0s autopkgtest [20:17:05]: starting date and time: 2024-11-15 20:17:05+0000 0s autopkgtest [20:17:05]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [20:17:05]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o5ttv07f/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scikit-learn --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-6build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-20.secgroup --name adt-plucky-arm64-mdanalysis-20241115-201705-juju-7f2275-prod-proposed-migration-environment-20-d7a0f08b-5fee-47ff-b1b6-18c4be39e2d4 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 1581s autopkgtest [20:43:26]: testbed dpkg architecture: arm64 1581s autopkgtest [20:43:26]: testbed apt version: 2.9.8 1581s autopkgtest [20:43:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1582s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 1583s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 1583s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [93.0 kB] 1583s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 1583s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1044 kB] 1583s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [171 kB] 1583s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 1583s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [789 kB] 1583s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6404 B] 1583s Fetched 2249 kB in 1s (2269 kB/s) 1583s Reading package lists... 1586s Reading package lists... 1587s Building dependency tree... 1587s Reading state information... 1588s Calculating upgrade... 1589s The following NEW packages will be installed: 1589s libassuan9 1589s The following packages will be upgraded: 1589s libgpgme11t64 libseccomp2 python3-cffi-backend python3-markupsafe 1589s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1589s Need to get 337 kB of archives. 1589s After this operation, 447 kB of additional disk space will be used. 1589s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libseccomp2 arm64 2.5.5-1ubuntu5 [51.4 kB] 1590s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cffi-backend arm64 1.17.1-2build1 [89.9 kB] 1590s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libassuan9 arm64 3.0.1-2 [40.6 kB] 1590s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgpgme11t64 arm64 1.24.0-2ubuntu1 [142 kB] 1590s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-markupsafe arm64 2.1.5-1build3 [13.0 kB] 1590s Fetched 337 kB in 0s (691 kB/s) 1591s (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 ... 79957 files and directories currently installed.) 1591s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu5_arm64.deb ... 1591s Unpacking libseccomp2:arm64 (2.5.5-1ubuntu5) over (2.5.5-1ubuntu4) ... 1591s Setting up libseccomp2:arm64 (2.5.5-1ubuntu5) ... 1591s (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 ... 79957 files and directories currently installed.) 1591s Preparing to unpack .../python3-cffi-backend_1.17.1-2build1_arm64.deb ... 1591s Unpacking python3-cffi-backend:arm64 (1.17.1-2build1) over (1.17.1-2) ... 1591s Selecting previously unselected package libassuan9:arm64. 1591s Preparing to unpack .../libassuan9_3.0.1-2_arm64.deb ... 1591s Unpacking libassuan9:arm64 (3.0.1-2) ... 1591s Preparing to unpack .../libgpgme11t64_1.24.0-2ubuntu1_arm64.deb ... 1591s Unpacking libgpgme11t64:arm64 (1.24.0-2ubuntu1) over (1.23.2-5ubuntu4) ... 1591s Preparing to unpack .../python3-markupsafe_2.1.5-1build3_arm64.deb ... 1591s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ... 1591s Setting up python3-markupsafe (2.1.5-1build3) ... 1591s Setting up libassuan9:arm64 (3.0.1-2) ... 1591s Setting up libgpgme11t64:arm64 (1.24.0-2ubuntu1) ... 1591s Setting up python3-cffi-backend:arm64 (1.17.1-2build1) ... 1591s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1592s Reading package lists... 1592s Building dependency tree... 1592s Reading state information... 1593s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1594s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 1594s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1594s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1594s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1596s Reading package lists... 1596s Reading package lists... 1596s Building dependency tree... 1596s Reading state information... 1596s Calculating upgrade... 1598s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1598s Reading package lists... 1598s Building dependency tree... 1598s Reading state information... 1599s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1602s autopkgtest [20:43:47]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 1602s autopkgtest [20:43:47]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 1606s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B] 1606s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB] 1606s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB] 1606s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC 1606s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 1606s gpgv: issuer "dparsons@debian.org" 1606s gpgv: Can't check signature: No public key 1606s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found 1608s autopkgtest [20:43:53]: testing package mdanalysis version 2.7.0-5 1608s autopkgtest [20:43:53]: build not needed 1613s autopkgtest [20:43:58]: test test-mdanalysis: preparing testbed 1615s Reading package lists... 1616s Building dependency tree... 1616s Reading state information... 1616s Starting pkgProblemResolver with broken count: 0 1616s Starting 2 pkgProblemResolver with broken count: 0 1616s Done 1617s The following additional packages will be installed: 1617s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 1617s cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper debugedit 1617s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 1617s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 1617s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 1617s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 1617s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 1617s libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 1617s libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl 1617s libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1 1617s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 1617s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 1617s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 1617s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 1617s libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 libpython3-all-dev 1617s libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 libsharpyuv0 1617s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 1617s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 1617s libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 1617s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 1617s python3-alabaster python3-all python3-all-dev python3-appdirs 1617s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 1617s python3-citeproc python3-contourpy python3-cycler python3-dateutil 1617s python3-decorator python3-defusedxml python3-dev python3-docutils 1617s python3-duecredit python3-fasteners python3-fonttools python3-freetype 1617s python3-fs python3-griddataformats python3-gsd python3-h5py 1617s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 1617s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 1617s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 1617s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 1617s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 1617s python3-netcdf4 python3-networkx python3-numpy python3-packaging 1617s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 1617s python3-pluggy python3-pybtex python3-pybtex-docutils 1617s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 1617s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 1617s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 1617s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 1617s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 1617s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 1617s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 1617s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 1617s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 1617s zlib1g-dev 1617s Suggested packages: 1617s autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales 1617s cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf 1617s fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 1617s gdb-aarch64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 1617s libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc 1617s liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran 1617s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl bwa clustalo clustalw 1617s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 1617s python3-mysqldb python3-rdflib python3-psycopg2 raxml samtools t-coffee wise 1617s python3-pip python3-venv python-build-doc python-cycler-doc docutils-doc 1617s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 1617s texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc 1617s python-hypothesis-doc python-installer-doc python-joblib-doc 1617s python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 1617s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 1617s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 1617s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 1617s texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal 1617s python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc 1617s python3-statsmodels python-pil-doc python-pybtex-doc 1617s python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools 1617s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 1617s python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm 1617s fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre 1617s texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic 1617s python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg 1617s python3.13-tk sgml-base-doc 1617s Recommended packages: 1617s libarchive-cpio-perl javascript-common libjson-xs-perl libltdl-dev 1617s libmail-sendmail-perl python-biopython-doc ncbi-blast+ libpaper-utils 1617s python3-click python3-simplejson python3-psutil python3-bs4 1617s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 1617s python3-odf python3-openpyxl python3-tables python3-olefile 1617s fonts-dejavu-extra isympy-common 1618s The following NEW packages will be installed: 1618s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 1618s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 1618s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 1618s docutils-common dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono 1618s fonts-font-awesome fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ 1618s g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 1618s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 1618s libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 1618s libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl 1618s libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1 1618s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 1618s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 1618s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 1618s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 1618s libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 libpython3-all-dev 1618s libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 libsharpyuv0 1618s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 1618s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 1618s libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 1618s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 1618s python3-alabaster python3-all python3-all-dev python3-appdirs 1618s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 1618s python3-citeproc python3-contourpy python3-cycler python3-dateutil 1618s python3-decorator python3-defusedxml python3-dev python3-docutils 1618s python3-duecredit python3-fasteners python3-fonttools python3-freetype 1618s python3-fs python3-griddataformats python3-gsd python3-h5py 1618s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 1618s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 1618s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 1618s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 1618s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 1618s python3-netcdf4 python3-networkx python3-numpy python3-packaging 1618s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 1618s python3-pluggy python3-pybtex python3-pybtex-docutils 1618s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 1618s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 1618s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 1618s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 1618s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 1618s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 1618s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 1618s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 1618s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 1618s zlib1g-dev 1618s 0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded. 1618s Need to get 200 MB/200 MB of archives. 1618s After this operation, 863 MB of additional disk space will be used. 1618s Get:1 /tmp/autopkgtest.QaPnxU/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [1016 B] 1618s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 1618s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 1618s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 1618s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 1618s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 1618s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 1618s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 1618s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 1618s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 1618s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 1618s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 1618s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 1618s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 1618s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 1618s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 1619s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 1619s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 1619s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 1619s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 1619s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 1619s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 1619s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 1619s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 1619s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 1619s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 1619s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 1619s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 1619s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 1619s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 1619s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 1619s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 1619s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 1619s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 1619s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 1619s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 1619s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 1619s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 1619s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 1619s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 1620s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 1620s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 1620s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 1620s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 1620s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 1620s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 1620s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 1620s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 1620s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 1620s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-1ubuntu2 [2977 kB] 1620s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 1620s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB] 1620s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 1620s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 1620s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 1620s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 1621s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB] 1621s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 1621s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 1621s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 1621s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 1621s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 1621s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB] 1621s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 1621s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 1621s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 1621s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 1621s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 1621s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 1621s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 1621s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 1621s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 1621s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 1621s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 1621s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 1621s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 1621s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 1621s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 1621s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 1621s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 1621s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 1621s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 1621s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 1621s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 1621s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 1621s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 1621s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 1621s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 1621s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 1621s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 1621s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 1621s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 1621s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 1621s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 1621s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 1621s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf19t64 arm64 1:4.9.2-6ubuntu1 [466 kB] 1621s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 