0s autopkgtest [16:12:45]: starting date and time: 2024-11-14 16:12:45+0000 0s autopkgtest [16:12:45]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:12:45]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zbicu8d0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-36.secgroup --name adt-plucky-arm64-mdanalysis-20241114-161245-juju-7f2275-prod-proposed-migration-environment-20-c8ebdb72-92b8-4fac-b7b0-ea6f6798520a --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/ 69s autopkgtest [16:13:54]: testbed dpkg architecture: arm64 70s autopkgtest [16:13:54]: testbed apt version: 2.9.8 70s autopkgtest [16:13:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 70s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 71s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [966 kB] 71s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 71s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 71s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 71s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [138 kB] 71s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 71s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [724 kB] 71s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6012 B] 71s Fetched 2085 kB in 1s (2225 kB/s) 71s Reading package lists... 74s Reading package lists... 75s Building dependency tree... 75s Reading state information... 76s Calculating upgrade... 77s The following packages will be upgraded: 77s pastebinit python3-systemd 78s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 61.6 kB of archives. 78s After this operation, 347 kB of additional disk space will be used. 78s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 78s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 78s Fetched 61.6 kB in 0s (174 kB/s) 79s (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 ... 79925 files and directories currently installed.) 79s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 79s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 79s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 79s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 79s Setting up pastebinit (1.7.1-1) ... 79s Setting up python3-systemd (235-1build5) ... 79s Processing triggers for man-db (2.12.1-3) ... 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 83s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 83s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 83s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 84s Reading package lists... 84s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s Calculating upgrade... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s autopkgtest [16:14:17]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 92s autopkgtest [16:14:17]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 97s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B] 97s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB] 97s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB] 97s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC 97s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 97s gpgv: issuer "dparsons@debian.org" 97s gpgv: Can't check signature: No public key 97s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found 98s autopkgtest [16:14:23]: testing package mdanalysis version 2.7.0-5 99s autopkgtest [16:14:24]: build not needed 103s autopkgtest [16:14:28]: test test-mdanalysis: preparing testbed 107s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Starting pkgProblemResolver with broken count: 0 109s Starting 2 pkgProblemResolver with broken count: 0 109s Done 110s The following additional packages will be installed: 110s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 110s cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper debugedit 110s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 110s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 110s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 110s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 110s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 110s libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 110s libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl 110s libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1 110s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 110s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 110s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 110s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 110s libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 libpython3-all-dev 110s libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 libsharpyuv0 110s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 110s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 110s libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 110s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 110s python3-alabaster python3-all python3-all-dev python3-appdirs 110s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 110s python3-citeproc python3-contourpy python3-cycler python3-dateutil 110s python3-decorator python3-defusedxml python3-dev python3-docutils 110s python3-duecredit python3-fasteners python3-fonttools python3-freetype 110s python3-fs python3-griddataformats python3-gsd python3-h5py 110s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 110s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 110s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 110s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 110s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 110s python3-netcdf4 python3-networkx python3-numpy python3-packaging 110s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 110s python3-pluggy python3-pybtex python3-pybtex-docutils 110s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 110s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 110s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 110s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 110s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 110s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 110s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 110s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 110s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 110s zlib1g-dev 110s Suggested packages: 110s autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales 110s cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf 110s fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 110s gdb-aarch64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 110s libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc 110s liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran 110s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl bwa clustalo clustalw 110s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 110s python3-mysqldb python3-rdflib python3-psycopg2 raxml samtools t-coffee wise 110s python3-pip python3-venv python-build-doc python-cycler-doc docutils-doc 110s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 110s texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc 110s python-hypothesis-doc python-installer-doc python-joblib-doc 110s python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 110s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 110s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 110s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 110s texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal 110s python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc 110s python3-statsmodels python-pil-doc python-pybtex-doc 110s python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools 110s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 110s python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm 110s fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre 110s texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic 110s python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg 110s python3.13-tk sgml-base-doc 110s Recommended packages: 110s libarchive-cpio-perl javascript-common libjson-xs-perl libltdl-dev 110s libmail-sendmail-perl python-biopython-doc ncbi-blast+ libpaper-utils 110s python3-click python3-simplejson python3-psutil python3-bs4 110s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 110s python3-odf python3-openpyxl python3-tables python3-olefile 110s fonts-dejavu-extra isympy-common 110s The following NEW packages will be installed: 110s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 110s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 110s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 110s docutils-common dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono 110s fonts-font-awesome fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ 110s g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 110s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 110s libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 110s libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl 110s libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1 110s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 110s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 110s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 110s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 110s libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 libpython3-all-dev 110s libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 libsharpyuv0 110s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 110s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 110s libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 110s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 110s python3-alabaster python3-all python3-all-dev python3-appdirs 110s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 110s python3-citeproc python3-contourpy python3-cycler python3-dateutil 110s python3-decorator python3-defusedxml python3-dev python3-docutils 110s python3-duecredit python3-fasteners python3-fonttools python3-freetype 110s python3-fs python3-griddataformats python3-gsd python3-h5py 110s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 110s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 110s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 110s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 110s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 110s python3-netcdf4 python3-networkx python3-numpy python3-packaging 110s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 110s python3-pluggy python3-pybtex python3-pybtex-docutils 110s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 110s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 110s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 110s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 110s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 110s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 110s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 110s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 110s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 110s zlib1g-dev 110s 0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded. 110s Need to get 197 MB/197 MB of archives. 