1518s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 1518s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 1518s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 1518s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 1518s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 1518s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 1518s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 1518s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 1518s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 1518s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 1518s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 1518s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 1518s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 1518s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 1518s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 1518s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 1518s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 1518s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 1518s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 1518s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 1518s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 1518s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 1518s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 1518s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 1518s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 1518s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 1518s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 1518s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 1518s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 1518s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 1518s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 1518s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 1518s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 1518s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 1518s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 1518s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 1518s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 1518s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 1518s Get:44 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 1518s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 1518s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 1518s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 1518s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 1518s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 1518s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 1518s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 1518s Get:52 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 1518s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 1518s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 1519s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 1519s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 1519s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 1519s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 1519s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 1519s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 1519s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 1519s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 1519s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 1519s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 1519s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 1519s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 1519s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 1519s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 1519s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 1519s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 1519s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 1519s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 1520s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 1520s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 1520s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bioframe all 0.4.1-1 [76.1 kB] 1520s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 1520s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 1520s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 1520s Fetched 74.1 MB in 3s (28.1 MB/s) 1520s Selecting previously unselected package libpython3.13-minimal:amd64. 1520s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75548 files and directories currently installed.) 1520s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 1520s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 1520s Selecting previously unselected package python3.13-minimal. 1520s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 1520s Unpacking python3.13-minimal (3.13.0-2) ... 1520s Selecting previously unselected package libtcl8.6:amd64. 1520s Preparing to unpack .../02-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 1520s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 1520s Selecting previously unselected package fonts-dejavu-mono. 1520s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... 1520s Unpacking fonts-dejavu-mono (2.37-8) ... 1520s Selecting previously unselected package fonts-dejavu-core. 1520s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ... 1520s Unpacking fonts-dejavu-core (2.37-8) ... 1520s Selecting previously unselected package fontconfig-config. 1520s Preparing to unpack .../05-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 1521s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 1521s Selecting previously unselected package libfontconfig1:amd64. 1521s Preparing to unpack .../06-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 1521s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 1521s Selecting previously unselected package libxrender1:amd64. 1521s Preparing to unpack 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libsharpyuv0:amd64 (1.4.0-0.1) ... 1522s Selecting previously unselected package libjbig0:amd64. 1522s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 1522s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 1522s Selecting previously unselected package libwebp7:amd64. 1522s Preparing to unpack .../35-libwebp7_1.4.0-0.1_amd64.deb ... 1522s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 1522s Selecting previously unselected package libtiff6:amd64. 1522s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 1522s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 1522s Selecting previously unselected package libwebpdemux2:amd64. 1522s Preparing to unpack .../37-libwebpdemux2_1.4.0-0.1_amd64.deb ... 