1621s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.7-3 [5565 kB] 1621s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.12.6-0ubuntu1 [10.2 kB] 1621s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.12.6-0ubuntu1 [916 B] 1621s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 1621s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 1622s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 1622s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 1622s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 1622s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 1622s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 1622s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 1622s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 1622s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 1622s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 1622s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-toml all 0.10.2-1 [16.5 kB] 1622s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wheel all 0.44.0-1 [54.2 kB] 1622s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-build all 1.2.2-1 [31.0 kB] 1622s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 1622s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-pyproject all 6.20241024 [1728 B] 1622s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 1622s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 1622s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-mdanalysis-doc all 2.7.0-5 [2323 kB] 1623s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 1623s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] 1623s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.12.6-0ubuntu1 [26.7 kB] 1623s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.12.6-0ubuntu1 [908 B] 1623s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 1623s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 1623s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 1623s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.6-1ubuntu1 [9806 B] 1623s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 1623s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 1623s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 1623s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 1623s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 1623s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 1623s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 1623s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 1623s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 1623s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 1623s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-1build1 [290 kB] 1623s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 1623s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-citeproc all 0.6.0-3 [98.4 kB] 1623s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2build1 [220 kB] 1623s Get:142 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 1623s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 1623s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 1623s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 1623s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-2 [42.0 kB] 1623s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 4.2-1 [10.0 kB] 1623s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 1623s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-looseversion all 1.3.0-3 [8354 B] 1623s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-duecredit all 0.10.2-2 [66.0 kB] 1623s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-monotonic all 1.6-2 [5732 B] 1623s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-fasteners all 0.18-2 [12.5 kB] 1623s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 1623s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 1623s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 1623s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 1624s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 1624s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 1624s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 1624s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 1624s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 1624s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 1624s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 1624s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mrcfile all 1.5.3-3 [114 kB] 1624s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-griddataformats all 1.0.2-2 [2107 kB] 1624s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gsd arm64 3.3.0-1 [200 kB] 1624s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 1624s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 1624s Get:169 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 1624s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hypothesis all 6.116.0-1 [326 kB] 1624s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 1624s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 1624s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 1624s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 1624s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-latexcodec all 3.0.0-1 [16.6 kB] 1624s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 1624s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 1624s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build2 [77.9 kB] 1624s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 1624s Get:180 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 1624s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.0-1 [91.6 kB] 1624s Get:182 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mdanalysis arm64 2.7.0-5 [2017 kB] 1624s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-common all 7.4.7-4 [775 kB] 1624s Get:184 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 1624s Get:185 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 1624s Get:186 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sphinx all 7.4.7-4 [593 kB] 1624s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 1624s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 1624s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-msmb-theme all 1.2.0-4 [35.4 kB] 1624s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1 [567 kB] 1624s Get:191 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 1624s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 1625s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 1625s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 1625s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex all 0.24.0-4 [70.0 kB] 1625s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex-docutils all 1.0.2-1 [7176 B] 1625s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 1625s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-seaborn all 0.13.2-4 [225 kB] 1625s Get:199 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6build1 [6350 kB] 1625s Get:200 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn all 1.4.2+dfsg-6build1 [2257 kB] 1625s Get:201 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-sitemap all 2.6.0-1 [6674 B] 1625s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 1626s Fetched 200 MB in 7s (27.0 MB/s) 1626s Selecting previously unselected package fonts-lato. 1626s (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.) 1626s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 1626s Unpacking fonts-lato (2.015-1) ... 1626s Selecting previously unselected package sgml-base. 1626s Preparing to unpack .../001-sgml-base_1.31_all.deb ... 1626s Unpacking sgml-base (1.31) ... 1626s Selecting previously unselected package m4. 1626s Preparing to unpack .../002-m4_1.4.19-4build1_arm64.deb ... 1626s Unpacking m4 (1.4.19-4build1) ... 1626s Selecting previously unselected package autoconf. 1626s Preparing to unpack .../003-autoconf_2.72-3_all.deb ... 1626s Unpacking autoconf (2.72-3) ... 1626s Selecting previously unselected package autotools-dev. 1626s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ... 1626s Unpacking autotools-dev (20220109.1) ... 1626s Selecting previously unselected package automake. 1626s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 1626s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 1627s Selecting previously unselected package autopoint. 1627s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ... 1627s Unpacking autopoint (0.22.5-2) ... 1627s Selecting previously unselected package libtcl8.6:arm64. 1627s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 1627s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 1627s Selecting previously unselected package fonts-dejavu-mono. 1627s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8_all.deb ... 1627s Unpacking fonts-dejavu-mono (2.37-8) ... 1627s Selecting previously unselected package fonts-dejavu-core. 1627s Preparing to unpack .../009-fonts-dejavu-core_2.37-8_all.deb ... 1627s Unpacking fonts-dejavu-core (2.37-8) ... 1627s Selecting previously unselected package libfontenc1:arm64. 1627s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 1627s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 1627s Selecting previously unselected package x11-common. 1627s Preparing to unpack .../011-x11-common_1%3a7.7+23ubuntu3_all.deb ... 1627s Unpacking x11-common (1:7.7+23ubuntu3) ... 1627s Selecting previously unselected package xfonts-encodings. 1627s Preparing to unpack .../012-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 1627s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 1627s Selecting previously unselected package xfonts-utils. 1627s Preparing to unpack .../013-xfonts-utils_1%3a7.7+7_arm64.deb ... 1627s Unpacking xfonts-utils (1:7.7+7) ... 1627s Selecting previously unselected package fonts-urw-base35. 1627s Preparing to unpack .../014-fonts-urw-base35_20200910-8_all.deb ... 1627s Unpacking fonts-urw-base35 (20200910-8) ... 1627s Selecting previously unselected package fontconfig-config. 1628s Preparing to unpack .../015-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 1628s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 1628s Selecting previously unselected package libfontconfig1:arm64. 1628s Preparing to unpack .../016-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 1628s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 1628s Selecting previously unselected package libxrender1:arm64. 1628s Preparing to unpack .../017-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 1628s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 1628s Selecting previously unselected package libxft2:arm64. 1628s Preparing to unpack .../018-libxft2_2.3.6-1build1_arm64.deb ... 1628s Unpacking libxft2:arm64 (2.3.6-1build1) ... 1628s Selecting previously unselected package libxss1:arm64. 1628s Preparing to unpack .../019-libxss1_1%3a1.2.3-1build3_arm64.deb ... 1628s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 1628s Selecting previously unselected package libtk8.6:arm64. 1628s Preparing to unpack .../020-libtk8.6_8.6.15-1_arm64.deb ... 1628s Unpacking libtk8.6:arm64 (8.6.15-1) ... 1628s Selecting previously unselected package tk8.6-blt2.5. 1628s Preparing to unpack .../021-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 1628s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 1628s Selecting previously unselected package blt. 1628s Preparing to unpack .../022-blt_2.5.3+dfsg-7build1_arm64.deb ... 1628s Unpacking blt (2.5.3+dfsg-7build1) ... 1628s Selecting previously unselected package libisl23:arm64. 1628s Preparing to unpack .../023-libisl23_0.27-1_arm64.deb ... 1628s Unpacking libisl23:arm64 (0.27-1) ... 1628s Selecting previously unselected package libmpc3:arm64. 1628s Preparing to unpack .../024-libmpc3_1.3.1-1build2_arm64.deb ... 1628s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 1628s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 1628s Preparing to unpack .../025-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 1628s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 1629s Selecting previously unselected package cpp-14. 1629s Preparing to unpack .../026-cpp-14_14.2.0-8ubuntu1_arm64.deb ... 1629s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 1629s Selecting previously unselected package cpp-aarch64-linux-gnu. 1629s Preparing to unpack .../027-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 1629s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 1629s Selecting previously unselected package cpp. 1629s Preparing to unpack .../028-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 1629s Unpacking cpp (4:14.1.0-2ubuntu1) ... 1629s Selecting previously unselected package libcc1-0:arm64. 1629s Preparing to unpack .../029-libcc1-0_14.2.0-8ubuntu1_arm64.deb ... 1629s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ... 1629s Selecting previously unselected package libgomp1:arm64. 1629s Preparing to unpack .../030-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 1629s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 1629s Selecting previously unselected package libitm1:arm64. 1629s Preparing to unpack .../031-libitm1_14.2.0-8ubuntu1_arm64.deb ... 1629s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 1629s Selecting previously unselected package libasan8:arm64. 1629s Preparing to unpack .../032-libasan8_14.2.0-8ubuntu1_arm64.deb ... 1629s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 1629s Selecting previously unselected package liblsan0:arm64. 1629s Preparing to unpack .../033-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 1629s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 1629s Selecting previously unselected package libtsan2:arm64. 1629s Preparing to unpack .../034-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 1629s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 1629s Selecting previously unselected package libubsan1:arm64. 1629s Preparing to unpack .../035-libubsan1_14.2.0-8ubuntu1_arm64.deb ... 1629s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ... 1629s Selecting previously unselected package libhwasan0:arm64. 1629s Preparing to unpack .../036-libhwasan0_14.2.0-8ubuntu1_arm64.deb ... 1629s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ... 1630s Selecting previously unselected package libgcc-14-dev:arm64. 1630s Preparing to unpack .../037-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ... 1630s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 1630s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 1630s Preparing to unpack .../038-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 1630s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 1630s Selecting previously unselected package gcc-14. 1630s Preparing to unpack .../039-gcc-14_14.2.0-8ubuntu1_arm64.deb ... 1630s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 1630s Selecting previously unselected package gcc-aarch64-linux-gnu. 1630s Preparing to unpack .../040-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 1630s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 1630s Selecting previously unselected package gcc. 1631s Preparing to unpack .../041-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 1631s Unpacking gcc (4:14.1.0-2ubuntu1) ... 1631s Selecting previously unselected package libstdc++-14-dev:arm64. 1631s Preparing to unpack .../042-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ... 1631s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 1631s Selecting previously unselected package g++-14-aarch64-linux-gnu. 1631s Preparing to unpack .../043-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 1631s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 1631s Selecting previously unselected package g++-14. 1631s Preparing to unpack .../044-g++-14_14.2.0-8ubuntu1_arm64.deb ... 1631s Unpacking g++-14 (14.2.0-8ubuntu1) ... 1631s Selecting previously unselected package g++-aarch64-linux-gnu. 1631s Preparing to unpack .../045-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 1631s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 1631s Selecting previously unselected package g++. 1631s Preparing to unpack .../046-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 1631s Unpacking g++ (4:14.1.0-2ubuntu1) ... 1631s Selecting previously unselected package build-essential. 1631s Preparing to unpack .../047-build-essential_12.10ubuntu1_arm64.deb ... 1631s Unpacking build-essential (12.10ubuntu1) ... 1631s Selecting previously unselected package cython3. 1631s Preparing to unpack .../048-cython3_3.0.11+dfsg-1ubuntu2_arm64.deb ... 1631s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ... 1632s Selecting previously unselected package libdebhelper-perl. 1632s Preparing to unpack .../049-libdebhelper-perl_13.20ubuntu1_all.deb ... 1632s Unpacking libdebhelper-perl (13.20ubuntu1) ... 1632s Selecting previously unselected package libtool. 1632s Preparing to unpack .../050-libtool_2.4.7-7build1_all.deb ... 1632s Unpacking libtool (2.4.7-7build1) ... 1632s Selecting previously unselected package dh-autoreconf. 1632s Preparing to unpack .../051-dh-autoreconf_20_all.deb ... 1632s Unpacking dh-autoreconf (20) ... 1632s Selecting previously unselected package libarchive-zip-perl. 1632s Preparing to unpack .../052-libarchive-zip-perl_1.68-1_all.deb ... 1632s Unpacking libarchive-zip-perl (1.68-1) ... 1632s Selecting previously unselected package libfile-stripnondeterminism-perl. 1632s Preparing to unpack .../053-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 1632s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 1632s Selecting previously unselected package dh-strip-nondeterminism. 1632s Preparing to unpack .../054-dh-strip-nondeterminism_1.14.0-1_all.deb ... 1632s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 1632s Selecting previously unselected package debugedit. 1632s Preparing to unpack .../055-debugedit_1%3a5.1-1_arm64.deb ... 1632s Unpacking debugedit (1:5.1-1) ... 1632s Selecting previously unselected package dwz. 1632s Preparing to unpack .../056-dwz_0.15-1build6_arm64.deb ... 1632s Unpacking dwz (0.15-1build6) ... 1632s Selecting previously unselected package gettext. 1632s Preparing to unpack .../057-gettext_0.22.5-2_arm64.deb ... 1632s Unpacking gettext (0.22.5-2) ... 1632s Selecting previously unselected package intltool-debian. 1632s Preparing to unpack .../058-intltool-debian_0.35.0+20060710.6_all.deb ... 1632s Unpacking intltool-debian (0.35.0+20060710.6) ... 1632s Selecting previously unselected package po-debconf. 1632s Preparing to unpack .../059-po-debconf_1.0.21+nmu1_all.deb ... 1632s Unpacking po-debconf (1.0.21+nmu1) ... 1632s Selecting previously unselected package debhelper. 1632s Preparing to unpack .../060-debhelper_13.20ubuntu1_all.deb ... 1632s Unpacking debhelper (13.20ubuntu1) ... 1632s Selecting previously unselected package dh-python. 1632s Preparing to unpack .../061-dh-python_6.20241024_all.deb ... 1632s Unpacking dh-python (6.20241024) ... 1633s Selecting previously unselected package xml-core. 1633s Preparing to unpack .../062-xml-core_0.19_all.deb ... 1633s Unpacking xml-core (0.19) ... 1633s Selecting previously unselected package docutils-common. 1633s Preparing to unpack .../063-docutils-common_0.21.2+dfsg-2_all.deb ... 1633s Unpacking docutils-common (0.21.2+dfsg-2) ... 