0s autopkgtest [15:56:26]: starting date and time: 2024-11-15 15:56:26+0000
  0s autopkgtest [15:56:26]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [15:56:26]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5dc2g107/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:matplotlib --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=matplotlib/3.8.3-3ubuntu1 -- lxd -r lxd-armhf-10.145.243.171 lxd-armhf-10.145.243.171:autopkgtest/ubuntu/plucky/armhf
 52s autopkgtest [15:57:18]: testbed dpkg architecture: armhf
 54s autopkgtest [15:57:20]: testbed apt version: 2.9.8
 54s autopkgtest [15:57:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 61s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 61s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 62s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB]
 62s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.2 kB]
 62s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1052 kB]
 62s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [146 kB]
 62s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [751 kB]
 62s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4428 B]
 62s Fetched 2144 kB in 1s (2130 kB/s)
 62s Reading package lists...
 79s tee: /proc/self/fd/2: Permission denied
101s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
101s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
101s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
101s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
103s Reading package lists...
103s Reading package lists...
103s Building dependency tree...
103s Reading state information...
104s Calculating upgrade...
104s The following packages will be upgraded:
104s   python3-markupsafe
104s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
104s Need to get 12.5 kB of archives.
104s After this operation, 10.2 kB of additional disk space will be used.
104s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf python3-markupsafe armhf 2.1.5-1build3 [12.5 kB]
105s Fetched 12.5 kB in 0s (81.8 kB/s)
105s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 59566 files and directories currently installed.)
105s Preparing to unpack .../python3-markupsafe_2.1.5-1build3_armhf.deb ...
105s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ...
105s Setting up python3-markupsafe (2.1.5-1build3) ...
106s Reading package lists...
106s Building dependency tree...
106s Reading state information...
107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
109s autopkgtest [15:58:15]: rebooting testbed after setup commands that affected boot
175s autopkgtest [15:59:21]: testbed running kernel: Linux 6.8.0-47-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Oct  2 16:39:14 UTC 2
202s autopkgtest [15:59:48]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis
218s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B]
218s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB]
218s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB]
219s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC
219s gpgv:                using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA
219s gpgv:                issuer "dparsons@debian.org"
219s gpgv: Can't check signature: No public key
219s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found
220s autopkgtest [16:00:06]: testing package mdanalysis version 2.7.0-5
222s autopkgtest [16:00:08]: build not needed
227s autopkgtest [16:00:13]: test test-mdanalysis: preparing testbed
238s Reading package lists...
238s Building dependency tree...
238s Reading state information...
239s Starting pkgProblemResolver with broken count: 0
239s Starting 2 pkgProblemResolver with broken count: 0
239s Done
240s The following additional packages will be installed:
240s   autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14
240s   cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cython3 debhelper
240s   debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
240s   dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome
240s   fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14
240s   g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14
240s   gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian
240s   libaec0 libarchive-zip-perl libasan8 libblas3 libc-dev-bin libc6-dev
240s   libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl libdeflate0 libexpat1-dev
240s   libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6
240s   libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
240s   libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libisl23 libjbig0
240s   libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-mathjax
240s   libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0
240s   liblcms2-2 liblerc4 liblzf1 libmpc3 libnetcdf19t64 libopenjp2-7
240s   libpixman-1-0 libpython3-all-dev libpython3-dev libpython3.12-dev
240s   libpython3.12t64 libqhull-r8.0 libraqm0 libsharpyuv0 libstdc++-14-dev libsz2
240s   libtcl8.6 libtiff6 libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2
240s   libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1
240s   libxss1 linux-libc-dev m4 po-debconf pybuild-plugin-pyproject
240s   python-matplotlib-data python-mdanalysis-doc python3-alabaster python3-all
240s   python3-all-dev python3-appdirs python3-biopython python3-brotli
240s   python3-build python3-cairo python3-cftime python3-citeproc
240s   python3-contourpy python3-cycler python3-dateutil python3-decorator
240s   python3-defusedxml python3-dev python3-docutils python3-duecredit
240s   python3-fasteners python3-fonttools python3-freetype python3-fs
240s   python3-griddataformats python3-gsd python3-h5py python3-h5py-serial
240s   python3-hypothesis python3-imagesize python3-iniconfig python3-installer
240s   python3-joblib python3-kiwisolver python3-latexcodec python3-looseversion
240s   python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib
240s   python3-mdanalysis python3-mmtf python3-monotonic python3-mpmath
240s   python3-mrcfile python3-msgpack python3-msmb-theme python3-netcdf4
240s   python3-networkx python3-numpy python3-packaging python3-pandas
240s   python3-pandas-lib python3-pil python3-pil.imagetk python3-pluggy
240s   python3-pybtex python3-pybtex-docutils python3-pyproject-hooks
240s   python3-pytest python3-reportlab python3-rlpycairo python3-roman
240s   python3-scipy python3-seaborn python3-six python3-sklearn
240s   python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
240s   python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap
240s   python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy
240s   python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz
240s   python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev
240s   python3.12-tk rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common
240s   tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings
240s   xfonts-utils xml-core zlib1g-dev
240s Suggested packages:
240s   autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales
240s   cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf
240s   fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
240s   gdb-arm-linux-gnueabihf gettext-doc libasprintf-dev libgettextpo-dev
240s   libc-devtools glibc-doc libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix
240s   libjs-mathjax-doc liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc
240s   gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl bwa clustalo
240s   clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank
240s   probcons python3-mysqldb python3-rdflib python3-psycopg2 raxml samtools
240s   t-coffee wise python3-pip python3-venv python-build-doc python-cycler-doc
240s   docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
240s   texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc
240s   python-hypothesis-doc python-installer-doc python-joblib-doc
240s   python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg
240s   fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common
240s   python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject
240s   python3-pyqt5 python3-sip python3-tornado texlive-extra-utils
240s   texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal
240s   python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc
240s   python3-statsmodels python-pil-doc python-pybtex-doc
240s   python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools
240s   python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap
240s   python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm
240s   fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre
240s   texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic
240s   python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg
240s   python3.13-tk sgml-base-doc
240s Recommended packages:
240s   manpages manpages-dev libarchive-cpio-perl javascript-common libjson-xs-perl
240s   libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+
240s   libpaper-utils python3-click python3-simplejson python3-psutil python3-bs4
240s   python3-cssselect python3-html5lib python3-bottleneck python3-numexpr
240s   python3-odf python3-openpyxl python3-tables python3-olefile
240s   fonts-dejavu-extra isympy-common
240s The following NEW packages will be installed:
240s   autoconf automake autopkgtest-satdep autopoint autotools-dev blt
240s   build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf
240s   cpp-arm-linux-gnueabihf cython3 debhelper debugedit dh-autoreconf dh-python
240s   dh-strip-nondeterminism docutils-common dwz fontconfig-config
240s   fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx
240s   fonts-mathjax fonts-urw-base35 g++ g++-14 g++-14-arm-linux-gnueabihf
240s   g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf
240s   gcc-arm-linux-gnueabihf gettext intltool-debian libaec0 libarchive-zip-perl
240s   libasan8 libblas3 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev
240s   libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl
240s   libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev libgfortran5 libgomp1
240s   libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64
240s   libimagequant0 libisl23 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery
240s   libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl
240s   liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblzf1 libmpc3 libnetcdf19t64
240s   libopenjp2-7 libpixman-1-0 libpython3-all-dev libpython3-dev
240s   libpython3.12-dev libpython3.12t64 libqhull-r8.0 libraqm0 libsharpyuv0
240s   libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libubsan1
240s   libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2
240s   libxrender1 libxslt1.1 libxss1 linux-libc-dev m4 po-debconf
240s   pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc
240s   python3-alabaster python3-all python3-all-dev python3-appdirs
240s   python3-biopython python3-brotli python3-build python3-cairo python3-cftime
240s   python3-citeproc python3-contourpy python3-cycler python3-dateutil
240s   python3-decorator python3-defusedxml python3-dev python3-docutils
240s   python3-duecredit python3-fasteners python3-fonttools python3-freetype
240s   python3-fs python3-griddataformats python3-gsd python3-h5py
240s   python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig
240s   python3-installer python3-joblib python3-kiwisolver python3-latexcodec
240s   python3-looseversion python3-lxml python3-lz4 python3-matplotlib
240s   python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic
240s   python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme
240s   python3-netcdf4 python3-networkx python3-numpy python3-packaging
240s   python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk
240s   python3-pluggy python3-pybtex python3-pybtex-docutils
240s   python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo
240s   python3-roman python3-scipy python3-seaborn python3-six python3-sklearn
240s   python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
240s   python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap
240s   python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy
240s   python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz
240s   python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev
240s   python3.12-tk rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common
240s   tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings
240s   xfonts-utils xml-core zlib1g-dev
240s 0 upgraded, 205 newly installed, 0 to remove and 0 not upgraded.
240s Need to get 188 MB/188 MB of archives.
240s After this operation, 726 MB of additional disk space will be used.
