0s autopkgtest [16:43:18]: starting date and time: 2024-11-16 16:43:18+0000 0s autopkgtest [16:43:18]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [16:43:18]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4ro6ksoc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:mdtraj --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=mdtraj/1.10.1-2build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-1.secgroup --name adt-plucky-arm64-mdtraj-20241116-164317-juju-7f2275-prod-proposed-migration-environment-2-ac61d91a-8502-445f-96b8-0e465b459773 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 66s autopkgtest [16:44:24]: testbed dpkg architecture: arm64 66s autopkgtest [16:44:24]: testbed apt version: 2.9.8 66s autopkgtest [16:44:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 67s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 67s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [91.9 kB] 67s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 67s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1004 kB] 68s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 68s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [168 kB] 68s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 68s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [787 kB] 68s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6404 B] 68s Fetched 2204 kB in 1s (2518 kB/s) 68s Reading package lists... 70s Reading package lists... 71s Building dependency tree... 71s Reading state information... 72s Calculating upgrade... 72s The following packages will be upgraded: 72s debianutils 72s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 92.9 kB of archives. 72s After this operation, 0 B of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 debianutils arm64 5.21 [92.9 kB] 73s Fetched 92.9 kB in 0s (323 kB/s) 73s (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 ... 79964 files and directories currently installed.) 73s Preparing to unpack .../debianutils_5.21_arm64.deb ... 73s Unpacking debianutils (5.21) over (5.20) ... 73s Setting up debianutils (5.21) ... 73s Processing triggers for man-db (2.13.0-1) ... 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 76s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 76s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 76s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 77s Reading package lists... 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 78s Calculating upgrade... 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s autopkgtest [16:44:39]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 81s autopkgtest [16:44:39]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 84s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe mdtraj 1.10.1-2build1 (dsc) [2701 B] 84s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe mdtraj 1.10.1-2build1 (tar) [21.9 MB] 84s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe mdtraj 1.10.1-2build1 (diff) [299 kB] 84s gpgv: Signature made Fri Nov 15 13:41:25 2024 UTC 84s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 84s gpgv: Can't check signature: No public key 84s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.1-2build1.dsc: no acceptable signature found 85s autopkgtest [16:44:43]: testing package mdtraj version 1.10.1-2build1 86s autopkgtest [16:44:44]: build not needed 89s autopkgtest [16:44:47]: test command1: preparing testbed 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Starting pkgProblemResolver with broken count: 0 91s Starting 2 pkgProblemResolver with broken count: 0 91s Done 91s The following additional packages will be installed: 91s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 91s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdebuginfod-common 91s libdebuginfod1t64 libdeflate0 libfontconfig1 libgfortran5 libgomp1 91s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 91s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 91s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libnetcdf19t64 libnorm1t64 91s libopenjp2-7 libpgm-5.3-0t64 libpython3.13-minimal libpython3.13-stdlib 91s libqhull-r8.0 libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 91s libsource-highlight-common libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 91s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 91s libxss1 libzmq5 python-matplotlib-data python-tables-data python3-appdirs 91s python3-asttokens python3-brotli python3-cftime python3-comm 91s python3-contourpy python3-coverage python3-cpuinfo python3-cycler 91s python3-dateutil python3-debugpy python3-decorator python3-executing 91s python3-fastjsonschema python3-fonttools python3-fs python3-gsd 91s python3-iniconfig python3-ipykernel python3-ipython python3-jedi 91s python3-joblib python3-jupyter-client python3-jupyter-core 91s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 91s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 91s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 91s python3-numpy python3-packaging python3-pandas python3-pandas-lib 91s python3-parso python3-pexpect python3-pil python3-pil.imagetk 91s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 91s python3-ptyprocess python3-pure-eval python3-py python3-pytest python3-scipy 91s python3-six python3-sklearn python3-sklearn-lib python3-stack-data 91s python3-sympy python3-tables python3-tables-lib python3-threadpoolctl 91s python3-tk python3-tornado python3-traitlets python3-typeshed python3-tz 91s python3-ufolib2 python3-unicodedata2 python3-wcwidth python3-zmq 91s python3.12-tk python3.13 python3.13-minimal tk8.6-blt2.5 unicode-data 91s x11-common 91s Suggested packages: 91s blt-demo gdb-doc gdbserver libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 91s python-coverage-doc python-cycler-doc python-fastjsonschema-doc 91s python-gsd-doc python-ipython-doc python-joblib-doc 91s python-jupyter-client-doc python3-pip python-lxml-doc cm-super-minimal 91s dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 91s librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi-cairo 91s python3-gobject python3-pyqt5 python3-sip texlive-extra-utils 91s texlive-latex-extra python-mdtraj-doc python-mpmath-doc python3-gmpy2 91s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 91s python3-dev python-pandas-doc python3-statsmodels python-pexpect-doc 91s python-pil-doc subversion python-scipy-doc python3-dap python-sklearn-doc 91s texlive-fonts-extra python-sympy-doc python-tables-doc vitables tix 91s python3-tk-dbg python3.13-tk python3-pycurl python-tornado-doc 91s python3-twisted python-traitlets-doc python3.13-venv python3.13-doc 91s binfmt-support 91s Recommended packages: 91s libc-dbg javascript-common python3-simplejson python3-bs4 python3-cssselect 91s python3-html5lib python3-bottleneck python3-odf python3-openpyxl 91s python3-olefile g++ | c++-compiler isympy-common 91s The following NEW packages will be installed: 91s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 91s fonts-lyx gdb libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 91s libdebuginfod-common libdebuginfod1t64 libdeflate0 libfontconfig1 91s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 91s libhdf5-hl-100t64 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 91s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 91s libnetcdf19t64 libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 91s libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0 91s libsharpyuv0 libsnappy1v5 libsodium23 libsource-highlight-common 91s libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 91s libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 91s python-matplotlib-data python-tables-data python3-appdirs python3-asttokens 91s python3-brotli python3-cftime python3-comm python3-contourpy 91s python3-coverage python3-cpuinfo python3-cycler python3-dateutil 91s python3-debugpy python3-decorator python3-executing python3-fastjsonschema 91s python3-fonttools python3-fs python3-gsd python3-iniconfig python3-ipykernel 91s python3-ipython python3-jedi python3-joblib python3-jupyter-client 91s python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 91s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 91s python3-nbformat python3-nest-asyncio python3-netcdf4 python3-networkx 91s python3-numexpr python3-numpy python3-packaging python3-pandas 91s python3-pandas-lib python3-parso python3-pexpect python3-pil 91s python3-pil.imagetk python3-platformdirs python3-pluggy 91s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 91s python3-py python3-pytest python3-scipy python3-six python3-sklearn 91s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 91s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 91s python3-traitlets python3-typeshed python3-tz python3-ufolib2 91s python3-unicodedata2 python3-wcwidth python3-zmq python3.12-tk python3.13 91s python3.13-minimal tk8.6-blt2.5 unicode-data x11-common 91s 0 upgraded, 135 newly installed, 0 to remove and 0 not upgraded. 91s Need to get 104 MB/104 MB of archives. 91s After this operation, 497 MB of additional disk space will be used. 91s Get:1 /tmp/autopkgtest.SpFfCJ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [776 B] 91s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebuginfod-common all 0.192-4 [15.4 kB] 91s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 92s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 92s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 92s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 92s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 92s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 92s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 92s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 92s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 92s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 92s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 92s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 92s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 92s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 92s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 92s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libbabeltrace1 arm64 1.5.11-4build1 [159 kB] 92s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebuginfod1t64 arm64 0.192-4 [20.8 kB] 92s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 92s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libsource-highlight4t64 arm64 3.1.9-4.3build1 [243 kB] 92s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 gdb arm64 15.1-1ubuntu2 [4550 kB] 92s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 92s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 92s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libsnappy1v5 arm64 1.2.1-1 [30.4 kB] 92s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc1 arm64 1.21.5+ds-1build1 [25.7 kB] 92s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libblosc2-4 arm64 2.15.1+ds-1 [157 kB] 92s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 92s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 92s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 92s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 92s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 92s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 92s Get:34 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 93s Get:35 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 93s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 93s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 93s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 93s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 93s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 93s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 93s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 93s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 93s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 93s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf19t64 