110s After this operation, 841 MB of additional disk space will be used. 110s Get:1 /tmp/autopkgtest.LPm1xd/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [1012 B] 110s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 111s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 111s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 111s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 111s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 111s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 111s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 111s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 111s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 111s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 111s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 111s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 111s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 111s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 111s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 111s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 111s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 111s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 111s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 111s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 111s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 111s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 111s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 111s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 111s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 111s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 112s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 112s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 112s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 112s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 112s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 112s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 112s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 112s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 112s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 112s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 112s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 112s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 112s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 113s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 113s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 113s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 113s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 113s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 113s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 113s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 113s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 113s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 113s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-1ubuntu1 [2355 kB] 113s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 113s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB] 113s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 113s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 113s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 113s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 113s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB] 113s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 113s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 113s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 113s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 113s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 113s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB] 113s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 113s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 113s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 113s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 113s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 113s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 113s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 113s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 113s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 113s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 113s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 113s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 113s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.2-2 [128 kB] 113s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 113s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 113s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 113s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 113s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 113s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 113s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 113s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 113s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 113s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 113s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 113s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 113s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 113s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 113s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 113s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 113s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 114s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 114s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 114s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf19t64 arm64 1:4.9.2-6ubuntu1 [466 kB] 114s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 114s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.7-3 [5565 kB] 114s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.12.6-0ubuntu1 [10.2 kB] 114s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.12.6-0ubuntu1 [916 B] 114s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 114s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 114s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 114s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 114s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 114s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 114s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 114s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 114s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 114s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 114s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 114s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-toml all 0.10.2-1 [16.5 kB] 114s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wheel all 0.44.0-1 [54.2 kB] 114s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-build all 1.2.2-1 [31.0 kB] 114s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 114s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-pyproject all 6.20241024 [1728 B] 114s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 114s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 115s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-mdanalysis-doc all 2.7.0-5 [2323 kB] 115s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 115s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] 115s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.12.6-0ubuntu1 [26.7 kB] 115s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.12.6-0ubuntu1 [908 B] 115s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 115s Get:125 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 115s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 115s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.6-1ubuntu1 [9806 B] 115s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 115s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 115s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 115s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 115s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 115s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 115s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 115s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 115s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 115s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 115s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-1 [195 kB] 115s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 115s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-citeproc all 0.6.0-3 [98.4 kB] 115s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 115s Get:142 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 115s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 115s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 115s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 115s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-2 [42.0 kB] 115s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 4.2-1 [10.0 kB] 115s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 115s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-looseversion all 1.3.0-3 [8354 B] 115s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-duecredit all 0.10.2-2 [66.0 kB] 115s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-monotonic all 1.6-2 [5732 B] 115s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-fasteners all 0.18-2 [12.5 kB] 115s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 116s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 116s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 116s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 116s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 116s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 116s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 116s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB] 116s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 116s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 117s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 