0s autopkgtest [13:34:59]: starting date and time: 2024-11-15 13:34:59+0000 0s autopkgtest [13:34:59]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [13:34:59]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5h1yupo3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:matplotlib --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=matplotlib/3.8.3-3ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu4-ram8-disk100 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-26.secgroup --name adt-plucky-amd64-mdanalysis-20241115-133459-juju-7f2275-prod-proposed-migration-environment-2-d6781674-b0c6-479e-832f-9194f03bc983 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 48s autopkgtest [13:35:47]: testbed dpkg architecture: amd64 48s autopkgtest [13:35:47]: testbed apt version: 2.9.8 48s autopkgtest [13:35:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 49s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 49s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.2 kB] 49s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1062 kB] 49s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 49s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 49s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [174 kB] 49s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [108 kB] 49s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 49s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [300 kB] 49s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [840 kB] 49s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B] 49s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B] 50s Fetched 2718 kB in 1s (3094 kB/s) 50s Reading package lists... 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 52s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 53s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 53s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 54s Reading package lists... 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 55s Calculating upgrade... 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s autopkgtest [13:35:57]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 58s autopkgtest [13:35:57]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 62s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B] 62s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB] 62s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB] 62s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC 62s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 62s gpgv: issuer "dparsons@debian.org" 62s gpgv: Can't check signature: No public key 62s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found 63s autopkgtest [13:36:02]: testing package mdanalysis version 2.7.0-5 64s autopkgtest [13:36:03]: build not needed 68s autopkgtest [13:36:07]: test test-mdanalysis: preparing testbed 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Starting pkgProblemResolver with broken count: 0 69s Starting 2 pkgProblemResolver with broken count: 0 69s Done 70s The following additional packages will be installed: 70s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 70s cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cython3 debhelper debugedit 70s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 70s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 70s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 70s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 70s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian libaec0 70s libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdebhelper-perl 70s libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 70s libfontenc1 libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 70s libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libimagequant0 libisl23 70s libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 70s libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 70s liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libnetcdf19t64 70s libopenjp2-7 libpixman-1-0 libpython3-all-dev libpython3-dev 70s libpython3.12-dev libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 70s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 70s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 70s libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 70s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 70s python3-alabaster python3-all python3-all-dev python3-appdirs 70s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 70s python3-citeproc python3-contourpy python3-cycler python3-dateutil 70s python3-decorator python3-defusedxml python3-dev python3-docutils 70s python3-duecredit python3-fasteners python3-fonttools python3-freetype 70s python3-fs python3-griddataformats python3-gsd python3-h5py 70s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 70s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 70s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 70s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 70s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 70s python3-netcdf4 python3-networkx python3-numpy python3-packaging 70s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 70s python3-pluggy python3-pybtex python3-pybtex-docutils 70s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 70s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 70s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 70s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 70s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 70s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 70s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 70s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 70s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 70s zlib1g-dev 70s Suggested packages: 70s autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales 70s cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf 70s fonts-texgyre g++-multilib g++-14-multilib gcc-14-doc gcc-multilib 70s manpages-dev flex bison gdb gcc-doc gcc-14-multilib gdb-x86-64-linux-gnu 70s gettext-doc libasprintf-dev libgettextpo-dev libjs-jquery-ui-docs 70s fonts-mathjax-extras fonts-stix libjs-mathjax-doc liblcms2-utils 70s libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler 70s gcj-jdk m4-doc libmail-box-perl bwa clustalo clustalw dialign dssp emboss 70s fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb 70s python3-rdflib python3-psycopg2 raxml samtools t-coffee wise python3-pip 70s python3-venv python-build-doc python-cycler-doc docutils-doc 70s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 70s texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc 70s python-hypothesis-doc python-installer-doc python-joblib-doc 70s python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 70s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 70s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 70s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 70s texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal 70s python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc 70s python3-statsmodels python-pil-doc python-pybtex-doc 70s python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools 70s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 70s python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm 70s fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre 70s texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic 70s python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg 70s python3.13-tk sgml-base-doc 70s Recommended packages: 70s libarchive-cpio-perl javascript-common libjson-xs-perl libltdl-dev 70s libmail-sendmail-perl python-biopython-doc ncbi-blast+ libpaper-utils 70s python3-click python3-simplejson python3-psutil python3-bs4 70s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 70s python3-odf python3-openpyxl python3-tables python3-numba python3-olefile 70s fonts-dejavu-extra isympy-common 70s The following NEW packages will be installed: 70s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 70s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 70s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 70s docutils-common dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono 70s fonts-font-awesome fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ 70s g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 70s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian libaec0 70s libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdebhelper-perl 70s libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 70s libfontenc1 libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 70s libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libimagequant0 libisl23 70s libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 70s libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 70s liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libnetcdf19t64 70s libopenjp2-7 