240s Get:1 /tmp/autopkgtest.dci7le/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [1012 B]
240s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB]
241s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB]
241s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB]
241s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB]
241s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB]
241s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB]
241s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB]
241s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.15+dfsg-2 [909 kB]
241s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB]
241s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB]
241s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB]
241s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB]
241s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB]
241s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
241s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB]
241s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB]
241s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB]
241s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB]
241s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB]
241s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB]
241s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B]
241s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.15-1 [685 kB]
241s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7build1 [525 kB]
241s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf blt armhf 2.5.3+dfsg-7build1 [4840 B]
241s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB]
241s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB]
241s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB]
241s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB]
241s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB]
241s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB]
241s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB]
241s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [9219 kB]
241s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-8ubuntu1 [1032 B]
241s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B]
241s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB]
241s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-8ubuntu1 [43.3 kB]
241s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB]
241s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-8ubuntu1 [2901 kB]
242s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-8ubuntu1 [1150 kB]
242s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-8ubuntu1 [897 kB]
242s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [18.0 MB]
242s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-8ubuntu1 [498 kB]
242s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B]
242s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B]
242s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-8ubuntu1 [2569 kB]
242s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [10.5 MB]
243s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-8ubuntu1 [19.9 kB]
243s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B]
243s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B]
243s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B]
243s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf cython3 armhf 3.0.11+dfsg-1ubuntu2 [3061 kB]
243s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB]
243s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-7build1 [166 kB]
243s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB]
243s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB]
243s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB]
243s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B]
243s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB]
243s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB]
243s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB]
243s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB]
243s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB]
243s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB]
243s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20241024 [112 kB]
243s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB]
243s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB]
243s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
243s Get:69 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lyx all 2.4.2.1-1 [171 kB]
243s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
243s Get:71 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB]
243s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB]
243s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB]
243s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB]
243s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B]
243s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB]
243s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB]
243s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.4-1 [121 kB]
243s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB]
243s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB]
243s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB]
243s Get:82 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B]
243s Get:83 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB]
243s Get:84 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB]
243s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB]
243s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB]
243s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B]
243s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
243s Get:89 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
244s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
244s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB]
244s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-perl all 4.10000-1 [81.9 kB]
244s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB]
244s Get:94 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB]
244s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB]
244s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB]
244s Get:97 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B]
244s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf libnetcdf19t64 armhf 1:4.9.2-6ubuntu1 [419 kB]
244s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.7-3 [2075 kB]
244s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB]
244s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.7-3 [4344 kB]
244s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-dev armhf 3.12.6-0ubuntu1 [10.2 kB]
244s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-all-dev armhf 3.12.6-0ubuntu1 [914 B]
244s Get:104 http://ftpmaster.internal/ubuntu plucky/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB]
244s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB]
244s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB]
244s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB]
244s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB]
244s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB]
244s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB]
244s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB]
244s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu1 [150 kB]
244s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB]
244s Get:114 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyproject-hooks all 1.2.0-1 [10.2 kB]
244s Get:115 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-toml all 0.10.2-1 [16.5 kB]
244s Get:116 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-wheel all 0.44.0-1 [54.2 kB]
244s Get:117 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-build all 1.2.2-1 [31.0 kB]
244s Get:118 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-installer all 0.7.0+dfsg1-3 [17.4 kB]
244s Get:119 http://ftpmaster.internal/ubuntu plucky/universe armhf pybuild-plugin-pyproject all 6.20241024 [1728 B]
245s Get:120 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB]
245s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
246s Get:122 http://ftpmaster.internal/ubuntu plucky/universe armhf python-mdanalysis-doc all 2.7.0-5 [2323 kB]
246s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B]
246s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.7-3 [505 kB]
246s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dev armhf 3.12.6-0ubuntu1 [26.7 kB]
246s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all-dev armhf 3.12.6-0ubuntu1 [908 B]
246s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf python3-appdirs all 1.4.4-4 [10.9 kB]
246s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB]
246s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-tk armhf 3.12.7-3 [112 kB]
246s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tk armhf 3.12.6-1ubuntu1 [9806 B]
246s Get:131 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pil.imagetk armhf 10.4.0-1ubuntu1 [8848 B]
246s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB]
246s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB]
246s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB]
246s Get:135 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB]
246s Get:136 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B]
246s Get:137 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB]
246s Get:138 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB]
246s Get:139 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB]
246s Get:140 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-brotli armhf 1.1.0-2build2 [321 kB]
246s Get:141 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cftime armhf 1.6.4-1 [202 kB]
246s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lxml armhf 5.3.0-1 [1234 kB]
246s Get:143 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-citeproc all 0.6.0-3 [98.4 kB]
246s Get:144 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-contourpy armhf 1.3.0-2 [192 kB]
246s Get:145 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cycler all 0.12.1-1 [9716 B]
246s Get:146 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB]
246s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-2 [80.3 kB]
246s Get:148 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB]
246s Get:149 http://ftpmaster.internal/ubuntu plucky/main armhf python3-defusedxml all 0.7.1-2 [42.0 kB]
246s Get:150 http://ftpmaster.internal/ubuntu plucky/main armhf python3-roman all 4.2-1 [10.0 kB]
246s Get:151 http://ftpmaster.internal/ubuntu plucky/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB]
246s Get:152 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-looseversion all 1.3.0-3 [8354 B]
246s Get:153 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-duecredit all 0.10.2-2 [66.0 kB]
246s Get:154 http://ftpmaster.internal/ubuntu plucky/main armhf python3-monotonic all 1.6-2 [5732 B]
246s Get:155 http://ftpmaster.internal/ubuntu plucky/main armhf python3-fasteners all 0.18-2 [12.5 kB]
246s Get:156 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB]
246s Get:157 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB]
246s Get:158 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mpmath all 1.3.0-1 [425 kB]
246s Get:159 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sympy all 1.13.3-1 [4228 kB]
246s Get:160 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB]
246s Get:161 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fs all 2.4.16-4 [91.3 kB]
246s Get:162 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-lz4 armhf 4.0.2+dfsg-1build4 [24.8 kB]
246s Get:163 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-unicodedata2 armhf 15.1.0+ds-1build2 [357 kB]
246s Get:164 http://ftpmaster.internal/ubuntu plucky/universe armhf unicode-data all 15.1.0-1 [8878 kB]
246s Get:165 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fonttools armhf 4.46.0-1build2 [1402 kB]
246s Get:166 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB]
246s Get:167 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mrcfile all 1.5.3-3 [114 kB]
246s Get:168 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-griddataformats all 1.0.2-2 [2107 kB]
246s Get:169 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-gsd armhf 3.3.0-1 [197 kB]
246s Get:170 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-5ubuntu1 [1061 kB]
246s Get:171 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-5ubuntu1 [7974 B]
246s Get:172 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sortedcontainers all 2.4.0-2 [27.6 kB]
246s Get:173 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-hypothesis all 6.116.0-1 [326 kB]
246s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf python3-imagesize all 1.4.1-1 [6844 B]
246s Get:175 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B]
246s Get:176 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.3.2-5 [206 kB]
246s Get:177 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-kiwisolver armhf 1.4.7-2build1 [71.1 kB]
246s Get:178 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-latexcodec all 3.0.0-1 [16.6 kB]
246s Get:179 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-matplotlib armhf 3.8.3-3ubuntu1 [4597 kB]
247s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mda-xdrlib all 0.2.0-3 [11.4 kB]
247s Get:181 http://ftpmaster.internal/ubuntu plucky/main armhf python3-msgpack armhf 1.0.3-3build2 [76.1 kB]
247s Get:182 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB]
247s Get:183 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-threadpoolctl all 3.1.0-1 [21.3 kB]
247s Get:184 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.0-1 [91.6 kB]
247s Get:185 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mdanalysis armhf 2.7.0-5 [1882 kB]
247s Get:186 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-common all 7.4.7-4 [775 kB]
247s Get:187 http://ftpmaster.internal/ubuntu plucky/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB]
247s Get:188 http://ftpmaster.internal/ubuntu plucky/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB]
247s Get:189 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sphinx all 7.4.7-4 [593 kB]
247s Get:190 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B]
247s Get:191 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB]
247s Get:192 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-msmb-theme all 1.2.0-4 [35.4 kB]
247s Get:193 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-netcdf4 armhf 1.7.2-1 [589 kB]
247s Get:194 http://ftpmaster.internal/ubuntu plucky/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB]
247s Get:195 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5 [4728 kB]
247s Get:196 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5 [3112 kB]
247s Get:197 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB]
247s Get:198 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex all 0.24.0-4 [70.0 kB]
247s Get:199 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex-docutils all 1.0.2-1 [7176 B]
247s Get:200 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.3-1 [251 kB]
247s Get:201 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-seaborn all 0.13.2-4 [225 kB]
247s Get:202 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn-lib armhf 1.4.2+dfsg-6 [3751 kB]
248s Get:203 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn all 1.4.2+dfsg-6 [2257 kB]
248s Get:204 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-sitemap all 2.6.0-1 [6674 B]
248s Get:205 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB]
249s Fetched 188 MB in 8s (23.4 MB/s)
249s Selecting previously unselected package fonts-lato.
249s (Reading database ... 
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(Reading database ... 59567 files and directories currently installed.)
249s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ...
249s Unpacking fonts-lato (2.015-1) ...
249s Selecting previously unselected package sgml-base.
249s Preparing to unpack .../001-sgml-base_1.31_all.deb ...
249s Unpacking sgml-base (1.31) ...
249s Selecting previously unselected package m4.