arm64 1:4.9.2-6ubuntu1 [466 kB] 93s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnorm1t64 arm64 1.5.9+dfsg-3.1build1 [150 kB] 93s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpgm-5.3-0t64 arm64 5.3.128~dfsg-2.1build1 [162 kB] 93s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 93s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 93s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 93s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 93s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libsodium23 arm64 1.0.18-1build3 [119 kB] 93s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 93s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 93s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 93s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 93s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 93s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 93s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 libzmq5 arm64 4.3.5-1build2 [247 kB] 93s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 93s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-tables-data all 3.10.1-1build1 [49.4 kB] 93s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 93s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-asttokens all 2.4.1-2 [20.8 kB] 93s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 93s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 93s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-1build1 [290 kB] 93s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 93s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-comm all 0.2.1-1 [7016 B] 93s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2build1 [220 kB] 93s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 93s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coverage arm64 7.4.4+dfsg1-0ubuntu3 [150 kB] 93s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cpuinfo all 9.0.0+git20221119-2 [21.6 kB] 93s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 93s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 93s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 93s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-debugpy arm64 1.8.8+ds-1ubuntu2 [1054 kB] 93s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 93s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-executing all 2.1.0-0.1 [24.4 kB] 93s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastjsonschema all 2.20.0-1 [20.1 kB] 93s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 94s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 94s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 94s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 94s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 94s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 94s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 94s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 94s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 94s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 94s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 94s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gsd arm64 3.3.0-1build1 [228 kB] 94s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 94s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-parso all 0.8.3-1 [67.2 kB] 94s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 94s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 94s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 94s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 94s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pexpect all 4.9-2 [48.1 kB] 94s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 94s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-prompt-toolkit all 3.0.48-1 [256 kB] 94s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pure-eval all 0.2.3-1 [11.4 kB] 94s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 95s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 95s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 95s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-core all 5.7.2-4 [28.0 kB] 95s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-psutil arm64 5.9.8-2build2 [196 kB] 95s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tornado arm64 6.4.1-3 [299 kB] 95s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-py all 1.11.0-2 [72.7 kB] 95s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-zmq arm64 24.0.1-5build1 [280 kB] 95s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-client all 8.6.2-3 [78.1 kB] 95s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nest-asyncio all 1.5.4-1 [6256 B] 95s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 95s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ipykernel all 6.29.5-1 [82.5 kB] 95s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 95s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 95s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 95s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 95s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 95s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.6-1ubuntu1 [9806 B] 95s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 95s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 95s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 96s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 96s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 96s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numexpr arm64 2.10.1-2 [114 kB] 96s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables-lib arm64 3.10.1-1build1 [739 kB] 96s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tables all 3.10.1-1build1 [354 kB] 96s Get:128 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-mdtraj arm64 1.10.1-2build1 [1548 kB] 96s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 96s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1build1 [798 kB] 96s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 96s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 96s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 96s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3806 kB] 96s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 97s Preconfiguring packages ... 97s Fetched 104 MB in 5s (20.8 MB/s) 97s Selecting previously unselected package libdebuginfod-common. 97s (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 ... 79964 files and directories currently installed.) 97s Preparing to unpack .../000-libdebuginfod-common_0.192-4_all.deb ... 97s Unpacking libdebuginfod-common (0.192-4) ... 97s Selecting previously unselected package libpython3.13-minimal:arm64. 97s Preparing to unpack .../001-libpython3.13-minimal_3.13.0-2_arm64.deb ... 97s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 97s Selecting previously unselected package python3.13-minimal. 97s Preparing to unpack .../002-python3.13-minimal_3.13.0-2_arm64.deb ... 97s Unpacking python3.13-minimal (3.13.0-2) ... 97s Selecting previously unselected package libtcl8.6:arm64. 97s Preparing to unpack .../003-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 97s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 97s Selecting previously unselected package fonts-dejavu-mono. 97s Preparing to unpack .../004-fonts-dejavu-mono_2.37-8_all.deb ... 97s Unpacking fonts-dejavu-mono (2.37-8) ... 97s Selecting previously unselected package fonts-dejavu-core. 97s Preparing to unpack .../005-fonts-dejavu-core_2.37-8_all.deb ... 97s Unpacking fonts-dejavu-core (2.37-8) ... 97s Selecting previously unselected package fontconfig-config. 97s Preparing to unpack .../006-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 97s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 97s Selecting previously unselected package libfontconfig1:arm64. 97s Preparing to unpack .../007-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 97s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 97s Selecting previously unselected package libxrender1:arm64. 97s Preparing to unpack .../008-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 97s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 97s Selecting previously unselected package libxft2:arm64. 97s Preparing to unpack .../009-libxft2_2.3.6-1build1_arm64.deb ... 97s Unpacking libxft2:arm64 (2.3.6-1build1) ... 97s Selecting previously unselected package x11-common. 97s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 97s Unpacking x11-common (1:7.7+23ubuntu3) ... 97s Selecting previously unselected package libxss1:arm64. 97s Preparing to unpack .../011-libxss1_1%3a1.2.3-1build3_arm64.deb ... 97s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 97s Selecting previously unselected package libtk8.6:arm64. 97s Preparing to unpack .../012-libtk8.6_8.6.15-1_arm64.deb ... 97s Unpacking libtk8.6:arm64 (8.6.15-1) ... 97s Selecting previously unselected package tk8.6-blt2.5. 97s Preparing to unpack .../013-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 97s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 97s Selecting previously unselected package blt. 98s Preparing to unpack .../014-blt_2.5.3+dfsg-7build1_arm64.deb ... 98s Unpacking blt (2.5.3+dfsg-7build1) ... 98s Selecting previously unselected package fonts-lyx. 98s Preparing to unpack .../015-fonts-lyx_2.4.2.1-1_all.deb ... 98s Unpacking fonts-lyx (2.4.2.1-1) ... 98s Selecting previously unselected package libbabeltrace1:arm64. 98s Preparing to unpack .../016-libbabeltrace1_1.5.11-4build1_arm64.deb ... 98s Unpacking libbabeltrace1:arm64 (1.5.11-4build1) ... 98s Selecting previously unselected package libdebuginfod1t64:arm64. 98s Preparing to unpack .../017-libdebuginfod1t64_0.192-4_arm64.deb ... 98s Unpacking libdebuginfod1t64:arm64 (0.192-4) ... 98s Selecting previously unselected package libsource-highlight-common. 98s Preparing to unpack .../018-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 98s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 98s Selecting previously unselected package libsource-highlight4t64:arm64. 98s Preparing to unpack .../019-libsource-highlight4t64_3.1.9-4.3build1_arm64.deb ... 98s Unpacking libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 98s Selecting previously unselected package gdb. 98s Preparing to unpack .../020-gdb_15.1-1ubuntu2_arm64.deb ... 98s Unpacking gdb (15.1-1ubuntu2) ... 98s Selecting previously unselected package libaec0:arm64. 98s Preparing to unpack .../021-libaec0_1.1.3-1_arm64.deb ... 98s Unpacking libaec0:arm64 (1.1.3-1) ... 98s Selecting previously unselected package libblas3:arm64. 98s Preparing to unpack .../022-libblas3_3.12.0-3build2_arm64.deb ... 98s Unpacking libblas3:arm64 (3.12.0-3build2) ... 98s Selecting previously unselected package libsnappy1v5:arm64. 98s Preparing to unpack .../023-libsnappy1v5_1.2.1-1_arm64.deb ... 98s Unpacking libsnappy1v5:arm64 (1.2.1-1) ... 98s Selecting previously unselected package libblosc1:arm64. 98s Preparing to unpack .../024-libblosc1_1.21.5+ds-1build1_arm64.deb ... 98s Unpacking libblosc1:arm64 (1.21.5+ds-1build1) ... 98s Selecting previously unselected package libblosc2-4:arm64. 98s Preparing to unpack .../025-libblosc2-4_2.15.1+ds-1_arm64.deb ... 98s Unpacking libblosc2-4:arm64 (2.15.1+ds-1) ... 98s Selecting previously unselected package libdeflate0:arm64. 98s Preparing to unpack .../026-libdeflate0_1.22-1_arm64.deb ... 98s Unpacking libdeflate0:arm64 (1.22-1) ... 98s Selecting previously unselected package libgfortran5:arm64. 98s Preparing to unpack .../027-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 98s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 98s Selecting previously unselected package libgomp1:arm64. 98s Preparing to unpack .../028-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 98s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 98s Selecting previously unselected package libgraphite2-3:arm64. 