libpixman-1-0 libpython3-all-dev libpython3-dev 70s libpython3.12-dev libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 70s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 70s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 70s libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 70s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 70s python3-alabaster python3-all python3-all-dev python3-appdirs 70s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 70s python3-citeproc python3-contourpy python3-cycler python3-dateutil 70s python3-decorator python3-defusedxml python3-dev python3-docutils 70s python3-duecredit python3-fasteners python3-fonttools python3-freetype 70s python3-fs python3-griddataformats python3-gsd python3-h5py 70s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 70s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 70s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 70s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 70s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 70s python3-netcdf4 python3-networkx python3-numpy python3-packaging 70s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 70s python3-pluggy python3-pybtex python3-pybtex-docutils 70s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 70s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 70s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 70s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 70s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 70s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 70s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 70s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 70s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 70s zlib1g-dev 70s 0 upgraded, 203 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 209 MB/209 MB of archives. 70s After this operation, 881 MB of additional disk space will be used. 70s Get:1 /tmp/autopkgtest.iPlIju/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [1012 B] 70s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 70s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 70s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 70s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 70s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 70s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 70s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 70s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 70s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 70s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 71s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 71s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 71s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 71s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 71s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 71s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 71s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 71s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 71s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 71s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 71s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 71s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 71s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 71s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 71s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 71s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 71s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 71s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 71s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 71s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 71s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 71s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 71s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 71s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 71s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 71s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 71s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 72s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 72s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 72s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 72s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 72s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 72s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 72s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 73s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 73s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 73s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 73s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 73s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 73s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-1ubuntu2 [3368 kB] 73s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 73s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 73s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 73s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 73s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 73s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 73s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 73s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 73s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 73s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 73s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 73s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 73s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB] 73s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 73s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 73s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 73s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 73s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 73s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 73s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 73s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 73s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 73s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 73s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 73s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 73s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB] 73s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 74s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 74s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 74s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 74s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 74s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 74s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 74s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 74s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 74s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 74s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 74s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 74s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 74s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 74s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 74s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 74s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 74s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 74s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 74s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf19t64 amd64 1:4.9.2-6ubuntu1 [472 kB] 74s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 74s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.7-3 [5699 kB] 74s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.12.6-0ubuntu1 [10.2 kB] 74s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-all-dev amd64 3.12.6-0ubuntu1 [916 B] 74s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 74s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 74s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 74s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 74s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 75s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 75s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 75s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 75s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 75s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 75s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 75s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] 75s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wheel all 0.44.0-1 [54.2 kB] 75s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-build all 1.2.2-1 [31.0 kB] 75s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 75s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-pyproject all 6.20241024 [1728 B] 75s Get:118 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 75s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 