249s Preparing to unpack .../002-m4_1.4.19-4build1_armhf.deb ...
249s Unpacking m4 (1.4.19-4build1) ...
249s Selecting previously unselected package autoconf.
249s Preparing to unpack .../003-autoconf_2.72-3_all.deb ...
249s Unpacking autoconf (2.72-3) ...
249s Selecting previously unselected package autotools-dev.
249s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ...
249s Unpacking autotools-dev (20220109.1) ...
249s Selecting previously unselected package automake.
249s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ...
249s Unpacking automake (1:1.16.5-1.3ubuntu1) ...
249s Selecting previously unselected package autopoint.
249s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ...
249s Unpacking autopoint (0.22.5-2) ...
249s Selecting previously unselected package libtcl8.6:armhf.
249s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_armhf.deb ...
249s Unpacking libtcl8.6:armhf (8.6.15+dfsg-2) ...
249s Selecting previously unselected package libfreetype6:armhf.
249s Preparing to unpack .../008-libfreetype6_2.13.3+dfsg-1_armhf.deb ...
249s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ...
249s Selecting previously unselected package fonts-dejavu-mono.
249s Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ...
249s Unpacking fonts-dejavu-mono (2.37-8) ...
249s Selecting previously unselected package fonts-dejavu-core.
249s Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ...
250s Unpacking fonts-dejavu-core (2.37-8) ...
250s Selecting previously unselected package libfontenc1:armhf.
250s Preparing to unpack .../011-libfontenc1_1%3a1.1.8-1build1_armhf.deb ...
250s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ...
250s Selecting previously unselected package x11-common.
250s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ...
250s Unpacking x11-common (1:7.7+23ubuntu3) ...
250s Selecting previously unselected package xfonts-encodings.
250s Preparing to unpack .../013-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
250s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
250s Selecting previously unselected package xfonts-utils.
250s Preparing to unpack .../014-xfonts-utils_1%3a7.7+7_armhf.deb ...
250s Unpacking xfonts-utils (1:7.7+7) ...
250s Selecting previously unselected package fonts-urw-base35.
250s Preparing to unpack .../015-fonts-urw-base35_20200910-8_all.deb ...
250s Unpacking fonts-urw-base35 (20200910-8) ...
250s Selecting previously unselected package fontconfig-config.
250s Preparing to unpack .../016-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ...
250s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
250s Selecting previously unselected package libfontconfig1:armhf.
250s Preparing to unpack .../017-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ...
250s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ...
250s Selecting previously unselected package libxrender1:armhf.
250s Preparing to unpack .../018-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ...
250s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ...
250s Selecting previously unselected package libxft2:armhf.
251s Preparing to unpack .../019-libxft2_2.3.6-1build1_armhf.deb ...
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251s Selecting previously unselected package libxss1:armhf.
251s Preparing to unpack .../020-libxss1_1%3a1.2.3-1build3_armhf.deb ...
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251s Selecting previously unselected package libtk8.6:armhf.
251s Preparing to unpack .../021-libtk8.6_8.6.15-1_armhf.deb ...
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251s Selecting previously unselected package tk8.6-blt2.5.
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251s Selecting previously unselected package blt.
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251s Selecting previously unselected package libc-dev-bin.
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251s Selecting previously unselected package linux-libc-dev:armhf.
251s Preparing to unpack .../025-linux-libc-dev_6.11.0-8.8_armhf.deb ...
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251s Selecting previously unselected package libcrypt-dev:armhf.
251s Preparing to unpack .../026-libcrypt-dev_1%3a4.4.36-4build1_armhf.deb ...
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251s Selecting previously unselected package rpcsvc-proto.
251s Preparing to unpack .../027-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ...
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251s Selecting previously unselected package libc6-dev:armhf.
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251s Selecting previously unselected package libisl23:armhf.
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251s Selecting previously unselected package libmpc3:armhf.
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251s Selecting previously unselected package cpp-14-arm-linux-gnueabihf.
251s Preparing to unpack .../031-cpp-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ...
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252s Selecting previously unselected package cpp-14.
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252s Unpacking cpp-14 (14.2.0-8ubuntu1) ...
252s Selecting previously unselected package cpp-arm-linux-gnueabihf.
252s Preparing to unpack .../033-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ...
252s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ...
252s Selecting previously unselected package cpp.
252s Preparing to unpack .../034-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ...
252s Unpacking cpp (4:14.1.0-2ubuntu1) ...
252s Selecting previously unselected package libcc1-0:armhf.
252s Preparing to unpack .../035-libcc1-0_14.2.0-8ubuntu1_armhf.deb ...
252s Unpacking libcc1-0:armhf (14.2.0-8ubuntu1) ...
252s Selecting previously unselected package libgomp1:armhf.
252s Preparing to unpack .../036-libgomp1_14.2.0-8ubuntu1_armhf.deb ...
252s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ...
252s Selecting previously unselected package libasan8:armhf.
252s Preparing to unpack .../037-libasan8_14.2.0-8ubuntu1_armhf.deb ...
252s Unpacking libasan8:armhf (14.2.0-8ubuntu1) ...
252s Selecting previously unselected package libubsan1:armhf.
252s Preparing to unpack .../038-libubsan1_14.2.0-8ubuntu1_armhf.deb ...
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252s Selecting previously unselected package libgcc-14-dev:armhf.
252s Preparing to unpack .../039-libgcc-14-dev_14.2.0-8ubuntu1_armhf.deb ...
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252s Selecting previously unselected package gcc-14-arm-linux-gnueabihf.
252s Preparing to unpack .../040-gcc-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ...
252s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ...
253s Selecting previously unselected package gcc-14.
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253s Selecting previously unselected package gcc-arm-linux-gnueabihf.
253s Preparing to unpack .../042-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ...
253s Unpacking gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ...
253s Selecting previously unselected package gcc.
253s Preparing to unpack .../043-gcc_4%3a14.1.0-2ubuntu1_armhf.deb ...
253s Unpacking gcc (4:14.1.0-2ubuntu1) ...
253s Selecting previously unselected package libstdc++-14-dev:armhf.
253s Preparing to unpack .../044-libstdc++-14-dev_14.2.0-8ubuntu1_armhf.deb ...
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253s Selecting previously unselected package g++-14-arm-linux-gnueabihf.
253s Preparing to unpack .../045-g++-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ...
253s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ...
253s Selecting previously unselected package g++-14.
253s Preparing to unpack .../046-g++-14_14.2.0-8ubuntu1_armhf.deb ...
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253s Selecting previously unselected package g++-arm-linux-gnueabihf.
253s Preparing to unpack .../047-g++-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ...
253s Unpacking g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ...
253s Selecting previously unselected package g++.
253s Preparing to unpack .../048-g++_4%3a14.1.0-2ubuntu1_armhf.deb ...
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253s Selecting previously unselected package build-essential.
253s Preparing to unpack .../049-build-essential_12.10ubuntu1_armhf.deb ...
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253s Selecting previously unselected package cython3.
253s Preparing to unpack .../050-cython3_3.0.11+dfsg-1ubuntu2_armhf.deb ...
253s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ...
254s Selecting previously unselected package libdebhelper-perl.
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254s Unpacking libdebhelper-perl (13.20ubuntu1) ...
254s Selecting previously unselected package libtool.
254s Preparing to unpack .../052-libtool_2.4.7-7build1_all.deb ...
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254s Selecting previously unselected package dh-autoreconf.
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254s Unpacking dh-autoreconf (20) ...
254s Selecting previously unselected package libarchive-zip-perl.
254s Preparing to unpack .../054-libarchive-zip-perl_1.68-1_all.deb ...
254s Unpacking libarchive-zip-perl (1.68-1) ...
254s Selecting previously unselected package libfile-stripnondeterminism-perl.
254s Preparing to unpack .../055-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
254s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
254s Selecting previously unselected package dh-strip-nondeterminism.
254s Preparing to unpack .../056-dh-strip-nondeterminism_1.14.0-1_all.deb ...
254s Unpacking dh-strip-nondeterminism (1.14.0-1) ...
254s Selecting previously unselected package debugedit.
254s Preparing to unpack .../057-debugedit_1%3a5.1-1_armhf.deb ...
254s Unpacking debugedit (1:5.1-1) ...
254s Selecting previously unselected package dwz.
254s Preparing to unpack .../058-dwz_0.15-1build6_armhf.deb ...
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254s Selecting previously unselected package gettext.
254s Preparing to unpack .../059-gettext_0.22.5-2_armhf.deb ...
254s Unpacking gettext (0.22.5-2) ...
254s Selecting previously unselected package intltool-debian.
254s Preparing to unpack .../060-intltool-debian_0.35.0+20060710.6_all.deb ...
254s Unpacking intltool-debian (0.35.0+20060710.6) ...
254s Selecting previously unselected package po-debconf.
254s Preparing to unpack .../061-po-debconf_1.0.21+nmu1_all.deb ...
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254s Selecting previously unselected package debhelper.
254s Preparing to unpack .../062-debhelper_13.20ubuntu1_all.deb ...
254s Unpacking debhelper (13.20ubuntu1) ...
254s Selecting previously unselected package dh-python.
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254s Unpacking dh-python (6.20241024) ...
254s Selecting previously unselected package xml-core.
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254s Selecting previously unselected package docutils-common.
254s Preparing to unpack .../065-docutils-common_0.21.2+dfsg-2_all.deb ...