117s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mrcfile all 1.5.3-3 [114 kB] 117s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-griddataformats all 1.0.2-2 [2107 kB] 117s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gsd arm64 3.3.0-1 [200 kB] 117s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 117s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 117s Get:169 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 117s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hypothesis all 6.116.0-1 [326 kB] 117s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 117s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 117s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 117s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 117s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-latexcodec all 3.0.0-1 [16.6 kB] 117s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 117s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 117s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build2 [77.9 kB] 117s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 117s Get:180 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 117s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.0-1 [91.6 kB] 117s Get:182 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mdanalysis arm64 2.7.0-5 [2017 kB] 117s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-common all 7.4.7-4 [775 kB] 117s Get:184 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 117s Get:185 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 117s Get:186 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sphinx all 7.4.7-4 [593 kB] 117s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 117s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 117s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-msmb-theme all 1.2.0-4 [35.4 kB] 117s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1 [567 kB] 117s Get:191 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 117s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 117s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 118s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 118s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex all 0.24.0-4 [70.0 kB] 118s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex-docutils all 1.0.2-1 [7176 B] 118s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 118s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-seaborn all 0.13.2-4 [225 kB] 118s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3806 kB] 118s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 118s Get:201 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-sitemap all 2.6.0-1 [6674 B] 118s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 119s Fetched 197 MB in 8s (25.6 MB/s) 119s Selecting previously unselected package fonts-lato. 119s (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 ... 79930 files and directories currently installed.) 119s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 119s Unpacking fonts-lato (2.015-1) ... 119s Selecting previously unselected package sgml-base. 119s Preparing to unpack .../001-sgml-base_1.31_all.deb ... 119s Unpacking sgml-base (1.31) ... 119s Selecting previously unselected package m4. 119s Preparing to unpack .../002-m4_1.4.19-4build1_arm64.deb ... 119s Unpacking m4 (1.4.19-4build1) ... 119s Selecting previously unselected package autoconf. 119s Preparing to unpack .../003-autoconf_2.72-3_all.deb ... 119s Unpacking autoconf (2.72-3) ... 119s Selecting previously unselected package autotools-dev. 119s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ... 119s Unpacking autotools-dev (20220109.1) ... 119s Selecting previously unselected package automake. 119s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 119s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 119s Selecting previously unselected package autopoint. 119s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ... 119s Unpacking autopoint (0.22.5-2) ... 119s Selecting previously unselected package libtcl8.6:arm64. 119s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 119s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 120s Selecting previously unselected package fonts-dejavu-mono. 120s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8_all.deb ... 120s Unpacking fonts-dejavu-mono (2.37-8) ... 120s Selecting previously unselected package fonts-dejavu-core. 120s Preparing to unpack .../009-fonts-dejavu-core_2.37-8_all.deb ... 120s Unpacking fonts-dejavu-core (2.37-8) ... 120s Selecting previously unselected package libfontenc1:arm64. 120s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 120s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 120s Selecting previously unselected package x11-common. 120s Preparing to unpack .../011-x11-common_1%3a7.7+23ubuntu3_all.deb ... 120s Unpacking x11-common (1:7.7+23ubuntu3) ... 120s Selecting previously unselected package xfonts-encodings. 120s Preparing to unpack .../012-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 120s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 120s Selecting previously unselected package xfonts-utils. 120s Preparing to unpack .../013-xfonts-utils_1%3a7.7+7_arm64.deb ... 120s Unpacking xfonts-utils (1:7.7+7) ... 120s Selecting previously unselected package fonts-urw-base35. 120s Preparing to unpack .../014-fonts-urw-base35_20200910-8_all.deb ... 120s Unpacking fonts-urw-base35 (20200910-8) ... 120s Selecting previously unselected package fontconfig-config. 120s Preparing to unpack .../015-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 121s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 121s Selecting previously unselected package libfontconfig1:arm64. 121s Preparing to unpack .../016-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 121s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 121s Selecting previously unselected package libxrender1:arm64. 121s Preparing to unpack .../017-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 121s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 121s Selecting previously unselected package libxft2:arm64. 121s Preparing to unpack .../018-libxft2_2.3.6-1build1_arm64.deb ... 121s Unpacking libxft2:arm64 (2.3.6-1build1) ... 121s Selecting previously unselected package 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unselected package libgomp1:arm64. 122s Preparing to unpack .../030-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 122s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 122s Selecting previously unselected package libitm1:arm64. 122s Preparing to unpack .../031-libitm1_14.2.0-8ubuntu1_arm64.deb ... 122s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 122s Selecting previously unselected package libasan8:arm64. 122s Preparing to unpack .../032-libasan8_14.2.0-8ubuntu1_arm64.deb ... 122s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 122s Selecting previously unselected package liblsan0:arm64. 122s Preparing to unpack .../033-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 122s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 122s Selecting previously unselected package libtsan2:arm64. 122s Preparing to unpack .../034-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 122s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 122s Selecting previously unselected package libubsan1:arm64. 122s Preparing to unpack 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.../045-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 125s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 125s Selecting previously unselected package g++. 125s Preparing to unpack .../046-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 125s Unpacking g++ (4:14.1.0-2ubuntu1) ... 125s Selecting previously unselected package build-essential. 125s Preparing to unpack .../047-build-essential_12.10ubuntu1_arm64.deb ... 125s Unpacking build-essential (12.10ubuntu1) ... 125s Selecting previously unselected package cython3. 125s Preparing to unpack .../048-cython3_3.0.11+dfsg-1ubuntu1_arm64.deb ... 125s Unpacking cython3 (3.0.11+dfsg-1ubuntu1) ... 125s Selecting previously unselected package libdebhelper-perl. 125s Preparing to unpack .../049-libdebhelper-perl_13.20ubuntu1_all.deb ... 125s Unpacking libdebhelper-perl (13.20ubuntu1) ... 125s Selecting previously unselected package libtool. 125s Preparing to unpack .../050-libtool_2.4.7-7build1_all.deb ... 125s Unpacking libtool 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package dwz. 125s Preparing to unpack .../056-dwz_0.15-1build6_arm64.deb ... 125s Unpacking dwz (0.15-1build6) ... 125s Selecting previously unselected package gettext. 125s Preparing to unpack .../057-gettext_0.22.5-2_arm64.deb ... 125s Unpacking gettext (0.22.5-2) ... 126s Selecting previously unselected package intltool-debian. 126s Preparing to unpack .../058-intltool-debian_0.35.0+20060710.6_all.deb ... 126s Unpacking intltool-debian (0.35.0+20060710.6) ... 126s Selecting previously unselected package po-debconf. 126s Preparing to unpack .../059-po-debconf_1.0.21+nmu1_all.deb ... 126s Unpacking po-debconf (1.0.21+nmu1) ... 126s Selecting previously unselected package debhelper. 126s Preparing to unpack .../060-debhelper_13.20ubuntu1_all.deb ... 126s Unpacking debhelper (13.20ubuntu1) ... 126s Selecting previously unselected package dh-python. 126s Preparing to unpack .../061-dh-python_6.20241024_all.deb ... 126s Unpacking dh-python (6.20241024) ... 126s Selecting previously 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126s Unpacking libaec0:arm64 (1.1.3-1) ... 127s Selecting previously unselected package libblas3:arm64. 127s Preparing to unpack .../068-libblas3_3.12.0-3build2_arm64.deb ... 127s Unpacking libblas3:arm64 (3.12.0-3build2) ... 127s Selecting previously unselected package libpixman-1-0:arm64. 127s Preparing to unpack .../069-libpixman-1-0_0.44.0-3_arm64.deb ... 127s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 127s Selecting previously unselected package libxcb-render0:arm64. 127s Preparing to unpack .../070-libxcb-render0_1.17.0-2_arm64.deb ... 127s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 127s Selecting previously unselected package libxcb-shm0:arm64. 127s Preparing to unpack .../071-libxcb-shm0_1.17.0-2_arm64.deb ... 127s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 127s Selecting previously unselected package libcairo2:arm64. 127s Preparing to unpack .../072-libcairo2_1.18.2-2_arm64.deb ... 127s Unpacking libcairo2:arm64 (1.18.2-2) ... 127s Selecting previously unselected package libdeflate0:arm64. 127s Preparing to unpack .../073-libdeflate0_1.22-1_arm64.deb ... 