0s autopkgtest [01:50:16]: starting date and time: 2024-11-15 01:50:16+0000 0s autopkgtest [01:50:16]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [01:50:16]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8l0qvey8/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 autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-8.secgroup --name adt-plucky-arm64-mdanalysis-20241115-015016-juju-7f2275-prod-proposed-migration-environment-15-744ef305-222e-4984-b9d7-c09e7f70786a --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 74s autopkgtest [01:51:30]: testbed dpkg architecture: arm64 74s autopkgtest [01:51:30]: testbed apt version: 2.9.8 74s autopkgtest [01:51:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 75s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 75s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1030 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [102 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 76s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 76s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [139 kB] 76s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 76s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [770 kB] 76s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6116 B] 76s Fetched 2193 kB in 1s (2446 kB/s) 76s Reading package lists... 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Calculating upgrade... 83s The following packages will be upgraded: 83s firmware-sof-signed libcap-ng0 lxd-installer man-db pastebinit 83s python3-systemd xfsprogs 83s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 9405 kB of archives. 83s After this operation, 548 kB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 410s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libcap-ng0 arm64 0.8.5-3build1 [15.0 kB] 410s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 man-db arm64 2.13.0-1 [1320 kB] 471s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 lxd-installer all 9 [5084 B] 471s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 471s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 471s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 xfsprogs arm64 6.8.0-2.2ubuntu2 [919 kB] 474s Preconfiguring packages ... 474s Fetched 9405 kB in 6min 30s (24.1 kB/s) 474s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79925 files and directories currently installed.) 474s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 474s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 474s Preparing to unpack .../libcap-ng0_0.8.5-3build1_arm64.deb ... 474s Unpacking libcap-ng0:arm64 (0.8.5-3build1) over (0.8.5-1) ... 474s Setting up libcap-ng0:arm64 (0.8.5-3build1) ... 474s (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 ... 79951 files and directories currently installed.) 474s Preparing to unpack .../man-db_2.13.0-1_arm64.deb ... 474s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 475s Preparing to unpack .../lxd-installer_9_all.deb ... 475s Unpacking lxd-installer (9) over (8) ... 475s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 475s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 475s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 475s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 475s Preparing to unpack .../xfsprogs_6.8.0-2.2ubuntu2_arm64.deb ... 475s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 475s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 475s Setting up pastebinit (1.7.1-1) ... 475s Setting up man-db (2.13.0-1) ... 475s Updating database of manual pages ... 477s man-db.service is a disabled or a static unit not running, not starting it. 477s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 477s update-initramfs: deferring update (trigger activated) 478s Setting up lxd-installer (9) ... 478s Setting up python3-systemd (235-1build5) ... 479s Processing triggers for libc-bin (2.40-1ubuntu3) ... 479s Processing triggers for initramfs-tools (0.142ubuntu34) ... 479s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 479s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 498s System running in EFI mode, skipping. 498s Reading package lists... 499s Building dependency tree... 499s Reading state information... 499s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 500s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 503s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [213 kB] 509s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 509s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 509s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1030 kB] 552s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 555s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [164 kB] 563s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [773 kB] 593s Get:9 http://ftpmaster.internal/ubuntu plucky/main Sources [1379 kB] 664s Get:10 http://ftpmaster.internal/ubuntu plucky/universe Sources [20.7 MB] 1552s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 Packages [1418 kB] 1608s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 Packages [15.3 MB] 2087s Fetched 41.1 MB in 26min 27s (25.9 kB/s) 2088s Reading package lists... 2088s Reading package lists... 2089s Building dependency tree... 2089s Reading state information... 2090s Calculating upgrade... 2091s The following packages will be upgraded: 2091s libexpat1 2091s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2091s Need to get 76.6 kB of archives. 2091s After this operation, 1024 B of additional disk space will be used. 2091s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1 arm64 2.6.4-1 [76.6 kB] 2092s Fetched 76.6 kB in 1s (57.9 kB/s) 2093s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79957 files and directories currently installed.) 2093s Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... 2093s Unpacking libexpat1:arm64 (2.6.4-1) over (2.6.2-2) ... 2093s Setting up libexpat1:arm64 (2.6.4-1) ... 2093s Processing triggers for libc-bin (2.40-1ubuntu3) ... 2093s Reading package lists... 2093s Building dependency tree... 2093s Reading state information... 2094s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2094s autopkgtest [02:25:10]: rebooting testbed after setup commands that affected boot 2124s autopkgtest [02:25:40]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 2131s autopkgtest [02:25:47]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 2142s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B] 2142s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB] 2142s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB] 2143s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC 2143s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 2143s gpgv: issuer "dparsons@debian.org" 2143s gpgv: Can't check signature: No public key 2143s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found 2144s autopkgtest [02:26:00]: testing package mdanalysis version 2.7.0-5 2145s autopkgtest [02:26:01]: build not needed 2167s autopkgtest [02:26:23]: test test-mdanalysis: preparing testbed 2172s Reading package lists... 2173s Building dependency tree... 2173s Reading state information... 2173s Starting pkgProblemResolver with broken count: 0 2173s Starting 2 pkgProblemResolver with broken count: 0 2173s Done 2174s The following additional packages will be installed: 2174s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 2174s cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper debugedit 2174s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 2174s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 2174s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 2174s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 2174s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 2174s libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 2174s libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl 2174s libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1 2174s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 2174s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 2174s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 2174s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 2174s libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 libpython3-all-dev 2174s libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 libsharpyuv0 2174s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 2174s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 2174s libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 2174s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 2174s python3-alabaster python3-all python3-all-dev python3-appdirs 2174s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 2174s python3-citeproc python3-contourpy python3-cycler python3-dateutil 2174s python3-decorator python3-defusedxml python3-dev python3-docutils 2174s python3-duecredit python3-fasteners python3-fonttools python3-freetype 2174s python3-fs python3-griddataformats python3-gsd python3-h5py 2174s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 2174s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 2174s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 2174s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 2174s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 2174s python3-netcdf4 python3-networkx python3-numpy python3-packaging 2174s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 2174s python3-pluggy python3-pybtex python3-pybtex-docutils 2174s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 2174s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 2174s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 2174s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 2174s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 2174s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 2174s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 2174s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 2174s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 2174s zlib1g-dev 2174s Suggested packages: 2174s autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales 2174s cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf 2174s fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 2174s gdb-aarch64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 2174s libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc 2174s liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran 2174s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl bwa clustalo clustalw 2174s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 2174s python3-mysqldb python3-rdflib python3-psycopg2 raxml samtools t-coffee wise 2174s python3-pip python3-venv python-build-doc python-cycler-doc docutils-doc 2174s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 2174s texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc 2174s python-hypothesis-doc python-installer-doc python-joblib-doc 2174s python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 2174s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 2174s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 2174s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 2174s texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal 2174s python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc 2174s python3-statsmodels python-pil-doc python-pybtex-doc 2174s python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools 2174s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 2174s python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm 2174s fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre 2174s texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic 2174s python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg 2174s python3.13-tk sgml-base-doc 2174s Recommended packages: 2174s libarchive-cpio-perl javascript-common libjson-xs-perl libltdl-dev 2174s libmail-sendmail-perl python-biopython-doc ncbi-blast+ libpaper-utils 2174s python3-click python3-simplejson python3-psutil python3-bs4 2174s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 2174s python3-odf python3-openpyxl