98s Preparing to unpack .../029-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 98s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 98s Selecting previously unselected package libharfbuzz0b:arm64. 98s Preparing to unpack .../030-libharfbuzz0b_10.0.1-1_arm64.deb ... 98s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 98s Selecting previously unselected package libsz2:arm64. 98s Preparing to unpack .../031-libsz2_1.1.3-1_arm64.deb ... 98s Unpacking libsz2:arm64 (1.1.3-1) ... 98s Selecting previously unselected package libhdf5-103-1t64:arm64. 98s Preparing to unpack .../032-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 98s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 98s Selecting previously unselected package libhdf5-hl-100t64:arm64. 98s Preparing to unpack .../033-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 98s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 98s Selecting previously unselected package libimagequant0:arm64. 98s Preparing to unpack .../034-libimagequant0_2.18.0-1build1_arm64.deb ... 98s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 98s Selecting previously unselected package libjpeg-turbo8:arm64. 98s Preparing to unpack .../035-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 98s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 98s Selecting previously unselected package libjpeg8:arm64. 98s Preparing to unpack .../036-libjpeg8_8c-2ubuntu11_arm64.deb ... 98s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 98s Selecting previously unselected package libjs-jquery. 98s Preparing to unpack .../037-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 98s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 98s Selecting previously unselected package libjs-jquery-ui. 98s Preparing to unpack .../038-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 98s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 98s Selecting previously unselected package liblapack3:arm64. 98s Preparing to unpack .../039-liblapack3_3.12.0-3build2_arm64.deb ... 98s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 98s Selecting previously unselected package liblbfgsb0:arm64. 98s Preparing to unpack .../040-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 98s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 99s Selecting previously unselected package liblcms2-2:arm64. 99s Preparing to unpack .../041-liblcms2-2_2.16-2_arm64.deb ... 99s Unpacking liblcms2-2:arm64 (2.16-2) ... 99s Selecting previously unselected package liblerc4:arm64. 99s Preparing to unpack .../042-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 99s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 99s Selecting previously unselected package libnetcdf19t64:arm64. 99s Preparing to unpack .../043-libnetcdf19t64_1%3a4.9.2-6ubuntu1_arm64.deb ... 99s Unpacking libnetcdf19t64:arm64 (1:4.9.2-6ubuntu1) ... 99s Selecting previously unselected package libnorm1t64:arm64. 99s Preparing to unpack .../044-libnorm1t64_1.5.9+dfsg-3.1build1_arm64.deb ... 99s Unpacking libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 99s Selecting previously unselected package libpgm-5.3-0t64:arm64. 99s Preparing to unpack .../045-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_arm64.deb ... 99s Unpacking libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 99s Selecting previously unselected package libpython3.13-stdlib:arm64. 99s Preparing to unpack .../046-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 99s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 99s Selecting previously unselected package libqhull-r8.0:arm64. 99s Preparing to unpack .../047-libqhull-r8.0_2020.2-6build1_arm64.deb ... 99s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 99s Selecting previously unselected package libraqm0:arm64. 99s Preparing to unpack .../048-libraqm0_0.10.1-1build1_arm64.deb ... 99s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 99s Selecting previously unselected package libsharpyuv0:arm64. 99s Preparing to unpack .../049-libsharpyuv0_1.4.0-0.1_arm64.deb ... 99s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 99s Selecting previously unselected package libsodium23:arm64. 99s Preparing to unpack .../050-libsodium23_1.0.18-1build3_arm64.deb ... 99s Unpacking libsodium23:arm64 (1.0.18-1build3) ... 99s Selecting previously unselected package libjbig0:arm64. 99s Preparing to unpack .../051-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 99s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 99s Selecting previously unselected package libwebp7:arm64. 99s Preparing to unpack .../052-libwebp7_1.4.0-0.1_arm64.deb ... 99s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 99s Selecting previously unselected package libtiff6:arm64. 99s Preparing to unpack .../053-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 99s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 99s Selecting previously unselected package libwebpdemux2:arm64. 99s Preparing to unpack .../054-libwebpdemux2_1.4.0-0.1_arm64.deb ... 99s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 99s Selecting previously unselected package libwebpmux3:arm64. 99s Preparing to unpack .../055-libwebpmux3_1.4.0-0.1_arm64.deb ... 99s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 99s Selecting previously unselected package libxslt1.1:arm64. 99s Preparing to unpack .../056-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 99s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 99s Selecting previously unselected package libzmq5:arm64. 99s Preparing to unpack .../057-libzmq5_4.3.5-1build2_arm64.deb ... 99s Unpacking libzmq5:arm64 (4.3.5-1build2) ... 99s Selecting previously unselected package python-matplotlib-data. 99s Preparing to unpack .../058-python-matplotlib-data_3.8.3-3_all.deb ... 99s Unpacking python-matplotlib-data (3.8.3-3) ... 99s Selecting previously unselected package python-tables-data. 99s Preparing to unpack .../059-python-tables-data_3.10.1-1build1_all.deb ... 99s Unpacking python-tables-data (3.10.1-1build1) ... 99s Selecting previously unselected package python3-appdirs. 99s Preparing to unpack .../060-python3-appdirs_1.4.4-4_all.deb ... 99s Unpacking python3-appdirs (1.4.4-4) ... 99s Selecting previously unselected package python3-asttokens. 99s Preparing to unpack .../061-python3-asttokens_2.4.1-2_all.deb ... 99s Unpacking python3-asttokens (2.4.1-2) ... 99s Selecting previously unselected package python3-brotli. 99s Preparing to unpack .../062-python3-brotli_1.1.0-2build2_arm64.deb ... 99s Unpacking python3-brotli (1.1.0-2build2) ... 99s Selecting previously unselected package python3-numpy. 99s Preparing to unpack .../063-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 99s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 99s Selecting previously unselected package python3-cftime. 99s Preparing to unpack .../064-python3-cftime_1.6.4-1build1_arm64.deb ... 99s Unpacking python3-cftime (1.6.4-1build1) ... 100s Selecting previously unselected package python3-traitlets. 100s Preparing to unpack .../065-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 100s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 100s Selecting previously unselected package python3-comm. 100s Preparing to unpack .../066-python3-comm_0.2.1-1_all.deb ... 100s Unpacking python3-comm (0.2.1-1) ... 100s Selecting previously unselected package python3-contourpy. 100s Preparing to unpack .../067-python3-contourpy_1.3.0-2build1_arm64.deb ... 100s Unpacking python3-contourpy (1.3.0-2build1) ... 100s Selecting previously unselected package python3.13. 100s Preparing to unpack .../068-python3.13_3.13.0-2_arm64.deb ... 100s Unpacking python3.13 (3.13.0-2) ... 100s Selecting previously unselected package python3-coverage. 100s Preparing to unpack .../069-python3-coverage_7.4.4+dfsg1-0ubuntu3_arm64.deb ... 100s Unpacking python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 100s Selecting previously unselected package python3-cpuinfo. 100s Preparing to unpack .../070-python3-cpuinfo_9.0.0+git20221119-2_all.deb ... 100s Unpacking python3-cpuinfo (9.0.0+git20221119-2) ... 100s Selecting previously unselected package python3-cycler. 100s Preparing to unpack .../071-python3-cycler_0.12.1-1_all.deb ... 100s Unpacking python3-cycler (0.12.1-1) ... 100s Selecting previously unselected package python3-six. 100s Preparing to unpack .../072-python3-six_1.16.0-7_all.deb ... 100s Unpacking python3-six (1.16.0-7) ... 100s Selecting previously unselected package python3-dateutil. 100s Preparing to unpack .../073-python3-dateutil_2.9.0-2_all.deb ... 100s Unpacking python3-dateutil (2.9.0-2) ... 100s Selecting previously unselected package python3-debugpy. 100s Preparing to unpack .../074-python3-debugpy_1.8.8+ds-1ubuntu2_arm64.deb ... 100s Unpacking python3-debugpy (1.8.8+ds-1ubuntu2) ... 100s Selecting previously unselected package python3-decorator. 100s Preparing to unpack .../075-python3-decorator_5.1.1-5_all.deb ... 100s Unpacking python3-decorator (5.1.1-5) ... 100s Selecting previously unselected package python3-executing. 100s Preparing to unpack .../076-python3-executing_2.1.0-0.1_all.deb ... 100s Unpacking python3-executing (2.1.0-0.1) ... 100s Selecting previously unselected package python3-fastjsonschema. 100s Preparing to unpack .../077-python3-fastjsonschema_2.20.0-1_all.deb ... 100s Unpacking python3-fastjsonschema (2.20.0-1) ... 100s Selecting previously unselected package python3-scipy. 100s Preparing to unpack .../078-python3-scipy_1.13.1-5_arm64.deb ... 100s Unpacking python3-scipy (1.13.1-5) ... 100s Selecting previously unselected package python3-ufolib2. 100s Preparing to unpack .../079-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 100s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 100s Selecting previously unselected package python3-mpmath. 100s Preparing to unpack .../080-python3-mpmath_1.3.0-1_all.deb ... 100s Unpacking python3-mpmath (1.3.0-1) ... 100s Selecting previously unselected package python3-sympy. 100s Preparing to unpack .../081-python3-sympy_1.13.3-1_all.deb ... 100s Unpacking python3-sympy (1.13.3-1) ... 101s Selecting previously unselected package python3-tz. 101s Preparing to unpack .../082-python3-tz_2024.1-2_all.deb ... 101s Unpacking python3-tz (2024.1-2) ... 101s Selecting previously unselected package python3-fs. 101s Preparing to unpack .../083-python3-fs_2.4.16-4_all.deb ... 101s Unpacking python3-fs (2.4.16-4) ... 101s Selecting previously unselected package python3-lxml:arm64. 101s Preparing to unpack .../084-python3-lxml_5.3.0-1_arm64.deb ... 101s Unpacking python3-lxml:arm64 (5.3.0-1) ... 101s Selecting previously unselected package python3-lz4. 101s Preparing to unpack .../085-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 101s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 101s Selecting previously unselected package python3-unicodedata2. 101s Preparing to unpack .../086-python3-unicodedata2_15.1.0+ds-1build2_arm64.deb ... 101s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 101s Selecting previously unselected package unicode-data. 101s Preparing to unpack .../087-unicode-data_15.1.0-1_all.deb ... 101s Unpacking unicode-data (15.1.0-1) ... 101s Selecting previously unselected package python3-fonttools. 101s Preparing to unpack .../088-python3-fonttools_4.46.0-1build2_arm64.deb ... 101s Unpacking python3-fonttools (4.46.0-1build2) ... 101s Selecting previously unselected package python3-gsd. 101s Preparing to unpack .../089-python3-gsd_3.3.0-1build1_arm64.deb ... 101s Unpacking python3-gsd (3.3.0-1build1) ... 101s Selecting previously unselected package python3-iniconfig. 101s Preparing to unpack .../090-python3-iniconfig_1.1.1-2_all.deb ... 101s Unpacking python3-iniconfig (1.1.1-2) ... 101s Selecting previously unselected package python3-parso. 101s Preparing to unpack .../091-python3-parso_0.8.3-1_all.deb ... 101s Unpacking python3-parso (0.8.3-1) ... 101s Selecting previously unselected package python3-typeshed. 