127s Unpacking libdeflate0:arm64 (1.22-1) ... 127s Selecting previously unselected package libexpat1-dev:arm64. 127s Preparing to unpack .../074-libexpat1-dev_2.6.2-2_arm64.deb ... 127s Unpacking libexpat1-dev:arm64 (2.6.2-2) ... 127s Selecting previously unselected package libgfortran5:arm64. 127s Preparing to unpack .../075-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 127s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 127s Selecting previously unselected package libgraphite2-3:arm64. 127s Preparing to unpack .../076-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 127s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 127s Selecting previously unselected package libharfbuzz0b:arm64. 127s Preparing to unpack .../077-libharfbuzz0b_10.0.1-1_arm64.deb ... 127s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 127s Selecting previously unselected package libsz2:arm64. 127s Preparing to unpack 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... 128s Unpacking libjson-perl (4.10000-1) ... 128s Selecting previously unselected package liblapack3:arm64. 128s Preparing to unpack .../089-liblapack3_3.12.0-3build2_arm64.deb ... 128s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 128s Selecting previously unselected package liblbfgsb0:arm64. 128s Preparing to unpack .../090-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 128s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 128s Selecting previously unselected package liblcms2-2:arm64. 128s Preparing to unpack .../091-liblcms2-2_2.16-2_arm64.deb ... 128s Unpacking liblcms2-2:arm64 (2.16-2) ... 128s Selecting previously unselected package liblerc4:arm64. 128s Preparing to unpack .../092-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 128s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 128s Selecting previously unselected package liblzf1:arm64. 128s Preparing to unpack .../093-liblzf1_3.6-4_arm64.deb ... 128s Unpacking liblzf1:arm64 (3.6-4) ... 128s Selecting previously unselected package libnetcdf19t64:arm64. 128s Preparing to unpack .../094-libnetcdf19t64_1%3a4.9.2-6ubuntu1_arm64.deb ... 128s Unpacking libnetcdf19t64:arm64 (1:4.9.2-6ubuntu1) ... 128s Selecting previously unselected package zlib1g-dev:arm64. 128s Preparing to unpack .../095-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 128s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 129s Selecting previously unselected package libpython3.12-dev:arm64. 129s Preparing to unpack .../096-libpython3.12-dev_3.12.7-3_arm64.deb ... 129s Unpacking libpython3.12-dev:arm64 (3.12.7-3) ... 129s Selecting previously unselected package libpython3-dev:arm64. 129s Preparing to unpack .../097-libpython3-dev_3.12.6-0ubuntu1_arm64.deb ... 129s Unpacking libpython3-dev:arm64 (3.12.6-0ubuntu1) ... 129s Selecting previously unselected package libpython3-all-dev:arm64. 129s Preparing to unpack .../098-libpython3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 129s Unpacking libpython3-all-dev:arm64 (3.12.6-0ubuntu1) ... 129s Selecting previously unselected package libqhull-r8.0:arm64. 129s Preparing to unpack .../099-libqhull-r8.0_2020.2-6build1_arm64.deb ... 129s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 129s Selecting previously unselected package libraqm0:arm64. 129s Preparing to unpack .../100-libraqm0_0.10.1-1build1_arm64.deb ... 129s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 129s Selecting previously unselected package libsharpyuv0:arm64. 129s Preparing to unpack .../101-libsharpyuv0_1.4.0-0.1_arm64.deb ... 129s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 129s Selecting previously unselected package libjbig0:arm64. 129s Preparing to unpack .../102-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 129s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 129s Selecting previously unselected package libwebp7:arm64. 129s Preparing to unpack .../103-libwebp7_1.4.0-0.1_arm64.deb ... 129s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 129s Selecting previously unselected package libtiff6:arm64. 129s Preparing to unpack .../104-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 129s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 129s Selecting previously unselected package libwebpdemux2:arm64. 129s Preparing to unpack .../105-libwebpdemux2_1.4.0-0.1_arm64.deb ... 129s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 129s Selecting previously unselected package libwebpmux3:arm64. 129s Preparing to unpack .../106-libwebpmux3_1.4.0-0.1_arm64.deb ... 129s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 129s Selecting previously unselected package libxslt1.1:arm64. 129s Preparing to unpack .../107-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 129s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 130s Selecting previously unselected package python3-packaging. 130s Preparing to unpack .../108-python3-packaging_24.1-1_all.deb ... 130s Unpacking python3-packaging (24.1-1) ... 130s Selecting previously unselected package python3-pyproject-hooks. 130s Preparing to unpack .../109-python3-pyproject-hooks_1.2.0-1_all.deb ... 130s Unpacking python3-pyproject-hooks (1.2.0-1) ... 130s Selecting previously unselected package python3-toml. 130s Preparing to unpack .../110-python3-toml_0.10.2-1_all.deb ... 130s Unpacking python3-toml (0.10.2-1) ... 130s Selecting previously unselected package python3-wheel. 130s Preparing to unpack .../111-python3-wheel_0.44.0-1_all.deb ... 130s Unpacking python3-wheel (0.44.0-1) ... 130s Selecting previously unselected package python3-build. 130s Preparing to unpack .../112-python3-build_1.2.2-1_all.deb ... 130s Unpacking python3-build (1.2.2-1) ... 130s Selecting previously unselected package python3-installer. 130s Preparing to unpack .../113-python3-installer_0.7.0+dfsg1-3_all.deb ... 130s Unpacking python3-installer (0.7.0+dfsg1-3) ... 130s Selecting previously unselected package pybuild-plugin-pyproject. 130s Preparing to unpack .../114-pybuild-plugin-pyproject_6.20241024_all.deb ... 130s Unpacking pybuild-plugin-pyproject (6.20241024) ... 130s Selecting previously unselected package python-matplotlib-data. 130s Preparing to unpack .../115-python-matplotlib-data_3.8.3-3_all.deb ... 130s Unpacking python-matplotlib-data (3.8.3-3) ... 130s Selecting previously unselected package libjs-mathjax. 130s Preparing to unpack .../116-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 130s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 131s Selecting previously unselected package python-mdanalysis-doc. 131s Preparing to unpack .../117-python-mdanalysis-doc_2.7.0-5_all.deb ... 131s Unpacking python-mdanalysis-doc (2.7.0-5) ... 131s Selecting previously unselected package python3-all. 131s Preparing to unpack .../118-python3-all_3.12.6-0ubuntu1_arm64.deb ... 131s Unpacking python3-all (3.12.6-0ubuntu1) ... 131s Selecting previously unselected package python3.12-dev. 131s Preparing to unpack .../119-python3.12-dev_3.12.7-3_arm64.deb ... 131s Unpacking python3.12-dev (3.12.7-3) ... 131s Selecting previously unselected package python3-dev. 131s Preparing to unpack .../120-python3-dev_3.12.6-0ubuntu1_arm64.deb ... 131s Unpacking python3-dev (3.12.6-0ubuntu1) ... 131s Selecting previously unselected package python3-all-dev. 131s Preparing to unpack .../121-python3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 131s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 131s Selecting previously unselected package python3-appdirs. 131s Preparing to unpack .../122-python3-appdirs_1.4.4-4_all.deb ... 131s Unpacking python3-appdirs (1.4.4-4) ... 131s Selecting previously unselected package python3-numpy. 131s Preparing to unpack .../123-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 131s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 132s Selecting previously unselected package python3.12-tk. 132s Preparing to unpack .../124-python3.12-tk_3.12.7-3_arm64.deb ... 132s Unpacking python3.12-tk (3.12.7-3) ... 132s Selecting previously unselected package python3-tk:arm64. 132s Preparing to unpack .../125-python3-tk_3.12.6-1ubuntu1_arm64.deb ... 132s Unpacking python3-tk:arm64 (3.12.6-1ubuntu1) ... 132s Selecting previously unselected package python3-pil.imagetk:arm64. 132s Preparing to unpack .../126-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 132s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 132s Selecting previously unselected package libopenjp2-7:arm64. 132s Preparing to unpack .../127-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 132s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 132s Selecting previously unselected package python3-pil:arm64. 132s Preparing to unpack .../128-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 132s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 132s Selecting previously unselected package python3-cairo. 132s Preparing to unpack .../129-python3-cairo_1.26.1-2_arm64.deb ... 132s Unpacking python3-cairo (1.26.1-2) ... 132s Selecting previously unselected package python3-freetype. 132s Preparing to unpack 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133s Selecting previously unselected package python3-cftime. 133s Preparing to unpack .../136-python3-cftime_1.6.4-1_arm64.deb ... 133s Unpacking python3-cftime (1.6.4-1) ... 133s Selecting previously unselected package python3-lxml:arm64. 133s Preparing to unpack .../137-python3-lxml_5.3.0-1_arm64.deb ... 133s Unpacking python3-lxml:arm64 (5.3.0-1) ... 133s Selecting previously unselected package python3-citeproc. 133s Preparing to unpack .../138-python3-citeproc_0.6.0-3_all.deb ... 133s Unpacking python3-citeproc (0.6.0-3) ... 133s Selecting previously unselected package python3-contourpy. 133s Preparing to unpack .../139-python3-contourpy_1.3.0-2_arm64.deb ... 133s Unpacking python3-contourpy (1.3.0-2) ... 133s Selecting previously unselected package python3-cycler. 133s Preparing to unpack .../140-python3-cycler_0.12.1-1_all.deb ... 133s Unpacking python3-cycler (0.12.1-1) ... 133s Selecting previously unselected package python3-six. 133s Preparing to unpack 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previously unselected package python3-looseversion. 134s Preparing to unpack .../147-python3-looseversion_1.3.0-3_all.deb ... 134s Unpacking python3-looseversion (1.3.0-3) ... 134s Selecting previously unselected package python3-duecredit. 134s Preparing to unpack .../148-python3-duecredit_0.10.2-2_all.deb ... 134s Unpacking python3-duecredit (0.10.2-2) ... 134s Selecting previously unselected package python3-monotonic. 134s Preparing to unpack .../149-python3-monotonic_1.6-2_all.deb ... 134s Unpacking python3-monotonic (1.6-2) ... 