python3-tables python3-olefile 2174s fonts-dejavu-extra isympy-common 2174s The following NEW packages will be installed: 2174s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 2174s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 2174s cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism 2174s docutils-common dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono 2174s fonts-font-awesome fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ 2174s g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 2174s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 2174s libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 2174s libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl 2174s libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1 2174s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 2174s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 2174s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 2174s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 2174s libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 libpython3-all-dev 2174s libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 libsharpyuv0 2174s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 2174s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 2174s libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 2174s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 2174s python3-alabaster python3-all python3-all-dev python3-appdirs 2174s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 2174s python3-citeproc python3-contourpy python3-cycler python3-dateutil 2174s python3-decorator python3-defusedxml python3-dev python3-docutils 2174s python3-duecredit python3-fasteners python3-fonttools python3-freetype 2174s python3-fs python3-griddataformats python3-gsd python3-h5py 2174s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 2174s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 2174s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 2174s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 2174s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 2174s python3-netcdf4 python3-networkx python3-numpy python3-packaging 2174s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 2174s python3-pluggy python3-pybtex python3-pybtex-docutils 2174s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 2174s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 2174s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 2174s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 2174s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 2174s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 2174s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 2174s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 2174s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 2174s zlib1g-dev 2174s 0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded. 2174s Need to get 197 MB/197 MB of archives. 2174s After this operation, 841 MB of additional disk space will be used. 2174s Get:1 /tmp/autopkgtest.1hvvHo/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [1016 B] 2174s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 2175s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 2175s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 2175s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 2175s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 2175s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 2175s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 2175s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 2175s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 2175s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 2175s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 2175s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 2175s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 2175s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 2175s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 2175s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 2175s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 2175s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 2175s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 2175s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 2175s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 2175s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 2175s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 2175s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 2176s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 2176s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 2176s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 2176s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 2176s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 2176s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 2176s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 2176s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 2176s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 2176s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 2176s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 2176s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 2176s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 2176s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 2176s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 2177s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 2177s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 2177s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 2177s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 2177s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 2177s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 2177s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 2177s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 2177s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 2177s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-1ubuntu2 [2977 kB] 2177s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 2177s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB] 2177s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 2177s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 2177s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 2177s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 2178s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB] 2178s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 2178s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 2178s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 2178s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 2178s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 2178s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB] 2178s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 2178s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 2178s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 2178s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 2178s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 2178s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 2178s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 2178s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 2178s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 2178s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 2178s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 2178s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 2178s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 2178s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 2178s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 2178s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 2178s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 2178s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 2178s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 2178s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 2178s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 2178s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 2178s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 2178s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 2178s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 2178s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 2178s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 2178s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 2178s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 2178s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 2178s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 2178s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 2178s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf19t64 arm64 1:4.9.2-6ubuntu1 [466 kB] 2178s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 2178s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.7-3 [5565 kB] 2178s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.12.6-0ubuntu1 [10.2 kB] 2178s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.12.6-0ubuntu1 [916 B] 2178s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 2178s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 2179s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 2179s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 2179s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 2179s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 2179s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 2179s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 2179s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 2179s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 2179s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 2179s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-toml all 0.10.2-1 [16.5 kB] 2179s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wheel all 0.44.0-1 [54.2 kB] 2179s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-build all 1.2.2-1 [31.0 kB] 2179s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 2179s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-pyproject all 6.20241024 [1728 B] 2179s Get:117 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 2179s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 2179s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-mdanalysis-doc all 2.7.0-5 [2323 kB] 2180s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 2180s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB] 2180s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.12.6-0ubuntu1 [26.7 kB] 2180s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.12.6-0ubuntu1 [908 B] 2180s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 2180s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 2180s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 2180s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.6-1ubuntu1 [9806 B] 2180s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 2180s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 2180s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 2180s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 2180s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 2180s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 2180s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 2180s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 2180s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 2180s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 2180s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-1 [195 kB] 2180s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 2180s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-citeproc all 0.6.0-3 [98.4 kB] 2180s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 2180s Get:142 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 2180s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 2180s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 2180s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 2180s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-2 [42.0 kB] 2180s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 