254s Unpacking docutils-common (0.21.2+dfsg-2) ...
254s Selecting previously unselected package fonts-font-awesome.
254s Preparing to unpack .../066-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
254s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
254s Selecting previously unselected package fonts-lyx.
254s Preparing to unpack .../067-fonts-lyx_2.4.2.1-1_all.deb ...
254s Unpacking fonts-lyx (2.4.2.1-1) ...
255s Selecting previously unselected package fonts-mathjax.
255s Preparing to unpack .../068-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
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255s Selecting previously unselected package libaec0:armhf.
255s Preparing to unpack .../069-libaec0_1.1.3-1_armhf.deb ...
255s Unpacking libaec0:armhf (1.1.3-1) ...
255s Selecting previously unselected package libblas3:armhf.
255s Preparing to unpack .../070-libblas3_3.12.0-3build2_armhf.deb ...
255s Unpacking libblas3:armhf (3.12.0-3build2) ...
255s Selecting previously unselected package libpixman-1-0:armhf.
255s Preparing to unpack .../071-libpixman-1-0_0.44.0-3_armhf.deb ...
255s Unpacking libpixman-1-0:armhf (0.44.0-3) ...
255s Selecting previously unselected package libxcb-render0:armhf.
255s Preparing to unpack .../072-libxcb-render0_1.17.0-2_armhf.deb ...
255s Unpacking libxcb-render0:armhf (1.17.0-2) ...
255s Selecting previously unselected package libxcb-shm0:armhf.
255s Preparing to unpack .../073-libxcb-shm0_1.17.0-2_armhf.deb ...
255s Unpacking libxcb-shm0:armhf (1.17.0-2) ...
255s Selecting previously unselected package libcairo2:armhf.
255s Preparing to unpack .../074-libcairo2_1.18.2-2_armhf.deb ...
255s Unpacking libcairo2:armhf (1.18.2-2) ...
255s Selecting previously unselected package libdeflate0:armhf.
255s Preparing to unpack .../075-libdeflate0_1.22-1_armhf.deb ...
255s Unpacking libdeflate0:armhf (1.22-1) ...
255s Selecting previously unselected package libexpat1-dev:armhf.
255s Preparing to unpack .../076-libexpat1-dev_2.6.4-1_armhf.deb ...
255s Unpacking libexpat1-dev:armhf (2.6.4-1) ...
255s Selecting previously unselected package libgfortran5:armhf.
255s Preparing to unpack .../077-libgfortran5_14.2.0-8ubuntu1_armhf.deb ...
255s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ...
255s Selecting previously unselected package libgraphite2-3:armhf.
255s Preparing to unpack .../078-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ...
255s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ...
255s Selecting previously unselected package libharfbuzz0b:armhf.
255s Preparing to unpack .../079-libharfbuzz0b_10.0.1-1_armhf.deb ...
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255s Selecting previously unselected package libsz2:armhf.
255s Preparing to unpack .../080-libsz2_1.1.3-1_armhf.deb ...
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255s Selecting previously unselected package libhdf5-103-1t64:armhf.
255s Preparing to unpack .../081-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ...
255s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ...
255s Selecting previously unselected package libhdf5-hl-100t64:armhf.
255s Preparing to unpack .../082-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ...
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255s Selecting previously unselected package libimagequant0:armhf.
255s Preparing to unpack .../083-libimagequant0_2.18.0-1build1_armhf.deb ...
255s Unpacking libimagequant0:armhf (2.18.0-1build1) ...
255s Selecting previously unselected package libjpeg-turbo8:armhf.
255s Preparing to unpack .../084-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ...
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255s Selecting previously unselected package libjpeg8:armhf.
255s Preparing to unpack .../085-libjpeg8_8c-2ubuntu11_armhf.deb ...
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255s Selecting previously unselected package libjs-jquery.
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256s Selecting previously unselected package libjs-jquery-ui.
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256s Selecting previously unselected package libjs-underscore.
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256s Selecting previously unselected package libjs-sphinxdoc.
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256s Selecting previously unselected package libjson-perl.
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256s Selecting previously unselected package liblapack3:armhf.
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256s Selecting previously unselected package liblbfgsb0:armhf.
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256s Selecting previously unselected package liblcms2-2:armhf.
256s Preparing to unpack .../093-liblcms2-2_2.16-2_armhf.deb ...
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256s Selecting previously unselected package liblerc4:armhf.
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256s Selecting previously unselected package liblzf1:armhf.
256s Preparing to unpack .../095-liblzf1_3.6-4_armhf.deb ...
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256s Selecting previously unselected package libnetcdf19t64:armhf.
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256s Selecting previously unselected package libpython3.12t64:armhf.
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256s Selecting previously unselected package zlib1g-dev:armhf.
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256s Selecting previously unselected package libpython3.12-dev:armhf.
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257s Selecting previously unselected package libpython3-dev:armhf.
257s Preparing to unpack .../100-libpython3-dev_3.12.6-0ubuntu1_armhf.deb ...
257s Unpacking libpython3-dev:armhf (3.12.6-0ubuntu1) ...
257s Selecting previously unselected package libpython3-all-dev:armhf.
257s Preparing to unpack .../101-libpython3-all-dev_3.12.6-0ubuntu1_armhf.deb ...
257s Unpacking libpython3-all-dev:armhf (3.12.6-0ubuntu1) ...
257s Selecting previously unselected package libqhull-r8.0:armhf.
257s Preparing to unpack .../102-libqhull-r8.0_2020.2-6build1_armhf.deb ...
257s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ...
257s Selecting previously unselected package libraqm0:armhf.
257s Preparing to unpack .../103-libraqm0_0.10.1-1build1_armhf.deb ...
257s Unpacking libraqm0:armhf (0.10.1-1build1) ...
257s Selecting previously unselected package libsharpyuv0:armhf.
257s Preparing to unpack .../104-libsharpyuv0_1.4.0-0.1_armhf.deb ...
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257s Selecting previously unselected package libjbig0:armhf.
257s Preparing to unpack .../105-libjbig0_2.1-6.1ubuntu2_armhf.deb ...
257s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ...
257s Selecting previously unselected package libwebp7:armhf.
257s Preparing to unpack .../106-libwebp7_1.4.0-0.1_armhf.deb ...
257s Unpacking libwebp7:armhf (1.4.0-0.1) ...
257s Selecting previously unselected package libtiff6:armhf.
257s Preparing to unpack .../107-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ...
257s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ...
257s Selecting previously unselected package libwebpdemux2:armhf.
257s Preparing to unpack .../108-libwebpdemux2_1.4.0-0.1_armhf.deb ...
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257s Selecting previously unselected package libwebpmux3:armhf.
257s Preparing to unpack .../109-libwebpmux3_1.4.0-0.1_armhf.deb ...
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257s Selecting previously unselected package libxslt1.1:armhf.
257s Preparing to unpack .../110-libxslt1.1_1.1.39-0exp1ubuntu1_armhf.deb ...
257s Unpacking libxslt1.1:armhf (1.1.39-0exp1ubuntu1) ...
257s Selecting previously unselected package python3-packaging.
257s Preparing to unpack .../111-python3-packaging_24.1-1_all.deb ...
257s Unpacking python3-packaging (24.1-1) ...
257s Selecting previously unselected package python3-pyproject-hooks.
257s Preparing to unpack .../112-python3-pyproject-hooks_1.2.0-1_all.deb ...
257s Unpacking python3-pyproject-hooks (1.2.0-1) ...
257s Selecting previously unselected package python3-toml.
257s Preparing to unpack .../113-python3-toml_0.10.2-1_all.deb ...
257s Unpacking python3-toml (0.10.2-1) ...
257s Selecting previously unselected package python3-wheel.
257s Preparing to unpack .../114-python3-wheel_0.44.0-1_all.deb ...
257s Unpacking python3-wheel (0.44.0-1) ...
257s Selecting previously unselected package python3-build.
257s Preparing to unpack .../115-python3-build_1.2.2-1_all.deb ...
257s Unpacking python3-build (1.2.2-1) ...
257s Selecting previously unselected package python3-installer.
257s Preparing to unpack .../116-python3-installer_0.7.0+dfsg1-3_all.deb ...
257s Unpacking python3-installer (0.7.0+dfsg1-3) ...
257s Selecting previously unselected package pybuild-plugin-pyproject.
257s Preparing to unpack .../117-pybuild-plugin-pyproject_6.20241024_all.deb ...
257s Unpacking pybuild-plugin-pyproject (6.20241024) ...
257s Selecting previously unselected package python-matplotlib-data.
257s Preparing to unpack .../118-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ...
257s Unpacking python-matplotlib-data (3.8.3-3ubuntu1) ...
258s Selecting previously unselected package libjs-mathjax.
258s Preparing to unpack .../119-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
258s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
258s Selecting previously unselected package python-mdanalysis-doc.
258s Preparing to unpack .../120-python-mdanalysis-doc_2.7.0-5_all.deb ...
258s Unpacking python-mdanalysis-doc (2.7.0-5) ...
258s Selecting previously unselected package python3-all.
258s Preparing to unpack .../121-python3-all_3.12.6-0ubuntu1_armhf.deb ...
258s Unpacking python3-all (3.12.6-0ubuntu1) ...
258s Selecting previously unselected package python3.12-dev.
258s Preparing to unpack .../122-python3.12-dev_3.12.7-3_armhf.deb ...