101s Preparing to unpack .../092-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 101s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 102s Selecting previously unselected package python3-jedi. 102s Preparing to unpack .../093-python3-jedi_0.19.1+ds1-1_all.deb ... 102s Unpacking python3-jedi (0.19.1+ds1-1) ... 102s Selecting previously unselected package python3-matplotlib-inline. 102s Preparing to unpack .../094-python3-matplotlib-inline_0.1.6-2_all.deb ... 102s Unpacking python3-matplotlib-inline (0.1.6-2) ... 102s Selecting previously unselected package python3-ptyprocess. 102s Preparing to unpack .../095-python3-ptyprocess_0.7.0-6_all.deb ... 102s Unpacking python3-ptyprocess (0.7.0-6) ... 102s Selecting previously unselected package python3-pexpect. 102s Preparing to unpack .../096-python3-pexpect_4.9-2_all.deb ... 102s Unpacking python3-pexpect (4.9-2) ... 102s Selecting previously unselected package python3-wcwidth. 102s Preparing to unpack .../097-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 102s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 102s Selecting previously unselected package python3-prompt-toolkit. 102s Preparing to unpack .../098-python3-prompt-toolkit_3.0.48-1_all.deb ... 102s Unpacking python3-prompt-toolkit (3.0.48-1) ... 102s Selecting previously unselected package python3-pure-eval. 102s Preparing to unpack .../099-python3-pure-eval_0.2.3-1_all.deb ... 102s Unpacking python3-pure-eval (0.2.3-1) ... 102s Selecting previously unselected package python3-stack-data. 102s Preparing to unpack .../100-python3-stack-data_0.6.3-1_all.deb ... 102s Unpacking python3-stack-data (0.6.3-1) ... 102s Selecting previously unselected package python3-ipython. 102s Preparing to unpack .../101-python3-ipython_8.20.0-1ubuntu1_all.deb ... 102s Unpacking python3-ipython (8.20.0-1ubuntu1) ... 102s Selecting previously unselected package python3-platformdirs. 102s Preparing to unpack .../102-python3-platformdirs_4.3.6-1_all.deb ... 102s Unpacking python3-platformdirs (4.3.6-1) ... 102s Selecting previously unselected package python3-jupyter-core. 102s Preparing to unpack .../103-python3-jupyter-core_5.7.2-4_all.deb ... 102s Unpacking python3-jupyter-core (5.7.2-4) ... 102s Selecting previously unselected package python3-psutil. 102s Preparing to unpack .../104-python3-psutil_5.9.8-2build2_arm64.deb ... 102s Unpacking python3-psutil (5.9.8-2build2) ... 102s Selecting previously unselected package python3-tornado. 102s Preparing to unpack .../105-python3-tornado_6.4.1-3_arm64.deb ... 102s Unpacking python3-tornado (6.4.1-3) ... 102s Selecting previously unselected package python3-py. 102s Preparing to unpack .../106-python3-py_1.11.0-2_all.deb ... 102s Unpacking python3-py (1.11.0-2) ... 102s Selecting previously unselected package python3-zmq. 102s Preparing to unpack .../107-python3-zmq_24.0.1-5build1_arm64.deb ... 102s Unpacking python3-zmq (24.0.1-5build1) ... 102s Selecting previously unselected package python3-jupyter-client. 102s Preparing to unpack .../108-python3-jupyter-client_8.6.2-3_all.deb ... 102s Unpacking python3-jupyter-client (8.6.2-3) ... 103s Selecting previously unselected package python3-nest-asyncio. 103s Preparing to unpack .../109-python3-nest-asyncio_1.5.4-1_all.deb ... 103s Unpacking python3-nest-asyncio (1.5.4-1) ... 103s Selecting previously unselected package python3-packaging. 103s Preparing to unpack .../110-python3-packaging_24.1-1_all.deb ... 103s Unpacking python3-packaging (24.1-1) ... 103s Selecting previously unselected package python3-ipykernel. 103s Preparing to unpack .../111-python3-ipykernel_6.29.5-1_all.deb ... 103s Unpacking python3-ipykernel (6.29.5-1) ... 103s Selecting previously unselected package python3-joblib. 103s Preparing to unpack .../112-python3-joblib_1.3.2-5_all.deb ... 103s Unpacking python3-joblib (1.3.2-5) ... 103s Selecting previously unselected package python3-kiwisolver. 103s Preparing to unpack .../113-python3-kiwisolver_1.4.7-2build1_arm64.deb ... 103s Unpacking python3-kiwisolver (1.4.7-2build1) ... 103s Selecting previously unselected package libopenjp2-7:arm64. 103s Preparing to unpack .../114-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 103s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 103s Selecting previously unselected package python3-pil:arm64. 103s Preparing to unpack .../115-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 103s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 103s Selecting previously unselected package python3.12-tk. 103s Preparing to unpack .../116-python3.12-tk_3.12.7-3_arm64.deb ... 103s Unpacking python3.12-tk (3.12.7-3) ... 103s Selecting previously unselected package python3-tk:arm64. 103s Preparing to unpack .../117-python3-tk_3.12.6-1ubuntu1_arm64.deb ... 103s Unpacking python3-tk:arm64 (3.12.6-1ubuntu1) ... 103s Selecting previously unselected package python3-pil.imagetk:arm64. 103s Preparing to unpack .../118-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 103s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 103s Selecting previously unselected package python3-matplotlib. 103s Preparing to unpack .../119-python3-matplotlib_3.8.3-3_arm64.deb ... 103s Unpacking python3-matplotlib (3.8.3-3) ... 103s Selecting previously unselected package python3-networkx. 103s Preparing to unpack .../120-python3-networkx_3.2.1-4ubuntu1_all.deb ... 103s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 104s Selecting previously unselected package python3-pandas-lib:arm64. 104s Preparing to unpack .../121-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 104s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 104s Selecting previously unselected package python3-pandas. 104s Preparing to unpack .../122-python3-pandas_2.2.3+dfsg-5_all.deb ... 104s Unpacking python3-pandas (2.2.3+dfsg-5) ... 104s Selecting previously unselected package python3-numexpr. 104s Preparing to unpack .../123-python3-numexpr_2.10.1-2_arm64.deb ... 104s Unpacking python3-numexpr (2.10.1-2) ... 104s Selecting previously unselected package python3-tables-lib. 104s Preparing to unpack .../124-python3-tables-lib_3.10.1-1build1_arm64.deb ... 104s Unpacking python3-tables-lib (3.10.1-1build1) ... 104s Selecting previously unselected package python3-tables. 104s Preparing to unpack .../125-python3-tables_3.10.1-1build1_all.deb ... 104s Unpacking python3-tables (3.10.1-1build1) ... 104s Selecting previously unselected package python3-mdtraj. 104s Preparing to unpack .../126-python3-mdtraj_1.10.1-2build1_arm64.deb ... 104s Unpacking python3-mdtraj (1.10.1-2build1) ... 104s Selecting previously unselected package python3-nbformat. 104s Preparing to unpack .../127-python3-nbformat_5.9.1-1_all.deb ... 104s Unpacking python3-nbformat (5.9.1-1) ... 104s Selecting previously unselected package python3-netcdf4. 104s Preparing to unpack .../128-python3-netcdf4_1.7.2-1build1_arm64.deb ... 104s Unpacking python3-netcdf4 (1.7.2-1build1) ... 104s Selecting previously unselected package python3-pluggy. 104s Preparing to unpack .../129-python3-pluggy_1.5.0-1_all.deb ... 104s Unpacking python3-pluggy (1.5.0-1) ... 104s Selecting previously unselected package python3-pytest. 104s Preparing to unpack .../130-python3-pytest_8.3.3-1_all.deb ... 104s Unpacking python3-pytest (8.3.3-1) ... 104s Selecting previously unselected package python3-threadpoolctl. 104s Preparing to unpack .../131-python3-threadpoolctl_3.1.0-1_all.deb ... 104s Unpacking python3-threadpoolctl (3.1.0-1) ... 104s Selecting previously unselected package python3-sklearn-lib:arm64. 104s Preparing to unpack .../132-python3-sklearn-lib_1.4.2+dfsg-6_arm64.deb ... 104s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ... 105s Selecting previously unselected package python3-sklearn. 105s Preparing to unpack .../133-python3-sklearn_1.4.2+dfsg-6_all.deb ... 105s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 105s Selecting previously unselected package autopkgtest-satdep. 105s Preparing to unpack .../134-1-autopkgtest-satdep.deb ... 105s Unpacking autopkgtest-satdep (0) ... 105s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 105s Setting up liblcms2-2:arm64 (2.16-2) ... 105s Setting up python3-iniconfig (1.1.1-2) ... 105s Setting up python3-tornado (6.4.1-3) ... 105s Setting up libnorm1t64:arm64 (1.5.9+dfsg-3.1build1) ... 105s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 105s Setting up python3-pure-eval (0.2.3-1) ... 105s Setting up libsodium23:arm64 (1.0.18-1build3) ... 105s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 105s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 105s Setting up python3-py (1.11.0-2) ... 105s Setting up libdebuginfod-common (0.192-4) ... 106s Setting up python3-joblib (1.3.2-5) ... 106s Setting up python3-parso (0.8.3-1) ... 106s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 106s Setting up python3-asttokens (2.4.1-2) ... 106s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 106s Setting up fonts-lyx (2.4.2.1-1) ... 106s Setting up python3-threadpoolctl (3.1.0-1) ... 106s Setting up x11-common (1:7.7+23ubuntu3) ... 107s Setting up libdeflate0:arm64 (1.22-1) ... 107s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 107s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 107s Setting up python3-networkx (3.2.1-4ubuntu1) ... 108s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 108s Setting up libaec0:arm64 (1.1.3-1) ... 108s Setting up python3-platformdirs (4.3.6-1) ... 108s Setting up python3-psutil (5.9.8-2build2) ... 108s Setting up libsource-highlight-common (3.1.9-4.3build1) ... 108s Setting up python3-tz (2024.1-2) ... 108s Setting up libsnappy1v5:arm64 (1.2.1-1) ... 108s Setting up unicode-data (15.1.0-1) ... 108s Setting up python3-six (1.16.0-7) ... 109s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 109s Setting up libpgm-5.3-0t64:arm64 (5.3.128~dfsg-2.1build1) ... 109s Setting up python3-decorator (5.1.1-5) ... 109s Setting up libblosc2-4:arm64 (2.15.1+ds-1) ... 109s Setting up libblas3:arm64 (3.12.0-3build2) ... 109s 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 109s Setting up python3-packaging (24.1-1) ... 109s Setting up python3-wcwidth (0.2.13+dfsg1-1) ... 109s Setting up python3-typeshed (0.0~git20231111.6764465-3) ... 109s Setting up python3-executing (2.1.0-0.1) ... 109s Setting up python3-nest-asyncio (1.5.4-1) ... 109s Setting up python3-brotli (1.1.0-2build2) ... 109s Setting up python3-cycler (0.12.1-1) ... 109s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 109s Setting up fonts-dejavu-mono (2.37-8) ... 109s Setting up python3-kiwisolver (1.4.7-2build1) ... 109s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 109s Setting up fonts-dejavu-core (2.37-8) ... 109s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 109s Setting up python3-cpuinfo (9.0.0+git20221119-2) ... 110s Setting up libbabeltrace1:arm64 (1.5.11-4build1) ... 110s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 110s Setting up python3-pluggy (1.5.0-1) ... 110s Setting up libwebp7:arm64 (1.4.0-0.1) ... 110s Setting up python3-fastjsonschema (2.20.0-1) ... 110s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 110s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 110s Setting up libblosc1:arm64 (1.21.5+ds-1build1) ... 110s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 110s Setting up python3.13-minimal (3.13.0-2) ... 111s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 111s Setting up python3-dateutil (2.9.0-2) ... 111s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 111s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 111s Setting up python3-mpmath (1.3.0-1) ... 112s Setting up python-matplotlib-data (3.8.3-3) ... 112s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 112s Setting up python3-appdirs (1.4.4-4) ... 112s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 112s Setting up python3-stack-data (0.6.3-1) ... 112s Setting up python-tables-data (3.10.1-1build1) ... 112s Setting up python3-jupyter-core (5.7.2-4) ... 112s Setting up libsz2:arm64 (1.1.3-1) ... 112s Setting up python3-ptyprocess (0.7.0-6) ... 