75s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-mdanalysis-doc all 2.7.0-5 [2323 kB] 75s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 75s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] 75s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.12.6-0ubuntu1 [26.7 kB] 75s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all-dev amd64 3.12.6-0ubuntu1 [908 B] 75s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 75s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 75s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 75s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.6-1ubuntu1 [9806 B] 75s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 75s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 75s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 75s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 75s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 75s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 75s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 75s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 75s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 75s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 76s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cftime amd64 1.6.4-1 [214 kB] 76s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 76s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-citeproc all 0.6.0-3 [98.4 kB] 76s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 76s Get:143 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 76s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 76s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 76s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 76s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-defusedxml all 0.7.1-2 [42.0 kB] 76s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-roman all 4.2-1 [10.0 kB] 76s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 76s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-looseversion all 1.3.0-3 [8354 B] 76s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-duecredit all 0.10.2-2 [66.0 kB] 76s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-monotonic all 1.6-2 [5732 B] 76s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-fasteners all 0.18-2 [12.5 kB] 76s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 76s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 76s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 76s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 76s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 76s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 76s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 76s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB] 76s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 77s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 77s Get:164 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 77s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mrcfile all 1.5.3-3 [114 kB] 77s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-griddataformats all 1.0.2-2 [2107 kB] 77s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-gsd amd64 3.3.0-1 [203 kB] 77s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB] 77s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 77s Get:170 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 77s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hypothesis all 6.116.0-1 [326 kB] 77s Get:172 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-imagesize all 1.4.1-1 [6844 B] 77s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 77s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 77s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 77s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-latexcodec all 3.0.0-1 [16.6 kB] 77s Get:177 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu1 [4691 kB] 77s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 77s Get:179 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-msgpack amd64 1.0.3-3build2 [80.1 kB] 77s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mmtf all 1.1.3-1 [16.2 kB] 77s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 77s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.0-1 [91.6 kB] 77s Get:183 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mdanalysis amd64 2.7.0-5 [1992 kB] 77s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-common all 7.4.7-4 [775 kB] 77s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 77s Get:186 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 77s Get:187 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sphinx all 7.4.7-4 [593 kB] 77s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 77s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 77s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-msmb-theme all 1.2.0-4 [35.4 kB] 77s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-netcdf4 amd64 1.7.2-1 [645 kB] 77s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 78s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 78s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 78s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 78s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pybtex all 0.24.0-4 [70.0 kB] 78s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pybtex-docutils all 1.0.2-1 [7176 B] 78s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 78s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-seaborn all 0.13.2-4 [225 kB] 78s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB] 78s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 78s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinx-sitemap all 2.6.0-1 [6674 B] 78s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 79s Fetched 209 MB in 9s (24.5 MB/s) 79s Selecting previously unselected package fonts-lato. 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 ... 75576 files and directories currently installed.) 79s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 79s Unpacking fonts-lato (2.015-1) ... 79s Selecting previously unselected package sgml-base. 79s Preparing to unpack .../001-sgml-base_1.31_all.deb ... 79s Unpacking sgml-base (1.31) ... 79s Selecting previously unselected package m4. 79s Preparing to unpack .../002-m4_1.4.19-4build1_amd64.deb ... 79s Unpacking m4 (1.4.19-4build1) ... 79s Selecting previously unselected package autoconf. 79s Preparing to unpack .../003-autoconf_2.72-3_all.deb ... 79s Unpacking autoconf (2.72-3) ... 79s Selecting previously unselected package autotools-dev. 79s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ... 79s Unpacking autotools-dev (20220109.1) ... 79s Selecting previously unselected package automake. 79s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 79s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 79s Selecting previously unselected package autopoint. 79s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ... 79s Unpacking autopoint (0.22.5-2) ... 79s Selecting previously unselected package libtcl8.6:amd64. 79s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 79s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 79s Selecting previously unselected package fonts-dejavu-mono. 79s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8_all.deb ... 79s Unpacking fonts-dejavu-mono (2.37-8) ... 79s Selecting previously unselected package fonts-dejavu-core. 79s Preparing to unpack .../009-fonts-dejavu-core_2.37-8_all.deb ... 79s Unpacking fonts-dejavu-core (2.37-8) ... 79s Selecting previously unselected package libfontenc1:amd64. 79s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 79s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 79s Selecting previously unselected package x11-common. 79s Preparing to unpack .../011-x11-common_1%3a7.7+23ubuntu3_all.deb ... 79s Unpacking x11-common (1:7.7+23ubuntu3) ... 79s Selecting previously unselected package xfonts-encodings. 79s Preparing to unpack .../012-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 79s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 79s Selecting previously unselected package xfonts-utils. 79s Preparing to unpack .../013-xfonts-utils_1%3a7.7+7_amd64.deb ... 79s Unpacking xfonts-utils (1:7.7+7) ... 79s Selecting previously unselected package fonts-urw-base35. 79s Preparing 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unselected package liblapack3:amd64. 83s Preparing to unpack .../090-liblapack3_3.12.0-3build2_amd64.deb ... 83s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 83s Selecting previously unselected package liblbfgsb0:amd64. 83s Preparing to unpack .../091-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 83s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 83s Selecting previously unselected package liblcms2-2:amd64. 83s Preparing to unpack .../092-liblcms2-2_2.16-2_amd64.deb ... 83s Unpacking liblcms2-2:amd64 (2.16-2) ... 