134s Selecting previously unselected package python3-fasteners. 134s Preparing to unpack .../150-python3-fasteners_0.18-2_all.deb ... 134s Unpacking python3-fasteners (0.18-2) ... 134s Selecting previously unselected package python3-scipy. 134s Preparing to unpack .../151-python3-scipy_1.13.1-5_arm64.deb ... 134s Unpacking python3-scipy (1.13.1-5) ... 135s Selecting previously unselected package python3-ufolib2. 135s Preparing to unpack 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package python3-unicodedata2. 135s Preparing to unpack .../158-python3-unicodedata2_15.1.0+ds-1build1_arm64.deb ... 135s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 135s Selecting previously unselected package unicode-data. 135s Preparing to unpack .../159-unicode-data_15.1.0-1_all.deb ... 135s Unpacking unicode-data (15.1.0-1) ... 136s Selecting previously unselected package python3-fonttools. 136s Preparing to unpack .../160-python3-fonttools_4.46.0-1build2_arm64.deb ... 136s Unpacking python3-fonttools (4.46.0-1build2) ... 136s Selecting previously unselected package sphinx-rtd-theme-common. 136s Preparing to unpack .../161-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 136s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 136s Selecting previously unselected package python3-mrcfile. 136s Preparing to unpack .../162-python3-mrcfile_1.5.3-3_all.deb ... 136s Unpacking python3-mrcfile (1.5.3-3) ... 136s Selecting previously unselected package python3-griddataformats. 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python3-latexcodec (3.0.0-1) ... 137s Selecting previously unselected package python3-matplotlib. 137s Preparing to unpack .../174-python3-matplotlib_3.8.3-3_arm64.deb ... 137s Unpacking python3-matplotlib (3.8.3-3) ... 137s Selecting previously unselected package python3-mda-xdrlib. 137s Preparing to unpack .../175-python3-mda-xdrlib_0.2.0-3_all.deb ... 137s Unpacking python3-mda-xdrlib (0.2.0-3) ... 137s Selecting previously unselected package python3-msgpack. 137s Preparing to unpack .../176-python3-msgpack_1.0.3-3build2_arm64.deb ... 137s Unpacking python3-msgpack (1.0.3-3build2) ... 137s Selecting previously unselected package python3-mmtf. 137s Preparing to unpack .../177-python3-mmtf_1.1.3-1_all.deb ... 137s Unpacking python3-mmtf (1.1.3-1) ... 137s Selecting previously unselected package python3-threadpoolctl. 137s Preparing to unpack .../178-python3-threadpoolctl_3.1.0-1_all.deb ... 137s Unpacking python3-threadpoolctl (3.1.0-1) ... 137s Selecting previously unselected package 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Unpacking python3-pybtex-docutils (1.0.2-1) ... 140s Selecting previously unselected package python3-pytest. 140s Preparing to unpack .../195-python3-pytest_8.3.3-1_all.deb ... 140s Unpacking python3-pytest (8.3.3-1) ... 140s Selecting previously unselected package python3-seaborn. 140s Preparing to unpack .../196-python3-seaborn_0.13.2-4_all.deb ... 140s Unpacking python3-seaborn (0.13.2-4) ... 140s Selecting previously unselected package python3-sklearn-lib:arm64. 140s Preparing to unpack .../197-python3-sklearn-lib_1.4.2+dfsg-6_arm64.deb ... 140s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ... 140s Selecting previously unselected package python3-sklearn. 140s Preparing to unpack .../198-python3-sklearn_1.4.2+dfsg-6_all.deb ... 140s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 141s Selecting previously unselected package python3-sphinx-sitemap. 141s Preparing to unpack .../199-python3-sphinx-sitemap_2.6.0-1_all.deb ... 141s Unpacking python3-sphinx-sitemap (2.6.0-1) ... 141s 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python3-lz4 (4.0.2+dfsg-1build4) ... 142s Setting up libxcb-render0:arm64 (1.17.0-2) ... 142s Setting up python3-defusedxml (0.7.1-2) ... 142s Setting up libarchive-zip-perl (1.68-1) ... 142s Setting up python3-alabaster (0.7.16-0.1) ... 142s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 142s Setting up fonts-lyx (2.4.2.1-1) ... 142s Setting up libdebhelper-perl (13.20ubuntu1) ... 142s Setting up python3-tqdm (4.67.0-1) ... 143s Setting up python3-threadpoolctl (3.1.0-1) ... 143s Setting up x11-common (1:7.7+23ubuntu3) ... 144s Setting up libdeflate0:arm64 (1.22-1) ... 144s Setting up m4 (1.4.19-4build1) ... 144s Setting up python3-latexcodec (3.0.0-1) ... 144s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 144s Setting up python3-all (3.12.6-0ubuntu1) ... 144s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 144s Setting up python3-sortedcontainers (2.4.0-2) ... 144s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 144s Setting up python3-freetype (2.5.1-1) ... 144s Setting up python3-networkx (3.2.1-4ubuntu1) ... 147s Setting up python3-wheel (0.44.0-1) ... 147s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 147s Setting up python3-mda-xdrlib (0.2.0-3) ... 147s Setting up libaec0:arm64 (1.1.3-1) ... 147s Setting up python3-tz (2024.1-2) ... 148s Setting up python3-monotonic (1.6-2) ... 148s Setting up unicode-data (15.1.0-1) ... 148s Setting up python3-six (1.16.0-7) ... 148s Setting up python3-roman (4.2-1) ... 148s Setting up python3-decorator (5.1.1-5) ... 149s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 149s Setting up autotools-dev (20220109.1) ... 149s Setting up libblas3:arm64 (3.12.0-3build2) ... 149s 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 149s Setting up python3-packaging (24.1-1) ... 149s Setting up libexpat1-dev:arm64 (2.6.2-2) ... 149s Setting up python3-pyproject-hooks (1.2.0-1) ... 149s Setting up 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[100%] 1078s 1078s =============================== warnings summary =============================== 1078s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39 1078s /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. 1078s 1078s Due to the on going maintenance burden of keeping command line application 1078s wrappers up to date, we have decided to deprecate and eventually remove these 1078s modules. 1078s 1078s We instead now recommend building your command line and invoking it directly 1078s with the subprocess module. 1078s warnings.warn( 1078s 1078s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings 1078s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings 1078s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings 1078s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings 1078s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings 1078s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings 1078s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings 1078s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings 1078s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings 1078s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings 1078s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings 1078s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings 1078s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1078s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings 1078s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings 1078s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings 1078s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings 1078s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings 1078s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings 1078s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings 1078s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings 1078s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings 1078s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings 1078s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings 1078s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings 1078s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings 1078s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1078s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings 1078s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1078s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings 1078s /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. 1078s warnings.warn("DCDReader currently makes independent timesteps" 1078s 1078s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 1078s /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. 1078s warnings.warn(wmsg, category=DeprecationWarning) 1078s 1078s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings 1078s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written 1078s warnings.warn(wmsg) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings 1078s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings 1078s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings 1078s /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 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings 1078s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1078s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings 1078s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning 1078s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'hc', 'oh', 'h1', 'ho', 'c3'}. These have been given an empty element record. 1078s warnings.warn("Unknown elements found for some " 1078s 1078s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning 1078s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings 1078s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings 1078s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1078s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings 1078s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings 1078s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps 1078s self.times[i] = ts.time 1078s 1078s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning 1078s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings 1078s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1078s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings 1078s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings 1078s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings 1078s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded 1078s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps 1078s results.append((ts.time, x.sum() / mask.sum())) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue 1078s /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. 