258s Unpacking python3.12-dev (3.12.7-3) ...
259s Selecting previously unselected package python3-dev.
259s Preparing to unpack .../123-python3-dev_3.12.6-0ubuntu1_armhf.deb ...
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259s Selecting previously unselected package python3-all-dev.
259s Preparing to unpack .../124-python3-all-dev_3.12.6-0ubuntu1_armhf.deb ...
259s Unpacking python3-all-dev (3.12.6-0ubuntu1) ...
259s Selecting previously unselected package python3-appdirs.
259s Preparing to unpack .../125-python3-appdirs_1.4.4-4_all.deb ...
259s Unpacking python3-appdirs (1.4.4-4) ...
259s Selecting previously unselected package python3-numpy.
259s Preparing to unpack .../126-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ...
259s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
259s Selecting previously unselected package python3.12-tk.
259s Preparing to unpack .../127-python3.12-tk_3.12.7-3_armhf.deb ...
259s Unpacking python3.12-tk (3.12.7-3) ...
259s Selecting previously unselected package python3-tk:armhf.
259s Preparing to unpack .../128-python3-tk_3.12.6-1ubuntu1_armhf.deb ...
259s Unpacking python3-tk:armhf (3.12.6-1ubuntu1) ...
259s Selecting previously unselected package python3-pil.imagetk:armhf.
259s Preparing to unpack .../129-python3-pil.imagetk_10.4.0-1ubuntu1_armhf.deb ...
259s Unpacking python3-pil.imagetk:armhf (10.4.0-1ubuntu1) ...
259s Selecting previously unselected package libopenjp2-7:armhf.
259s Preparing to unpack .../130-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ...
259s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ...
259s Selecting previously unselected package python3-pil:armhf.
259s Preparing to unpack .../131-python3-pil_10.4.0-1ubuntu1_armhf.deb ...
259s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ...
259s Selecting previously unselected package python3-cairo.
259s Preparing to unpack .../132-python3-cairo_1.26.1-2_armhf.deb ...
259s Unpacking python3-cairo (1.26.1-2) ...
259s Selecting previously unselected package python3-freetype.
259s Preparing to unpack .../133-python3-freetype_2.5.1-1_all.deb ...
259s Unpacking python3-freetype (2.5.1-1) ...
259s Selecting previously unselected package python3-rlpycairo.
259s Preparing to unpack .../134-python3-rlpycairo_0.3.0-3_all.deb ...
259s Unpacking python3-rlpycairo (0.3.0-3) ...
259s Selecting previously unselected package python3-reportlab.
259s Preparing to unpack .../135-python3-reportlab_4.2.5-1_all.deb ...
259s Unpacking python3-reportlab (4.2.5-1) ...
260s Selecting previously unselected package w3c-sgml-lib.
260s Preparing to unpack .../136-w3c-sgml-lib_1.3-3_all.deb ...
260s Unpacking w3c-sgml-lib (1.3-3) ...
260s Selecting previously unselected package python3-biopython.
260s Preparing to unpack .../137-python3-biopython_1.84+dfsg-4_armhf.deb ...
260s Unpacking python3-biopython (1.84+dfsg-4) ...
260s Selecting previously unselected package python3-brotli.
260s Preparing to unpack .../138-python3-brotli_1.1.0-2build2_armhf.deb ...
260s Unpacking python3-brotli (1.1.0-2build2) ...
260s Selecting previously unselected package python3-cftime.
260s Preparing to unpack .../139-python3-cftime_1.6.4-1_armhf.deb ...
260s Unpacking python3-cftime (1.6.4-1) ...
260s Selecting previously unselected package python3-lxml:armhf.
260s Preparing to unpack .../140-python3-lxml_5.3.0-1_armhf.deb ...
260s Unpacking python3-lxml:armhf (5.3.0-1) ...
260s Selecting previously unselected package python3-citeproc.
260s Preparing to unpack .../141-python3-citeproc_0.6.0-3_all.deb ...
260s Unpacking python3-citeproc (0.6.0-3) ...
260s Selecting previously unselected package python3-contourpy.
260s Preparing to unpack .../142-python3-contourpy_1.3.0-2_armhf.deb ...
260s Unpacking python3-contourpy (1.3.0-2) ...
260s Selecting previously unselected package python3-cycler.
260s Preparing to unpack .../143-python3-cycler_0.12.1-1_all.deb ...
260s Unpacking python3-cycler (0.12.1-1) ...
260s Selecting previously unselected package python3-six.
260s Preparing to unpack .../144-python3-six_1.16.0-7_all.deb ...
260s Unpacking python3-six (1.16.0-7) ...
260s Selecting previously unselected package python3-dateutil.
260s Preparing to unpack .../145-python3-dateutil_2.9.0-2_all.deb ...
260s Unpacking python3-dateutil (2.9.0-2) ...
260s Selecting previously unselected package python3-decorator.
260s Preparing to unpack .../146-python3-decorator_5.1.1-5_all.deb ...
260s Unpacking python3-decorator (5.1.1-5) ...
260s Selecting previously unselected package python3-defusedxml.
260s Preparing to unpack .../147-python3-defusedxml_0.7.1-2_all.deb ...
260s Unpacking python3-defusedxml (0.7.1-2) ...
260s Selecting previously unselected package python3-roman.
260s Preparing to unpack .../148-python3-roman_4.2-1_all.deb ...
260s Unpacking python3-roman (4.2-1) ...
260s Selecting previously unselected package python3-docutils.
260s Preparing to unpack .../149-python3-docutils_0.21.2+dfsg-2_all.deb ...
260s Unpacking python3-docutils (0.21.2+dfsg-2) ...
260s Selecting previously unselected package python3-looseversion.
261s Preparing to unpack .../150-python3-looseversion_1.3.0-3_all.deb ...
261s Unpacking python3-looseversion (1.3.0-3) ...
261s Selecting previously unselected package python3-duecredit.
261s Preparing to unpack .../151-python3-duecredit_0.10.2-2_all.deb ...
261s Unpacking python3-duecredit (0.10.2-2) ...
261s Selecting previously unselected package python3-monotonic.
261s Preparing to unpack .../152-python3-monotonic_1.6-2_all.deb ...
261s Unpacking python3-monotonic (1.6-2) ...
261s Selecting previously unselected package python3-fasteners.
261s Preparing to unpack .../153-python3-fasteners_0.18-2_all.deb ...
261s Unpacking python3-fasteners (0.18-2) ...
261s Selecting previously unselected package python3-scipy.
261s Preparing to unpack .../154-python3-scipy_1.13.1-5_armhf.deb ...
261s Unpacking python3-scipy (1.13.1-5) ...
261s Selecting previously unselected package python3-ufolib2.
261s Preparing to unpack .../155-python3-ufolib2_0.16.1+dfsg1-1_all.deb ...
261s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ...
261s Selecting previously unselected package python3-mpmath.
261s Preparing to unpack .../156-python3-mpmath_1.3.0-1_all.deb ...
261s Unpacking python3-mpmath (1.3.0-1) ...
261s Selecting previously unselected package python3-sympy.
261s Preparing to unpack .../157-python3-sympy_1.13.3-1_all.deb ...
261s Unpacking python3-sympy (1.13.3-1) ...
262s Selecting previously unselected package python3-tz.
262s Preparing to unpack .../158-python3-tz_2024.1-2_all.deb ...
262s Unpacking python3-tz (2024.1-2) ...
262s Selecting previously unselected package python3-fs.
262s Preparing to unpack .../159-python3-fs_2.4.16-4_all.deb ...
262s Unpacking python3-fs (2.4.16-4) ...
262s Selecting previously unselected package python3-lz4.
262s Preparing to unpack .../160-python3-lz4_4.0.2+dfsg-1build4_armhf.deb ...
262s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ...
262s Selecting previously unselected package python3-unicodedata2.
262s Preparing to unpack .../161-python3-unicodedata2_15.1.0+ds-1build2_armhf.deb ...
262s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ...
262s Selecting previously unselected package unicode-data.
262s Preparing to unpack .../162-unicode-data_15.1.0-1_all.deb ...
262s Unpacking unicode-data (15.1.0-1) ...
262s Selecting previously unselected package python3-fonttools.
263s Preparing to unpack .../163-python3-fonttools_4.46.0-1build2_armhf.deb ...
263s Unpacking python3-fonttools (4.46.0-1build2) ...
263s Selecting previously unselected package sphinx-rtd-theme-common.
263s Preparing to unpack .../164-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ...
263s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ...
263s Selecting previously unselected package python3-mrcfile.
263s Preparing to unpack .../165-python3-mrcfile_1.5.3-3_all.deb ...
263s Unpacking python3-mrcfile (1.5.3-3) ...
263s Selecting previously unselected package python3-griddataformats.
263s Preparing to unpack .../166-python3-griddataformats_1.0.2-2_all.deb ...
263s Unpacking python3-griddataformats (1.0.2-2) ...
263s Selecting previously unselected package python3-gsd.
263s Preparing to unpack .../167-python3-gsd_3.3.0-1_armhf.deb ...
263s Unpacking python3-gsd (3.3.0-1) ...
263s Selecting previously unselected package python3-h5py-serial.
263s Preparing to unpack .../168-python3-h5py-serial_3.11.0-5ubuntu1_armhf.deb ...