83s Selecting previously unselected package liblerc4:amd64. 83s Preparing to unpack .../093-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 83s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 83s Selecting previously unselected package liblzf1:amd64. 83s Preparing to unpack .../094-liblzf1_3.6-4_amd64.deb ... 83s Unpacking liblzf1:amd64 (3.6-4) ... 83s Selecting previously unselected package libnetcdf19t64:amd64. 83s Preparing to unpack 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... 84s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 84s Selecting previously unselected package libwebpdemux2:amd64. 84s Preparing to unpack .../106-libwebpdemux2_1.4.0-0.1_amd64.deb ... 84s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 84s Selecting previously unselected package libwebpmux3:amd64. 84s Preparing to unpack .../107-libwebpmux3_1.4.0-0.1_amd64.deb ... 84s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 84s Selecting previously unselected package libxslt1.1:amd64. 84s Preparing to unpack .../108-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 84s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 84s Selecting previously unselected package python3-packaging. 84s Preparing to unpack .../109-python3-packaging_24.1-1_all.deb ... 84s Unpacking python3-packaging (24.1-1) ... 84s Selecting previously unselected package python3-pyproject-hooks. 84s Preparing to unpack .../110-python3-pyproject-hooks_1.2.0-1_all.deb ... 84s Unpacking python3-pyproject-hooks (1.2.0-1) ... 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python3-pil.imagetk:amd64. 85s Preparing to unpack .../127-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 85s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 85s Selecting previously unselected package libopenjp2-7:amd64. 85s Preparing to unpack .../128-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 85s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 85s Selecting previously unselected package python3-pil:amd64. 85s Preparing to unpack .../129-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 85s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 85s Selecting previously unselected package python3-cairo. 85s Preparing to unpack .../130-python3-cairo_1.26.1-2_amd64.deb ... 85s Unpacking python3-cairo (1.26.1-2) ... 85s Selecting previously unselected package python3-freetype. 85s Preparing to unpack .../131-python3-freetype_2.5.1-1_all.deb ... 85s Unpacking python3-freetype (2.5.1-1) ... 85s Selecting previously unselected package python3-rlpycairo. 85s Preparing to unpack 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unselected package python3-lxml:amd64. 86s Preparing to unpack .../138-python3-lxml_5.3.0-1_amd64.deb ... 86s Unpacking python3-lxml:amd64 (5.3.0-1) ... 86s Selecting previously unselected package python3-citeproc. 86s Preparing to unpack .../139-python3-citeproc_0.6.0-3_all.deb ... 86s Unpacking python3-citeproc (0.6.0-3) ... 86s Selecting previously unselected package python3-contourpy. 86s Preparing to unpack .../140-python3-contourpy_1.3.0-2_amd64.deb ... 86s Unpacking python3-contourpy (1.3.0-2) ... 86s Selecting previously unselected package python3-cycler. 86s Preparing to unpack .../141-python3-cycler_0.12.1-1_all.deb ... 86s Unpacking python3-cycler (0.12.1-1) ... 86s Selecting previously unselected package python3-six. 86s Preparing to unpack .../142-python3-six_1.16.0-7_all.deb ... 86s Unpacking python3-six (1.16.0-7) ... 86s Selecting previously unselected package python3-dateutil. 86s Preparing to unpack .../143-python3-dateutil_2.9.0-2_all.deb ... 86s Unpacking python3-dateutil (2.9.0-2) ... 86s Selecting previously unselected package python3-decorator. 86s Preparing to unpack .../144-python3-decorator_5.1.1-5_all.deb ... 86s Unpacking python3-decorator (5.1.1-5) ... 86s Selecting previously unselected package python3-defusedxml. 86s Preparing to unpack .../145-python3-defusedxml_0.7.1-2_all.deb ... 86s Unpacking python3-defusedxml (0.7.1-2) ... 86s Selecting previously unselected package python3-roman. 86s Preparing to unpack .../146-python3-roman_4.2-1_all.deb ... 86s Unpacking python3-roman (4.2-1) ... 86s Selecting previously unselected package python3-docutils. 86s Preparing to unpack .../147-python3-docutils_0.21.2+dfsg-2_all.deb ... 86s Unpacking python3-docutils (0.21.2+dfsg-2) ... 86s Selecting previously unselected package python3-looseversion. 86s Preparing to unpack .../148-python3-looseversion_1.3.0-3_all.deb ... 86s Unpacking python3-looseversion (1.3.0-3) ... 86s Selecting previously unselected package python3-duecredit. 86s 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previously unselected package python3-h5py-serial. 87s Preparing to unpack .../166-python3-h5py-serial_3.11.0-5ubuntu1_amd64.deb ... 87s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 87s Selecting previously unselected package python3-h5py. 87s Preparing to unpack .../167-python3-h5py_3.11.0-5ubuntu1_all.deb ... 87s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 87s Selecting previously unselected package python3-sortedcontainers. 87s Preparing to unpack .../168-python3-sortedcontainers_2.4.0-2_all.deb ... 87s Unpacking python3-sortedcontainers (2.4.0-2) ... 87s Selecting previously unselected package python3-hypothesis. 87s Preparing to unpack .../169-python3-hypothesis_6.116.0-1_all.deb ... 87s Unpacking python3-hypothesis (6.116.0-1) ... 87s Selecting previously unselected package python3-imagesize. 87s Preparing to unpack .../170-python3-imagesize_1.4.1-1_all.deb ... 87s Unpacking python3-imagesize (1.4.1-1) ... 87s Selecting previously unselected package python3-iniconfig. 87s 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[100%] 651s 651s =============================== warnings summary =============================== 651s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39 651s /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. 651s 651s Due to the on going maintenance burden of keeping command line application 651s wrappers up to date, we have decided to deprecate and eventually remove these 651s modules. 651s 651s We instead now recommend building your command line and invoking it directly 651s with the subprocess module. 651s warnings.warn( 651s 651s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings 651s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings 651s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings 651s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings 651s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings 651s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings 651s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings 651s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings 651s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings 651s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings 651s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings 651s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings 651s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings 651s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings 651s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings 651s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 651s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings 651s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings 651s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings 651s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings 651s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings 651s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings 651s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings 651s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings 651s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings 651s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings 651s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings 651s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings 651s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings 651s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 651s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings 651s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 651s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings 651s /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. 651s warnings.warn("DCDReader currently makes independent timesteps" 651s 651s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 651s /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. 