1522s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 1522s Selecting previously unselected package libwebpmux3:amd64. 1522s Preparing to unpack .../38-libwebpmux3_1.4.0-0.1_amd64.deb ... 1522s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 1522s Selecting previously 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... 1524s Setting up python3-tz (2024.1-2) ... 1525s Setting up unicode-data (15.1.0-1) ... 1525s Setting up python3-six (1.16.0-7) ... 1525s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 1525s Setting up python3-decorator (5.1.1-5) ... 1525s Setting up libblas3:amd64 (3.12.0-3build2) ... 1525s 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 1525s Setting up python3-packaging (24.1-1) ... 1525s Setting up python3-brotli (1.1.0-2build2) ... 1525s Setting up python3-cycler (0.12.1-1) ... 1525s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 1525s Setting up fonts-dejavu-mono (2.37-8) ... 1525s Setting up python3-kiwisolver (1.4.7-2) ... 1525s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 1525s Setting up fonts-dejavu-core (2.37-8) ... 1525s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 1525s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 1525s Setting up python3-pluggy (1.5.0-1) ... 1526s Setting up libwebp7:amd64 (1.4.0-0.1) ... 1526s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 1526s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 1526s Setting up python3.13-minimal (3.13.0-2) ... 1526s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 1526s Setting up python3-dateutil (2.9.0-2) ... 1526s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 1526s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1526s Setting up python3-mpmath (1.3.0-1) ... 1527s Setting up python-matplotlib-data (3.8.3-3) ... 1527s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 1527s Setting up python3-appdirs (1.4.4-4) ... 1527s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 1527s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 1527s Setting up python3-sympy (1.13.3-1) ... 1537s Setting up liblapack3:amd64 (3.12.0-3build2) ... 1537s 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 1537s Setting up python3.13 (3.13.0-2) ... 1537s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 1538s Setting up python3-pytest (8.3.3-1) ... 1538s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 1538s Setting up python3-all (3.12.7-1) ... 1538s Setting up python3-fs (2.4.16-4) ... 1538s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 1538s Setting up libraqm0:amd64 (0.10.1-1build1) ... 1538s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 1541s Setting up python3-lxml:amd64 (5.3.0-1) ... 1541s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 1541s Setting up python3-contourpy (1.3.0-2) ... 1541s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 1541s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 1541s Setting up libxft2:amd64 (2.3.6-1build1) ... 1541s Setting up python3-scipy (1.13.1-5) ... 1546s Setting up libtk8.6:amd64 (8.6.15-1) ... 1546s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 1546s Setting up python3.12-tk (3.12.7-3) ... 1546s Setting up python3.13-tk (3.13.0-2) ... 1546s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 1547s Setting up python3-pandas (2.2.3+dfsg-5) ... 1554s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 1554s Setting up blt (2.5.3+dfsg-7build1) ... 1554s Setting up python3-tk:amd64 (3.12.7-1) ... 1554s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 1554s Setting up python3-fonttools (4.46.0-1build2) ... 1556s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 1556s Setting up python3-matplotlib (3.8.3-3) ... 1558s Setting up python3-bioframe (0.4.1-1) ... 1558s Setting up autopkgtest-satdep (0) ... 1558s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1558s Processing triggers for systemd (256.5-2ubuntu4) ... 1558s Processing triggers for man-db (2.12.1-3) ... 1561s (Reading database ... 85213 files and directories currently installed.) 1561s Removing autopkgtest-satdep (0) ... 1562s autopkgtest [11:05:12]: test run-unit-test: [----------------------- 1563s ============================= test session starts ============================== 1563s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 1563s cachedir: .pytest_cache 1563s rootdir: /tmp/autopkgtest.QOBEE0/autopkgtest_tmp 1563s plugins: typeguard-4.4.1 1563s collecting ... collected 0 items / 8 errors 1563s 1563s ==================================== ERRORS ==================================== 1563s __________________ ERROR collecting tests/test_core_checks.py __________________ 1563s ImportError while importing test module '/tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_core_checks.py'. 1563s Hint: make sure your test modules/packages have valid Python names. 1563s Traceback: 1563s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1563s return _bootstrap._gcd_import(name[level:], package, level) 1563s tests/test_core_checks.py:3: in 1563s import pandas as pd 1563s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 1563s raise ImportError( 1563s E ImportError: Unable to import required dependencies: 1563s E numpy: Error importing numpy: you should not try to import numpy from 1563s E its source directory; please exit the numpy source tree, and relaunch 1563s E your python interpreter from there. 1563s _______________ ERROR collecting tests/test_core_construction.py _______________ 1563s ImportError while importing test module '/tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_core_construction.py'. 1563s Hint: make sure your test modules/packages have valid Python names. 1563s Traceback: 1563s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1563s return _bootstrap._gcd_import(name[level:], package, level) 1563s tests/test_core_construction.py:3: in 1563s import pandas as pd 1563s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 1563s raise ImportError( 1563s E ImportError: Unable to import required dependencies: 1563s E numpy: Error importing numpy: you should not try to import numpy from 1563s E its source directory; please exit the numpy source tree, and relaunch 1563s E your python interpreter from there. 1563s __________________ ERROR collecting tests/test_core_specs.py ___________________ 1563s ImportError while importing test module '/tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_core_specs.py'. 1563s Hint: make sure your test modules/packages have valid Python names. 