1078s warnings.warn(msg) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1078s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding 1078s /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 1078s warnings.warn(msg) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1078s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1078s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1078s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings 1078s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning 1078s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings 1078s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings 1078s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings 1078s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1078s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings 1078s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings 1078s /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. 1078s warnings.warn("Element information is missing, elements attribute " 1078s 1078s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran 1078s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame 1078s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections 1078s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues 1078s warnings.warn("Cannot determine phi and psi angles for the first " 1078s 1078s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin 1078s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr 1078s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame 1078s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot 1078s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning 1078s /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. 1078s warnings.warn(f"All residues selected with '{select_remove}' " 1078s 1078s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings 1078s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings 1078s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=6506) is multi-threaded, use of fork() may lead to deadlocks in the child. 1078s self.pid = os.fork() 1078s 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes 1078s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide 1078s cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms 1078s 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide 1078s local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1078s /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice 1078s ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1078s /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide 1078s ret = um.true_divide( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1078s /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide 1078s ret = ret.dtype.type(ret / rcount) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1078s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning 1078s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning 1078s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1078s /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. 1078s warnings.warn("1 A^3 CRYST1 record," 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. 1078s warnings.warn("Unit cell dimensions not found. " 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings 1078s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings 1078s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings 1078s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1078s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings 1078s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1078s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning 1078s /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 1078s warnings.warn(wmsg, DeprecationWarning) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 1078s warnings.warn("Desired number of sample points too high, using {0}" 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbond = HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbond = HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbond = HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbond = HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbond = HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbond = HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbond = HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbond = HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s HBAC( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1078s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1078s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbond = HBAC(u, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1078s `find_hydrogen_donors` will be removed in release 3.0.0. 1078s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s D = hbonds.find_hydrogen_donors(H) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1078s `find_hydrogen_donors` will be removed in release 3.0.0. 1078s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1078s hbonds.find_hydrogen_donors(u.atoms) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1078s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1078s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. 1078s return _methods._mean(a, axis=axis, dtype=dtype, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1078s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1078s /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide 1078s ret = ret.dtype.type(ret / rcount) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1078s /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. 1078s warnings.warn(msg.format(sel)) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1078s /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. 1078s warnings.warn(msg.format(sel)) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1078s /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. 1078s warnings.warn(msg.format(sel)) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. 1078s warnings.warn("Empty string to select atoms, empty group returned.", 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1078s /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, . 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1078s /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, . 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1078s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1078s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1078s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1078s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1078s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1078s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple 1078s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content 1078s /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. 1078s warnings.warn(wmsg) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning 1078s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning 1078s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1078s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1078s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1078s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1078s /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.) 1078s phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi 1078s 1078s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j 1078s /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 1078s warnings.warn("Column index entered (j = {:d} is smaller than row " 1078s 1078s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps 1078s dt=self.trajectory.ts.dt * step, 1078s 1078s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] 1078s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] 1078s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] 1078s /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 1078s warnings.warn(wmsg, DeprecationWarning) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1078s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings 1078s /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. 1078s warnings.warn("The `u` attribute is superflous and will be removed " 1078s 1078s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] 1078s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm 1078s /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. 1078s warnings.warn("The `density` attribute was deprecated in " 1078s 1078s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata 1078s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. 1078s warnings.warn(msg, category=MissingDataWarning) 1078s 1078s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps 1078s self.timesteps.append(self._ts.time) 1078s 1078s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning 1078s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default 1078s warnings.warn("{} does not support time selection. Reverting to " 1078s 1078s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default 1078s warnings.warn("{} does not support data selection. Reverting to " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1078s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings 1078s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps 1078s return self.ts.dt 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1078s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps 1078s ts.data['time'] = step_num * ts.dt 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_ts_time[universe0] 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1078s self.close() 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close 1078s self._apply('close') 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply 1078s return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] 1078s ^^^^^^^^^^^^ 1078s AttributeError: 'ChainReader' object has no attribute 'readers' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing 1078s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain 1078s warnings.warn("Missing frame in continuous chain", UserWarning) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps 1078s time_frame_0 = ts.time - ts.frame*ts.dt # assumes ts.dt is constant 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps 1078s frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps 1078s step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps 1078s self._add_step_to_frame_data(ts.time) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps 1078s if not np.allclose(A.time, B.time): 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] 1078s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array 1078s /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 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1078s self.close() 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close 1078s self._file.close() 1078s ^^^^^^^^^^ 1078s AttributeError: 'DCDReader' object has no attribute '_file' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms 1078s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit 1078s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__ 1078s self.close() 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close 1078s self._file.close() 1078s ^^^^^^^^^^ 1078s AttributeError: 'DCDWriter' object has no attribute '_file' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings 1078s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings 1078s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1078s /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. 