651s warnings.warn(wmsg, category=DeprecationWarning) 651s 651s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings 651s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings 651s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written 651s warnings.warn(wmsg) 651s 651s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings 651s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings 651s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings 651s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings 651s /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 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings 651s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 651s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings 651s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning 651s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 651s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'ho', 'h1', 'hc', 'c3', 'oh'}. These have been given an empty element record. 651s warnings.warn("Unknown elements found for some " 651s 651s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 651s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning 651s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings 651s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings 651s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 651s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings 651s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings 651s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps 651s self.times[i] = ts.time 651s 651s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings 651s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning 651s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings 651s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 651s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings 651s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings 651s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings 651s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded 651s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps 651s results.append((ts.time, x.sum() / mask.sum())) 651s 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue 651s /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. 651s warnings.warn(msg) 651s 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 651s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding 651s /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 651s warnings.warn(msg) 651s 651s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 651s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 651s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings 651s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 651s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 651s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings 651s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning 651s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings 651s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings 651s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings 651s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 651s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings 651s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings 651s /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. 651s warnings.warn("Element information is missing, elements attribute " 651s 651s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran 651s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame 651s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections 651s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning 651s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues 651s warnings.warn("Cannot determine phi and psi angles for the first " 651s 651s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin 651s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr 651s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame 651s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot 651s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning 651s /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. 651s warnings.warn(f"All residues selected with '{select_remove}' " 651s 651s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings 651s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings 651s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=6481) is multi-threaded, use of fork() may lead to deadlocks in the child. 651s self.pid = os.fork() 651s 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes 651s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide 651s cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms 651s 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide 651s local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) 651s 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 651s /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice 651s ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, 651s 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 651s /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide 651s ret = um.true_divide( 651s 651s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 651s /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide 651s ret = ret.dtype.type(ret / rcount) 651s 651s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 651s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning 651s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning 651s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 651s /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. 651s warnings.warn("1 A^3 CRYST1 record," 651s 651s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. 651s warnings.warn("Unit cell dimensions not found. " 651s 651s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings 651s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings 651s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings 651s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 651s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings 651s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 651s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning 651s /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 651s warnings.warn(wmsg, DeprecationWarning) 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 651s warnings.warn("Desired number of sample points too high, using {0}" 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbond = HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbond = HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbond = HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbond = HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbond = HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbond = HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbond = HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbond = HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s HBAC( 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 651s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 651s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbond = HBAC(u, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! 651s `find_hydrogen_donors` will be removed in release 3.0.0. 651s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s D = hbonds.find_hydrogen_donors(H) 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! 651s `find_hydrogen_donors` will be removed in release 3.0.0. 651s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 651s hbonds.find_hydrogen_donors(u.atoms) 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 651s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 651s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. 651s return _methods._mean(a, axis=axis, dtype=dtype, 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 651s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 651s /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide 651s ret = ret.dtype.type(ret / rcount) 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 651s /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. 651s warnings.warn(msg.format(sel)) 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 651s /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. 651s warnings.warn(msg.format(sel)) 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 651s /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. 651s warnings.warn(msg.format(sel)) 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 651s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. 651s warnings.warn("Empty string to select atoms, empty group returned.", 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 651s /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, . 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 651s /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, . 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 651s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 651s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 651s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 651s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 651s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 651s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple 651s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content 651s /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. 