1563s Traceback: 1563s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1563s return _bootstrap._gcd_import(name[level:], package, level) 1563s tests/test_core_specs.py:3: in 1563s import pandas as pd 1563s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 1563s raise ImportError( 1563s E ImportError: Unable to import required dependencies: 1563s E numpy: Error importing numpy: you should not try to import numpy from 1563s E its source directory; please exit the numpy source tree, and relaunch 1563s E your python interpreter from there. 1563s ________________ ERROR collecting tests/test_core_stringops.py _________________ 1563s ImportError while importing test module '/tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_core_stringops.py'. 1563s Hint: make sure your test modules/packages have valid Python names. 1563s Traceback: 1563s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1563s return _bootstrap._gcd_import(name[level:], package, level) 1563s tests/test_core_stringops.py:1: in 1563s import pandas as pd 1563s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 1563s raise ImportError( 1563s E ImportError: Unable to import required dependencies: 1563s E numpy: Error importing numpy: you should not try to import numpy from 1563s E its source directory; please exit the numpy source tree, and relaunch 1563s E your python interpreter from there. 1563s ____________________ ERROR collecting tests/test_extras.py _____________________ 1563s ImportError while importing test module '/tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_extras.py'. 1563s Hint: make sure your test modules/packages have valid Python names. 1563s Traceback: 1563s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1563s return _bootstrap._gcd_import(name[level:], package, level) 1563s tests/test_extras.py:4: in 1563s import pandas as pd 1563s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 1563s raise ImportError( 1563s E ImportError: Unable to import required dependencies: 1563s E numpy: Error importing numpy: you should not try to import numpy from 1563s E its source directory; please exit the numpy source tree, and relaunch 1563s E your python interpreter from there. 1563s ______________________ ERROR collecting tests/test_io.py _______________________ 1563s ImportError while importing test module '/tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_io.py'. 1563s Hint: make sure your test modules/packages have valid Python names. 1563s Traceback: 1563s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1563s return _bootstrap._gcd_import(name[level:], package, level) 1563s tests/test_io.py:3: in 1563s import pandas as pd 1563s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 1563s raise ImportError( 1563s E ImportError: Unable to import required dependencies: 1563s E numpy: Error importing numpy: you should not try to import numpy from 1563s E its source directory; please exit the numpy source tree, and relaunch 1563s E your python interpreter from there. 1563s ______________________ ERROR collecting tests/test_ops.py ______________________ 1563s ImportError while importing test module '/tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_ops.py'. 1563s Hint: make sure your test modules/packages have valid Python names. 1563s Traceback: 1563s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1563s return _bootstrap._gcd_import(name[level:], package, level) 1563s tests/test_ops.py:3: in 1563s import pandas as pd 1563s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 1563s raise ImportError( 1563s E ImportError: Unable to import required dependencies: 1563s E numpy: Error importing numpy: you should not try to import numpy from 1563s E its source directory; please exit the numpy source tree, and relaunch 1563s E your python interpreter from there. 1563s __________________ ERROR collecting tests/test_ops_select.py ___________________ 1563s ImportError while importing test module '/tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_ops_select.py'. 1563s Hint: make sure your test modules/packages have valid Python names. 1563s Traceback: 1563s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 1563s return _bootstrap._gcd_import(name[level:], package, level) 1563s tests/test_ops_select.py:1: in 1563s import pandas as pd 1563s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 1563s raise ImportError( 1563s E ImportError: Unable to import required dependencies: 1563s E numpy: Error importing numpy: you should not try to import numpy from 1563s E its source directory; please exit the numpy source tree, and relaunch 1563s E your python interpreter from there. 1563s =============================== warnings summary =============================== 1563s tests/test_io.py:23 1563s /tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_io.py:23: SyntaxWarning: invalid escape sequence '\s' 1563s assert bioframe.read_table(StringIO(d), schema="bed3", sep="\s+").shape == (3, 3) 1563s 1563s tests/test_io.py:24 1563s /tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_io.py:24: SyntaxWarning: invalid escape sequence '\s' 1563s assert bioframe.read_table(StringIO(d), schema="bed6", sep="\s+").shape == (3, 6) 1563s 1563s tests/test_io.py:25 1563s /tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_io.py:25: SyntaxWarning: invalid escape sequence '\s' 1563s assert bioframe.read_table(StringIO(d), schema="bed12", sep="\s+").shape == (3, 12) 1563s 1563s tests/test_io.py:33 1563s /tmp/autopkgtest.QOBEE0/autopkgtest_tmp/tests/test_io.py:33: SyntaxWarning: invalid escape sequence '\s' 1563s StringIO(d), schema="bedpe", sep="\s+", schema_is_strict=True 1563s 1563s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1563s =========================== short test summary info ============================ 1563s ERROR tests/test_core_checks.py 1563s ERROR tests/test_core_construction.py 1563s ERROR tests/test_core_specs.py 1563s ERROR tests/test_core_stringops.py 1563s ERROR tests/test_extras.py 1563s ERROR tests/test_io.py 1563s ERROR tests/test_ops.py 1563s ERROR tests/test_ops_select.py 1563s !!!!!!!!!!!!!!!!!!! Interrupted: 8 errors during collection !!!!!!!!!!!!!!!!!!!! 1563s ======================== 4 warnings, 8 errors in 0.39s ========================= 1563s autopkgtest [11:05:13]: test run-unit-test: -----------------------] 1564s autopkgtest [11:05:14]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1564s run-unit-test FAIL non-zero exit status 2 1564s autopkgtest [11:05:14]: @@@@@@@@@@@@@@@@@@@@ summary 1564s run-unit-test FAIL non-zero exit status 2 1801s nova [W] Skipping flock for amd64 1801s Creating nova instance adt-plucky-amd64-python-bioframe-20241113-103910-juju-7f2275-prod-proposed-migration-environment-15-8b3b138b-62f1-42f1-923e-afad2b260e8e from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...