4.2-1 [10.0 kB] 2180s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 2180s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-looseversion all 1.3.0-3 [8354 B] 2180s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-duecredit all 0.10.2-2 [66.0 kB] 2180s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-monotonic all 1.6-2 [5732 B] 2180s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-fasteners all 0.18-2 [12.5 kB] 2180s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 2181s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 2181s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 2181s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 2181s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 2181s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 2181s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 2181s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 2181s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 2181s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 2181s Get:163 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 2181s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mrcfile all 1.5.3-3 [114 kB] 2181s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-griddataformats all 1.0.2-2 [2107 kB] 2181s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gsd arm64 3.3.0-1 [200 kB] 2181s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 2181s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 2181s Get:169 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 2181s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hypothesis all 6.116.0-1 [326 kB] 2181s Get:171 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 2181s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 2181s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 2181s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB] 2181s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-latexcodec all 3.0.0-1 [16.6 kB] 2181s Get:176 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu1 [4612 kB] 2181s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 2181s Get:178 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build2 [77.9 kB] 2181s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 2181s Get:180 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 2181s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.0-1 [91.6 kB] 2181s Get:182 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mdanalysis arm64 2.7.0-5 [2017 kB] 2182s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-common all 7.4.7-4 [775 kB] 2182s Get:184 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 2182s Get:185 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 2182s Get:186 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sphinx all 7.4.7-4 [593 kB] 2182s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 2182s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 2182s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-msmb-theme all 1.2.0-4 [35.4 kB] 2182s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1 [567 kB] 2182s Get:191 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 2182s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 2182s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 2182s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 2182s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex all 0.24.0-4 [70.0 kB] 2182s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex-docutils all 1.0.2-1 [7176 B] 2182s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 2182s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-seaborn all 0.13.2-4 [225 kB] 2182s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3806 kB] 2182s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 2182s Get:201 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-sitemap all 2.6.0-1 [6674 B] 2182s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 2183s Fetched 197 MB in 8s (24.1 MB/s) 2183s Selecting previously unselected package fonts-lato. 2183s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79957 files and directories currently installed.) 2183s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 2183s Unpacking fonts-lato (2.015-1) ... 2184s Selecting previously unselected package sgml-base. 2184s Preparing to unpack .../001-sgml-base_1.31_all.deb ... 2184s Unpacking sgml-base (1.31) ... 2184s Selecting previously unselected package m4. 2184s Preparing to unpack .../002-m4_1.4.19-4build1_arm64.deb ... 2184s Unpacking m4 (1.4.19-4build1) ... 2184s Selecting previously unselected package autoconf. 2184s Preparing to unpack .../003-autoconf_2.72-3_all.deb ... 2184s Unpacking autoconf (2.72-3) ... 2184s Selecting previously unselected package autotools-dev. 2184s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ... 2184s Unpacking autotools-dev (20220109.1) ... 2184s Selecting previously unselected package automake. 2184s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 2184s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 2184s Selecting previously unselected package autopoint. 2184s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ... 2184s Unpacking autopoint (0.22.5-2) ... 2184s Selecting previously unselected package libtcl8.6:arm64. 2184s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 2184s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 2184s Selecting previously unselected package fonts-dejavu-mono. 2184s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8_all.deb ... 2184s Unpacking fonts-dejavu-mono (2.37-8) ... 2184s Selecting previously unselected package fonts-dejavu-core. 2184s Preparing to unpack .../009-fonts-dejavu-core_2.37-8_all.deb ... 2184s Unpacking fonts-dejavu-core (2.37-8) ... 2184s Selecting previously unselected package libfontenc1:arm64. 2184s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 2184s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 2184s Selecting previously unselected package x11-common. 2184s Preparing to unpack .../011-x11-common_1%3a7.7+23ubuntu3_all.deb ... 2184s Unpacking x11-common (1:7.7+23ubuntu3) ... 2184s Selecting previously unselected package xfonts-encodings. 2184s Preparing to unpack .../012-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 2184s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 2184s Selecting previously unselected package xfonts-utils. 2184s Preparing to unpack .../013-xfonts-utils_1%3a7.7+7_arm64.deb ... 2184s Unpacking xfonts-utils (1:7.7+7) ... 2184s Selecting previously unselected package fonts-urw-base35. 2184s Preparing to unpack .../014-fonts-urw-base35_20200910-8_all.deb ... 2184s Unpacking fonts-urw-base35 (20200910-8) ... 2184s Selecting previously unselected package fontconfig-config. 2185s Preparing to unpack .../015-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 2185s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 2185s Selecting previously unselected package libfontconfig1:arm64. 2185s Preparing to unpack .../016-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 2185s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 2185s Selecting previously unselected package libxrender1:arm64. 2185s Preparing to unpack .../017-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 2185s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 2185s Selecting previously unselected package libxft2:arm64. 2185s Preparing to unpack .../018-libxft2_2.3.6-1build1_arm64.deb ... 2185s Unpacking libxft2:arm64 (2.3.6-1build1) ... 2185s Selecting previously unselected package libxss1:arm64. 2185s Preparing to unpack .../019-libxss1_1%3a1.2.3-1build3_arm64.deb ... 2185s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 2185s Selecting previously unselected package libtk8.6:arm64. 2185s Preparing to unpack .../020-libtk8.6_8.6.15-1_arm64.deb ... 2185s Unpacking libtk8.6:arm64 (8.6.15-1) ... 2185s Selecting previously unselected package tk8.6-blt2.5. 2185s Preparing to unpack .../021-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 2185s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 2185s Selecting previously unselected package blt. 2185s Preparing to unpack .../022-blt_2.5.3+dfsg-7build1_arm64.deb ... 2185s Unpacking blt (2.5.3+dfsg-7build1) ... 2185s Selecting previously unselected package libisl23:arm64. 2185s Preparing to unpack .../023-libisl23_0.27-1_arm64.deb ... 2185s Unpacking libisl23:arm64 (0.27-1) ... 2185s Selecting previously unselected package libmpc3:arm64. 2185s Preparing to unpack .../024-libmpc3_1.3.1-1build2_arm64.deb ... 2185s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 2185s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 2185s Preparing to unpack .../025-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 2185s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 2185s Selecting previously unselected package cpp-14. 2185s Preparing to unpack .../026-cpp-14_14.2.0-8ubuntu1_arm64.deb ... 2185s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 2185s Selecting previously unselected package cpp-aarch64-linux-gnu. 2186s Preparing to unpack .../027-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 2186s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 2186s Selecting previously unselected package cpp. 2186s Preparing to unpack .../028-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 2186s Unpacking cpp (4:14.1.0-2ubuntu1) ... 2186s Selecting previously unselected package libcc1-0:arm64. 2186s Preparing to unpack .../029-libcc1-0_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ... 2186s Selecting previously unselected package libgomp1:arm64. 2186s Preparing to unpack .../030-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 2186s Selecting previously unselected package libitm1:arm64. 2186s Preparing to unpack .../031-libitm1_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 2186s Selecting previously unselected package libasan8:arm64. 2186s Preparing to unpack .../032-libasan8_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 2186s Selecting previously unselected package liblsan0:arm64. 2186s Preparing to unpack .../033-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 2186s Selecting previously unselected package libtsan2:arm64. 2186s Preparing to unpack .../034-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 2186s Selecting previously unselected package libubsan1:arm64. 2186s Preparing to unpack .../035-libubsan1_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ... 2186s Selecting previously unselected package libhwasan0:arm64. 2186s Preparing to unpack .../036-libhwasan0_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ... 2186s Selecting previously unselected package libgcc-14-dev:arm64. 2186s Preparing to unpack .../037-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 2186s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 2186s Preparing to unpack .../038-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 2186s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 2187s Selecting previously unselected package gcc-14. 2187s Preparing to unpack .../039-gcc-14_14.2.0-8ubuntu1_arm64.deb ... 2187s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 2187s Selecting previously unselected package gcc-aarch64-linux-gnu. 2187s Preparing to unpack .../040-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 2187s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 2187s Selecting previously unselected package gcc. 2187s Preparing to unpack .../041-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 2187s Unpacking gcc (4:14.1.0-2ubuntu1) ... 2187s Selecting previously unselected package libstdc++-14-dev:arm64. 2187s Preparing to unpack .../042-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ... 2187s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 2187s Selecting previously unselected package g++-14-aarch64-linux-gnu. 2187s Preparing to unpack .../043-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 2187s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 2188s Selecting previously unselected package g++-14. 