651s warnings.warn(wmsg) 651s 651s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning 651s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning 651s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 651s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 651s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 651s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 651s /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.) 651s phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi 651s 651s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j 651s /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 651s warnings.warn("Column index entered (j = {:d} is smaller than row " 651s 651s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps 651s dt=self.trajectory.ts.dt * step, 651s 651s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] 651s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] 651s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] 651s /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 651s warnings.warn(wmsg, DeprecationWarning) 651s 651s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 651s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings 651s /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. 651s warnings.warn("The `u` attribute is superflous and will be removed " 651s 651s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] 651s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm 651s /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. 651s warnings.warn("The `density` attribute was deprecated in " 651s 651s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata 651s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. 651s warnings.warn(msg, category=MissingDataWarning) 651s 651s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps 651s self.timesteps.append(self._ts.time) 651s 651s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning 651s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default 651s warnings.warn("{} does not support time selection. Reverting to " 651s 651s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default 651s warnings.warn("{} does not support data selection. Reverting to " 651s 651s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings 651s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings 651s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 651s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings 651s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps 651s return self.ts.dt 651s 651s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings 651s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 651s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps 651s ts.data['time'] = step_num * ts.dt 651s 651s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats 651s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_unsupported_filetypes 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 651s self.close() 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close 651s self._apply('close') 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply 651s return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] 651s ^^^^^^^^^^^^ 651s AttributeError: 'ChainReader' object has no attribute 'readers' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing 651s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain 651s warnings.warn("Missing frame in continuous chain", UserWarning) 651s 651s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps 651s time_frame_0 = ts.time - ts.frame*ts.dt # assumes ts.dt is constant 651s 651s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps 651s frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps 651s step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps 651s self._add_step_to_frame_data(ts.time) 651s 651s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings 651s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 651s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps 651s if not np.allclose(A.time, B.time): 651s 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] 651s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array 651s /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 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 651s self.close() 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close 651s self._file.close() 651s ^^^^^^^^^^ 651s AttributeError: 'DCDReader' object has no attribute '_file' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms 651s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit 651s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__ 651s self.close() 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close 651s self._file.close() 651s ^^^^^^^^^^ 651s AttributeError: 'DCDWriter' object has no attribute '_file' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings 651s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings 651s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 651s /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. 651s warnings.warn(msg) 651s 651s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps 651s return self.ts.time 651s 651s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps 651s assert_equal(reader.ts.dt, reader.dt) 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps 651s time_frame = time_frame_0 + frame_index*ts.dt 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps 651s reader_p = pickle.loads(pickle.dumps(reader)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings 651s /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 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] 651s warnings.warn(wmsg) 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 651s /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`. 651s warnings.warn(wmsg) 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. 651s warnings.warn("Not all velocities were present. " 651s 651s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps 651s reader_p = pickle.loads(pickle.dumps(reader)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader 651s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps 651s reader_p = pickle.loads(pickle.dumps(reader)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 651s self.close() 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close 651s self._file.close() 651s ^^^^^^^^^^ 651s AttributeError: 'H5MDReader' object has no attribute '_file' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 651s for aux in self.aux_list: 651s ^^^^^^^^^^^^^ 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 651s return self._auxs.keys() 651s ^^^^^^^^^^ 651s AttributeError: 'H5MDReader' object has no attribute '_auxs' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings 651s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 651s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 651s warnings.warn('Guessed all Masses to 1.0') 651s 651s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit 651s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 651s for aux in self.aux_list: 651s ^^^^^^^^^^^^^ 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 651s return self._auxs.keys() 651s ^^^^^^^^^^ 651s AttributeError: 'DCDReader' object has no attribute '_auxs' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view 651s /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 651s warnings.warn("MemoryReader.timeseries inclusive `stop` " 651s 651s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader 651s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps 651s reader_p = pickle.loads(pickle.dumps(reader)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 651s /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 651s warnings.warn(wmsg) 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps 651s ts.time) # in-place ! (hope this works...) 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps 651s time_list = [ts.time for ts in u.trajectory] 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps 651s assert u.trajectory.ts.dt == pytest.approx(ref) 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 651s /tmp/autopkgtest.iPlIju/build.D5q/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.) 651s return self._test_write_trajectory(universe, outfile) 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] 651s /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. 651s warnings.warn(wmsg) 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 651s /tmp/autopkgtest.iPlIju/build.D5q/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.) 651s return self._test_write_trajectory(universe, outfile) 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings 651s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 651s warnings.warn("Found missing chainIDs." 