1078s warnings.warn(msg) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps 1078s return self.ts.time 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps 1078s assert_equal(reader.ts.dt, reader.dt) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps 1078s time_frame = time_frame_0 + frame_index*ts.dt 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps 1078s reader_p = pickle.loads(pickle.dumps(reader)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings 1078s /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 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] 1078s warnings.warn(wmsg) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1078s /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`. 1078s warnings.warn(wmsg) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. 1078s warnings.warn("Not all velocities were present. " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps 1078s reader_p = pickle.loads(pickle.dumps(reader)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader 1078s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps 1078s reader_p = pickle.loads(pickle.dumps(reader)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1078s self.close() 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close 1078s self._file.close() 1078s ^^^^^^^^^^ 1078s AttributeError: 'H5MDReader' object has no attribute '_file' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1078s for aux in self.aux_list: 1078s ^^^^^^^^^^^^^ 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1078s return self._auxs.keys() 1078s ^^^^^^^^^^ 1078s AttributeError: 'H5MDReader' object has no attribute '_auxs' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1078s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 1078s warnings.warn('Guessed all Masses to 1.0') 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit 1078s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1078s for aux in self.aux_list: 1078s ^^^^^^^^^^^^^ 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1078s return self._auxs.keys() 1078s ^^^^^^^^^^ 1078s AttributeError: 'DCDReader' object has no attribute '_auxs' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view 1078s /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 1078s warnings.warn("MemoryReader.timeseries inclusive `stop` " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader 1078s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps 1078s reader_p = pickle.loads(pickle.dumps(reader)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1078s /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 1078s warnings.warn(wmsg) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps 1078s ts.time) # in-place ! (hope this works...) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps 1078s time_list = [ts.time for ts in u.trajectory] 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps 1078s assert u.trajectory.ts.dt == pytest.approx(ref) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 1078s /tmp/autopkgtest.LPm1xd/build.vUr/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.) 1078s return self._test_write_trajectory(universe, outfile) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] 1078s /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. 1078s warnings.warn(wmsg) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1078s /tmp/autopkgtest.LPm1xd/build.vUr/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.) 1078s return self._test_write_trajectory(universe, outfile) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 1078s warnings.warn("Found missing chainIDs." 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom] 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond] 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom] 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree] 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond] 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom] 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps 1078s time = ts.time 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1078s self.close() 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close 1078s if self.trjfile is not None: 1078s ^^^^^^^^^^^^ 1078s AttributeError: 'NCDFWriter' object has no attribute 'trjfile' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' 1078s warnings.warn("Found no information for attr: '{}'" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' 1078s warnings.warn("Found chainIDs using unnaccepted character." 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' 1078s warnings.warn("Found chainIDs with invalid length." 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed 1078s warnings.warn("Serial numbers went over 100,000. " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed 1078s warnings.warn("Invalid atom serials were present, bonds will not" 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed 1078s warnings.warn("Invalid atom serials were present, " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment 1078s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1078s /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. 1078s warnings.warn(wmsg) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1078s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1078s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1078s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1078s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges 1078s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps 1078s assert_equal(ts.dt, 1.0) # default value 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps 1078s assert_equal(ts.time, 0.0) # default to 1.0 (dt) * 0 (frame) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps 1078s assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1078s for aux in self.aux_list: 1078s ^^^^^^^^^^^^^ 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1078s return self._auxs.keys() 1078s ^^^^^^^^^^ 1078s AttributeError: 'TNGReader' object has no attribute '_auxs' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms 1078s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe 1078s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe 1078s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1078s self.close() 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close 1078s if self.trjfile is None: 1078s ^^^^^^^^^^^^ 1078s AttributeError: 'TRJReader' object has no attribute 'trjfile' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps 1078s data['time'] = ts.time 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1078s /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 1078s warnings.warn("Timestep didn't have the following attributes: '{0}', " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1078s /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. 1078s warnings.warn("Timestep didn't have velocity information, " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1078s /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 1078s warnings.warn("Timestep didn't have dimensions information, " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1078s self.close() 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close 1078s if self.trzfile is None: 1078s ^^^^^^^^^^^^ 1078s AttributeError: 'TRZWriter' object has no attribute 'trzfile' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1078s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1078s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1078s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1078s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1078s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1078s /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. 1078s warnings.warn("Element information is missing, elements attribute " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1078s /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 1078s warnings.warn(wmsg, DeprecationWarning) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] 1078s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] 1078s /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' 1078s warnings.warn(wmsg) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD 1078s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps 1078s time = ts.time 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD 1078s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps 1078s time = ts.time 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1078s self.close() 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1078s self._xdr.close() 1078s ^^^^^^^^^ 1078s AttributeError: 'XTCWriter' object has no attribute '_xdr' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container 1078s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1078s 1078s Traceback (most recent call last): 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1078s self.close() 1078s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1078s self._xdr.close() 1078s ^^^^^^^^^ 1078s AttributeError: 'TRRWriter' object has no attribute '_xdr' 1078s 1078s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1078s /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. 1078s Consider setting 'refresh_offsets=True' when loading your Universe. 1078s warnings.warn(f"Reading offsets from {fname} failed, " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly 1078s /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. 1078s warnings.warn(f"Cannot write lock/offset file in same location as " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1078s /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. 1078s Consider setting 'refresh_offsets=True' when loading your Universe. 1078s warnings.warn(f"Reading offsets from {fname} failed, " 1078s 1078s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly 1078s /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. 1078s warnings.warn(f"Cannot write lock/offset file in same location as " 1078s 1078s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] 1078s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] 1078s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] 1078s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce 1078s return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1078s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1078s /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. 