2188s Preparing to unpack .../044-g++-14_14.2.0-8ubuntu1_arm64.deb ... 2188s Unpacking g++-14 (14.2.0-8ubuntu1) ... 2188s Selecting previously unselected package g++-aarch64-linux-gnu. 2188s Preparing to unpack .../045-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 2188s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 2188s Selecting previously unselected package g++. 2188s Preparing to unpack .../046-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 2188s Unpacking g++ (4:14.1.0-2ubuntu1) ... 2188s Selecting previously unselected package build-essential. 2188s Preparing to unpack .../047-build-essential_12.10ubuntu1_arm64.deb ... 2188s Unpacking build-essential (12.10ubuntu1) ... 2188s Selecting previously unselected package cython3. 2188s Preparing to unpack .../048-cython3_3.0.11+dfsg-1ubuntu2_arm64.deb ... 2188s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ... 2188s Selecting previously unselected package libdebhelper-perl. 2188s Preparing to unpack .../049-libdebhelper-perl_13.20ubuntu1_all.deb ... 2188s Unpacking libdebhelper-perl (13.20ubuntu1) ... 2188s Selecting previously unselected package libtool. 2188s Preparing to unpack .../050-libtool_2.4.7-7build1_all.deb ... 2188s Unpacking libtool (2.4.7-7build1) ... 2188s Selecting previously unselected package dh-autoreconf. 2188s Preparing to unpack .../051-dh-autoreconf_20_all.deb ... 2188s Unpacking dh-autoreconf (20) ... 2188s Selecting previously unselected package libarchive-zip-perl. 2188s Preparing to unpack .../052-libarchive-zip-perl_1.68-1_all.deb ... 2188s Unpacking libarchive-zip-perl (1.68-1) ... 2188s Selecting previously unselected package libfile-stripnondeterminism-perl. 2188s Preparing to unpack .../053-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 2188s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 2188s Selecting previously unselected package dh-strip-nondeterminism. 2188s Preparing to unpack .../054-dh-strip-nondeterminism_1.14.0-1_all.deb ... 2188s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 2188s Selecting previously unselected package debugedit. 2188s Preparing to unpack .../055-debugedit_1%3a5.1-1_arm64.deb ... 2188s Unpacking debugedit (1:5.1-1) ... 2188s Selecting previously unselected package dwz. 2188s Preparing to unpack .../056-dwz_0.15-1build6_arm64.deb ... 2188s Unpacking dwz (0.15-1build6) ... 2188s Selecting previously unselected package gettext. 2188s Preparing to unpack .../057-gettext_0.22.5-2_arm64.deb ... 2188s Unpacking gettext (0.22.5-2) ... 2188s Selecting previously unselected package intltool-debian. 2188s Preparing to unpack .../058-intltool-debian_0.35.0+20060710.6_all.deb ... 2188s Unpacking intltool-debian (0.35.0+20060710.6) ... 2188s Selecting previously unselected package po-debconf. 2188s Preparing to unpack .../059-po-debconf_1.0.21+nmu1_all.deb ... 2188s Unpacking po-debconf (1.0.21+nmu1) ... 2189s Selecting previously unselected package debhelper. 2189s Preparing to unpack .../060-debhelper_13.20ubuntu1_all.deb ... 2189s Unpacking debhelper (13.20ubuntu1) ... 2189s Selecting previously unselected package dh-python. 2189s Preparing to unpack .../061-dh-python_6.20241024_all.deb ... 2189s Unpacking dh-python (6.20241024) ... 2189s Selecting previously unselected package xml-core. 2189s Preparing to unpack .../062-xml-core_0.19_all.deb ... 2189s Unpacking xml-core (0.19) ... 2189s Selecting previously unselected package docutils-common. 2189s Preparing to unpack .../063-docutils-common_0.21.2+dfsg-2_all.deb ... 2189s Unpacking docutils-common (0.21.2+dfsg-2) ... 2189s Selecting previously unselected package fonts-font-awesome. 2189s Preparing to unpack .../064-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 2189s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 2189s Selecting previously unselected package fonts-lyx. 2189s Preparing to unpack .../065-fonts-lyx_2.4.2.1-1_all.deb ... 2189s Unpacking fonts-lyx (2.4.2.1-1) ... 2189s Selecting previously unselected package fonts-mathjax. 2189s Preparing to unpack .../066-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 2189s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 2189s Selecting previously unselected package libaec0:arm64. 2189s Preparing to unpack .../067-libaec0_1.1.3-1_arm64.deb ... 2189s Unpacking libaec0:arm64 (1.1.3-1) ... 2189s Selecting previously unselected package libblas3:arm64. 2189s Preparing to unpack .../068-libblas3_3.12.0-3build2_arm64.deb ... 2189s Unpacking libblas3:arm64 (3.12.0-3build2) ... 2189s Selecting previously unselected package libpixman-1-0:arm64. 2189s Preparing to unpack .../069-libpixman-1-0_0.44.0-3_arm64.deb ... 2189s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 2189s Selecting previously unselected package libxcb-render0:arm64. 2189s Preparing to unpack .../070-libxcb-render0_1.17.0-2_arm64.deb ... 2189s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 2189s Selecting previously unselected package libxcb-shm0:arm64. 2189s Preparing to unpack .../071-libxcb-shm0_1.17.0-2_arm64.deb ... 2189s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 2189s Selecting previously unselected package libcairo2:arm64. 2189s Preparing to unpack .../072-libcairo2_1.18.2-2_arm64.deb ... 2189s Unpacking libcairo2:arm64 (1.18.2-2) ... 2189s Selecting previously unselected package libdeflate0:arm64. 2189s Preparing to unpack .../073-libdeflate0_1.22-1_arm64.deb ... 2189s Unpacking libdeflate0:arm64 (1.22-1) ... 2189s Selecting previously unselected package libexpat1-dev:arm64. 2189s Preparing to unpack .../074-libexpat1-dev_2.6.4-1_arm64.deb ... 2189s Unpacking libexpat1-dev:arm64 (2.6.4-1) ... 2189s Selecting previously unselected package libgfortran5:arm64. 2189s Preparing to unpack .../075-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 2189s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 2190s Selecting previously unselected package libgraphite2-3:arm64. 2190s Preparing to unpack .../076-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 2190s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 2190s Selecting previously unselected package libharfbuzz0b:arm64. 2190s Preparing to unpack .../077-libharfbuzz0b_10.0.1-1_arm64.deb ... 2190s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 2190s Selecting previously unselected package libsz2:arm64. 2190s Preparing to unpack .../078-libsz2_1.1.3-1_arm64.deb ... 2190s Unpacking libsz2:arm64 (1.1.3-1) ... 2190s Selecting previously unselected package libhdf5-103-1t64:arm64. 2190s Preparing to unpack .../079-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 2190s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 2190s Selecting previously unselected package libhdf5-hl-100t64:arm64. 2190s Preparing to unpack .../080-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 2190s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 2190s Selecting previously unselected package libimagequant0:arm64. 2190s Preparing to unpack .../081-libimagequant0_2.18.0-1build1_arm64.deb ... 2190s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 2190s Selecting previously unselected package libjpeg-turbo8:arm64. 2190s Preparing to unpack .../082-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 2190s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 2190s Selecting previously unselected package libjpeg8:arm64. 2190s Preparing to unpack .../083-libjpeg8_8c-2ubuntu11_arm64.deb ... 2190s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 2190s Selecting previously unselected package libjs-jquery. 2190s Preparing to unpack .../084-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 2190s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 2190s Selecting previously unselected package libjs-jquery-ui. 2190s Preparing to unpack .../085-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 2190s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 2190s Selecting previously unselected package libjs-underscore. 2190s Preparing to unpack .../086-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 2190s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 2190s Selecting previously unselected package libjs-sphinxdoc. 2190s Preparing to unpack .../087-libjs-sphinxdoc_7.4.7-4_all.deb ... 2190s Unpacking libjs-sphinxdoc (7.4.7-4) ... 2190s Selecting previously unselected package libjson-perl. 2190s Preparing to unpack .../088-libjson-perl_4.10000-1_all.deb ... 2190s Unpacking libjson-perl (4.10000-1) ... 2190s Selecting previously unselected package liblapack3:arm64. 2190s Preparing to unpack .../089-liblapack3_3.12.0-3build2_arm64.deb ... 2190s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 2190s Selecting previously unselected package liblbfgsb0:arm64. 2190s Preparing to unpack .../090-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 2190s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 2190s Selecting previously unselected package liblcms2-2:arm64. 2190s Preparing to unpack .../091-liblcms2-2_2.16-2_arm64.deb ... 2190s Unpacking liblcms2-2:arm64 (2.16-2) ... 2190s Selecting previously unselected package liblerc4:arm64. 2190s Preparing to unpack .../092-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 2190s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 2190s Selecting previously unselected package liblzf1:arm64. 2191s Preparing to unpack .../093-liblzf1_3.6-4_arm64.deb ... 2191s Unpacking liblzf1:arm64 (3.6-4) ... 2191s Selecting previously unselected package libnetcdf19t64:arm64. 2191s Preparing to unpack .../094-libnetcdf19t64_1%3a4.9.2-6ubuntu1_arm64.deb ... 2191s Unpacking libnetcdf19t64:arm64 (1:4.9.2-6ubuntu1) ... 2191s Selecting previously unselected package zlib1g-dev:arm64. 2191s Preparing to unpack .../095-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 2191s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 2191s Selecting previously unselected package libpython3.12-dev:arm64. 2191s Preparing to unpack .../096-libpython3.12-dev_3.12.7-3_arm64.deb ... 2191s Unpacking libpython3.12-dev:arm64 (3.12.7-3) ... 2191s Selecting previously unselected package libpython3-dev:arm64. 2191s Preparing to unpack .../097-libpython3-dev_3.12.6-0ubuntu1_arm64.deb ... 2191s Unpacking libpython3-dev:arm64 (3.12.6-0ubuntu1) ... 2191s Selecting previously unselected package libpython3-all-dev:arm64. 2191s Preparing to unpack .../098-libpython3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 2191s Unpacking libpython3-all-dev:arm64 (3.12.6-0ubuntu1) ... 2191s Selecting previously unselected package libqhull-r8.0:arm64. 2191s Preparing to unpack .../099-libqhull-r8.0_2020.2-6build1_arm64.deb ... 2191s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 2191s Selecting previously unselected package libraqm0:arm64. 2191s Preparing to unpack .../100-libraqm0_0.10.1-1build1_arm64.deb ... 2191s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 2191s Selecting previously unselected package libsharpyuv0:arm64. 2191s Preparing to unpack .../101-libsharpyuv0_1.4.0-0.1_arm64.deb ... 2191s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 2191s Selecting previously unselected package libjbig0:arm64. 2191s Preparing to unpack .../102-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 2191s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 2191s Selecting previously unselected package libwebp7:arm64. 2191s Preparing to unpack .../103-libwebp7_1.4.0-0.1_arm64.deb ... 2191s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 2191s Selecting previously unselected package libtiff6:arm64. 2191s Preparing to unpack .../104-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 2191s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 2191s Selecting previously unselected package libwebpdemux2:arm64. 2191s Preparing to unpack .../105-libwebpdemux2_1.4.0-0.1_arm64.deb ... 2191s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 2191s Selecting previously unselected package libwebpmux3:arm64. 2191s Preparing to unpack .../106-libwebpmux3_1.4.0-0.1_arm64.deb ... 2191s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 2191s Selecting previously unselected package libxslt1.1:arm64. 