263s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ...
263s Selecting previously unselected package python3-h5py.
263s Preparing to unpack .../169-python3-h5py_3.11.0-5ubuntu1_all.deb ...
263s Unpacking python3-h5py (3.11.0-5ubuntu1) ...
263s Selecting previously unselected package python3-sortedcontainers.
263s Preparing to unpack .../170-python3-sortedcontainers_2.4.0-2_all.deb ...
263s Unpacking python3-sortedcontainers (2.4.0-2) ...
263s Selecting previously unselected package python3-hypothesis.
263s Preparing to unpack .../171-python3-hypothesis_6.116.0-1_all.deb ...
263s Unpacking python3-hypothesis (6.116.0-1) ...
263s Selecting previously unselected package python3-imagesize.
263s Preparing to unpack .../172-python3-imagesize_1.4.1-1_all.deb ...
263s Unpacking python3-imagesize (1.4.1-1) ...
263s Selecting previously unselected package python3-iniconfig.
263s Preparing to unpack .../173-python3-iniconfig_1.1.1-2_all.deb ...
263s Unpacking python3-iniconfig (1.1.1-2) ...
263s Selecting previously unselected package python3-joblib.
263s Preparing to unpack .../174-python3-joblib_1.3.2-5_all.deb ...
263s Unpacking python3-joblib (1.3.2-5) ...
263s Selecting previously unselected package python3-kiwisolver.
263s Preparing to unpack .../175-python3-kiwisolver_1.4.7-2build1_armhf.deb ...
263s Unpacking python3-kiwisolver (1.4.7-2build1) ...
263s Selecting previously unselected package python3-latexcodec.
263s Preparing to unpack .../176-python3-latexcodec_3.0.0-1_all.deb ...
263s Unpacking python3-latexcodec (3.0.0-1) ...
263s Selecting previously unselected package python3-matplotlib.
263s Preparing to unpack .../177-python3-matplotlib_3.8.3-3ubuntu1_armhf.deb ...
263s Unpacking python3-matplotlib (3.8.3-3ubuntu1) ...
264s Selecting previously unselected package python3-mda-xdrlib.
264s Preparing to unpack .../178-python3-mda-xdrlib_0.2.0-3_all.deb ...
264s Unpacking python3-mda-xdrlib (0.2.0-3) ...
264s Selecting previously unselected package python3-msgpack.
264s Preparing to unpack .../179-python3-msgpack_1.0.3-3build2_armhf.deb ...
264s Unpacking python3-msgpack (1.0.3-3build2) ...
264s Selecting previously unselected package python3-mmtf.
264s Preparing to unpack .../180-python3-mmtf_1.1.3-1_all.deb ...
264s Unpacking python3-mmtf (1.1.3-1) ...
264s Selecting previously unselected package python3-threadpoolctl.
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264s Unpacking python3-threadpoolctl (3.1.0-1) ...
264s Selecting previously unselected package python3-tqdm.
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264s Unpacking python3-tqdm (4.67.0-1) ...
264s Selecting previously unselected package python3-mdanalysis.
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264s Unpacking python3-mdanalysis (2.7.0-5) ...
264s Selecting previously unselected package sphinx-common.
264s Preparing to unpack .../184-sphinx-common_7.4.7-4_all.deb ...
264s Unpacking sphinx-common (7.4.7-4) ...
264s Selecting previously unselected package python3-alabaster.
264s Preparing to unpack .../185-python3-alabaster_0.7.16-0.1_all.deb ...
264s Unpacking python3-alabaster (0.7.16-0.1) ...
264s Selecting previously unselected package python3-snowballstemmer.
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264s Unpacking python3-snowballstemmer (2.2.0-4build1) ...
264s Selecting previously unselected package python3-sphinx.
264s Preparing to unpack .../187-python3-sphinx_7.4.7-4_all.deb ...
264s Unpacking python3-sphinx (7.4.7-4) ...
264s Selecting previously unselected package python3-sphinxcontrib.jquery.
264s Preparing to unpack .../188-python3-sphinxcontrib.jquery_4.1-5_all.deb ...
264s Unpacking python3-sphinxcontrib.jquery (4.1-5) ...
264s Selecting previously unselected package python3-sphinx-rtd-theme.
264s Preparing to unpack .../189-python3-sphinx-rtd-theme_3.0.1+dfsg-1_all.deb ...
264s Unpacking python3-sphinx-rtd-theme (3.0.1+dfsg-1) ...
264s Selecting previously unselected package python3-msmb-theme.
264s Preparing to unpack .../190-python3-msmb-theme_1.2.0-4_all.deb ...
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264s Selecting previously unselected package python3-netcdf4.
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265s Selecting previously unselected package python3-networkx.
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265s Unpacking python3-networkx (3.2.1-4ubuntu1) ...
265s Selecting previously unselected package python3-pandas-lib:armhf.
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266s Selecting previously unselected package python3-pandas.
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266s Selecting previously unselected package python3-pluggy.
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266s Selecting previously unselected package python3-pybtex.
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266s Selecting previously unselected package python3-pybtex-docutils.
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266s Selecting previously unselected package python3-pytest.
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266s Selecting previously unselected package python3-seaborn.
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266s Selecting previously unselected package python3-sklearn-lib:armhf.
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267s Selecting previously unselected package python3-sphinx-sitemap.
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267s Selecting previously unselected package python3-sphinxcontrib.bibtex.
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267s Selecting previously unselected package autopkgtest-satdep.
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267s Setting up dh-python (6.20241024) ...
267s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ...
267s Setting up liblcms2-2:armhf (2.16-2) ...
267s Setting up python3-iniconfig (1.1.1-2) ...
267s Setting up libpixman-1-0:armhf (0.44.0-3) ...
267s Setting up libsharpyuv0:armhf (1.4.0-0.1) ...
267s Setting up fonts-lato (2.015-1) ...
267s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
267s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ...
267s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
267s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ...
267s Setting up python3-joblib (1.3.2-5) ...
267s Setting up python3-lz4 (4.0.2+dfsg-1build4) ...
268s Setting up libxcb-render0:armhf (1.17.0-2) ...
268s Setting up python3-defusedxml (0.7.1-2) ...
268s Setting up libarchive-zip-perl (1.68-1) ...
268s Setting up python3-alabaster (0.7.16-0.1) ...
268s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ...
268s Setting up fonts-lyx (2.4.2.1-1) ...
268s Setting up libdebhelper-perl (13.20ubuntu1) ...
268s Setting up python3-tqdm (4.67.0-1) ...
268s Setting up python3-threadpoolctl (3.1.0-1) ...
268s Setting up x11-common (1:7.7+23ubuntu3) ...
269s Setting up libdeflate0:armhf (1.22-1) ...
269s Setting up linux-libc-dev:armhf (6.11.0-8.8) ...
269s Setting up m4 (1.4.19-4build1) ...
269s Setting up python3-latexcodec (3.0.0-1) ...
269s Setting up libqhull-r8.0:armhf (2020.2-6build1) ...
269s Setting up python3-all (3.12.6-0ubuntu1) ...
269s Setting up libxcb-shm0:armhf (1.17.0-2) ...
269s Setting up python3-sortedcontainers (2.4.0-2) ...
269s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ...
269s Setting up python3-networkx (3.2.1-4ubuntu1) ...
271s Setting up python3-wheel (0.44.0-1) ...
271s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ...
271s Setting up python3-mda-xdrlib (0.2.0-3) ...
271s Setting up libaec0:armhf (1.1.3-1) ...
271s Setting up python3-tz (2024.1-2) ...
271s Setting up python3-monotonic (1.6-2) ...
271s Setting up unicode-data (15.1.0-1) ...
271s Setting up python3-six (1.16.0-7) ...
271s Setting up libpython3.12t64:armhf (3.12.7-3) ...
271s Setting up python3-roman (4.2-1) ...
272s Setting up python3-decorator (5.1.1-5) ...
272s Setting up libfontenc1:armhf (1:1.1.8-1build1) ...
272s Setting up autotools-dev (20220109.1) ...
272s Setting up libblas3:armhf (3.12.0-3build2) ...
272s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
272s Setting up python3-packaging (24.1-1) ...
272s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ...
272s Setting up python3-pyproject-hooks (1.2.0-1) ...
272s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ...
272s Setting up python3-snowballstemmer (2.2.0-4build1) ...
272s Setting up python3-brotli (1.1.0-2build2) ...
272s Setting up liblzf1:armhf (3.6-4) ...
272s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
272s Setting up python3-cycler (0.12.1-1) ...
273s Setting up libimagequant0:armhf (2.18.0-1build1) ...
273s Setting up fonts-dejavu-mono (2.37-8) ...
273s Setting up python3-kiwisolver (1.4.7-2build1) ...
273s Setting up libmpc3:armhf (1.3.1-1build2) ...
273s Setting up cython3 (3.0.11+dfsg-1ubuntu2) ...
274s Setting up libtcl8.6:armhf (8.6.15+dfsg-2) ...
274s Setting up autopoint (0.22.5-2) ...
274s Setting up fonts-dejavu-core (2.37-8) ...
274s Setting up python3-fasteners (0.18-2) ...
274s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ...
274s Setting up python3-toml (0.10.2-1) ...
274s Setting up python3-installer (0.7.0+dfsg1-3) ...
274s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ...
274s Setting up autoconf (2.72-3) ...