1078s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings 1078s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings 1078s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings 1078s /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. 1078s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1078s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1078s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide 1078s return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() 1078s 1078s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings 1078s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide 1078s _centers /= _weights.sum(axis=1)[:, None] 1078s 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1078s /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`. 1078s warnings.warn(msg, category=SelectionWarning) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1078s /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`. 1078s warnings.warn(msg, category=SelectionWarning) 1078s 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] 1078s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] 1078s /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`. 1078s warnings.warn(msg, category=SelectionWarning) 1078s 1078s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] 1078s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] 1078s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] 1078s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] 1078s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] 1078s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc 1078s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc 1078s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options 1078s /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 1078s warnings.warn("The 'pbc' kwarg has been deprecated and will be " 1078s 1078s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel 1078s /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`. 1078s warnings.warn(msg, category=SelectionWarning) 1078s 1078s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] 1078s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] 1078s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] 1078s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] 1078s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] 1078s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide 1078s x = np.dot(a, b) / (norm(a) * norm(b)) 1078s 1078s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt 1078s ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) 1078s 1078s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt 1078s box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - 1078s 1078s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide 1078s a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) 1078s 1078s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide 1078s b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) 1078s 1078s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide 1078s c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) 1078s 1078s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide 1078s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1078s 1078s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide 1078s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1078s 1078s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 1078s /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps 1078s cls(buf, protocol).dump(obj) 1078s 1078s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps 1078s ps = pickle.dumps(ref_reader) 1078s 1078s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] 1078s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd 1078s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd 1078s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset 1078s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific 1078s /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. 1078s warnings.warn('Cannot average position for non sequential' 1078s 1078s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name] 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname] 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type] 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid] 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' 1078s warnings.warn("PDB file is missing resid information. " 1078s 1078s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX 1078s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1078s 1078s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2] 1078s /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. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2] 1078s /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. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2] 1078s /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. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2] 1078s /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. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1078s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings 1078s /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. 1078s warnings.warn(msg) 1078s 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts 1078s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr] 1078s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file. 1078s warnings.warn('No coordinate reader found for {}. Skipping ' 1078s 1078s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses 1078s /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. 1078s warnings.warn(msg, category=SelectionWarning) 1078s 1078s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 1078s /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. 1078s warnings.warn( 1078s 1078s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps 1078s return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1078s 1078s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps 1078s pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1078s 1078s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps 1078s return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL) 1078s 1078s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps 1078s return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL) 1078s 1078s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps 1078s return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL) 1078s 1078s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps 1078s pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL) 1078s 1078s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag 1078s /tmp/autopkgtest.LPm1xd/build.vUr/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps 1078s pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL) 1078s 1078s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings 1078s /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream 1078s warnings.warn("Constructed NamedStream from a NamedStream", 1078s 1078s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] 1078s /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. 1078s warnings.warn(wmsg, DeprecationWarning) 1078s 1078s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1078s = 18631 passed, 594 skipped, 7 xfailed, 3 xpassed, 8130 warnings in 810.19s (0:13:30) = 1103s 1103s DueCredit Report: 1103s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] 1103s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] 1103s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] 1103s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] 1103s - HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] 1103s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] 1103s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] 1103s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] 1103s - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] 1103s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] 1103s - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] 1103s - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 2.7.0, 1.1) [15, 16] 1103s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] 1103s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] 1103s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] 1103s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] 1103s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] 1103s - Scientific tools library / numpy (v 1.26.4) [22] 1103s 1103s 2 packages cited 1103s 16 modules cited 1103s 0 functions cited 1103s 1103s References 1103s ---------- 1103s 1103s [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. 1103s [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. 1103s [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. 1103s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 1103s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 1103s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460. 1103s [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. 1103s [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. 1103s [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. 1103s [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). 1103s [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. 1103s [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. 1103s [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. 1103s [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. 1103s [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. 1103s [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. 1103s [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. 1103s [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. 1103s [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. 1103s [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. 1103s [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. 1103s [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. 1107s autopkgtest [16:31:12]: test test-mdanalysis: -----------------------] 1108s test-mdanalysis PASS 1108s autopkgtest [16:31:13]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 1108s autopkgtest [16:31:13]: @@@@@@@@@@@@@@@@@@@@ summary 1108s test-mdanalysis PASS 1128s nova [W] Skipping flock in bos03-arm64 1128s Creating nova instance adt-plucky-arm64-mdanalysis-20241114-161245-juju-7f2275-prod-proposed-migration-environment-20-c8ebdb72-92b8-4fac-b7b0-ea6f6798520a from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...