112s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 112s Setting up python3-prompt-toolkit (3.0.48-1) ... 112s Setting up python3-sympy (1.13.3-1) ... 119s Setting up libdebuginfod1t64:arm64 (0.192-4) ... 119s Setting up liblapack3:arm64 (3.12.0-3build2) ... 119s 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 119s Setting up libzmq5:arm64 (4.3.5-1build2) ... 119s Setting up python3-jedi (0.19.1+ds1-1) ... 119s Setting up python3.13 (3.13.0-2) ... 120s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 120s Setting up python3-pytest (8.3.3-1) ... 121s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 121s Setting up python3-coverage (7.4.4+dfsg1-0ubuntu3) ... 121s Setting up libsource-highlight4t64:arm64 (3.1.9-4.3build1) ... 121s Setting up python3-nbformat (5.9.1-1) ... 121s Setting up python3-matplotlib-inline (0.1.6-2) ... 121s Setting up python3-comm (0.2.1-1) ... 121s Setting up python3-fs (2.4.16-4) ... 121s Setting up gdb (15.1-1ubuntu2) ... 121s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 121s Setting up python3-pexpect (4.9-2) ... 121s Setting up python3-zmq (24.0.1-5build1) ... 122s Setting up libraqm0:arm64 (0.10.1-1build1) ... 122s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 124s Setting up python3-lxml:arm64 (5.3.0-1) ... 124s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 124s Setting up python3-jupyter-client (8.6.2-3) ... 124s Setting up python3-contourpy (1.3.0-2build1) ... 124s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 124s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 124s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 124s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 124s Setting up libnetcdf19t64:arm64 (1:4.9.2-6ubuntu1) ... 124s Setting up libxft2:arm64 (2.3.6-1build1) ... 124s Setting up python3-scipy (1.13.1-5) ... 127s Setting up python3-tables-lib (3.10.1-1build1) ... 127s Setting up libtk8.6:arm64 (8.6.15-1) ... 127s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 127s Setting up python3.12-tk (3.12.7-3) ... 127s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ... 127s Setting up python3-gsd (3.3.0-1build1) ... 128s Setting up python3-debugpy (1.8.8+ds-1ubuntu2) ... 128s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 129s Setting up python3-pandas (2.2.3+dfsg-5) ... 134s Setting up python3-ipython (8.20.0-1ubuntu1) ... 134s Setting up python3-ipykernel (6.29.5-1) ... 135s Setting up python3-sklearn (1.4.2+dfsg-6) ... 137s Setting up python3-cftime (1.6.4-1build1) ... 137s Setting up python3-numexpr (2.10.1-2) ... 137s Setting up python3-netcdf4 (1.7.2-1build1) ... 137s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 137s Setting up blt (2.5.3+dfsg-7build1) ... 137s Setting up python3-tk:arm64 (3.12.6-1ubuntu1) ... 137s Setting up python3-tables (3.10.1-1build1) ... 138s Setting up python3-mdtraj (1.10.1-2build1) ... 138s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 138s Setting up python3-fonttools (4.46.0-1build2) ... 139s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 139s Setting up python3-matplotlib (3.8.3-3) ... 141s Setting up autopkgtest-satdep (0) ... 141s Processing triggers for libc-bin (2.40-1ubuntu3) ... 141s Processing triggers for systemd (256.5-2ubuntu4) ... 141s Processing triggers for man-db (2.13.0-1) ... 148s (Reading database ... 103284 files and directories currently installed.) 148s Removing autopkgtest-satdep (0) ... 148s autopkgtest [16:45:46]: test command1: pytest-3 -k 'not nmr.ipynb and not test_image_molecules' 148s autopkgtest [16:45:46]: test command1: [----------------------- 149s ============================= test session starts ============================== 149s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 149s cachedir: .pytest_cache 149s rootdir: /tmp/autopkgtest.SpFfCJ/build.MyK/src 149s configfile: pytest.ini 149s testpaths: tests, examples 149s plugins: typeguard-4.4.1 151s collecting ... collected 1129 items / 2 deselected / 1127 selected 151s 151s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 151s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 151s tests/test_alignment.py::test_transform PASSED [ 0%] 151s tests/test_alignment.py::test_transform2 PASSED [ 0%] 152s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 152s tests/test_angles.py::test_generator PASSED [ 0%] 152s tests/test_angles.py::test_angle_180[True] PASSED [ 0%] 152s tests/test_angles.py::test_angle_180[False] PASSED [ 0%] 152s tests/test_arc.py::test_read_0 PASSED [ 0%] 152s tests/test_arc.py::test_read_arctraj PASSED [ 0%] 152s tests/test_arc.py::test_read_pbc PASSED [ 0%] 152s tests/test_capi.py::test_1 PASSED [ 1%] 152s tests/test_contact.py::test_contact_0 PASSED [ 1%] 152s 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[ 37%] 381s tests/test_restart.py::test_read_after_close PASSED [ 37%] 381s tests/test_restart.py::test_shape PASSED [ 38%] 381s tests/test_restart.py::test_shape_2 PASSED [ 38%] 381s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 381s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 381s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 382s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 382s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 382s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 382s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 382s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 382s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 382s tests/test_rmsd.py::test_superpose_2 PASSED [ 39%] 382s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 382s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 382s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 383s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 383s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 383s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 383s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 383s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 383s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 383s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 383s tests/test_sasa.py::test_sasa_1 PASSED [ 40%] 383s tests/test_sasa.py::test_sasa_2 PASSED [ 40%] 383s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 384s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 384s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 384s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 384s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 384s tests/test_selection.py::test_range PASSED [ 40%] 384s tests/test_selection.py::test_unary_2 PASSED [ 40%] 385s tests/test_selection.py::test_unary_3 PASSED [ 40%] 385s tests/test_selection.py::test_binary_1 PASSED [ 40%] 385s tests/test_selection.py::test_binary_2 PASSED [ 40%] 385s tests/test_selection.py::test_simple PASSED [ 41%] 385s tests/test_selection.py::test_alias PASSED [ 41%] 385s tests/test_selection.py::test_unary_1 PASSED [ 41%] 385s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 385s tests/test_selection.py::test_raises PASSED [ 41%] 385s tests/test_selection.py::test_raises2 PASSED [ 41%] 385s tests/test_selection.py::test_bool PASSED [ 41%] 385s tests/test_selection.py::test_nested_bool PASSED [ 41%] 385s tests/test_selection.py::test_values PASSED [ 41%] 385s tests/test_selection.py::test_element PASSED [ 41%] 385s tests/test_selection.py::test_not PASSED [ 41%] 385s tests/test_selection.py::test_re PASSED [ 42%] 385s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 385s tests/test_selection.py::test_quotes PASSED [ 42%] 385s tests/test_selection.py::test_top PASSED [ 42%] 385s tests/test_selection.py::test_top_2 PASSED [ 42%] 386s tests/test_selection.py::test_backbone PASSED [ 42%] 386s tests/test_selection.py::test_sidechain PASSED [ 42%] 387s tests/test_selection.py::test_literal PASSED [ 42%] 387s tests/test_selection.py::test_in PASSED [ 42%] 387s tests/test_shape.py::test_gyration PASSED [ 42%] 387s tests/test_shape.py::test_principal_moments PASSED [ 42%] 387s tests/test_shape.py::test_asphericity PASSED [ 43%] 388s tests/test_shape.py::test_shape_metrics PASSED [ 43%] 388s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 388s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 388s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 388s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 388s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 388s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 388s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 388s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 388s tests/test_topology.py::test_topology_pandas PASSED [ 43%] 388s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 388s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 388s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 388s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 389s tests/test_topology.py::test_chain PASSED [ 44%] 389s tests/test_topology.py::test_residue PASSED [ 44%] 389s tests/test_topology.py::test_segment_id PASSED [ 44%] 389s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 389s tests/test_topology.py::test_pickle PASSED [ 44%] 389s tests/test_topology.py::test_atoms_by_name PASSED [ 44%] 389s tests/test_topology.py::test_select_atom_indices PASSED [ 44%] 389s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 44%] 389s tests/test_topology.py::test_n_bonds PASSED [ 45%] 389s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 389s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 390s tests/test_topology.py::test_select_pairs PASSED [ 45%] 390s tests/test_topology.py::test_to_fasta PASSED [ 45%] 391s tests/test_topology.py::test_subset PASSED [ 45%] 391s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 391s tests/test_topology.py::test_molecules PASSED [ 45%] 391s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 391s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 45%] 391s tests/test_topology.py::test_topology_join PASSED [ 45%] 392s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 392s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 392s tests/test_trajectory.py::test_box PASSED [ 46%] 392s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 392s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 392s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 392s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 392s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 392s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 392s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 46%] 392s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 46%] 392s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 392s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 392s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 392s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 392s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 392s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 392s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 392s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 392s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 392s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 47%] 392s tests/test_trajectory.py::test_slice PASSED [ 47%] 392s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 392s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 392s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 392s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 392s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 392s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 392s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 392s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 392s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 392s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 393s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 48%] 393s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 48%] 393s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 