2191s Preparing to unpack .../107-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 2191s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 2191s Selecting previously unselected package python3-packaging. 2191s Preparing to unpack .../108-python3-packaging_24.1-1_all.deb ... 2192s Unpacking python3-packaging (24.1-1) ... 2192s Selecting previously unselected package python3-pyproject-hooks. 2192s Preparing to unpack .../109-python3-pyproject-hooks_1.2.0-1_all.deb ... 2192s Unpacking python3-pyproject-hooks (1.2.0-1) ... 2192s Selecting previously unselected package python3-toml. 2192s Preparing to unpack .../110-python3-toml_0.10.2-1_all.deb ... 2192s Unpacking python3-toml (0.10.2-1) ... 2192s Selecting previously unselected package python3-wheel. 2192s Preparing to unpack .../111-python3-wheel_0.44.0-1_all.deb ... 2192s Unpacking python3-wheel (0.44.0-1) ... 2192s Selecting previously unselected package python3-build. 2192s Preparing to unpack .../112-python3-build_1.2.2-1_all.deb ... 2192s Unpacking python3-build (1.2.2-1) ... 2192s Selecting previously unselected package python3-installer. 2192s Preparing to unpack .../113-python3-installer_0.7.0+dfsg1-3_all.deb ... 2192s Unpacking python3-installer (0.7.0+dfsg1-3) ... 2192s Selecting previously unselected package pybuild-plugin-pyproject. 2192s Preparing to unpack .../114-pybuild-plugin-pyproject_6.20241024_all.deb ... 2192s Unpacking pybuild-plugin-pyproject (6.20241024) ... 2192s Selecting previously unselected package python-matplotlib-data. 2192s Preparing to unpack .../115-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ... 2192s Unpacking python-matplotlib-data (3.8.3-3ubuntu1) ... 2192s Selecting previously unselected package libjs-mathjax. 2192s Preparing to unpack .../116-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 2192s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 2193s Selecting previously unselected package python-mdanalysis-doc. 2193s Preparing to unpack .../117-python-mdanalysis-doc_2.7.0-5_all.deb ... 2193s Unpacking python-mdanalysis-doc (2.7.0-5) ... 2193s Selecting previously unselected package python3-all. 2193s Preparing to unpack .../118-python3-all_3.12.6-0ubuntu1_arm64.deb ... 2193s Unpacking python3-all (3.12.6-0ubuntu1) ... 2193s Selecting previously unselected package python3.12-dev. 2193s Preparing to unpack .../119-python3.12-dev_3.12.7-3_arm64.deb ... 2193s Unpacking python3.12-dev (3.12.7-3) ... 2193s Selecting previously unselected package python3-dev. 2193s Preparing to unpack .../120-python3-dev_3.12.6-0ubuntu1_arm64.deb ... 2193s Unpacking python3-dev (3.12.6-0ubuntu1) ... 2193s Selecting previously unselected package python3-all-dev. 2193s Preparing to unpack .../121-python3-all-dev_3.12.6-0ubuntu1_arm64.deb ... 2193s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 2193s Selecting previously unselected package python3-appdirs. 2193s Preparing to unpack .../122-python3-appdirs_1.4.4-4_all.deb ... 2193s Unpacking python3-appdirs (1.4.4-4) ... 2193s Selecting previously unselected package python3-numpy. 2193s Preparing to unpack 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.../128-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 2193s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 2193s Selecting previously unselected package python3-cairo. 2193s Preparing to unpack .../129-python3-cairo_1.26.1-2_arm64.deb ... 2193s Unpacking python3-cairo (1.26.1-2) ... 2194s Selecting previously unselected package python3-freetype. 2194s Preparing to unpack .../130-python3-freetype_2.5.1-1_all.deb ... 2194s Unpacking python3-freetype (2.5.1-1) ... 2194s Selecting previously unselected package python3-rlpycairo. 2194s Preparing to unpack .../131-python3-rlpycairo_0.3.0-3_all.deb ... 2194s Unpacking python3-rlpycairo (0.3.0-3) ... 2194s Selecting previously unselected package python3-reportlab. 2194s Preparing to unpack .../132-python3-reportlab_4.2.5-1_all.deb ... 2194s Unpacking python3-reportlab (4.2.5-1) ... 2194s Selecting previously unselected package w3c-sgml-lib. 2194s Preparing to unpack .../133-w3c-sgml-lib_1.3-3_all.deb ... 2194s Unpacking w3c-sgml-lib (1.3-3) ... 2194s Selecting previously unselected package python3-biopython. 2194s Preparing to unpack .../134-python3-biopython_1.84+dfsg-4_arm64.deb ... 2194s Unpacking python3-biopython (1.84+dfsg-4) ... 2194s Selecting previously unselected package python3-brotli. 2194s Preparing to unpack .../135-python3-brotli_1.1.0-2build2_arm64.deb ... 2194s Unpacking python3-brotli (1.1.0-2build2) ... 2194s Selecting previously unselected package python3-cftime. 2194s Preparing to unpack .../136-python3-cftime_1.6.4-1_arm64.deb ... 2194s Unpacking python3-cftime (1.6.4-1) ... 2194s Selecting previously unselected package python3-lxml:arm64. 2194s Preparing to unpack .../137-python3-lxml_5.3.0-1_arm64.deb ... 2194s Unpacking python3-lxml:arm64 (5.3.0-1) ... 2194s Selecting previously unselected package python3-citeproc. 2194s Preparing to unpack .../138-python3-citeproc_0.6.0-3_all.deb ... 2194s Unpacking python3-citeproc (0.6.0-3) ... 2194s Selecting previously unselected package python3-contourpy. 2194s 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python3-defusedxml (0.7.1-2) ... 2195s Selecting previously unselected package python3-roman. 2195s Preparing to unpack .../145-python3-roman_4.2-1_all.deb ... 2195s Unpacking python3-roman (4.2-1) ... 2195s Selecting previously unselected package python3-docutils. 2195s Preparing to unpack .../146-python3-docutils_0.21.2+dfsg-2_all.deb ... 2195s Unpacking python3-docutils (0.21.2+dfsg-2) ... 2195s Selecting previously unselected package python3-looseversion. 2195s Preparing to unpack .../147-python3-looseversion_1.3.0-3_all.deb ... 2195s Unpacking python3-looseversion (1.3.0-3) ... 2195s Selecting previously unselected package python3-duecredit. 2195s Preparing to unpack .../148-python3-duecredit_0.10.2-2_all.deb ... 2195s Unpacking python3-duecredit (0.10.2-2) ... 2195s Selecting previously unselected package python3-monotonic. 2195s Preparing to unpack .../149-python3-monotonic_1.6-2_all.deb ... 2195s Unpacking python3-monotonic (1.6-2) ... 2195s Selecting previously unselected package python3-fasteners. 2195s Preparing to unpack .../150-python3-fasteners_0.18-2_all.deb ... 2195s Unpacking python3-fasteners (0.18-2) ... 2195s Selecting previously unselected package python3-scipy. 2195s Preparing to unpack .../151-python3-scipy_1.13.1-5_arm64.deb ... 2195s Unpacking python3-scipy (1.13.1-5) ... 2195s Selecting previously unselected package python3-ufolib2. 2195s Preparing to unpack .../152-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 2195s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 2195s Selecting previously unselected package python3-mpmath. 2195s Preparing to unpack .../153-python3-mpmath_1.3.0-1_all.deb ... 2195s Unpacking python3-mpmath (1.3.0-1) ... 2196s Selecting previously unselected package python3-sympy. 2196s Preparing to unpack .../154-python3-sympy_1.13.3-1_all.deb ... 2196s Unpacking python3-sympy (1.13.3-1) ... 2196s Selecting previously unselected package python3-tz. 2196s Preparing to unpack .../155-python3-tz_2024.1-2_all.deb ... 2196s Unpacking python3-tz (2024.1-2) ... 2196s Selecting previously unselected package python3-fs. 2196s Preparing to unpack .../156-python3-fs_2.4.16-4_all.deb ... 2196s Unpacking python3-fs (2.4.16-4) ... 2196s Selecting previously unselected package python3-lz4. 2196s Preparing to unpack .../157-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 2196s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 2196s Selecting previously unselected package python3-unicodedata2. 2196s Preparing to unpack .../158-python3-unicodedata2_15.1.0+ds-1build2_arm64.deb ... 2196s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 2196s Selecting previously unselected package unicode-data. 2196s Preparing to unpack .../159-unicode-data_15.1.0-1_all.deb ... 2196s Unpacking unicode-data (15.1.0-1) ... 2196s Selecting previously unselected package python3-fonttools. 2196s Preparing to unpack .../160-python3-fonttools_4.46.0-1build2_arm64.deb ... 2196s Unpacking python3-fonttools (4.46.0-1build2) ... 2197s Selecting previously unselected package sphinx-rtd-theme-common. 2197s Preparing to unpack .../161-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 2197s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 2197s Selecting previously unselected package python3-mrcfile. 2197s Preparing to unpack .../162-python3-mrcfile_1.5.3-3_all.deb ... 2197s Unpacking python3-mrcfile (1.5.3-3) ... 2197s Selecting previously unselected package python3-griddataformats. 2197s Preparing to unpack .../163-python3-griddataformats_1.0.2-2_all.deb ... 2197s Unpacking python3-griddataformats (1.0.2-2) ... 2197s Selecting previously unselected package python3-gsd. 2197s Preparing to unpack .../164-python3-gsd_3.3.0-1_arm64.deb ... 2197s Unpacking python3-gsd (3.3.0-1) ... 2197s Selecting previously unselected package python3-h5py-serial. 2197s Preparing to unpack .../165-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ... 2197s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 2197s Selecting previously unselected package python3-h5py. 2197s Preparing to unpack .../166-python3-h5py_3.11.0-5ubuntu1_all.deb ... 2197s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 2197s Selecting previously unselected package python3-sortedcontainers. 2197s Preparing to unpack .../167-python3-sortedcontainers_2.4.0-2_all.deb ... 2197s Unpacking python3-sortedcontainers (2.4.0-2) ... 2197s Selecting previously unselected package python3-hypothesis. 2197s Preparing to unpack .../168-python3-hypothesis_6.116.0-1_all.deb ... 2197s Unpacking python3-hypothesis (6.116.0-1) ... 2197s Selecting previously unselected package python3-imagesize. 2197s Preparing to unpack .../169-python3-imagesize_1.4.1-1_all.deb ... 2197s Unpacking python3-imagesize (1.4.1-1) ... 2197s Selecting previously unselected package python3-iniconfig. 2197s Preparing to unpack .../170-python3-iniconfig_1.1.1-2_all.deb ... 2197s Unpacking python3-iniconfig (1.1.1-2) ... 2197s Selecting previously unselected package python3-joblib. 2197s Preparing to unpack .../171-python3-joblib_1.3.2-5_all.deb ... 2197s Unpacking python3-joblib (1.3.2-5) ... 2197s Selecting previously unselected package python3-kiwisolver. 2197s Preparing to unpack .../172-python3-kiwisolver_1.4.7-2build1_arm64.deb ... 2197s Unpacking python3-kiwisolver (1.4.7-2build1) ... 2197s Selecting previously unselected package python3-latexcodec. 2197s Preparing to unpack .../173-python3-latexcodec_3.0.0-1_all.deb ... 2197s Unpacking python3-latexcodec (3.0.0-1) ... 2197s Selecting previously unselected package python3-matplotlib. 2197s Preparing to unpack .../174-python3-matplotlib_3.8.3-3ubuntu1_arm64.deb ... 2197s Unpacking python3-matplotlib (3.8.3-3ubuntu1) ... 2198s Selecting previously unselected package python3-mda-xdrlib. 2198s Preparing to unpack .../175-python3-mda-xdrlib_0.2.0-3_all.deb ... 2198s Unpacking python3-mda-xdrlib (0.2.0-3) ... 2198s Selecting previously unselected package python3-msgpack. 2198s Preparing to unpack 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[100%] 3027s 3027s =============================== warnings summary =============================== 3027s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39 3027s /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. 3027s 3027s Due to the on going maintenance burden of keeping command line application 3027s wrappers up to date, we have decided to deprecate and eventually remove these 3027s modules. 3027s 3027s We instead now recommend building your command line and invoking it directly 3027s with the subprocess module. 