274s Setting up python3-pluggy (1.5.0-1) ...
274s Setting up libwebp7:armhf (1.4.0-0.1) ...
274s Setting up python3-pybtex (0.24.0-4) ...
275s Setting up libubsan1:armhf (14.2.0-8ubuntu1) ...
275s Setting up dwz (0.15-1build6) ...
275s Setting up python3-looseversion (1.3.0-3) ...
275s Setting up libcrypt-dev:armhf (1:4.4.36-4build1) ...
275s Setting up libasan8:armhf (14.2.0-8ubuntu1) ...
275s Setting up libjson-perl (4.10000-1) ...
275s Setting up libxslt1.1:armhf (1.1.39-0exp1ubuntu1) ...
275s Setting up debugedit (1:5.1-1) ...
275s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ...
275s Setting up libharfbuzz0b:armhf (10.0.1-1) ...
275s Setting up python3-dateutil (2.9.0-2) ...
275s Setting up sgml-base (1.31) ...
275s Setting up python3-msgpack (1.0.3-3build2) ...
275s Setting up libxss1:armhf (1:1.2.3-1build3) ...
275s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
275s Setting up libgcc-14-dev:armhf (14.2.0-8ubuntu1) ...
275s Setting up python3-mpmath (1.3.0-1) ...
276s Setting up libisl23:armhf (0.27-1) ...
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348s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ...
348s Setting up python3-msmb-theme (1.2.0-4) ...
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379s (Reading database ... 86868 files and directories currently installed.)
379s Removing autopkgtest-satdep (0) ...
385s autopkgtest [16:02:51]: test test-mdanalysis: [-----------------------
387s skipping tests with SKIP_TEST_LIST=
399s ============================= test session starts ==============================
399s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
399s rootdir: /tmp/autopkgtest.dci7le/build.glK/src
399s plugins: typeguard-4.4.1, hypothesis-6.116.0
399s collected 19229 items / 6 skipped
399s 
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1062s ..s                                                                      [ 53%]
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1114s ....                                                                     [ 85%]
1114s testsuite/MDAnalysisTests/test_api.py ............................       [ 86%]
1120s testsuite/MDAnalysisTests/topology/test_altloc.py ...                    [ 86%]
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1120s testsuite/MDAnalysisTests/topology/test_dlpoly.py ...................... [ 86%]
1120s ..........................................                               [ 86%]
1122s testsuite/MDAnalysisTests/topology/test_dms.py ....................      [ 86%]
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1122s .....                                                                    [ 86%]
1125s testsuite/MDAnalysisTests/topology/test_gro.py ...............           [ 86%]
1125s testsuite/MDAnalysisTests/topology/test_gsd.py ......................... [ 86%]
1125s ......                                                                   [ 86%]
1125s testsuite/MDAnalysisTests/topology/test_guessers.py .................... [ 87%]
1125s ..............ssssssssss                                                 [ 87%]
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1134s testsuite/MDAnalysisTests/topology/test_mol2.py ........................ [ 89%]
1134s .......                                                                  [ 89%]
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1138s ..........................                                               [ 89%]
1139s testsuite/MDAnalysisTests/topology/test_pdbqt.py .........               [ 89%]
1140s testsuite/MDAnalysisTests/topology/test_pqr.py ....................      [ 89%]
1148s testsuite/MDAnalysisTests/topology/test_psf.py ......................... [ 89%]
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1160s ...........                                                              [ 91%]
1160s testsuite/MDAnalysisTests/topology/test_topology_base.py ...             [ 91%]
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1231s testsuite/MDAnalysisTests/topology/test_xyz.py ........................  [ 96%]
1231s testsuite/MDAnalysisTests/transformations/test_base.py .....             [ 96%]
1231s testsuite/MDAnalysisTests/transformations/test_boxdimensions.py ........ [ 96%]
1231s ......                                                                   [ 96%]
1231s testsuite/MDAnalysisTests/transformations/test_fit.py .................. [ 96%]
1231s .........................................                                [ 96%]
1233s testsuite/MDAnalysisTests/transformations/test_nojump.py ............    [ 96%]
1233s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py .... [ 96%]
1233s .                                                                        [ 96%]
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1244s .......                                                                  [ 97%]
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1244s testsuite/MDAnalysisTests/utils/test_datafiles.py ....                   [ 97%]
1244s testsuite/MDAnalysisTests/utils/test_duecredit.py ..............         [ 97%]
1244s testsuite/MDAnalysisTests/utils/test_failure.py .                        [ 97%]
1244s testsuite/MDAnalysisTests/utils/test_imports.py ........................ [ 97%]
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1244s ...................                                                      [ 98%]
1244s testsuite/MDAnalysisTests/utils/test_log.py .                            [ 98%]
1244s testsuite/MDAnalysisTests/utils/test_meta.py ....                        [ 98%]
1246s testsuite/MDAnalysisTests/utils/test_modelling.py .............          [ 98%]
1247s testsuite/MDAnalysisTests/utils/test_persistence.py .......              [ 98%]
1259s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%]
1259s ..............ss..                                                       [ 98%]
1259s testsuite/MDAnalysisTests/utils/test_qcprot.py ......                    [ 98%]
1261s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%]
1261s                                                                          [ 98%]
1261s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 98%]
1262s ...............                                                          [ 99%]
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1262s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%]
1262s .......                                                                  [ 99%]
1263s testsuite/MDAnalysisTests/visualization/test_streamlines.py ...          [100%]
1263s 
1263s =============================== warnings summary ===============================
1263s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39
1263s   /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
1263s   
1263s   Due to the on going maintenance burden of keeping command line application
1263s   wrappers up to date, we have decided to deprecate and eventually remove these
1263s   modules.
1263s   
1263s   We instead now recommend building your command line and invoking it directly
1263s   with the subprocess module.
1263s     warnings.warn(
1263s 
1263s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings
1263s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings
1263s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings
1263s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings
1263s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings
1263s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings
1263s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings
1263s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings
1263s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings
1263s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings
1263s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings
1263s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings
1263s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
1263s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings
1263s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings
1263s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings
1263s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings
1263s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings
1263s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings
1263s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings
1263s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings
1263s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings
1263s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings
1263s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings
1263s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings
1263s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings
1263s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
1263s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings
1263s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
1263s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings
1263s   /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.
1263s     warnings.warn("DCDReader currently makes independent timesteps"
1263s 
1263s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52
1263s   /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.
1263s     warnings.warn(wmsg, category=DeprecationWarning)
1263s 
1263s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles'
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings
1263s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written
1263s     warnings.warn(wmsg)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings
1263s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings
1263s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings
1263s   /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
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings
1263s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
1263s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings
1263s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning
1263s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'h1', 'hc', 'c3', 'oh', 'ho'}. These have been given an empty element record.
1263s     warnings.warn("Unknown elements found for some "
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning
1263s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings
1263s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings
1263s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
1263s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings
1263s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings
1263s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     self.times[i] = ts.time
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning
1263s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings
1263s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
1263s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings
1263s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings
1263s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings
1263s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded
1263s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     results.append((ts.time, x.sum() / mask.sum()))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue
1263s   /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.
1263s     warnings.warn(msg)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
1263s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding
1263s   /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
1263s     warnings.warn(msg)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
1263s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1263s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
1263s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings
1263s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning
1263s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings
1263s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings
1263s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings
1263s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
1263s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings
1263s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings
1263s   /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.
1263s     warnings.warn("Element information is missing, elements attribute "
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran
1263s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame
1263s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections
1263s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues
1263s     warnings.warn("Cannot determine phi and psi angles for the first "
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin
1263s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr
1263s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame
1263s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot
1263s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning
1263s   /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.
1263s     warnings.warn(f"All residues selected with '{select_remove}' "
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings
1263s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings
1263s   /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=5347) is multi-threaded, use of fork() may lead to deadlocks in the child.
1263s     self.pid = os.fork()
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes
1263s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide
1263s     cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide
1263s     local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T  # (n_res-3, 3)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
1263s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice
1263s     ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
1263s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide
1263s     ret = um.true_divide(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
1263s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide
1263s     ret = ret.dtype.type(ret / rcount)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
1263s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning
1263s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning
1263s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
1263s   /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.
1263s     warnings.warn("1 A^3 CRYST1 record,"
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values.
1263s     warnings.warn("Unit cell dimensions not found. "
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' '
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings
1263s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings
1263s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings
1263s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
1263s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings
1263s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
1263s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning
1263s   /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
1263s     warnings.warn(wmsg, DeprecationWarning)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6
1263s     warnings.warn("Desired number of sample points too high, using {0}"
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbond = HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbond = HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbond = HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbond = HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbond = HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbond = HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbond = HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbond = HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     HBAC(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1263s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1263s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbond = HBAC(u,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated!
1263s   `find_hydrogen_donors` will be removed in release 3.0.0.
1263s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     D = hbonds.find_hydrogen_donors(H)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated!
1263s   `find_hydrogen_donors` will be removed in release 3.0.0.
1263s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1263s     hbonds.find_hydrogen_donors(u.atoms)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
1263s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
1263s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
1263s     return _methods._mean(a, axis=axis, dtype=dtype,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
1263s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
1263s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
1263s     ret = ret.dtype.type(ret / rcount)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1263s   /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.