393s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 393s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 393s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 393s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 393s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 393s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 393s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 393s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 393s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 49%] 393s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 49%] 394s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 394s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 394s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 394s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 394s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 394s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 394s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 394s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 394s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 394s tests/test_trajectory.py::test_write_path[gro] PASSED [ 50%] 394s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 50%] 394s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 394s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 394s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 394s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 394s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 397s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 397s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 398s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 398s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 398s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 399s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 51%] 401s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 51%] 401s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 401s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 401s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 401s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 401s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 401s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 401s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 401s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 401s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 403s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 52%] 403s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 52%] 403s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 403s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 403s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 404s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 405s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 405s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 405s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 405s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 405s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 405s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 53%] 405s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 53%] 405s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 405s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 405s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 406s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 407s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 407s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 407s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 407s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 407s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 408s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 408s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 54%] 408s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 408s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 408s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 408s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 408s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 409s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 409s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 409s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 411s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 411s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 411s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 55%] 411s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 55%] 411s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 412s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 412s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 412s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 412s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 412s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 412s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 412s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 412s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 412s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 56%] 412s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 56%] 412s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 415s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 415s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 415s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 415s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 415s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 416s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 416s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 416s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 416s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 417s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 57%] 417s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 417s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 417s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 417s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 417s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 417s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 417s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 418s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 418s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 418s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 418s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 58%] 419s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 421s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 421s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 421s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 421s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 421s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 421s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 421s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 421s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 421s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 421s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 59%] 422s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 59%] 422s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 422s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 423s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 423s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 423s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 424s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 424s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 424s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 424s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 424s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 424s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 60%] 424s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 424s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 424s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 424s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 424s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 425s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 425s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 425s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 425s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 426s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 426s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 61%] 426s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 426s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 426s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 426s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 426s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 427s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 427s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 427s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 427s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 427s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 427s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 62%] 427s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 62%] 427s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 427s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 428s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 429s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 429s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 429s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 429s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 429s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 429s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 429s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 429s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 63%] 429s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 429s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 431s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 431s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 431s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 431s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 431s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 432s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 64%] 433s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 433s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 433s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 433s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 433s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 433s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 433s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 433s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 433s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 65%] 434s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 434s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 435s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 435s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 436s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 436s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 436s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 436s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 436s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 66%] 438s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 438s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 439s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 439s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 439s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 440s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 441s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 441s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 441s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 442s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 442s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 67%] 