1633s Selecting previously unselected package fonts-font-awesome. 1633s Preparing to unpack .../064-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 1633s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 1633s Selecting previously unselected package fonts-lyx. 1633s Preparing to unpack .../065-fonts-lyx_2.4.2.1-1_all.deb ... 1633s Unpacking fonts-lyx (2.4.2.1-1) ... 1633s Selecting previously unselected package fonts-mathjax. 1633s Preparing to unpack .../066-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 1633s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 1633s Selecting previously unselected package libaec0:arm64. 1633s Preparing to unpack .../067-libaec0_1.1.3-1_arm64.deb ... 1633s Unpacking libaec0:arm64 (1.1.3-1) ... 1633s Selecting previously unselected package libblas3:arm64. 1633s Preparing to unpack .../068-libblas3_3.12.0-3build2_arm64.deb ... 1633s Unpacking libblas3:arm64 (3.12.0-3build2) ... 1633s Selecting previously unselected package libpixman-1-0:arm64. 1633s Preparing to unpack .../069-libpixman-1-0_0.44.0-3_arm64.deb ... 1633s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 1633s Selecting previously unselected package libxcb-render0:arm64. 1633s Preparing to unpack .../070-libxcb-render0_1.17.0-2_arm64.deb ... 1633s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 1633s Selecting previously unselected package libxcb-shm0:arm64. 1633s Preparing to unpack .../071-libxcb-shm0_1.17.0-2_arm64.deb ... 1633s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 1633s Selecting previously unselected package libcairo2:arm64. 1633s Preparing to unpack .../072-libcairo2_1.18.2-2_arm64.deb ... 1633s Unpacking libcairo2:arm64 (1.18.2-2) ... 1633s Selecting previously unselected package libdeflate0:arm64. 1633s Preparing to unpack .../073-libdeflate0_1.22-1_arm64.deb ... 1633s Unpacking libdeflate0:arm64 (1.22-1) ... 1633s Selecting previously unselected package libexpat1-dev:arm64. 1633s Preparing to unpack .../074-libexpat1-dev_2.6.4-1_arm64.deb ... 1633s Unpacking libexpat1-dev:arm64 (2.6.4-1) ... 1633s Selecting previously unselected package libgfortran5:arm64. 1634s Preparing to unpack .../075-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 1634s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 1634s Selecting previously unselected package libgraphite2-3:arm64. 1634s Preparing to unpack .../076-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 1634s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 1634s Selecting previously unselected package libharfbuzz0b:arm64. 1634s Preparing to unpack .../077-libharfbuzz0b_10.0.1-1_arm64.deb ... 1634s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 1634s Selecting previously unselected package libsz2:arm64. 1634s Preparing to unpack .../078-libsz2_1.1.3-1_arm64.deb ... 1634s Unpacking libsz2:arm64 (1.1.3-1) ... 1634s Selecting previously unselected package libhdf5-103-1t64:arm64. 1634s Preparing to unpack .../079-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 1634s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 1634s Selecting previously unselected package libhdf5-hl-100t64:arm64. 1634s Preparing to unpack .../080-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 1634s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 1634s Selecting previously unselected package libimagequant0:arm64. 1634s Preparing to unpack .../081-libimagequant0_2.18.0-1build1_arm64.deb ... 1634s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 1634s Selecting previously unselected package libjpeg-turbo8:arm64. 1634s Preparing to unpack .../082-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 1634s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 1634s Selecting previously unselected package libjpeg8:arm64. 1634s Preparing to unpack .../083-libjpeg8_8c-2ubuntu11_arm64.deb ... 1634s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 1634s Selecting previously unselected package libjs-jquery. 1634s Preparing to unpack .../084-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 1634s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1634s Selecting previously unselected package libjs-jquery-ui. 1634s Preparing to unpack .../085-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 1634s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 1634s Selecting previously unselected package libjs-underscore. 1634s Preparing to unpack .../086-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 1634s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 1634s Selecting previously unselected package libjs-sphinxdoc. 1634s Preparing to unpack .../087-libjs-sphinxdoc_7.4.7-4_all.deb ... 1634s Unpacking libjs-sphinxdoc (7.4.7-4) ... 1634s Selecting previously unselected package libjson-perl. 1634s Preparing to unpack .../088-libjson-perl_4.10000-1_all.deb ... 1634s Unpacking libjson-perl (4.10000-1) ... 1634s Selecting previously unselected package liblapack3:arm64. 1634s Preparing to unpack .../089-liblapack3_3.12.0-3build2_arm64.deb ... 1634s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 1635s Selecting previously unselected package liblbfgsb0:arm64. 1635s Preparing to unpack .../090-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 1635s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 1635s Selecting previously unselected package liblcms2-2:arm64. 1635s Preparing to unpack .../091-liblcms2-2_2.16-2_arm64.deb ... 1635s Unpacking liblcms2-2:arm64 (2.16-2) ... 1635s Selecting previously unselected package liblerc4:arm64. 1635s Preparing to unpack .../092-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 1635s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 1635s Selecting previously unselected package liblzf1:arm64. 1635s Preparing to unpack .../093-liblzf1_3.6-4_arm64.deb ... 1635s Unpacking liblzf1:arm64 (3.6-4) ... 1635s Selecting previously unselected package libnetcdf19t64:arm64. 1635s Preparing to unpack .../094-libnetcdf19t64_1%3a4.9.2-6ubuntu1_arm64.deb ... 1635s Unpacking libnetcdf19t64:arm64 (1:4.9.2-6ubuntu1) ... 1635s Selecting previously unselected package zlib1g-dev:arm64. 1635s Preparing to unpack .../095-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 1635s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 1635s Selecting previously unselected package libpython3.12-dev:arm64. 1635s Preparing to unpack .../096-libpython3.12-dev_3.12.7-3_arm64.deb ... 1635s Unpacking libpython3.12-dev:arm64 (3.12.7-3) ... 1635s Selecting previously unselected package libpython3-dev:arm64. 1635s Preparing to unpack .../097-libpython3-dev_3.12.6-0ubuntu1_arm64.deb ... 1635s Unpacking libpython3-dev:arm64 (3.12.6-0ubuntu1) ... 1635s Selecting previously unselected package libpython3-all-dev:arm64. 1635s Preparing to unpack .../098-libpython3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 1635s Unpacking libpython3-all-dev:arm64 (3.12.6-0ubuntu1) ... 1635s Selecting previously unselected package libqhull-r8.0:arm64. 1635s Preparing to unpack .../099-libqhull-r8.0_2020.2-6build1_arm64.deb ... 1635s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 1635s Selecting previously unselected package libraqm0:arm64. 1635s Preparing to unpack .../100-libraqm0_0.10.1-1build1_arm64.deb ... 1635s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 1635s Selecting previously unselected package libsharpyuv0:arm64. 1635s Preparing to unpack .../101-libsharpyuv0_1.4.0-0.1_arm64.deb ... 1635s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 1635s Selecting previously unselected package libjbig0:arm64. 1635s Preparing to unpack .../102-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 1635s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 1635s Selecting previously unselected package libwebp7:arm64. 1636s Preparing to unpack .../103-libwebp7_1.4.0-0.1_arm64.deb ... 1636s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 1636s Selecting previously unselected package libtiff6:arm64. 1636s Preparing to unpack .../104-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 1636s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 1636s Selecting previously unselected package libwebpdemux2:arm64. 1636s Preparing to unpack .../105-libwebpdemux2_1.4.0-0.1_arm64.deb ... 1636s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 1636s Selecting previously unselected package libwebpmux3:arm64. 1636s Preparing to unpack .../106-libwebpmux3_1.4.0-0.1_arm64.deb ... 1636s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 1636s Selecting previously unselected package libxslt1.1:arm64. 1636s Preparing to unpack .../107-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 1636s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 1636s Selecting previously unselected package python3-packaging. 1636s Preparing to unpack .../108-python3-packaging_24.1-1_all.deb ... 1636s Unpacking python3-packaging (24.1-1) ... 1636s Selecting previously unselected package python3-pyproject-hooks. 1636s Preparing to unpack .../109-python3-pyproject-hooks_1.2.0-1_all.deb ... 1636s Unpacking python3-pyproject-hooks (1.2.0-1) ... 1636s Selecting previously unselected package python3-toml. 1636s Preparing to unpack .../110-python3-toml_0.10.2-1_all.deb ... 1636s Unpacking python3-toml (0.10.2-1) ... 1636s Selecting previously unselected package python3-wheel. 1636s Preparing to unpack .../111-python3-wheel_0.44.0-1_all.deb ... 1636s Unpacking python3-wheel (0.44.0-1) ... 1636s Selecting previously unselected package python3-build. 1636s Preparing to unpack .../112-python3-build_1.2.2-1_all.deb ... 1636s Unpacking python3-build (1.2.2-1) ... 1636s Selecting previously unselected package python3-installer. 1636s Preparing to unpack .../113-python3-installer_0.7.0+dfsg1-3_all.deb ... 1636s Unpacking python3-installer (0.7.0+dfsg1-3) ... 1636s Selecting previously unselected package pybuild-plugin-pyproject. 1636s Preparing to unpack .../114-pybuild-plugin-pyproject_6.20241024_all.deb ... 1636s Unpacking pybuild-plugin-pyproject (6.20241024) ... 1636s Selecting previously unselected package python-matplotlib-data. 1636s Preparing to unpack .../115-python-matplotlib-data_3.8.3-3_all.deb ... 1636s Unpacking python-matplotlib-data (3.8.3-3) ... 1636s Selecting previously unselected package libjs-mathjax. 1636s Preparing to unpack .../116-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 1636s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 1637s Selecting previously unselected package python-mdanalysis-doc. 1637s Preparing to unpack .../117-python-mdanalysis-doc_2.7.0-5_all.deb ... 1637s Unpacking python-mdanalysis-doc (2.7.0-5) ... 1637s Selecting previously unselected package python3-all. 1637s Preparing to unpack .../118-python3-all_3.12.6-0ubuntu1_arm64.deb ... 1637s Unpacking python3-all (3.12.6-0ubuntu1) ... 1637s Selecting previously unselected package python3.12-dev. 1637s Preparing to unpack .../119-python3.12-dev_3.12.7-3_arm64.deb ... 1637s Unpacking python3.12-dev (3.12.7-3) ... 1637s Selecting previously unselected package python3-dev. 1638s Preparing to unpack .../120-python3-dev_3.12.6-0ubuntu1_arm64.deb ... 1638s Unpacking python3-dev (3.12.6-0ubuntu1) ... 1638s Selecting previously unselected package python3-all-dev. 1638s Preparing to unpack .../121-python3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 1638s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 1638s Selecting previously unselected package python3-appdirs. 1638s Preparing to unpack .../122-python3-appdirs_1.4.4-4_all.deb ... 1638s Unpacking python3-appdirs (1.4.4-4) ... 1638s Selecting previously unselected package python3-numpy. 1638s Preparing to unpack .../123-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 1638s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 1638s Selecting previously unselected package python3.12-tk. 1638s Preparing to unpack .../124-python3.12-tk_3.12.7-3_arm64.deb ... 1638s Unpacking python3.12-tk (3.12.7-3) ... 1638s Selecting previously unselected package python3-tk:arm64. 1638s Preparing to unpack .../125-python3-tk_3.12.6-1ubuntu1_arm64.deb ... 1638s Unpacking python3-tk:arm64 (3.12.6-1ubuntu1) ... 1638s Selecting previously unselected package python3-pil.imagetk:arm64. 1638s Preparing to unpack .../126-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 1638s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 1638s Selecting previously unselected package libopenjp2-7:arm64. 1638s Preparing to unpack .../127-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 1638s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 1638s Selecting previously unselected package python3-pil:arm64. 1638s Preparing to unpack .../128-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 1638s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 1638s Selecting previously unselected package python3-cairo. 1638s Preparing to unpack .../129-python3-cairo_1.26.1-2_arm64.deb ... 1638s Unpacking python3-cairo (1.26.1-2) ... 1638s Selecting previously unselected package python3-freetype. 1638s Preparing to unpack .../130-python3-freetype_2.5.1-1_all.deb ... 1638s Unpacking python3-freetype (2.5.1-1) ... 1638s Selecting previously unselected package python3-rlpycairo. 1638s Preparing to unpack .../131-python3-rlpycairo_0.3.0-3_all.deb ... 1638s Unpacking python3-rlpycairo (0.3.0-3) ... 1638s Selecting previously unselected package python3-reportlab. 1638s Preparing to unpack .../132-python3-reportlab_4.2.5-1_all.deb ... 1638s Unpacking python3-reportlab (4.2.5-1) ... 1639s Selecting previously unselected package w3c-sgml-lib. 1639s Preparing to unpack .../133-w3c-sgml-lib_1.3-3_all.deb ... 1639s Unpacking w3c-sgml-lib (1.3-3) ... 1639s Selecting previously unselected package python3-biopython. 1639s Preparing to unpack .../134-python3-biopython_1.84+dfsg-4_arm64.deb ... 1639s Unpacking python3-biopython (1.84+dfsg-4) ... 1639s Selecting previously unselected package python3-brotli. 1639s Preparing to unpack .../135-python3-brotli_1.1.0-2build2_arm64.deb ... 1639s Unpacking python3-brotli (1.1.0-2build2) ... 1639s Selecting previously unselected package python3-cftime. 1639s Preparing to unpack .../136-python3-cftime_1.6.4-1build1_arm64.deb ... 1639s Unpacking python3-cftime (1.6.4-1build1) ... 1639s Selecting previously unselected package python3-lxml:arm64. 1639s Preparing to unpack .../137-python3-lxml_5.3.0-1_arm64.deb ... 1639s Unpacking python3-lxml:arm64 (5.3.0-1) ... 1639s Selecting previously unselected package python3-citeproc. 1639s Preparing to unpack .../138-python3-citeproc_0.6.0-3_all.deb ... 1639s Unpacking python3-citeproc (0.6.0-3) ... 1639s Selecting previously unselected package python3-contourpy. 1639s Preparing to unpack .../139-python3-contourpy_1.3.0-2build1_arm64.deb ... 1639s Unpacking python3-contourpy (1.3.0-2build1) ... 1639s Selecting previously unselected package python3-cycler. 1639s Preparing to unpack .../140-python3-cycler_0.12.1-1_all.deb ... 1639s Unpacking python3-cycler (0.12.1-1) ... 1639s Selecting previously unselected package python3-six. 1639s Preparing to unpack .../141-python3-six_1.16.0-7_all.deb ... 1639s Unpacking python3-six (1.16.0-7) ... 1639s Selecting previously unselected package python3-dateutil. 1639s Preparing to unpack .../142-python3-dateutil_2.9.0-2_all.deb ... 1639s Unpacking python3-dateutil (2.9.0-2) ... 1639s Selecting previously unselected package python3-decorator. 1639s Preparing to unpack .../143-python3-decorator_5.1.1-5_all.deb ... 1639s Unpacking python3-decorator (5.1.1-5) ... 1639s Selecting previously unselected package python3-defusedxml. 1639s Preparing to unpack .../144-python3-defusedxml_0.7.1-2_all.deb ... 1639s Unpacking python3-defusedxml (0.7.1-2) ... 1639s Selecting previously unselected package python3-roman. 1639s Preparing to unpack .../145-python3-roman_4.2-1_all.deb ... 1639s Unpacking python3-roman (4.2-1) ... 1639s Selecting previously unselected package python3-docutils. 1640s Preparing to unpack .../146-python3-docutils_0.21.2+dfsg-2_all.deb ... 1640s Unpacking python3-docutils (0.21.2+dfsg-2) ... 1640s Selecting previously unselected package python3-looseversion. 1640s Preparing to unpack .../147-python3-looseversion_1.3.0-3_all.deb ... 1640s Unpacking python3-looseversion (1.3.0-3) ... 1640s Selecting previously unselected package python3-duecredit. 1640s Preparing to unpack .../148-python3-duecredit_0.10.2-2_all.deb ... 1640s Unpacking python3-duecredit (0.10.2-2) ... 1640s Selecting previously unselected package python3-monotonic. 1640s Preparing to unpack .../149-python3-monotonic_1.6-2_all.deb ... 1640s Unpacking python3-monotonic (1.6-2) ... 1640s Selecting previously unselected package python3-fasteners. 1640s Preparing to unpack .../150-python3-fasteners_0.18-2_all.deb ... 1640s Unpacking python3-fasteners (0.18-2) ... 1640s Selecting previously unselected package python3-scipy. 1640s Preparing to unpack .../151-python3-scipy_1.13.1-5_arm64.deb ... 1640s Unpacking python3-scipy (1.13.1-5) ... 1640s Selecting previously unselected package python3-ufolib2. 1640s Preparing to unpack .../152-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 1640s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 1640s Selecting previously unselected package python3-mpmath. 1640s Preparing to unpack .../153-python3-mpmath_1.3.0-1_all.deb ... 1640s Unpacking python3-mpmath (1.3.0-1) ... 1641s Selecting previously unselected package python3-sympy. 1641s Preparing to unpack .../154-python3-sympy_1.13.3-1_all.deb ... 1641s Unpacking python3-sympy (1.13.3-1) ... 1641s Selecting previously unselected package python3-tz. 1641s Preparing to unpack .../155-python3-tz_2024.1-2_all.deb ... 1641s Unpacking python3-tz (2024.1-2) ... 1641s Selecting previously unselected package python3-fs. 1641s Preparing to unpack .../156-python3-fs_2.4.16-4_all.deb ... 1641s Unpacking python3-fs (2.4.16-4) ... 1641s Selecting previously unselected package python3-lz4. 1641s Preparing to unpack .../157-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 1641s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 1641s Selecting previously unselected package python3-unicodedata2. 1641s Preparing to unpack .../158-python3-unicodedata2_15.1.0+ds-1build2_arm64.deb ... 1641s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 1641s Selecting previously unselected package unicode-data. 1641s Preparing to unpack .../159-unicode-data_15.1.0-1_all.deb ... 1641s Unpacking unicode-data (15.1.0-1) ... 1641s Selecting previously unselected package python3-fonttools. 1641s Preparing to unpack .../160-python3-fonttools_4.46.0-1build2_arm64.deb ... 1641s Unpacking python3-fonttools (4.46.0-1build2) ... 1642s Selecting previously unselected package sphinx-rtd-theme-common. 1642s Preparing to unpack .../161-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 1642s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 1642s Selecting previously unselected package python3-mrcfile. 1642s Preparing to unpack .../162-python3-mrcfile_1.5.3-3_all.deb ... 1642s Unpacking python3-mrcfile (1.5.3-3) ... 1642s Selecting previously unselected package python3-griddataformats. 1642s Preparing to unpack .../163-python3-griddataformats_1.0.2-2_all.deb ... 1642s Unpacking python3-griddataformats (1.0.2-2) ... 