3027s warnings.warn( 3027s 3027s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings 3027s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings 3027s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings 3027s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings 3027s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings 3027s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings 3027s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings 3027s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings 3027s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings 3027s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings 3027s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings 3027s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings 3027s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 3027s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings 3027s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings 3027s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings 3027s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings 3027s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings 3027s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings 3027s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings 3027s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings 3027s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings 3027s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings 3027s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings 3027s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings 3027s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings 3027s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 3027s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings 3027s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 3027s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings 3027s /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. 3027s warnings.warn("DCDReader currently makes independent timesteps" 3027s 3027s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 3027s /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. 3027s warnings.warn(wmsg, category=DeprecationWarning) 3027s 3027s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings 3027s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written 3027s warnings.warn(wmsg) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings 3027s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings 3027s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings 3027s /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 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings 3027s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 3027s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings 3027s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning 3027s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'h1', 'c3', 'hc', 'ho', 'oh'}. These have been given an empty element record. 3027s warnings.warn("Unknown elements found for some " 3027s 3027s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning 3027s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings 3027s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings 3027s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 3027s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings 3027s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings 3027s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps 3027s self.times[i] = ts.time 3027s 3027s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning 3027s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings 3027s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 3027s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings 3027s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings 3027s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings 3027s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded 3027s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps 3027s results.append((ts.time, x.sum() / mask.sum())) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue 3027s /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. 3027s warnings.warn(msg) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 3027s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding 3027s /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 3027s warnings.warn(msg) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 3027s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 3027s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 3027s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings 3027s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning 3027s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings 3027s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings 3027s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings 3027s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 3027s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings 3027s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings 3027s /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. 3027s warnings.warn("Element information is missing, elements attribute " 3027s 3027s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran 3027s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame 3027s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections 3027s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues 3027s warnings.warn("Cannot determine phi and psi angles for the first " 3027s 3027s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin 3027s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr 3027s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame 3027s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot 3027s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning 3027s /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. 3027s warnings.warn(f"All residues selected with '{select_remove}' " 3027s 3027s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings 3027s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings 3027s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=5767) is multi-threaded, use of fork() may lead to deadlocks in the child. 3027s self.pid = os.fork() 3027s 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes 3027s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide 3027s cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms 3027s 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide 3027s local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 3027s /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice 3027s ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 3027s /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide 3027s ret = um.true_divide( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 3027s /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide 3027s ret = ret.dtype.type(ret / rcount) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 3027s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning 3027s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning 3027s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 3027s /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. 3027s warnings.warn("1 A^3 CRYST1 record," 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. 3027s warnings.warn("Unit cell dimensions not found. " 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings 3027s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings 3027s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings 3027s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 3027s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings 3027s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 3027s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning 3027s /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 3027s warnings.warn(wmsg, DeprecationWarning) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 3027s warnings.warn("Desired number of sample points too high, using {0}" 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbond = HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbond = HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbond = HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbond = HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbond = HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbond = HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbond = HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbond = HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s HBAC( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 3027s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 3027s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbond = HBAC(u, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! 3027s `find_hydrogen_donors` will be removed in release 3.0.0. 3027s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s D = hbonds.find_hydrogen_donors(H) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! 3027s `find_hydrogen_donors` will be removed in release 3.0.0. 3027s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 3027s hbonds.find_hydrogen_donors(u.atoms) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 3027s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 3027s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. 3027s return _methods._mean(a, axis=axis, dtype=dtype, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 3027s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 3027s /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide 3027s ret = ret.dtype.type(ret / rcount) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 3027s /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. 3027s warnings.warn(msg.format(sel)) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 3027s /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. 3027s warnings.warn(msg.format(sel)) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 3027s /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. 3027s warnings.warn(msg.format(sel)) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. 3027s warnings.warn("Empty string to select atoms, empty group returned.", 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 3027s /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, . 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 3027s /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, . 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 3027s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 3027s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 3027s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 3027s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 3027s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 3027s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple 3027s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content 3027s /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. 3027s warnings.warn(wmsg) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning 3027s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning 3027s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 3027s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 3027s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 3027s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 3027s /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.) 3027s phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi 3027s 3027s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j 3027s /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 3027s warnings.warn("Column index entered (j = {:d} is smaller than row " 3027s 3027s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps 3027s dt=self.trajectory.ts.dt * step, 3027s 3027s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] 3027s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] 3027s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] 3027s /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 3027s warnings.warn(wmsg, DeprecationWarning) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 3027s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings 3027s /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. 3027s warnings.warn("The `u` attribute is superflous and will be removed " 3027s 3027s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] 3027s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm 3027s /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. 