443s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 443s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 443s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 443s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 443s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 445s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 445s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 446s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 446s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 446s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 447s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 68%] 448s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 448s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 448s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 449s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 449s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 449s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 449s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 449s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 449s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 449s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 449s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 449s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 449s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 449s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 449s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 449s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 449s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 449s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 449s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 449s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 449s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 449s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 449s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 70%] 449s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 71%] 449s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 449s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 450s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 450s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 450s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 450s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 450s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 450s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 451s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 451s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 452s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 452s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 452s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 453s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 453s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 453s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 453s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 454s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 454s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 454s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 454s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 454s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 454s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 454s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 454s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 454s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 454s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 455s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 455s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 457s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 459s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 459s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 459s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 459s tests/test_trajectory.py::test_load[gro] PASSED [ 74%] 460s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 460s tests/test_trajectory.py::test_center PASSED [ 75%] 460s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 460s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 460s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 460s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 460s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 460s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 460s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 77%] 461s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 462s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 462s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 462s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 462s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 462s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 462s tests/test_trajectory.py::test_join PASSED [ 78%] 462s tests/test_trajectory.py::test_md_join PASSED [ 78%] 462s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 462s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 462s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 462s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 462s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 462s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 462s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 462s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 462s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 463s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 463s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 463s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 463s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 463s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 463s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 463s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 463s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 464s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 464s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 464s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 464s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 464s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 465s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 465s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 465s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 465s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 465s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 465s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 465s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 465s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 465s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 465s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 465s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 465s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 465s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 465s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 466s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 466s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 466s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 470s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 473s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 474s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 475s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 476s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 479s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 479s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 480s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 481s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 483s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 485s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 485s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 485s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 485s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 485s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 485s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 486s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 486s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 486s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 486s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 486s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 486s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 486s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 486s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 486s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 486s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 487s tests/test_trajectory.py::test_length PASSED [ 89%] 487s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 487s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 487s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 487s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 487s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 487s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 487s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 487s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 487s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 487s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 487s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 487s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 487s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 487s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 487s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 487s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 487s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 487s tests/test_trajectory.py::test_hashing PASSED [ 90%] 487s tests/test_trajectory.py::test_smooth PASSED [ 90%] 487s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 487s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] 488s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 488s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 488s tests/test_trr.py::test_1 PASSED [ 91%] 488s tests/test_trr.py::test_read_stride PASSED [ 91%] 488s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 488s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 488s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 488s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 488s tests/test_trr.py::test_write_read PASSED [ 91%] 488s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 488s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 488s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 488s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 488s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 488s tests/test_trr.py::test_malformed PASSED [ 92%] 488s tests/test_trr.py::test_tell PASSED [ 92%] 488s tests/test_trr.py::test_seek PASSED [ 92%] 488s tests/test_trr.py::test_get_velocities PASSED [ 92%] 488s tests/test_trr.py::test_get_forces PASSED [ 92%] 488s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 488s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 488s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 92%] 488s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 488s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 488s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 488s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 488s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 488s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 488s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 488s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 488s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 488s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 488s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 488s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 488s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 488s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 