1642s Selecting previously unselected package python3-gsd. 1642s Preparing to unpack .../164-python3-gsd_3.3.0-1_arm64.deb ... 1642s Unpacking python3-gsd (3.3.0-1) ... 1642s Selecting previously unselected package python3-h5py-serial. 1642s Preparing to unpack .../165-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ... 1642s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 1642s Selecting previously unselected package python3-h5py. 1642s Preparing to unpack .../166-python3-h5py_3.11.0-5ubuntu1_all.deb ... 1642s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 1642s Selecting previously unselected package python3-sortedcontainers. 1642s Preparing to unpack .../167-python3-sortedcontainers_2.4.0-2_all.deb ... 1642s Unpacking python3-sortedcontainers (2.4.0-2) ... 1642s Selecting previously unselected package python3-hypothesis. 1642s Preparing to unpack .../168-python3-hypothesis_6.116.0-1_all.deb ... 1642s Unpacking python3-hypothesis (6.116.0-1) ... 1642s Selecting previously unselected package python3-imagesize. 1642s Preparing to unpack .../169-python3-imagesize_1.4.1-1_all.deb ... 1642s Unpacking python3-imagesize (1.4.1-1) ... 1642s Selecting previously unselected package python3-iniconfig. 1642s Preparing to unpack .../170-python3-iniconfig_1.1.1-2_all.deb ... 1642s Unpacking python3-iniconfig (1.1.1-2) ... 1642s Selecting previously unselected package python3-joblib. 1642s Preparing to unpack .../171-python3-joblib_1.3.2-5_all.deb ... 1642s Unpacking python3-joblib (1.3.2-5) ... 1642s Selecting previously unselected package python3-kiwisolver. 1642s Preparing to unpack .../172-python3-kiwisolver_1.4.7-2build1_arm64.deb ... 1642s Unpacking python3-kiwisolver (1.4.7-2build1) ... 1642s Selecting previously unselected package python3-latexcodec. 1643s Preparing to unpack .../173-python3-latexcodec_3.0.0-1_all.deb ... 1643s Unpacking python3-latexcodec (3.0.0-1) ... 1643s Selecting previously unselected package python3-matplotlib. 1643s Preparing to unpack .../174-python3-matplotlib_3.8.3-3_arm64.deb ... 1643s Unpacking python3-matplotlib (3.8.3-3) ... 1643s Selecting previously unselected package python3-mda-xdrlib. 1643s Preparing to unpack .../175-python3-mda-xdrlib_0.2.0-3_all.deb ... 1643s Unpacking python3-mda-xdrlib (0.2.0-3) ... 1643s Selecting previously unselected package python3-msgpack. 1643s Preparing to unpack .../176-python3-msgpack_1.0.3-3build2_arm64.deb ... 1643s Unpacking python3-msgpack (1.0.3-3build2) ... 1643s Selecting previously unselected package python3-mmtf. 1643s Preparing to unpack .../177-python3-mmtf_1.1.3-1_all.deb ... 1643s Unpacking python3-mmtf (1.1.3-1) ... 1643s Selecting previously unselected package python3-threadpoolctl. 1643s Preparing to unpack .../178-python3-threadpoolctl_3.1.0-1_all.deb ... 1643s Unpacking python3-threadpoolctl (3.1.0-1) ... 1643s Selecting previously unselected package python3-tqdm. 1643s Preparing to unpack .../179-python3-tqdm_4.67.0-1_all.deb ... 1643s Unpacking python3-tqdm (4.67.0-1) ... 1643s Selecting previously unselected package python3-mdanalysis. 1643s Preparing to unpack .../180-python3-mdanalysis_2.7.0-5_arm64.deb ... 1643s Unpacking python3-mdanalysis (2.7.0-5) ... 1643s Selecting previously unselected package sphinx-common. 1643s Preparing to unpack .../181-sphinx-common_7.4.7-4_all.deb ... 1643s Unpacking sphinx-common (7.4.7-4) ... 1643s Selecting previously unselected package python3-alabaster. 1643s Preparing to unpack .../182-python3-alabaster_0.7.16-0.1_all.deb ... 1643s Unpacking python3-alabaster (0.7.16-0.1) ... 1644s Selecting previously unselected package python3-snowballstemmer. 1644s Preparing to unpack .../183-python3-snowballstemmer_2.2.0-4build1_all.deb ... 1644s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 1644s Selecting previously unselected package python3-sphinx. 1644s Preparing to unpack .../184-python3-sphinx_7.4.7-4_all.deb ... 1644s Unpacking python3-sphinx (7.4.7-4) ... 1644s Selecting previously unselected package python3-sphinxcontrib.jquery. 1644s Preparing to unpack .../185-python3-sphinxcontrib.jquery_4.1-5_all.deb ... 1644s Unpacking python3-sphinxcontrib.jquery (4.1-5) ... 1644s Selecting previously unselected package python3-sphinx-rtd-theme. 1644s Preparing to unpack .../186-python3-sphinx-rtd-theme_3.0.1+dfsg-1_all.deb ... 1644s Unpacking python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 1644s Selecting previously unselected package python3-msmb-theme. 1644s Preparing to unpack .../187-python3-msmb-theme_1.2.0-4_all.deb ... 1644s Unpacking python3-msmb-theme (1.2.0-4) ... 1644s Selecting previously unselected package python3-netcdf4. 1644s Preparing to unpack .../188-python3-netcdf4_1.7.2-1_arm64.deb ... 1644s Unpacking python3-netcdf4 (1.7.2-1) ... 1644s Selecting previously unselected package python3-networkx. 1644s Preparing to unpack .../189-python3-networkx_3.2.1-4ubuntu1_all.deb ... 1644s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 1645s Selecting previously unselected package python3-pandas-lib:arm64. 1645s Preparing to unpack .../190-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 1645s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 1645s Selecting previously unselected package python3-pandas. 1645s Preparing to unpack .../191-python3-pandas_2.2.3+dfsg-5_all.deb ... 1645s Unpacking python3-pandas (2.2.3+dfsg-5) ... 1645s Selecting previously unselected package python3-pluggy. 1645s Preparing to unpack .../192-python3-pluggy_1.5.0-1_all.deb ... 1645s Unpacking python3-pluggy (1.5.0-1) ... 1645s Selecting previously unselected package python3-pybtex. 1645s Preparing to unpack .../193-python3-pybtex_0.24.0-4_all.deb ... 1645s Unpacking python3-pybtex (0.24.0-4) ... 1645s Selecting previously unselected package python3-pybtex-docutils. 1645s Preparing to unpack .../194-python3-pybtex-docutils_1.0.2-1_all.deb ... 1645s Unpacking python3-pybtex-docutils (1.0.2-1) ... 1646s Selecting previously unselected package python3-pytest. 1646s Preparing to unpack .../195-python3-pytest_8.3.3-1_all.deb ... 1646s Unpacking python3-pytest (8.3.3-1) ... 1646s Selecting previously unselected package python3-seaborn. 1646s Preparing to unpack .../196-python3-seaborn_0.13.2-4_all.deb ... 1646s Unpacking python3-seaborn (0.13.2-4) ... 1646s Selecting previously unselected package python3-sklearn-lib:arm64. 1646s Preparing to unpack .../197-python3-sklearn-lib_1.4.2+dfsg-6build1_arm64.deb ... 1646s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-6build1) ... 1646s Selecting previously unselected package python3-sklearn. 1646s Preparing to unpack .../198-python3-sklearn_1.4.2+dfsg-6build1_all.deb ... 1646s Unpacking python3-sklearn (1.4.2+dfsg-6build1) ... 1646s Selecting previously unselected package python3-sphinx-sitemap. 1646s Preparing to unpack .../199-python3-sphinx-sitemap_2.6.0-1_all.deb ... 1646s Unpacking python3-sphinx-sitemap (2.6.0-1) ... 1646s Selecting previously unselected package python3-sphinxcontrib.bibtex. 1646s Preparing to unpack .../200-python3-sphinxcontrib.bibtex_2.6.2-1_all.deb ... 1646s Unpacking python3-sphinxcontrib.bibtex (2.6.2-1) ... 1646s Selecting previously unselected package autopkgtest-satdep. 1646s Preparing to unpack .../201-1-autopkgtest-satdep.deb ... 1646s Unpacking autopkgtest-satdep (0) ... 1646s Setting up dh-python (6.20241024) ... 1647s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 1647s Setting up liblcms2-2:arm64 (2.16-2) ... 1647s Setting up python3-iniconfig (1.1.1-2) ... 1647s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 1647s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 1647s Setting up fonts-lato (2.015-1) ... 1647s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 1647s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 1647s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 1647s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 1647s Setting up python3-joblib (1.3.2-5) ... 1647s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 1648s Setting up libxcb-render0:arm64 (1.17.0-2) ... 1648s Setting up python3-defusedxml (0.7.1-2) ... 1648s Setting up libarchive-zip-perl (1.68-1) ... 1648s Setting up python3-alabaster (0.7.16-0.1) ... 1648s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 1648s Setting up fonts-lyx (2.4.2.1-1) ... 1648s Setting up libdebhelper-perl (13.20ubuntu1) ... 1648s Setting up python3-tqdm (4.67.0-1) ... 1648s Setting up python3-threadpoolctl (3.1.0-1) ... 1649s Setting up x11-common (1:7.7+23ubuntu3) ... 1649s Setting up libdeflate0:arm64 (1.22-1) ... 1649s Setting up m4 (1.4.19-4build1) ... 1649s Setting up python3-latexcodec (3.0.0-1) ... 1649s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 1649s Setting up python3-all (3.12.6-0ubuntu1) ... 1649s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 1649s Setting up python3-sortedcontainers (2.4.0-2) ... 1649s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 1649s Setting up python3-freetype (2.5.1-1) ... 1650s Setting up python3-networkx (3.2.1-4ubuntu1) ... 1652s Setting up python3-wheel (0.44.0-1) ... 1652s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 1652s Setting up python3-mda-xdrlib (0.2.0-3) ... 1652s Setting up libaec0:arm64 (1.1.3-1) ... 1652s Setting up python3-tz (2024.1-2) ... 1652s Setting up python3-monotonic (1.6-2) ... 1652s Setting up unicode-data (15.1.0-1) ... 1652s Setting up python3-six (1.16.0-7) ... 1653s Setting up python3-roman (4.2-1) ... 1653s Setting up python3-decorator (5.1.1-5) ... 1653s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 1653s Setting up autotools-dev (20220109.1) ... 1653s Setting up libblas3:arm64 (3.12.0-3build2) ... 1653s 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 1653s Setting up python3-packaging (24.1-1) ... 1653s Setting up libexpat1-dev:arm64 (2.6.4-1) ... 1653s Setting up python3-pyproject-hooks (1.2.0-1) ... 1654s Setting up python3-snowballstemmer (2.2.0-4build1) ... 1654s Setting up python3-brotli (1.1.0-2build2) ... 1654s Setting up liblzf1:arm64 (3.6-4) ... 1654s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 1654s Setting up python3-cycler (0.12.1-1) ... 1654s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 1654s Setting up fonts-dejavu-mono (2.37-8) ... 1654s Setting up python3-kiwisolver (1.4.7-2build1) ... 1655s Setting up libmpc3:arm64 (1.3.1-1build2) ... 1655s Setting up cython3 (3.0.11+dfsg-1ubuntu2) ... 1656s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 1656s Setting up autopoint (0.22.5-2) ... 1656s Setting up fonts-dejavu-core (2.37-8) ... 1656s Setting up python3-fasteners (0.18-2) ... 1656s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 1656s Setting up python3-toml (0.10.2-1) ... 1656s Setting up python3-installer (0.7.0+dfsg1-3) ... 1657s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 1657s Setting up autoconf (2.72-3) ... 1657s Setting up python3-pluggy (1.5.0-1) ... 1657s Setting up libwebp7:arm64 (1.4.0-0.1) ... 1657s Setting up python3-pybtex (0.24.0-4) ... 1657s Setting up libubsan1:arm64 (14.2.0-8ubuntu1) ... 1657s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 1657s Setting up dwz (0.15-1build6) ... 1657s Setting up python3-looseversion (1.3.0-3) ... 1657s Setting up libhwasan0:arm64 (14.2.0-8ubuntu1) ... 1657s Setting up libasan8:arm64 (14.2.0-8ubuntu1) ... 1657s Setting up libjson-perl (4.10000-1) ... 1657s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 1657s Setting up debugedit (1:5.1-1) ... 1657s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 1657s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 1657s Setting up python3-dateutil (2.9.0-2) ... 1658s Setting up sgml-base (1.31) ... 1658s Setting up python3-msgpack (1.0.3-3build2) ... 1658s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 1658s Setting up libtsan2:arm64 (14.2.0-8ubuntu1) ... 1658s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1658s Setting up python3-mpmath (1.3.0-1) ... 1659s Setting up libisl23:arm64 (0.27-1) ... 1659s Setting up python3-build (1.2.2-1) ... 1659s Setting up python-matplotlib-data (3.8.3-3) ... 1659s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 1659s Setting up python3-appdirs (1.4.4-4) ... 1659s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 1659s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 1659s Setting up libcc1-0:arm64 (14.2.0-8ubuntu1) ... 1659s Setting up liblsan0:arm64 (14.2.0-8ubuntu1) ... 1659s Setting up libsz2:arm64 (1.1.3-1) ... 1659s Setting up libitm1:arm64 (14.2.0-8ubuntu1) ... 1659s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 1659s Setting up python3-imagesize (1.4.1-1) ... 1659s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 1659s Setting up automake (1:1.16.5-1.3ubuntu1) ... 1659s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 1659s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 1659s Setting up python3-sympy (1.13.3-1) ... 1667s Setting up liblapack3:arm64 (3.12.0-3build2) ... 1667s 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 1667s Setting up gettext (0.22.5-2) ... 1667s Setting up pybuild-plugin-pyproject (6.20241024) ... 1667s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 1668s Setting up python3-pytest (8.3.3-1) ... 1668s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 1668s Setting up python3-hypothesis (6.116.0-1) ... 1669s Setting up libpython3.12-dev:arm64 (3.12.7-3) ... 1669s Setting up xfonts-utils (1:7.7+7) ... 1669s Setting up intltool-debian (0.35.0+20060710.6) ... 1669s Setting up python3-fs (2.4.16-4) ... 1669s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 1669s Setting up libraqm0:arm64 (0.10.1-1build1) ... 1669s Setting up python3.12-dev (3.12.7-3) ... 1669s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 1672s Setting up libjs-sphinxdoc (7.4.7-4) ... 1672s Setting up dh-strip-nondeterminism (1.14.0-1) ... 1672s Setting up cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 1672s Setting up python3-lxml:arm64 (5.3.0-1) ... 1672s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 1672s Setting up xml-core (0.19) ... 1672s Setting up python3-contourpy (1.3.0-2build1) ... 1672s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 1672s Setting up libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 1672s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 1672s Setting up libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 1672s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 1672s Setting up python3-mrcfile (1.5.3-3) ... 1672s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 1672s Setting up libnetcdf19t64:arm64 (1:4.9.2-6ubuntu1) ... 1672s Setting up libxft2:arm64 (2.3.6-1build1) ... 1672s Setting up python3-scipy (1.13.1-5) ... 1678s Setting up libpython3-dev:arm64 (3.12.6-0ubuntu1) ... 1678s Setting up python3-citeproc (0.6.0-3) ... 1678s Setting up po-debconf (1.0.21+nmu1) ... 1678s Setting up libtk8.6:arm64 (8.6.15-1) ... 1678s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 1678s Setting up python3.12-tk (3.12.7-3) ... 1679s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-6build1) ... 1679s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 1679s Setting up python3-gsd (3.3.0-1) ... 1679s Setting up python3-mmtf (1.1.3-1) ... 1679s Setting up fonts-urw-base35 (20200910-8) ... 1680s Setting up libcairo2:arm64 (1.18.2-2) ... 1680s Setting up python-mdanalysis-doc (2.7.0-5) ... 1680s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 1680s Setting up cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 1680s Setting up python3-griddataformats (1.0.2-2) ... 1680s Setting up python3-pandas (2.2.3+dfsg-5) ... 1687s Setting up libpython3-all-dev:arm64 (3.12.6-0ubuntu1) ... 1687s Setting up sphinx-common (7.4.7-4) ... 1687s Setting up python3-dev (3.12.6-0ubuntu1) ... 1687s Setting up python3-h5py (3.11.0-5ubuntu1) ... 1687s Setting up python3-sklearn (1.4.2+dfsg-6build1) ... 1690s Setting up python3-cftime (1.6.4-1build1) ... 1690s Setting up cpp-14 (14.2.0-8ubuntu1) ... 1690s Setting up cpp (4:14.1.0-2ubuntu1) ... 1690s Setting up gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 1690s Setting up python3-netcdf4 (1.7.2-1) ... 1690s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 1690s Setting up gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 1690s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 1690s Setting up g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 1690s Setting up python3-cairo (1.26.1-2) ... 1690s Setting up python3-duecredit (0.10.2-2) ... 1691s Setting up blt (2.5.3+dfsg-7build1) ... 1691s Setting up python3-tk:arm64 (3.12.6-1ubuntu1) ... 1691s Setting up gcc-14 (14.2.0-8ubuntu1) ... 1691s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 1691s Setting up python3-rlpycairo (0.3.0-3) ... 1691s Setting up python3-reportlab (4.2.5-1) ... 1692s Setting up g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 1692s Setting up g++-14 (14.2.0-8ubuntu1) ... 1692s Setting up libtool (2.4.7-7build1) ... 1692s Setting up gcc (4:14.1.0-2ubuntu1) ... 1692s Setting up dh-autoreconf (20) ... 1692s Setting up g++ (4:14.1.0-2ubuntu1) ... 1692s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1692s Setting up build-essential (12.10ubuntu1) ... 1692s Setting up debhelper (13.20ubuntu1) ... 1692s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 1692s Setting up python3-fonttools (4.46.0-1build2) ... 1693s Setting up python3-matplotlib (3.8.3-3) ... 1695s Setting up python3-mdanalysis (2.7.0-5) ... 1695s Setting up python3-seaborn (0.13.2-4) ... 1696s Processing triggers for man-db (2.13.0-1) ... 1697s Processing triggers for install-info (7.1.1-1) ... 1698s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1698s Processing triggers for sgml-base (1.31) ... 1698s Setting up docutils-common (0.21.2+dfsg-2) ... 1698s Setting up w3c-sgml-lib (1.3-3) ... 1732s Setting up python3-biopython (1.84+dfsg-4) ... 1733s Processing triggers for sgml-base (1.31) ... 1733s Setting up python3-docutils (0.21.2+dfsg-2) ... 1734s Setting up python3-pybtex-docutils (1.0.2-1) ... 1734s Setting up python3-sphinx (7.4.7-4) ... 1735s Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ... 1735s Setting up python3-sphinx-sitemap (2.6.0-1) ... 1735s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 1735s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 1735s Setting up python3-msmb-theme (1.2.0-4) ... 1735s Setting up autopkgtest-satdep (0) ... 1744s (Reading database ... 105745 files and directories currently installed.) 1744s Removing autopkgtest-satdep (0) ... 1745s autopkgtest [20:46:10]: test test-mdanalysis: [----------------------- 1745s skipping tests with SKIP_TEST_LIST= 1756s ============================= test session starts ============================== 1756s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 1756s rootdir: /tmp/autopkgtest.QaPnxU/build.ecx/src 1756s plugins: typeguard-4.4.1, hypothesis-6.116.0 1756s collected 19229 items / 6 skipped 1756s 1760s testsuite/MDAnalysisTests/analysis/test_align.py ....................... [ 0%] 1769s ....................s.ss.s... [ 0%] 1769s testsuite/MDAnalysisTests/analysis/test_atomicdistances.py ... [ 0%] 1769s testsuite/MDAnalysisTests/analysis/test_base.py ........................ [ 0%] 1769s ........................................................................ [ 0%] 1773s ....................................................................... [ 1%] 1775s testsuite/MDAnalysisTests/analysis/test_bat.py ............ [ 1%] 1777s testsuite/MDAnalysisTests/analysis/test_contacts.py .................... [ 1%] 1780s .............. [ 1%] 1780s testsuite/MDAnalysisTests/analysis/test_data.py . [ 1%] 1780s testsuite/MDAnalysisTests/analysis/test_density.py ..................... [ 1%] 1787s ...................... [ 1%] 1788s testsuite/MDAnalysisTests/analysis/test_dielectric.py ...... [ 1%] 1789s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py .......... [ 1%] 1796s testsuite/MDAnalysisTests/analysis/test_dihedrals.py ................... [ 1%] 1797s .... [ 1%] 1803s testsuite/MDAnalysisTests/analysis/test_distances.py ............ [ 1%] 1831s testsuite/MDAnalysisTests/analysis/test_encore.py .................X..X. [ 2%] 1844s ..................................... [ 2%] 1855s testsuite/MDAnalysisTests/analysis/test_gnm.py ...... [ 2%] 1855s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py .............. [ 2%] 1857s ................................ [ 2%] 1857s testsuite/MDAnalysisTests/analysis/test_hole2.py ....sssssssssssssssssss [ 2%] 1857s ssssssssssssssssssssssssssssssss [ 2%] 1857s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py ...... [ 2%] 1857s ......... [ 2%] 1858s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py . [ 2%] 1858s ................. [ 2%] 1858s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py ...... [ 2%] 1859s ...................................... [ 3%] 1861s testsuite/MDAnalysisTests/analysis/test_leaflet.py s............ [ 3%] 1861s testsuite/MDAnalysisTests/analysis/test_lineardensity.py ........ [ 3%] 1863s testsuite/MDAnalysisTests/analysis/test_msd.py .......................ss [ 3%] 1863s sssssssssssssssssssssssssssss [ 3%] 1864s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py ................ [ 3%] 1864s [ 3%] 1865s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py .................... [ 3%] 1865s .............. [ 3%] 1867s testsuite/MDAnalysisTests/analysis/test_pca.py ......................... [ 3%] 1868s ...................... [ 4%] 1871s testsuite/MDAnalysisTests/analysis/test_persistencelength.py ........... [ 4%] 1871s ....... [ 4%] 1893s testsuite/MDAnalysisTests/analysis/test_psa.py ......................... [ 4%] 1893s .................... [ 4%] 1894s testsuite/MDAnalysisTests/analysis/test_rdf.py .................... [ 4%] 1894s testsuite/MDAnalysisTests/analysis/test_rdf_s.py ..................... [ 4%] 1896s testsuite/MDAnalysisTests/analysis/test_rms.py ......................... [ 4%] 1900s ................ [ 4%] 1900s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py ............... [ 4%] 1900s ........... [ 4%] 1900s testsuite/MDAnalysisTests/analysis/test_wbridge.py ..................... [ 5%] 1900s ........................... [ 5%] 1900s testsuite/MDAnalysisTests/auxiliary/test_core.py ..... [ 5%] 1900s testsuite/MDAnalysisTests/auxiliary/test_edr.py .sssssssssssssssssssssss [ 5%] 1900s ssssssssssssssssssssssssssssssssssssssssssss [ 5%] 1900s testsuite/MDAnalysisTests/auxiliary/test_xvg.py ........................ [ 5%] 1900s ........................................................................ [ 6%] 1900s .... [ 6%] 1900s testsuite/MDAnalysisTests/converters/test_base.py .. [ 6%] 1900s testsuite/MDAnalysisTests/converters/test_rdkit.py .ssssssssssssssssssss [ 6%] 1900s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 6%] 1900s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 6%] 1900s ssssssssssssssssssssssssssssss [ 7%] 1900s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py ... [ 7%] 1904s testsuite/MDAnalysisTests/coordinates/test_chainreader.py .............. [ 7%] 1915s ....................................................... [ 7%] 1916s testsuite/MDAnalysisTests/coordinates/test_copying.py .................. [ 7%] 1924s ...............................................................ss.ss.s.s [ 7%] 1933s s.sss....ss...s.ssss.ss.s.ss.sss....ss...s.ssss.ss.s.ss.sss....ss.s.ssss [ 8%] 1938s .......................................................s [ 8%] 1939s testsuite/MDAnalysisTests/coordinates/test_crd.py .............. [ 8%] 1939s testsuite/MDAnalysisTests/coordinates/test_dcd.py ...................... [ 8%] 1941s .......x.......ss....................................................... [ 9%] 1943s ..........................................s [ 9%] 1943s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py ................... [ 9%] 1943s .................................... [ 9%] 1944s testsuite/MDAnalysisTests/coordinates/test_dms.py ......... [ 9%] 1944s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py .................. [ 9%] 1944s ....... [ 9%] 1945s testsuite/MDAnalysisTests/coordinates/test_gms.py .................. [ 9%] 1946s testsuite/MDAnalysisTests/coordinates/test_gro.py ...................... [ 10%] 1947s .......................sss.............................................. [ 10%] 1948s ..............sss...................................................sss. [ 10%] 1967s ..................................................sss................... [ 11%] 1978s .................... [ 11%] 1978s testsuite/MDAnalysisTests/coordinates/test_gsd.py ss.... [ 11%] 1979s testsuite/MDAnalysisTests/coordinates/test_h5md.py ..................... [ 11%] 1984s ..............ss........................................................ [ 11%] 2001s .......x................................................... [ 12%] 2002s testsuite/MDAnalysisTests/coordinates/test_lammps.py ................... [ 12%] 2012s ........................................................................ [ 12%] 2046s ............................................................ [ 12%] 2048s testsuite/MDAnalysisTests/coordinates/test_memory.py ................... [ 13%] 2058s ........x......xxx...................................................... [ 13%] 2058s .......................... [ 13%] 2058s testsuite/MDAnalysisTests/coordinates/test_mmtf.py ........... [ 13%] 2059s testsuite/MDAnalysisTests/coordinates/test_mol2.py ..................... [ 13%] 2059s [ 13%] 2060s testsuite/MDAnalysisTests/coordinates/test_namdbin.py .................. [ 13%] 2060s ..... [ 13%] 2060s testsuite/MDAnalysisTests/coordinates/test_netcdf.py ................... [ 13%] 2063s ........................................................................ [ 14%] 2067s ........................................................................ [ 14%] 2067s .................. [ 14%] 2068s testsuite/MDAnalysisTests/coordinates/test_null.py . [ 14%] 2069s testsuite/MDAnalysisTests/coordinates/test_pdb.py ...................... [ 14%] 2095s ........................................................................ [ 15%] 2099s ........................................................................ [ 15%] 2100s ................ [ 15%] 2100s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py ............... [ 15%] 2101s testsuite/MDAnalysisTests/coordinates/test_pqr.py ...................... [ 15%] 2102s ........ [ 15%] 2102s testsuite/MDAnalysisTests/coordinates/test_reader_api.py ............... [ 16%] 2102s ........................................................................ [ 16%] 2102s ........................................................................ [ 16%] 2102s ............................. [ 16%] 2102s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py ............. [ 16%] 2102s ........................................................................ [ 17%] 2106s ........................................................................ [ 17%] 2107s ................. [ 17%] 2107s testsuite/MDAnalysisTests/coordinates/test_tng.py ..ssssssssssssssssssss [ 17%] 2107s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 18%] 2107s s [ 18%] 2108s testsuite/MDAnalysisTests/coordinates/test_trc.py ...................... [ 18%] 2108s .......... [ 18%] 2108s testsuite/MDAnalysisTests/coordinates/test_trj.py ...................... [ 18%] 2109s .............. [ 18%] 2110s testsuite/MDAnalysisTests/coordinates/test_trz.py ...................... [ 18%] 2110s .. [ 18%] 2110s testsuite/MDAnalysisTests/coordinates/test_txyz.py ...... [ 18%] 2110s testsuite/MDAnalysisTests/coordinates/test_windows.py .................. [ 18%] 2111s ................................................. [ 19%] 2111s testsuite/MDAnalysisTests/coordinates/test_writer_api.py .ss............ [ 19%] 2111s ......ss.....s............ss.....s........... [ 19%] 2111s testsuite/MDAnalysisTests/coordinates/test_writer_registration.py .... [ 19%] 2113s testsuite/MDAnalysisTests/coordinates/test_xdr.py ...................... [ 19%] 2124s ........................................................................ [ 19%] 2124s ....ss.................................................................. [ 20%] 2125s .ss......................................................... [ 20%] 2125s testsuite/MDAnalysisTests/coordinates/test_xyz.py ...................... [ 20%] 2126s ...............ss....................................................... [ 21%] 2126s .................ss....................................... [ 21%] 2126s testsuite/MDAnalysisTests/core/test_accessors.py ssss..s [ 21%] 2127s testsuite/MDAnalysisTests/core/test_accumulate.py ...................... [ 21%] 2134s ................................................................... [ 21%] 2136s testsuite/MDAnalysisTests/core/test_atom.py ................... [ 22%] 2141s testsuite/MDAnalysisTests/core/test_atomgroup.py ....................... [ 22%] 2154s ........................................................................ [ 22%] 2155s ........................................................................ [ 22%] 2168s ........................................................................ [ 23%] 2187s ........................................................................ [ 23%] 2205s ........................................................................ [ 24%] 2209s .................................................... [ 24%] 2209s testsuite/MDAnalysisTests/core/test_atomselections.py .................. [ 24%] 2210s ........................................................................ [ 24%] 2210s ........................................................................ [ 25%] 2226s ..................sssssssssssssssssss................................... [ 25%] 2227s ........................................................................ [ 25%] 2227s ........................................................................ [ 26%] 2228s ........................................................................ [ 26%] 2241s .....................................sssss...........ssssss.... [ 26%] 2241s testsuite/MDAnalysisTests/core/test_copying.py ......................... [ 27%] 2242s .................... [ 27%] 2244s testsuite/MDAnalysisTests/core/test_fragments.py ................ [ 27%] 2244s testsuite/MDAnalysisTests/core/test_group_traj_access.py ............... [ 27%] 2247s ................................................. [ 27%] 2247s testsuite/MDAnalysisTests/core/test_groups.py .......................... [ 27%] 2247s ........................................................................ [ 28%] 2247s ........................................................................ [ 28%] 2247s ........................................................................ [ 28%] 2248s ........................................................................ [ 29%] 2249s ........................................................................ [ 29%] 2249s ........................................................................ [ 30%] 2249s ........................................................................ [ 30%] 2274s ....................................................................... [ 30%] 2274s testsuite/MDAnalysisTests/core/test_index_dtype.py ............... [ 30%] 2274s testsuite/MDAnalysisTests/core/test_requires.py .... [ 30%] 2275s testsuite/MDAnalysisTests/core/test_residue.py .... [ 30%] 2277s testsuite/MDAnalysisTests/core/test_residuegroup.py s..................s [ 30%] 2278s ssss..... [ 31%] 2278s testsuite/MDAnalysisTests/core/test_segment.py ....... [ 31%] 2279s testsuite/MDAnalysisTests/core/test_segmentgroup.py ........... [ 31%] 2279s testsuite/MDAnalysisTests/core/test_topology.py ........................ [ 31%] 2279s ........................................ [ 31%] 2280s testsuite/MDAnalysisTests/core/test_topologyattrs.py ................... [ 31%] 2280s ................................................................x....... [ 31%] 2281s ..................................................... [ 32%] 2281s testsuite/MDAnalysisTests/core/test_topologyobjects.py ................. [ 32%] 2284s ...................................................................... [ 32%] 2286s testsuite/MDAnalysisTests/core/test_universe.py .................sssssss [ 32%] 2290s s....................................................................... [ 33%] 2296s ........................................................................ [ 33%] 2297s ........................................................................ [ 33%] 2299s .................. [ 34%] 2299s testsuite/MDAnalysisTests/core/test_unwrap.py .......................... [ 34%] 2300s ........................................................................ [ 34%] 2300s ........................................................................ [ 34%] 2301s ........................................................................ [ 35%] 2301s ........................................................................ [ 35%] 2301s ........................................................................ [ 36%] 2301s ........................................................................ [ 36%] 2302s ................................................... [ 36%] 2305s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py .............. [ 36%] 2305s . [ 36%] 2305s testsuite/MDAnalysisTests/core/test_wrap.py ............................ [ 36%] 2306s ........................................................................ [ 37%] 2307s ........................................................................ [ 37%] 2307s ........................................................................ [ 37%] 2307s ........................................................................ [ 38%] 2307s ........................................................................ [ 38%] 2308s ........................................................................ [ 39%] 2309s ......................................................... [ 39%] 2309s testsuite/MDAnalysisTests/formats/test_libdcd.py ....................... [ 39%] 2310s .......................X................................................ [ 39%] 2310s ...... [ 39%] 2310s testsuite/MDAnalysisTests/formats/test_libmdaxdr.py .................... [ 40%] 2310s ........................................................................ [ 40%] 2310s ... [ 40%] 2314s testsuite/MDAnalysisTests/import/test_import.py .. [ 40%] 2314s testsuite/MDAnalysisTests/lib/test_augment.py .......................... [ 40%] 2314s .......... [ 40%] 2314s testsuite/MDAnalysisTests/lib/test_cutil.py ............. [ 40%] 2314s testsuite/MDAnalysisTests/lib/test_distances.py ........................ [ 40%] 2315s ........................................................................ [ 41%] 2315s ........................................................................ [ 41%] 2315s ........................................................................ [ 41%] 2315s ........................................................................ [ 42%] 2315s ........................................................................ [ 42%] 2316s ........................................................................ [ 43%] 2321s ........................................................................ [ 43%] 2323s ........................................................................ [ 43%] 2324s ........................................................................ [ 44%] 2324s ........................................................................ [ 44%] 2324s ........................................................................ [ 44%] 2324s ........................................................................ [ 45%] 2324s ........................................................................ [ 45%] 2325s ........................................................................ [ 46%] 2325s ........................................................................ [ 46%] 2325s ........................................................................ [ 46%] 2325s ........................................................................ [ 47%] 2325s ........................................................................ [ 47%] 2325s ........................................................................ [ 47%] 2325s ........................................................................ [ 48%] 2325s ........................................................................ [ 48%] 2325s ........................................................................ [ 49%] 2325s ........................................................................ [ 49%] 2325s ........................................................................ [ 49%] 2326s ........................................................................ [ 50%] 2326s ........................................................................ [ 50%] 2326s ........................................................................ [ 50%] 2326s ........................................................................ [ 51%] 2326s ........................................................................ [ 51%] 2326s ........................................................................ [ 52%] 2326s ........................................................................ [ 52%] 2326s ........................................................................ [ 52%] 2327s ........................................................................ [ 53%] 2327s ........................................................................ [ 53%] 2327s .............................................. [ 53%] 2327s testsuite/MDAnalysisTests/lib/test_log.py ... [ 53%] 2327s testsuite/MDAnalysisTests/lib/test_neighborsearch.py .. [ 53%] 2332s testsuite/MDAnalysisTests/lib/test_nsgrid.py ........................... [ 53%] 2333s ..s [ 53%] 2333s testsuite/MDAnalysisTests/lib/test_pkdtree.py ................. [ 54%] 2333s testsuite/MDAnalysisTests/lib/test_qcprot.py .... [ 54%] 2333s testsuite/MDAnalysisTests/lib/test_util.py ............................. [ 54%] 2333s ........................................................................ [ 54%] 2333s ........................................................................ [ 54%] 2333s ........................................................................ [ 55%] 2333s ........................................................................ [ 55%] 2333s ........................................................................ [ 56%] 2333s ........................................................................ [ 56%] 2333s ........................................................................ [ 56%] 2334s ........................................................................ [ 57%] 2334s ........................................................................ [ 57%] 2334s ........................................................................ [ 57%] 2334s ........................................................................ [ 58%] 2334s ........................................................................ [ 58%] 2334s ........................................................................ [ 59%] 2334s ........................................................................ [ 59%] 2334s ........................................................................ [ 59%] 2334s ........................................................................ [ 60%] 2334s ........................................................................ [ 60%] 2334s ........................................................................ [ 60%] 2334s ........................................................................ [ 61%] 2334s ........................................................................ [ 61%] 2335s ........................................................................ [ 62%] 2335s ........................................................................ [ 62%] 2335s ........................................................................ [ 62%] 2335s ........................................................................ [ 63%] 2335s ........................................................................ [ 63%] 2335s ........................................................................ [ 63%] 2335s ........................................................................ [ 64%] 2335s ........................................................................ [ 64%] 2335s ........................................................................ [ 65%] 2335s ........................................................................ [ 65%] 2335s ........................................................................ [ 65%] 2335s ........................................................................ [ 66%] 2336s ........................................................................ [ 66%] 2336s ........................................................................ [ 66%] 2336s ........................................................................ [ 67%] 2336s ........................................................................ [ 67%] 2336s ........................................................................ [ 68%] 2336s ........................................................................ [ 68%] 2336s ........................................................................ [ 68%] 2336s ........................................................................ [ 69%] 2336s ........................................................................ [ 69%] 2336s ........................................................................ [ 69%] 2336s ........................................................................ [ 70%] 2336s ........................................................................ [ 70%] 2337s ........................................................................ [ 71%] 2337s ........................................................................ [ 71%] 2337s ........................................................................ [ 71%] 2337s ........................................................................ [ 72%] 2337s ........................................................................ [ 72%] 2337s ........................................................................ [ 72%] 2337s ........................................................................ [ 73%] 2337s ........................................................................ [ 73%] 2337s ........................................................................ [ 74%] 2337s ........................................................................ [ 74%] 2337s ........................................................................ [ 74%] 2337s ........................................................................ [ 75%] 2337s ........................................................................ [ 75%] 2337s ........................................................................ [ 75%] 2338s ........................................................................ [ 76%] 2338s ........................................................................ [ 76%] 2338s ........................................................................ [ 77%] 2338s ........................................................................ [ 77%] 2338s ........................................................................ [ 77%] 2338s ........................................................................ [ 78%] 2338s ........................................................................ [ 78%] 2338s ........................................................................ [ 78%] 2338s ........................................................................ [ 79%] 2338s ........................................................................ [ 79%] 2338s ........................................................................ [ 80%] 2338s ........................................................................ [ 80%] 2338s ........................................................................ [ 80%] 2340s ........................................................................ [ 81%] 2340s ........................................................................ [ 81%] 2340s ........................................................................ [ 81%] 2340s ........................................................................ [ 82%] 2340s ........................................................................ [ 82%] 2340s ........................................................................ [ 83%] 2340s ........................................................................ [ 83%] 2340s ........................................................................ [ 83%] 2341s .........................................s.............................. [ 84%] 2341s ........................................................................ [ 84%] 2342s .............s.......................................................... [ 84%] 2347s ........................................................................ [ 85%] 2347s .................................................. [ 85%] 2350s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py .......... [ 85%] 2377s ....................................... [ 85%] 2377s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py .... [ 85%] 2378s .... [ 85%] 2378s testsuite/MDAnalysisTests/test_api.py ............................ [ 86%] 2383s testsuite/MDAnalysisTests/topology/test_altloc.py ... [ 86%] 2384s testsuite/MDAnalysisTests/topology/test_crd.py ........ [ 86%] 2384s testsuite/MDAnalysisTests/topology/test_dlpoly.py ...................... [ 86%] 2384s .......................................... [ 86%] 2385s testsuite/MDAnalysisTests/topology/test_dms.py .................... [ 86%] 2385s testsuite/MDAnalysisTests/topology/test_fhiaims.py ............ [ 86%] 2385s testsuite/MDAnalysisTests/topology/test_gms.py ......................... [ 86%] 2385s ..... [ 86%] 2388s testsuite/MDAnalysisTests/topology/test_gro.py ............... [ 86%] 2388s testsuite/MDAnalysisTests/topology/test_gsd.py ......................... [ 86%] 2388s ...... [ 86%] 2388s testsuite/MDAnalysisTests/topology/test_guessers.py .................... [ 87%] 2389s ..............ssssssssss [ 87%] 2389s testsuite/MDAnalysisTests/topology/test_hoomdxml.py .................. [ 87%] 2389s testsuite/MDAnalysisTests/topology/test_itp.py ......................... [ 87%] 2389s ........................................................................ [ 87%] 2390s .......................... [ 87%] 2394s testsuite/MDAnalysisTests/topology/test_lammpsdata.py .................. [ 88%] 2395s ........................................................................ [ 88%] 2395s ....................................................... [ 88%] 2395s testsuite/MDAnalysisTests/topology/test_minimal.py ..................... [ 88%] 2395s ........... [ 88%] 2396s testsuite/MDAnalysisTests/topology/test_mmtf.py ........................ [ 88%] 2396s ...................................................... [ 89%] 2396s testsuite/MDAnalysisTests/topology/test_mol2.py ........................ [ 89%] 2396s ....... [ 89%] 2400s testsuite/MDAnalysisTests/topology/test_pdb.py ......................... [ 89%] 2401s .......................... [ 89%] 2401s testsuite/MDAnalysisTests/topology/test_pdbqt.py ......... [ 89%] 2402s testsuite/MDAnalysisTests/topology/test_pqr.py .................... [ 89%] 2407s testsuite/MDAnalysisTests/topology/test_psf.py ......................... [ 89%] 2410s ....................................... [ 90%] 2410s testsuite/MDAnalysisTests/topology/test_top.py ......................... [ 90%] 2415s ........................................................................ [ 90%] 2416s ........................................................................ [ 91%] 2416s ........... [ 91%] 2416s testsuite/MDAnalysisTests/topology/test_topology_base.py ... [ 91%] 2416s testsuite/MDAnalysisTests/topology/test_topology_str_types.py .......... [ 91%] 2424s ........................................................................ [ 91%] 2425s .................. [ 91%] 2432s testsuite/MDAnalysisTests/topology/test_tprparser.py ................... [ 91%] 2442s ........................................................................ [ 92%] 2452s ........................................................................ [ 92%] 2463s ........................................................................ [ 92%] 2474s ........................................................................ [ 93%] 2482s ........................................................................ [ 93%] 2483s ........................................................................ [ 93%] 2483s ........................................................................ [ 94%] 2483s ........................................................................ [ 94%] 2483s ........................................................................ [ 95%] 2483s ........................................................................ [ 95%] 2485s ........................................................................ [ 95%] 2488s ...................................... [ 96%] 2488s testsuite/MDAnalysisTests/topology/test_txyz.py ...................... [ 96%] 2488s testsuite/MDAnalysisTests/topology/test_xpdb.py ........ [ 96%] 2488s testsuite/MDAnalysisTests/topology/test_xyz.py ........................ [ 96%] 2488s testsuite/MDAnalysisTests/transformations/test_base.py ..... [ 96%] 2488s testsuite/MDAnalysisTests/transformations/test_boxdimensions.py ........ [ 96%] 2488s ...... [ 96%] 2488s testsuite/MDAnalysisTests/transformations/test_fit.py .................. [ 96%] 2488s ......................................... [ 96%] 2490s testsuite/MDAnalysisTests/transformations/test_nojump.py ............ [ 96%] 2490s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py .... [ 96%] 2490s . [ 96%] 2490s testsuite/MDAnalysisTests/transformations/test_rotate.py ............... [ 96%] 2490s ............................ [ 97%] 2490s testsuite/MDAnalysisTests/transformations/test_translate.py ............ [ 97%] 2490s ............ [ 97%] 2499s testsuite/MDAnalysisTests/transformations/test_wrap.py ................. [ 97%] 2500s ....... [ 97%] 2500s testsuite/MDAnalysisTests/utils/test_authors.py . [ 97%] 2500s testsuite/MDAnalysisTests/utils/test_datafiles.py .... [ 97%] 2500s testsuite/MDAnalysisTests/utils/test_duecredit.py .............. [ 97%] 2500s testsuite/MDAnalysisTests/utils/test_failure.py . [ 97%] 2500s testsuite/MDAnalysisTests/utils/test_imports.py ........................ [ 97%] 2500s ........................................................................ [ 97%] 2500s ........................................................................ [ 98%] 2500s ................... [ 98%] 2500s testsuite/MDAnalysisTests/utils/test_log.py . [ 98%] 2500s testsuite/MDAnalysisTests/utils/test_meta.py .... [ 98%] 2501s testsuite/MDAnalysisTests/utils/test_modelling.py ............. [ 98%] 2502s testsuite/MDAnalysisTests/utils/test_persistence.py ....... [ 98%] 2513s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%] 2513s ..............ss.. [ 98%] 2513s testsuite/MDAnalysisTests/utils/test_qcprot.py ...... [ 98%] 2515s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%] 2515s [ 98%] 2515s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 98%] 2516s ............... [ 99%] 2516s testsuite/MDAnalysisTests/utils/test_transformations.py ................ [ 99%] 2516s ........................................................................ [ 99%] 2516s ........................................................ [ 99%] 2516s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%] 2516s ....... [ 99%] 2516s testsuite/MDAnalysisTests/visualization/test_streamlines.py ... [100%] 2516s 2516s =============================== warnings summary =============================== 2516s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39 2516s /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. 2516s 2516s Due to the on going maintenance burden of keeping command line application 2516s wrappers up to date, we have decided to deprecate and eventually remove these 2516s modules. 2516s 2516s We instead now recommend building your command line and invoking it directly 2516s with the subprocess module. 2516s warnings.warn( 2516s 2516s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings 2516s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings 2516s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings 2516s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings 2516s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings 2516s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings 2516s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings 2516s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings 2516s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings 2516s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings 2516s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings 2516s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings 2516s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 2516s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings 2516s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings 2516s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings 2516s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings 2516s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings 2516s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings 2516s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings 2516s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings 2516s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings 2516s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings 2516s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings 2516s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings 2516s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings 2516s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings 2516s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 2516s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings 2516s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 2516s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you. 2516s warnings.warn("DCDReader currently makes independent timesteps" 2516s 2516s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0. 2516s warnings.warn(wmsg, category=DeprecationWarning) 2516s 2516s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings 2516s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written 2516s warnings.warn(wmsg) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings 2516s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings 2516s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/memory.py:535: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings 2516s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 2516s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings 2516s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning 2516s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings 2516s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file. 2516s warnings.warn('No coordinate reader found for {}. Skipping ' 2516s 2516s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'c3', 'hc', 'ho', 'h1', 'oh'}. These have been given an empty element record. 2516s warnings.warn("Unknown elements found for some " 2516s 2516s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning 2516s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings 2516s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings 2516s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 2516s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings 2516s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings 2516s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps 2516s self.times[i] = ts.time 2516s 2516s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning 2516s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings 2516s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 2516s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings 2516s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 2516s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings 2516s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings 2516s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded 2516s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps 2516s results.append((ts.time, x.sum() / mask.sum())) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/density.py:423: UserWarning: Box padding (currently set at 2.0) is not used in user defined grids. 2516s warnings.warn(msg) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 2516s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/density.py:556: UserWarning: Atom selection does not fit grid --- you may want to define a larger box 2516s warnings.warn(msg) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 2516s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 2516s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 2516s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings 2516s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning 2516s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings 2516s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings 2516s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings 2516s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings 2516s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings 2516s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 2516s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings 2516s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:331: UserWarning: Element information is missing, elements attribute will not be populated. If needed these can be guessed using MDAnalysis.topology.guessers. 