3027s warnings.warn("The `density` attribute was deprecated in " 3027s 3027s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata 3027s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. 3027s warnings.warn(msg, category=MissingDataWarning) 3027s 3027s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps 3027s self.timesteps.append(self._ts.time) 3027s 3027s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning 3027s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default 3027s warnings.warn("{} does not support time selection. Reverting to " 3027s 3027s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default 3027s warnings.warn("{} does not support data selection. Reverting to " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 3027s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings 3027s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps 3027s return self.ts.dt 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 3027s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps 3027s ts.data['time'] = step_num * ts.dt 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_ts_time[universe0] 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 3027s self.close() 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close 3027s self._apply('close') 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply 3027s return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] 3027s ^^^^^^^^^^^^ 3027s AttributeError: 'ChainReader' object has no attribute 'readers' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing 3027s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain 3027s warnings.warn("Missing frame in continuous chain", UserWarning) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps 3027s time_frame_0 = ts.time - ts.frame*ts.dt # assumes ts.dt is constant 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps 3027s frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps 3027s step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps 3027s self._add_step_to_frame_data(ts.time) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps 3027s if not np.allclose(A.time, B.time): 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] 3027s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array 3027s /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 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 3027s self.close() 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close 3027s self._file.close() 3027s ^^^^^^^^^^ 3027s AttributeError: 'DCDReader' object has no attribute '_file' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms 3027s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit 3027s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__ 3027s self.close() 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close 3027s self._file.close() 3027s ^^^^^^^^^^ 3027s AttributeError: 'DCDWriter' object has no attribute '_file' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings 3027s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings 3027s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 3027s /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. 3027s warnings.warn(msg) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps 3027s return self.ts.time 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps 3027s assert_equal(reader.ts.dt, reader.dt) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps 3027s time_frame = time_frame_0 + frame_index*ts.dt 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps 3027s reader_p = pickle.loads(pickle.dumps(reader)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings 3027s /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 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] 3027s warnings.warn(wmsg) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 3027s /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`. 3027s warnings.warn(wmsg) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. 3027s warnings.warn("Not all velocities were present. " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps 3027s reader_p = pickle.loads(pickle.dumps(reader)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader 3027s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps 3027s reader_p = pickle.loads(pickle.dumps(reader)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 3027s self.close() 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close 3027s self._file.close() 3027s ^^^^^^^^^^ 3027s AttributeError: 'H5MDReader' object has no attribute '_file' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 3027s for aux in self.aux_list: 3027s ^^^^^^^^^^^^^ 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 3027s return self._auxs.keys() 3027s ^^^^^^^^^^ 3027s AttributeError: 'H5MDReader' object has no attribute '_auxs' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 3027s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 3027s warnings.warn('Guessed all Masses to 1.0') 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit 3027s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 3027s for aux in self.aux_list: 3027s ^^^^^^^^^^^^^ 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 3027s return self._auxs.keys() 3027s ^^^^^^^^^^ 3027s AttributeError: 'DCDReader' object has no attribute '_auxs' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view 3027s /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 3027s warnings.warn("MemoryReader.timeseries inclusive `stop` " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader 3027s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps 3027s reader_p = pickle.loads(pickle.dumps(reader)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 3027s /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 3027s warnings.warn(wmsg) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps 3027s ts.time) # in-place ! (hope this works...) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps 3027s time_list = [ts.time for ts in u.trajectory] 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps 3027s assert u.trajectory.ts.dt == pytest.approx(ref) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 3027s /tmp/autopkgtest.1hvvHo/build.Cds/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.) 3027s return self._test_write_trajectory(universe, outfile) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] 3027s /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. 3027s warnings.warn(wmsg) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 3027s /tmp/autopkgtest.1hvvHo/build.Cds/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.) 3027s return self._test_write_trajectory(universe, outfile) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 3027s warnings.warn("Found missing chainIDs." 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom] 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond] 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom] 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree] 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond] 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom] 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps 3027s time = ts.time 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 3027s self.close() 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close 3027s if self.trjfile is not None: 3027s ^^^^^^^^^^^^ 3027s AttributeError: 'NCDFWriter' object has no attribute 'trjfile' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' 3027s warnings.warn("Found no information for attr: '{}'" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' 3027s warnings.warn("Found chainIDs using unnaccepted character." 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' 3027s warnings.warn("Found chainIDs with invalid length." 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed 3027s warnings.warn("Serial numbers went over 100,000. " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed 3027s warnings.warn("Invalid atom serials were present, bonds will not" 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed 3027s warnings.warn("Invalid atom serials were present, " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment 3027s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 3027s /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. 3027s warnings.warn(wmsg) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 3027s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 3027s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 3027s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 3027s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges 3027s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps 3027s assert_equal(ts.dt, 1.0) # default value 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps 3027s assert_equal(ts.time, 0.0) # default to 1.0 (dt) * 0 (frame) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps 3027s assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 3027s for aux in self.aux_list: 3027s ^^^^^^^^^^^^^ 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 3027s return self._auxs.keys() 3027s ^^^^^^^^^^ 3027s AttributeError: 'TNGReader' object has no attribute '_auxs' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms 3027s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe 3027s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe 3027s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 3027s self.close() 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close 3027s if self.trjfile is None: 3027s ^^^^^^^^^^^^ 3027s AttributeError: 'TRJReader' object has no attribute 'trjfile' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps 3027s data['time'] = ts.time 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 3027s /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 3027s warnings.warn("Timestep didn't have the following attributes: '{0}', " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 3027s /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. 3027s warnings.warn("Timestep didn't have velocity information, " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 3027s /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 3027s warnings.warn("Timestep didn't have dimensions information, " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 3027s self.close() 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close 3027s if self.trzfile is None: 3027s ^^^^^^^^^^^^ 3027s AttributeError: 'TRZWriter' object has no attribute 'trzfile' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 3027s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 3027s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 3027s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 3027s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 3027s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 3027s /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. 3027s warnings.warn("Element information is missing, elements attribute " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 3027s /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 3027s warnings.warn(wmsg, DeprecationWarning) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] 3027s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] 3027s /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' 3027s warnings.warn(wmsg) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD 3027s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps 3027s time = ts.time 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD 3027s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps 3027s time = ts.time 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 3027s self.close() 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 3027s self._xdr.close() 3027s ^^^^^^^^^ 3027s AttributeError: 'XTCWriter' object has no attribute '_xdr' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container 3027s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 3027s 3027s Traceback (most recent call last): 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 3027s self.close() 3027s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 3027s self._xdr.close() 3027s ^^^^^^^^^ 3027s AttributeError: 'TRRWriter' object has no attribute '_xdr' 3027s 3027s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 3027s /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. 