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom] 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond] 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom] 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree] 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond] 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom] 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps 651s time = ts.time 651s 651s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 651s self.close() 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close 651s if self.trjfile is not None: 651s ^^^^^^^^^^^^ 651s AttributeError: 'NCDFWriter' object has no attribute 'trjfile' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 651s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 651s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 651s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' 651s warnings.warn("Found no information for attr: '{}'" 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' 651s warnings.warn("Found chainIDs using unnaccepted character." 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' 651s warnings.warn("Found chainIDs with invalid length." 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed 651s warnings.warn("Serial numbers went over 100,000. " 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed 651s warnings.warn("Invalid atom serials were present, bonds will not" 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed 651s warnings.warn("Invalid atom serials were present, " 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment 651s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 651s /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. 651s warnings.warn(wmsg) 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 651s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 651s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 651s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 651s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges 651s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps 651s assert_equal(ts.dt, 1.0) # default value 651s 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps 651s assert_equal(ts.time, 0.0) # default to 1.0 (dt) * 0 (frame) 651s 651s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps 651s assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt) 651s 651s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 651s for aux in self.aux_list: 651s ^^^^^^^^^^^^^ 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 651s return self._auxs.keys() 651s ^^^^^^^^^^ 651s AttributeError: 'TNGReader' object has no attribute '_auxs' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms 651s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe 651s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe 651s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 651s self.close() 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close 651s if self.trjfile is None: 651s ^^^^^^^^^^^^ 651s AttributeError: 'TRJReader' object has no attribute 'trjfile' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps 651s data['time'] = ts.time 651s 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 651s /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 651s warnings.warn("Timestep didn't have the following attributes: '{0}', " 651s 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 651s /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. 651s warnings.warn("Timestep didn't have velocity information, " 651s 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 651s /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 651s warnings.warn("Timestep didn't have dimensions information, " 651s 651s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 651s self.close() 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close 651s if self.trzfile is None: 651s ^^^^^^^^^^^^ 651s AttributeError: 'TRZWriter' object has no attribute 'trzfile' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 651s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 651s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 651s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 651s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 651s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 651s /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. 651s warnings.warn("Element information is missing, elements attribute " 651s 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 651s /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 651s warnings.warn(wmsg, DeprecationWarning) 651s 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] 651s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] 651s /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' 651s warnings.warn(wmsg) 651s 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD 651s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps 651s time = ts.time 651s 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD 651s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps 651s time = ts.time 651s 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 651s self.close() 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 651s self._xdr.close() 651s ^^^^^^^^^ 651s AttributeError: 'XTCWriter' object has no attribute '_xdr' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container 651s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 651s 651s Traceback (most recent call last): 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 651s self.close() 651s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 651s self._xdr.close() 651s ^^^^^^^^^ 651s AttributeError: 'TRRWriter' object has no attribute '_xdr' 651s 651s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 651s 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 651s /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. 651s Consider setting 'refresh_offsets=True' when loading your Universe. 651s warnings.warn(f"Reading offsets from {fname} failed, " 651s 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly 651s /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. 651s warnings.warn(f"Cannot write lock/offset file in same location as " 651s 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 651s /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. 651s Consider setting 'refresh_offsets=True' when loading your Universe. 651s warnings.warn(f"Reading offsets from {fname} failed, " 651s 651s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly 651s /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. 651s warnings.warn(f"Cannot write lock/offset file in same location as " 651s 651s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] 651s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] 651s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] 651s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce 651s return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 651s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 651s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 651s /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. 651s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings 651s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings 651s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings 651s /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. 651s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 651s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 651s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 651s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide 651s return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() 651s 651s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings 651s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide 651s _centers /= _weights.sum(axis=1)[:, None] 651s 651s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 651s /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`. 651s warnings.warn(msg, category=SelectionWarning) 651s 651s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 651s /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`. 651s warnings.warn(msg, category=SelectionWarning) 651s 651s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] 651s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] 651s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] 651s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] 651s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] 651s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] 651s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] 651s /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`. 