2516s warnings.warn("Element information is missing, elements attribute " 2516s 2516s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran 2516s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame 2516s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections 2516s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues 2516s warnings.warn("Cannot determine phi and psi angles for the first " 2516s 2516s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin 2516s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr 2516s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame 2516s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot 2516s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:582: UserWarning: All residues selected with 'resname ALA CYS* GLY PRO SER THR VAL' have been removed from the selection. 2516s warnings.warn(f"All residues selected with '{select_remove}' " 2516s 2516s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings 2516s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings 2516s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings 2516s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=6533) is multi-threaded, use of fork() may lead to deadlocks in the child. 2516s self.pid = os.fork() 2516s 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide 2516s cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms 2516s 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide 2516s local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 2516s /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice 2516s ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 2516s /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide 2516s ret = um.true_divide( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 2516s /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide 2516s ret = ret.dtype.type(ret / rcount) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 2516s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning 2516s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning 2516s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:453: UserWarning: 1 A^3 CRYST1 record, this is usually a placeholder. Unit cell dimensions will be set to None. 2516s warnings.warn("1 A^3 CRYST1 record," 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. 2516s warnings.warn("Unit cell dimensions not found. " 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings 2516s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings 2516s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings 2516s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 2516s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings 2516s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings 2516s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 2516s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:119: DeprecationWarning: The TRZ reader is deprecated and will be removed in MDAnalysis version 3.0.0 2516s warnings.warn(wmsg, DeprecationWarning) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 2516s warnings.warn("Desired number of sample points too high, using {0}" 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbond = HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbond = HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbond = HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbond = HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbond = HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbond = HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbond = HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbond = HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s HBAC( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 2516s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 2516s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbond = HBAC(u, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! 2516s `find_hydrogen_donors` will be removed in release 3.0.0. 2516s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s D = hbonds.find_hydrogen_donors(H) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! 2516s `find_hydrogen_donors` will be removed in release 3.0.0. 2516s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 2516s hbonds.find_hydrogen_donors(u.atoms) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, name O, and Acceptor, name O. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, name O, and Acceptor, name O. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 2516s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 2516s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. 2516s return _methods._mean(a, axis=axis, dtype=dtype, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 2516s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 2516s /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide 2516s ret = ret.dtype.type(ret / rcount) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, type O, and Acceptor, type O. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, type O, and Acceptor, type O. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, None, and Acceptor, name OH2. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, None, and Acceptor, name OH2. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: donors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection. 2516s warnings.warn(msg.format(sel)) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: hydrogens_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection. 2516s warnings.warn(msg.format(sel)) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: acceptors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection. 2516s warnings.warn(msg.format(sel)) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 2516s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. 2516s warnings.warn("Empty string to select atoms, empty group returned.", 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, , and Acceptor, . 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 150 between Donor, , and Acceptor, . 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 2516s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 2516s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 2516s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 2516s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 2516s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 2516s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple 2516s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:348: UserWarning: Unknown element X found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers. 2516s warnings.warn(wmsg) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning 2516s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning 2516s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 2516s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 2516s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 2516s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/nuclinfo.py:302: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 2516s phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi 2516s 2516s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/psa.py:733: UserWarning: Column index entered (j = 3 is smaller than row index (i = 4). Using symmetric element in upper triangle of distance matrix instead: i --> j, j --> i 2516s warnings.warn("Column index entered (j = {:d} is smaller than row " 2516s 2516s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps 2516s dt=self.trajectory.ts.dt * step, 2516s 2516s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] 2516s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] 2516s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/rdf.py:347: DeprecationWarning: The `rdf` attribute was deprecated in MDAnalysis 2.0.0 and will be removed in MDAnalysis 3.0.0. Please use `results.rdf` instead 2516s warnings.warn(wmsg, DeprecationWarning) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 2516s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/rdf.py:554: DeprecationWarning: The `u` attribute is superflous and will be removed in MDAnalysis 3.0.0. 2516s warnings.warn("The `u` attribute is superflous and will be removed " 2516s 2516s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] 2516s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/rdf.py:567: DeprecationWarning: The `density` attribute was deprecated in MDAnalysis 2.3.0 and will be removed in MDAnalysis 3.0.0. Please use `norm=density` instead. 2516s warnings.warn("The `density` attribute was deprecated in " 2516s 2516s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. 2516s warnings.warn(msg, category=MissingDataWarning) 2516s 2516s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps 2516s self.timesteps.append(self._ts.time) 2516s 2516s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning 2516s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default 2516s warnings.warn("{} does not support time selection. Reverting to " 2516s 2516s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default 2516s warnings.warn("{} does not support data selection. Reverting to " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 2516s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning 2516s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings 2516s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps 2516s return self.ts.dt 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 2516s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 2516s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps 2516s ts.data['time'] = step_num * ts.dt 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_ts_time[universe0] 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 2516s self.close() 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close 2516s self._apply('close') 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply 2516s return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] 2516s ^^^^^^^^^^^^ 2516s AttributeError: 'ChainReader' object has no attribute 'readers' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing 2516s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain 2516s warnings.warn("Missing frame in continuous chain", UserWarning) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps 2516s time_frame_0 = ts.time - ts.frame*ts.dt # assumes ts.dt is constant 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps 2516s frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps 2516s step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps 2516s self._add_step_to_frame_data(ts.time) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, tempfactors. These will be written with default values. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resids, tempfactors. These will be written with default values. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: names, tempfactors. These will be written with default values. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: tempfactors, tempfactors. These will be written with default values. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps 2516s if not np.allclose(A.time, B.time): 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] 2516s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:326: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 2516s self.close() 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close 2516s self._file.close() 2516s ^^^^^^^^^^ 2516s AttributeError: 'DCDReader' object has no attribute '_file' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms 2516s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit 2516s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__ 2516s self.close() 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close 2516s self._file.close() 2516s ^^^^^^^^^^ 2516s AttributeError: 'DCDWriter' object has no attribute '_file' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings 2516s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings 2516s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings 2516s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/TOPParser.py:299: UserWarning: ATOMIC_NUMBER record not found, elements attribute will not be populated. If needed these can be guessed using MDAnalysis.topology.guessers. 2516s warnings.warn(msg) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps 2516s return self.ts.time 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/FHIAIMS.py:281: UserWarning: Supplied AtomGroup was missing the following attributes: names, ids. These will be written with default values. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps 2516s assert_equal(reader.ts.dt, reader.dt) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps 2516s time_frame = time_frame_0 + frame_index*ts.dt 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps 2516s reader_p = pickle.loads(pickle.dumps(reader)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:1034: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] 2516s warnings.warn(wmsg) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:228: UserWarning: Empty box [0., 0., 0.] found - treating as missing unit cell. Dimensions set to `None`. 2516s warnings.warn(wmsg) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resids. These will be written with default values. Alternatively these can be supplied as keyword arguments. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names. These will be written with default values. Alternatively these can be supplied as keyword arguments. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. 2516s warnings.warn("Not all velocities were present. " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps 2516s reader_p = pickle.loads(pickle.dumps(reader)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader 2516s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps 2516s reader_p = pickle.loads(pickle.dumps(reader)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 2516s self.close() 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close 2516s self._file.close() 2516s ^^^^^^^^^^ 2516s AttributeError: 'H5MDReader' object has no attribute '_file' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 2516s for aux in self.aux_list: 2516s ^^^^^^^^^^^^^ 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 2516s return self._auxs.keys() 2516s ^^^^^^^^^^ 2516s AttributeError: 'H5MDReader' object has no attribute '_auxs' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 2516s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 2516s warnings.warn('Guessed all Masses to 1.0') 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit 2516s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 2516s for aux in self.aux_list: 2516s ^^^^^^^^^^^^^ 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 2516s return self._auxs.keys() 2516s ^^^^^^^^^^ 2516s AttributeError: 'DCDReader' object has no attribute '_auxs' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/memory.py:545: DeprecationWarning: MemoryReader.timeseries inclusive `stop` indexing will be removed in 3.0 in favour of exclusive indexing 2516s warnings.warn("MemoryReader.timeseries inclusive `stop` " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader 2516s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps 2516s reader_p = pickle.loads(pickle.dumps(reader)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:554: UserWarning: NCDF trajectory does not contain `time` information; `time` will be set as an increasing index 2516s warnings.warn(wmsg) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps 2516s ts.time) # in-place ! (hope this works...) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps 2516s time_list = [ts.time for ts in u.trajectory] 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps 2516s assert u.trajectory.ts.dt == pytest.approx(ref) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:700: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.) 2516s return self._test_write_trajectory(universe, outfile) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:969: UserWarning: Could not find netCDF4 module. Falling back to MUCH slower scipy.io.netcdf implementation for writing. 2516s warnings.warn(wmsg) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:711: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.) 2516s return self._test_write_trajectory(universe, outfile) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 2516s warnings.warn("Found missing chainIDs." 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom] 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond] 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom] 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree] 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond] 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps 2516s time = ts.time 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 2516s self.close() 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close 2516s if self.trjfile is not None: 2516s ^^^^^^^^^^^^ 2516s AttributeError: 'NCDFWriter' object has no attribute 'trjfile' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 2516s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' 2516s warnings.warn("Found no information for attr: '{}'" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' 2516s warnings.warn("Found chainIDs using unnaccepted character." 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' 2516s warnings.warn("Found chainIDs with invalid length." 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed 2516s warnings.warn("Serial numbers went over 100,000. " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed 2516s warnings.warn("Invalid atom serials were present, bonds will not" 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed 2516s warnings.warn("Invalid atom serials were present, " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment 2516s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:348: UserWarning: Unknown element found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers. 2516s warnings.warn(wmsg) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 2516s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 2516s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 2516s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 2516s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 2516s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 2516s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges 2516s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDBQT.py:296: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, occupancies, tempfactors. These will be written with default values. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps 2516s assert_equal(ts.dt, 1.0) # default value 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps 2516s assert_equal(ts.time, 0.0) # default to 1.0 (dt) * 0 (frame) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 2516s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps 2516s assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 2516s for aux in self.aux_list: 2516s ^^^^^^^^^^^^^ 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 2516s return self._auxs.keys() 2516s ^^^^^^^^^^ 2516s AttributeError: 'TNGReader' object has no attribute '_auxs' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms 2516s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe 2516s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe 2516s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 2516s self.close() 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close 2516s if self.trjfile is None: 2516s ^^^^^^^^^^^^ 2516s AttributeError: 'TRJReader' object has no attribute 'trjfile' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps 2516s data['time'] = ts.time 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:551: UserWarning: Timestep didn't have the following attributes: 'pressure, pressure_tensor, total_energy, potential_energy, kinetic_energy, temperature, step', these will be set to 0 in the output trajectory 2516s warnings.warn("Timestep didn't have the following attributes: '{0}', " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:567: UserWarning: Timestep didn't have velocity information, this will be set to zero in output trajectory. 2516s warnings.warn("Timestep didn't have velocity information, " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:559: UserWarning: Timestep didn't have dimensions information, box will be written as all zero values 2516s warnings.warn("Timestep didn't have dimensions information, " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 2516s self.close() 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close 2516s if self.trzfile is None: 2516s ^^^^^^^^^^^^ 2516s AttributeError: 'TRZWriter' object has no attribute 'trzfile' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 2516s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 2516s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 2516s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 2516s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 2516s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/TXYZParser.py:139: UserWarning: Element information is missing, elements attribute will not be populated. If needed these can be guessed using MDAnalysis.topology.guessers. 2516s warnings.warn("Element information is missing, elements attribute " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:428: DeprecationWarning: The TRZ writer is deprecated and will be removed in MDAnalysis version 3.0.0 2516s warnings.warn(wmsg, DeprecationWarning) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, resids, names, tempfactors, tempfactors. These will be written with default values. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids. These will be written with default values. Alternatively these can be supplied as keyword arguments. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDBQT.py:296: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, names, occupancies, resids, resnames, tempfactors, types, chainids. These will be written with default values. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PQR.py:301: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids, charges, radii. These will be written with default values. 2516s warnings.warn( 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] 2516s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XYZ.py:193: UserWarning: Input AtomGroup or Universe does not have atom elements or names attributes, writer will default atom names to 'X' 2516s warnings.warn(wmsg) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD 2516s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps 2516s time = ts.time 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps 2516s time = ts.time 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 2516s self.close() 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 2516s self._xdr.close() 2516s ^^^^^^^^^ 2516s AttributeError: 'XTCWriter' object has no attribute '_xdr' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container 2516s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 2516s 2516s Traceback (most recent call last): 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 2516s self.close() 2516s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 2516s self._xdr.close() 2516s ^^^^^^^^^ 2516s AttributeError: 'TRRWriter' object has no attribute '_xdr' 2516s 2516s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-ubuntu/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz failed, reading offsets from trajectory instead. 2516s Consider setting 'refresh_offsets=True' when loading your Universe. 2516s warnings.warn(f"Reading offsets from {fname} failed, " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-ubuntu/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.xtc. Using slow offset calculation. 2516s warnings.warn(f"Cannot write lock/offset file in same location as " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-ubuntu/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz failed, reading offsets from trajectory instead. 2516s Consider setting 'refresh_offsets=True' when loading your Universe. 2516s warnings.warn(f"Reading offsets from {fname} failed, " 2516s 2516s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly 2516s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-ubuntu/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.trr. Using slow offset calculation. 2516s warnings.warn(f"Cannot write lock/offset file in same location as " 2516s 2516s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] 2516s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] 2516s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] 2516s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce 2516s return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2516s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3 2516s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2516s 2516s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 2517s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:833: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead. 2517s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings 2517s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings 2517s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/topologyattrs.py:295: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead. 2517s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 2517s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings 2517s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 2517s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide 2517s return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() 2517s 2517s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings 2517s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide 2517s _centers /= _weights.sum(axis=1)[:, None] 2517s 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -11.0 to -9.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. 2517s warnings.warn(msg, category=SelectionWarning) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -4.0 to -2.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. 2517s warnings.warn(msg, category=SelectionWarning) 2517s 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] 2517s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -0.7 to 1.3'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. 2517s warnings.warn(msg, category=SelectionWarning) 2517s 2517s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] 2517s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] 2517s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] 2517s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] 2517s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] 2517s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc 2517s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc 2517s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:445: DeprecationWarning: The 'pbc' kwarg has been deprecated and will be removed in version 3.0., please use 'wrap' instead 2517s warnings.warn("The 'pbc' kwarg has been deprecated and will be " 2517s 2517s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'bfactor 2.0 to 4.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`. 2517s warnings.warn(msg, category=SelectionWarning) 2517s 2517s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] 2517s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] 2517s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] 2517s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] 2517s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] 2517s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide 2517s x = np.dot(a, b) / (norm(a) * norm(b)) 2517s 2517s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt 2517s ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) 2517s 2517s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt 2517s box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - 2517s 2517s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide 2517s a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) 2517s 2517s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide 2517s b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) 2517s 2517s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide 2517s c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) 2517s 2517s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide 2517s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 2517s 2517s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide 2517s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 2517s 2517s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 2517s /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps 2517s cls(buf, protocol).dump(obj) 2517s 2517s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps 2517s ps = pickle.dumps(ref_reader) 2517s 2517s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] 2517s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd 2517s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd 2517s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset 2517s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific 2517s /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. 2517s warnings.warn('Cannot average position for non sequential' 2517s 2517s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name] 2517s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname] 2517s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type] 2517s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid] 2517s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' 2517s warnings.warn("PDB file is missing resid information. " 2517s 2517s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX 2517s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 2517s 2517s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/pytest-of-ubuntu/pytest-0/test_creates_universe_bz2_0/file.psf.bz2. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/pytest-of-ubuntu/pytest-0/test_bonds_atom_counts_bz2_0/file.psf.bz2. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/pytest-of-ubuntu/pytest-0/test_angles_atom_counts_bz2_0/file.psf.bz2. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/pytest-of-ubuntu/pytest-0/test_dihedrals_atom_counts_bz20/file.psf.bz2. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 2517s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 2517s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 2517s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/topology/TOPParser.py:306: UserWarning: Unknown ATOMIC_NUMBER value found for some atoms, these have been given an empty element record. If needed these can be guessed using MDAnalysis.topology.guessers. 2517s warnings.warn(msg) 2517s 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts 2517s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr] 2517s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file. 2517s warnings.warn('No coordinate reader found for {}. Skipping ' 2517s 2517s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses 2517s /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. 2517s warnings.warn(msg, category=SelectionWarning) 2517s 2517s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 2517s /usr/lib/python3/dist-packages/MDAnalysis/transformations/nojump.py:139: UserWarning: NoJump detected that the interval between frames is unequal.We are resetting the reference frame to the current timestep. 2517s warnings.warn( 2517s 2517s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps 2517s return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 2517s 2517s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps 2517s pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 2517s 2517s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps 2517s return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL) 2517s 2517s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps 2517s return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL) 2517s 2517s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps 2517s return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL) 2517s 2517s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps 2517s pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL) 2517s 2517s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag 2517s /tmp/autopkgtest.QaPnxU/build.ecx/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps 2517s pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL) 2517s 2517s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings 2517s /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream 2517s warnings.warn("Constructed NamedStream from a NamedStream", 2517s 2517s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] 2517s /usr/lib/python3/dist-packages/MDAnalysis/units.py:183: DeprecationWarning: Please use 'Boltzmann_constant' henceforth. The key 'Boltzman_constant' was a typo and will be removed in MDAnalysis 2.8.0. 2517s warnings.warn(wmsg, DeprecationWarning) 2517s 2517s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 2517s = 18631 passed, 594 skipped, 7 xfailed, 3 xpassed, 8130 warnings in 771.06s (0:12:51) = 2541s 2541s DueCredit Report: 2541s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] 2541s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] 2541s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] 2541s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] 2541s - HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] 2541s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] 2541s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] 2541s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] 2541s - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] 2541s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] 2541s - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] 2541s - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 1.1, 2.7.0) [15, 16] 2541s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] 2541s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] 2541s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] 2541s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] 2541s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] 2541s - Scientific tools library / numpy (v 1.26.4) [22] 2541s 2541s 2 packages cited 2541s 16 modules cited 2541s 0 functions cited 2541s 2541s References 2541s ---------- 2541s 2541s [1] Gowers, R. et al., 2016. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In Proceedings of the 15th Python in Science Conference. SciPy. SciPy, pp. 98–105. 2541s [2] Michaud‐Agrawal, N. et al., 2011. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10), pp.2319–2327. 2541s [3] Minh, D.D.L., 2019. Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors. Journal of Computational Chemistry, 41(7), pp.715–730. 2541s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 2541s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 2541s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460. 2541s [7] Smart, O.S. et al., 1996. HOLE: A program for the analysis of the pore dimensions of ion channel structural models. Journal of Molecular Graphics, 14(6), pp.354–360. 2541s [8] Stelzl, L.S. et al., 2014. Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY. Journal of Molecular Biology, 426(3), pp.735–751. 2541s [9] Smith, P. et al., 2019. On the interaction of hyaluronic acid with synovial fluid lipid membranes. Physical Chemistry Chemical Physics, 21(19), pp.9845–9857. 2541s [10] Gowers, R.J. & Carbone, P., 2015. A multiscale approach to model hydrogen bonding: The case of polyamide. The Journal of Chemical Physics, 142(22). 2541s [11] de Buyl, P., 2018. tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3(28), p.877. 2541s [12] Calandrini, V. et al., 2011. nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. École thématique de la Société Française de la Neutronique, 12, pp.201–232. 2541s [13] Yang, L. et al., 2008. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure, 16(2), pp.321–330. 2541s [14] Seyler, S.L. et al., 2015. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways E. Tajkhorshid, ed.. PLOS Computational Biology, 11(10), p.1004568. 2541s [15] Jakupovic, E. & Beckstein, O., 2021. MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. In Proceedings of the 20th Python in Science Conference. SciPy. SciPy, pp. 40–48. 2541s [16] de Buyl, P., Colberg, P.H. & Höfling, F., 2014. H5MD: A structured, efficient, and portable file format for molecular data. Computer Physics Communications, 185(6), pp.1546–1553. 2541s [17] Bradley, A.R. et al., 2017. MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures D. Schneidman, ed.. PLOS Computational Biology, 13(6), p.1005575. 2541s [18] Lundborg, M. et al., 2013. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. Journal of Computational Chemistry, 35(3), pp.260–269. 2541s [19] Theobald, D.L., 2005. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A Foundations of Crystallography, 61(4), pp.478–480. 2541s [20] Liu, P., Agrafiotis, D.K. & Theobald, D.L., Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7), pp.1561–1563. 2541s [21] Kulke, M. & Vermaas, J.V., 2022. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 18(10), pp.6161–6171. 2541s [22] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30. 2544s autopkgtest [20:59:29]: test test-mdanalysis: -----------------------] 2545s autopkgtest [20:59:30]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 2545s test-mdanalysis PASS 2545s autopkgtest [20:59:30]: @@@@@@@@@@@@@@@@@@@@ summary 2545s test-mdanalysis PASS 2557s nova [W] Skipping flock in bos03-arm64 2557s Creating nova instance adt-plucky-arm64-mdanalysis-20241115-201705-juju-7f2275-prod-proposed-migration-environment-20-d7a0f08b-5fee-47ff-b1b6-18c4be39e2d4 from image adt/ubuntu-plucky-arm64-server-20241115.img (UUID bf337bb2-b8c9-4fc7-87ba-f6e99408dba6)... 2557s nova [W] nova quota exceeded (attempt #0) 2557s nova [W] nova quota exceeded (attempt #1) 2557s nova [W] nova quota exceeded (attempt #2) 2557s nova [W] nova quota exceeded (attempt #3) 2557s nova [W] nova quota exceeded (attempt #4)