488s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 488s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 488s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 488s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 488s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 488s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 488s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 488s tests/test_utils.py::test_delay_import PASSED [ 94%] 488s tests/test_utils.py::test_unit_0 PASSED [ 95%] 488s tests/test_utils.py::test_unit_1 PASSED [ 95%] 488s tests/test_utils.py::test_unit_2 PASSED [ 95%] 488s tests/test_utils.py::test_unit_3 PASSED [ 95%] 488s tests/test_xml.py::test_xml PASSED [ 95%] 488s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 488s tests/test_xtc.py::test_read_stride PASSED [ 95%] 488s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 488s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 488s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 488s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 488s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 488s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 488s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 488s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 488s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 488s tests/test_xtc.py::test_write_0 PASSED [ 96%] 488s tests/test_xtc.py::test_write_1 PASSED [ 96%] 488s tests/test_xtc.py::test_write_2 PASSED [ 96%] 488s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 488s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 488s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 488s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 488s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 488s tests/test_xtc.py::test_tell PASSED [ 97%] 488s tests/test_xtc.py::test_seek PASSED [ 97%] 488s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 488s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 488s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 488s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 488s tests/test_xtc.py::test_short_traj PASSED [ 97%] 488s tests/test_xtc.py::test_flush PASSED [ 97%] 488s tests/test_xyz.py::test_read_0 PASSED [ 97%] 489s tests/test_xyz.py::test_read_1 PASSED [ 97%] 489s tests/test_xyz.py::test_read_gz PASSED [ 98%] 489s tests/test_xyz.py::test_read_write PASSED [ 98%] 489s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 489s tests/test_xyz.py::test_multiread PASSED [ 98%] 489s tests/test_xyz.py::test_seek PASSED [ 98%] 489s tests/test_xyz.py::test_len PASSED [ 98%] 489s tests/test_zipped.py::test_read_gz PASSED [ 98%] 489s tests/test_zipped.py::test_write_gz PASSED [ 98%] 489s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 489s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 489s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 98%] 489s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 492s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 494s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 496s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 498s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 499s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 500s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 502s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 505s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 507s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 509s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 509s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [100%] 509s 509s =============================== warnings summary =============================== 509s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 509s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 509s given by the platformdirs library. To remove this warning and 509s see the appropriate new directories, set the environment variable 509s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 509s The use of platformdirs will be the default in `jupyter_core` v6 509s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 509s 509s examples/test_examples.py:26 509s /tmp/autopkgtest.SpFfCJ/build.MyK/src/examples/test_examples.py:26: PytestUnknownMarkWarning: Unknown pytest.mark.flaky - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 509s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 509s 509s tests/test_arc.py::test_read_arctraj 509s tests/test_order.py::test_nematic_order 509s tests/test_order.py::test_director 509s tests/test_order.py::test_inertia 509s tests/test_order.py::test_nematic_order_args 509s tests/test_shape.py::test_gyration 509s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:204: RuntimeWarning: divide by zero encountered in divide 509s particle_density = traj.top.n_atoms / traj.unitcell_volumes[0] 509s 509s tests/test_arc.py: 1 warning 509s tests/test_gro.py: 3 warnings 509s tests/test_order.py: 4 warnings 509s tests/test_pdb.py: 1 warning 509s tests/test_shape.py: 4 warnings 509s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:206: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 509s warnings.warn( 509s 509s tests/test_contact.py::test_contact_0 509s tests/test_contact.py::test_contact_4 509s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:220: UserWarning: selected topology includes at least one glycine residue, which has no heavy atoms in its sidechain. The distances involving glycine residues will be computed using the sidechain hydrogen instead. 509s warnings.warn( 509s 509s tests/test_contact.py::test_contact_3 509s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 509s np.exp( 509s 509s tests/test_contact.py::test_contact_3 509s /tmp/autopkgtest.SpFfCJ/build.MyK/src/tests/test_contact.py:114: RuntimeWarning: divide by zero encountered in divide 509s assert np.allclose( 509s 509s tests/test_dcd.py::test_do_overwrite 509s tests/test_dcd.py::test_ragged_1 509s tests/test_dcd.py::test_ragged_2 509s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 509s warnings.warn( 509s 509s tests/test_distance.py::test_6 509s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 509s 509s tests/test_drid.py::test_drid_2 509s /tmp/autopkgtest.SpFfCJ/build.MyK/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 509s recip = 1 / squareform(pdist(t.xyz[i])) 509s 509s tests/test_geometry.py::test_dihedral_indices 509s tests/test_geometry.py::test_dihedral_indices 509s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 509s warnings.warn( 509s 509s tests/test_gro.py::test_load 509s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 509s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 509s warnings.warn( 509s 509s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 509s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 509s warnings.warn("atom_indices are not monotonically increasing") 509s 509s tests/test_trajectory.py::test_array_vs_matrix 509s /tmp/autopkgtest.SpFfCJ/build.MyK/src/tests/test_trajectory.py:419: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 509s xyz_mat = np.matrix(xyz) 509s 509s tests/test_utils.py::test_ensure_type_8 509s tests/test_utils.py::test_ensure_type_9 509s tests/test_utils.py::test_ensure_type_13 509s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 509s warnings.warn( 509s 509s tests/test_utils.py::test_ensure_type_11 509s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 509s warnings.warn( 509s 509s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 509s =========================== short test summary info ============================ 509s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 509s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 509s SKIPPED [15] tests/test_docstrings.py:37: Skip checking certain modules' docstrings 509s SKIPPED [1] tests/test_dssp.py:48: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 509s SKIPPED [1] tests/test_dssp.py:56: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 509s SKIPPED [1] tests/test_dssp.py:63: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 509s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 509s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 509s SKIPPED [1] tests/test_hbonds.py:44: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 509s SKIPPED [1] tests/test_hdf5.py:103: requires openmm.units 509s SKIPPED [1] tests/test_hdf5.py:154: requires openmm.units 509s SKIPPED [1] tests/test_hdf5.py:221: requires openmm.units 509s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 509s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 509s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 509s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 509s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 509s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 509s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 509s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 509s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 509s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 509s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 509s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 509s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 509s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 509s SKIPPED [1] tests/test_topology.py:44: needs OpenMM 509s SKIPPED [1] tests/test_topology.py:61: needs OpenMM 509s SKIPPED [1] tests/test_topology.py:192: needs OpenMM 509s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 509s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 509s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 509s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 509s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 509s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 509s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 509s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 509s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 509s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 509s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 509s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 509s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 509s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 509s SKIPPED [2] examples/test_examples.py:77: Network access required 509s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 509s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 509s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 509s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 509s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 509s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 509s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 509s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 509s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 509s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 509s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 509s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 509s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 509s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 509s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 509s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 509s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 509s = 959 passed, 107 skipped, 2 deselected, 61 xfailed, 40 warnings in 359.34s (0:05:59) = 510s autopkgtest [16:51:48]: test command1: -----------------------] 510s command1 PASS 510s autopkgtest [16:51:48]: test command1: - - - - - - - - - - results - - - - - - - - - - 511s autopkgtest [16:51:49]: @@@@@@@@@@@@@@@@@@@@ summary 511s command1 PASS 522s virt: nova [W] Skipping flock in bos03-arm64 522s virt: Creating nova instance adt-plucky-arm64-mdtraj-20241116-164317-juju-7f2275-prod-proposed-migration-environment-2-ac61d91a-8502-445f-96b8-0e465b459773 from image adt/ubuntu-plucky-arm64-server-20241116.img (UUID b01758a6-21f8-4caa-9834-062ee0544e32)...