651s warnings.warn(msg, category=SelectionWarning) 651s 651s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] 651s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] 651s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] 651s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] 651s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] 651s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc 651s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc 651s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options 651s /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 651s warnings.warn("The 'pbc' kwarg has been deprecated and will be " 651s 651s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel 651s /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`. 651s warnings.warn(msg, category=SelectionWarning) 651s 651s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] 651s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] 651s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] 651s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] 651s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] 651s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide 651s x = np.dot(a, b) / (norm(a) * norm(b)) 651s 651s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt 651s ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) 651s 651s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt 651s box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - 651s 651s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide 651s a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) 651s 651s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide 651s b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) 651s 651s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide 651s c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) 651s 651s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide 651s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 651s 651s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide 651s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 651s 651s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 651s /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps 651s cls(buf, protocol).dump(obj) 651s 651s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps 651s ps = pickle.dumps(ref_reader) 651s 651s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] 651s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd 651s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd 651s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset 651s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific 651s /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. 651s warnings.warn('Cannot average position for non sequential' 651s 651s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name] 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname] 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type] 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid] 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' 651s warnings.warn("PDB file is missing resid information. " 651s 651s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX 651s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 651s 651s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2] 651s /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. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2] 651s /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. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2] 651s /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. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2] 651s /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. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 651s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings 651s /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. 651s warnings.warn(msg) 651s 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts 651s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr] 651s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file. 651s warnings.warn('No coordinate reader found for {}. Skipping ' 651s 651s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses 651s /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. 651s warnings.warn(msg, category=SelectionWarning) 651s 651s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 651s /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. 651s warnings.warn( 651s 651s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps 651s return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 651s 651s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps 651s pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 651s 651s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps 651s return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL) 651s 651s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps 651s return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL) 651s 651s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps 651s return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL) 651s 651s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps 651s pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL) 651s 651s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag 651s /tmp/autopkgtest.iPlIju/build.D5q/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps 651s pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL) 651s 651s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings 651s /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream 651s warnings.warn("Constructed NamedStream from a NamedStream", 651s 651s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] 651s /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. 651s warnings.warn(wmsg, DeprecationWarning) 651s 651s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 651s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8130 warnings in 501.93s (0:08:21) = 672s 672s DueCredit Report: 672s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] 672s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] 672s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] 672s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] 672s - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] 672s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] 672s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] 672s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] 672s - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] 672s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] 672s - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] 672s - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 1.1, 2.7.0) [15, 16] 672s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] 672s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] 672s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] 672s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] 672s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] 672s - Scientific tools library / numpy (v 1.26.4) [22] 672s 672s 2 packages cited 672s 16 modules cited 672s 0 functions cited 672s 672s References 672s ---------- 672s 672s [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. 672s [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. 672s [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. 672s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 672s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 672s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460. 672s [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. 672s [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. 672s [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. 672s [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). 672s [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. 672s [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. 672s [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. 672s [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. 672s [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. 672s [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. 672s [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. 672s [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. 672s [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. 672s [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. 672s [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. 672s [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. 675s autopkgtest [13:46:14]: test test-mdanalysis: -----------------------] 676s autopkgtest [13:46:15]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 676s test-mdanalysis PASS 676s autopkgtest [13:46:15]: @@@@@@@@@@@@@@@@@@@@ summary 676s test-mdanalysis PASS 688s virt: nova [W] Skipping flock for amd64 688s virt: Creating nova instance adt-plucky-amd64-mdanalysis-20241115-133459-juju-7f2275-prod-proposed-migration-environment-2-d6781674-b0c6-479e-832f-9194f03bc983 from image adt/ubuntu-plucky-amd64-server-20241115.img (UUID 9bb4dd9c-454f-45da-a125-77b9d27ed145)...