3027s Consider setting 'refresh_offsets=True' when loading your Universe. 3027s warnings.warn(f"Reading offsets from {fname} failed, " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly 3027s /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. 3027s warnings.warn(f"Cannot write lock/offset file in same location as " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 3027s /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. 3027s Consider setting 'refresh_offsets=True' when loading your Universe. 3027s warnings.warn(f"Reading offsets from {fname} failed, " 3027s 3027s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly 3027s /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. 3027s warnings.warn(f"Cannot write lock/offset file in same location as " 3027s 3027s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] 3027s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] 3027s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] 3027s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce 3027s return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 3027s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 3027s /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. 3027s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings 3027s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings 3027s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings 3027s /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. 3027s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 3027s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 3027s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide 3027s return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() 3027s 3027s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings 3027s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide 3027s _centers /= _weights.sum(axis=1)[:, None] 3027s 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 3027s /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`. 3027s warnings.warn(msg, category=SelectionWarning) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 3027s /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`. 3027s warnings.warn(msg, category=SelectionWarning) 3027s 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] 3027s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] 3027s /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`. 3027s warnings.warn(msg, category=SelectionWarning) 3027s 3027s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] 3027s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] 3027s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] 3027s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] 3027s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] 3027s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc 3027s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc 3027s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options 3027s /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 3027s warnings.warn("The 'pbc' kwarg has been deprecated and will be " 3027s 3027s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel 3027s /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`. 3027s warnings.warn(msg, category=SelectionWarning) 3027s 3027s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] 3027s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] 3027s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] 3027s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] 3027s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] 3027s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide 3027s x = np.dot(a, b) / (norm(a) * norm(b)) 3027s 3027s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt 3027s ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) 3027s 3027s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt 3027s box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - 3027s 3027s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide 3027s a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) 3027s 3027s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide 3027s b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) 3027s 3027s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide 3027s c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) 3027s 3027s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide 3027s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 3027s 3027s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide 3027s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 3027s 3027s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 3027s /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps 3027s cls(buf, protocol).dump(obj) 3027s 3027s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps 3027s ps = pickle.dumps(ref_reader) 3027s 3027s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] 3027s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd 3027s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd 3027s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset 3027s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific 3027s /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. 3027s warnings.warn('Cannot average position for non sequential' 3027s 3027s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name] 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname] 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type] 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid] 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' 3027s warnings.warn("PDB file is missing resid information. " 3027s 3027s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX 3027s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 3027s 3027s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2] 3027s /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. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2] 3027s /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. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2] 3027s /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. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2] 3027s /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. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 3027s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings 3027s /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. 3027s warnings.warn(msg) 3027s 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts 3027s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr] 3027s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file. 3027s warnings.warn('No coordinate reader found for {}. Skipping ' 3027s 3027s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses 3027s /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. 3027s warnings.warn(msg, category=SelectionWarning) 3027s 3027s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 3027s /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. 3027s warnings.warn( 3027s 3027s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps 3027s return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 3027s 3027s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps 3027s pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 3027s 3027s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps 3027s return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL) 3027s 3027s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps 3027s return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL) 3027s 3027s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps 3027s return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL) 3027s 3027s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps 3027s pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL) 3027s 3027s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag 3027s /tmp/autopkgtest.1hvvHo/build.Cds/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps 3027s pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL) 3027s 3027s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings 3027s /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream 3027s warnings.warn("Constructed NamedStream from a NamedStream", 3027s 3027s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] 3027s /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. 3027s warnings.warn(wmsg, DeprecationWarning) 3027s 3027s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 3027s = 18631 passed, 594 skipped, 7 xfailed, 3 xpassed, 8130 warnings in 744.17s (0:12:24) = 3049s 3049s DueCredit Report: 3049s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] 3049s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] 3049s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] 3049s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] 3049s - HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] 3049s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] 3049s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] 3049s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] 3049s - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] 3049s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] 3049s - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] 3049s - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 2.7.0, 1.1) [15, 16] 3049s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] 3049s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] 3049s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] 3049s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] 3049s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] 3049s - Scientific tools library / numpy (v 1.26.4) [22] 3049s 3049s 2 packages cited 3049s 16 modules cited 3049s 0 functions cited 3049s 3049s References 3049s ---------- 3049s 3049s [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. 3049s [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. 3049s [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. 3049s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 3049s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 3049s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460. 3049s [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. 3049s [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. 3049s [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. 3049s [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). 3049s [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. 3049s [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. 3049s [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. 3049s [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. 3049s [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. 3049s [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. 3049s [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. 3049s [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. 3049s [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. 3049s [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. 3049s [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. 3049s [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. 3053s autopkgtest [02:41:09]: test test-mdanalysis: -----------------------] 3054s autopkgtest [02:41:10]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 3054s test-mdanalysis PASS 3054s autopkgtest [02:41:10]: @@@@@@@@@@@@@@@@@@@@ summary 3054s test-mdanalysis PASS 3067s nova [W] Skipping flock in bos03-arm64 3067s Creating nova instance adt-plucky-arm64-mdanalysis-20241115-015016-juju-7f2275-prod-proposed-migration-environment-15-744ef305-222e-4984-b9d7-c09e7f70786a from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...