1263s     warnings.warn(msg.format(sel))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1263s   /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.
1263s     warnings.warn(msg.format(sel))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1263s   /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.
1263s     warnings.warn(msg.format(sel))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned.
1263s     warnings.warn("Empty string to select atoms, empty group returned.",
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1263s   /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, .
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1263s   /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, .
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
1263s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
1263s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
1263s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
1263s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
1263s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
1263s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple
1263s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content
1263s   /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.
1263s     warnings.warn(wmsg)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning
1263s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning
1263s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
1263s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
1263s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
1263s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
1263s   /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.)
1263s     phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j
1263s   /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
1263s     warnings.warn("Column index entered (j = {:d} is smaller than row "
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     dt=self.trajectory.ts.dt * step,
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8]
1263s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0]
1263s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8]
1263s   /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
1263s     warnings.warn(wmsg, DeprecationWarning)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
1263s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings
1263s   /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.
1263s     warnings.warn("The `u` attribute is superflous and will be removed "
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267]
1263s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm
1263s   /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.
1263s     warnings.warn("The `density` attribute was deprecated in "
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata
1263s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first.
1263s     warnings.warn(msg, category=MissingDataWarning)
1263s 
1263s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     self.timesteps.append(self._ts.time)
1263s 
1263s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning
1263s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default
1263s     warnings.warn("{} does not support time selection. Reverting to "
1263s 
1263s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default
1263s     warnings.warn("{} does not support data selection. Reverting to "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
1263s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings
1263s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     return self.ts.dt
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
1263s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     ts.data['time'] = step_num * ts.dt
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats
1263s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_unsupported_filetypes
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xeeeca3e8>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
1263s       self.close()
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close
1263s       self._apply('close')
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply
1263s       return [reader.__getattribute__(method)(**kwargs) for reader in self.readers]
1263s                                                                       ^^^^^^^^^^^^
1263s   AttributeError: 'ChainReader' object has no attribute 'readers'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing
1263s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain
1263s     warnings.warn("Missing frame in continuous chain", UserWarning)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     time_frame_0 = ts.time - ts.frame*ts.dt  # assumes ts.dt is constant
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     self._add_step_to_frame_data(ts.time)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames]
1263s   /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. 
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids]
1263s   /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. 
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names]
1263s   /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. 
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors]
1263s   /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. 
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     if not np.allclose(A.time, B.time):
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1]
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2]
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3]
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0]
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1]
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2]
1263s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array
1263s   /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
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xeeeca3e8>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
1263s       self.close()
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close
1263s       self._file.close()
1263s       ^^^^^^^^^^
1263s   AttributeError: 'DCDReader' object has no attribute '_file'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms
1263s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit
1263s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function DCDWriter.__del__ at 0xeee41988>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__
1263s       self.close()
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close
1263s       self._file.close()
1263s       ^^^^^^^^^^
1263s   AttributeError: 'DCDWriter' object has no attribute '_file'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings
1263s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings
1263s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
1263s   /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.
1263s     warnings.warn(msg)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     return self.ts.time
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter]
1263s   /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. 
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     assert_equal(reader.ts.dt, reader.dt)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     time_frame = time_frame_0 + frame_index*ts.dt
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     reader_p = pickle.loads(pickle.dumps(reader))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings
1263s   /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
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.]
1263s     warnings.warn(wmsg)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
1263s   /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`.
1263s     warnings.warn(wmsg)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present.  Unset velocities set to zero.
1263s     warnings.warn("Not all velocities were present.  "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     reader_p = pickle.loads(pickle.dumps(reader))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader
1263s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     reader_p = pickle.loads(pickle.dumps(reader))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xeeeca3e8>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
1263s       self.close()
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close
1263s       self._file.close()
1263s       ^^^^^^^^^^
1263s   AttributeError: 'H5MDReader' object has no attribute '_file'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM'
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xeeeca3e8>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
1263s       for aux in self.aux_list:
1263s                  ^^^^^^^^^^^^^
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
1263s       return self._auxs.keys()
1263s              ^^^^^^^^^^
1263s   AttributeError: 'H5MDReader' object has no attribute '_auxs'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
1263s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0
1263s     warnings.warn('Guessed all Masses to 1.0')
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit
1263s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xeeeca3e8>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
1263s       for aux in self.aux_list:
1263s                  ^^^^^^^^^^^^^
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
1263s       return self._auxs.keys()
1263s              ^^^^^^^^^^
1263s   AttributeError: 'DCDReader' object has no attribute '_auxs'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view
1263s   /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
1263s     warnings.warn("MemoryReader.timeseries inclusive `stop` "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader
1263s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     reader_p = pickle.loads(pickle.dumps(reader))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
1263s   /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
1263s     warnings.warn(wmsg)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     ts.time)  # in-place ! (hope this works...)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     time_list = [ts.time for ts in u.trajectory]
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     assert u.trajectory.ts.dt == pytest.approx(ref)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4
1263s   /tmp/autopkgtest.dci7le/build.glK/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.)
1263s     return self._test_write_trajectory(universe, outfile)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0]
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0]
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0]
1263s   /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.
1263s     warnings.warn(wmsg)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
1263s   /tmp/autopkgtest.dci7le/build.glK/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.)
1263s     return self._test_write_trajectory(universe, outfile)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of ''
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'
1263s     warnings.warn("Found missing chainIDs."
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom]
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond]
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom]
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree]
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond]
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     time = ts.time
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0xeeeca528>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
1263s       self.close()
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close
1263s       if self.trjfile is not None:
1263s          ^^^^^^^^^^^^
1263s   AttributeError: 'NCDFWriter' object has no attribute 'trjfile'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK'
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' '
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1'
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X'
1263s     warnings.warn("Found no information for attr: '{}'"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X'
1263s     warnings.warn("Found chainIDs using unnaccepted character."
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X'
1263s     warnings.warn("Found chainIDs with invalid length."
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000.  Higher serials have been guessed
1263s     warnings.warn("Serial numbers went over 100,000.  "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed
1263s     warnings.warn("Invalid atom serials were present, bonds will not"
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed
1263s     warnings.warn("Invalid atom serials were present, "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment
1263s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
1263s   /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.
1263s     warnings.warn(wmsg)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
1263s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1263s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
1263s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1263s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges
1263s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
1263s   /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. 
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     assert_equal(ts.dt, 1.0)  # default value
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     assert_equal(ts.time, 0.0)  # default to 1.0 (dt) * 0 (frame)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xeeeca3e8>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
1263s       for aux in self.aux_list:
1263s                  ^^^^^^^^^^^^^
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
1263s       return self._auxs.keys()
1263s              ^^^^^^^^^^
1263s   AttributeError: 'TNGReader' object has no attribute '_auxs'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms
1263s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe
1263s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe
1263s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks!
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xeeeca3e8>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
1263s       self.close()
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close
1263s       if self.trjfile is None:
1263s          ^^^^^^^^^^^^
1263s   AttributeError: 'TRJReader' object has no attribute 'trjfile'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     data['time'] = ts.time
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
1263s   /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
1263s     warnings.warn("Timestep didn't have the following attributes: '{0}', "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
1263s   /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. 
1263s     warnings.warn("Timestep didn't have velocity information, "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
1263s   /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
1263s     warnings.warn("Timestep didn't have dimensions information, "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0xeeeca528>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
1263s       self.close()
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close
1263s       if self.trzfile is None:
1263s          ^^^^^^^^^^^^
1263s   AttributeError: 'TRZWriter' object has no attribute 'trzfile'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
1263s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
1263s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
1263s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
1263s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
1263s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
1263s   /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.
1263s     warnings.warn("Element information is missing, elements attribute "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
1263s   /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
1263s     warnings.warn(wmsg, DeprecationWarning)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter]
1263s   /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. 
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter]
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter]
1263s   /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. 
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter]
1263s   /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. 
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter]
1263s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter]
1263s   /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'
1263s     warnings.warn(wmsg)
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD
1263s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     time = ts.time
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD
1263s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     time = ts.time
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0xebe32618>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
1263s       self.close()
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
1263s       self._xdr.close()
1263s       ^^^^^^^^^
1263s   AttributeError: 'XTCWriter' object has no attribute '_xdr'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container
1263s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0xebe32618>
1263s   
1263s   Traceback (most recent call last):
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
1263s       self.close()
1263s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
1263s       self._xdr.close()
1263s       ^^^^^^^^^
1263s   AttributeError: 'TRRWriter' object has no attribute '_xdr'
1263s   
1263s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
1263s   /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.
1263s   Consider setting 'refresh_offsets=True' when loading your Universe.
1263s     warnings.warn(f"Reading offsets from {fname} failed, "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly
1263s   /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.
1263s     warnings.warn(f"Cannot write lock/offset file in same location as "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
1263s   /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.
1263s   Consider setting 'refresh_offsets=True' when loading your Universe.
1263s     warnings.warn(f"Reading offsets from {fname} failed, "
1263s 
1263s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly
1263s   /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.
1263s     warnings.warn(f"Cannot write lock/offset file in same location as "
1263s 
1263s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms]
1263s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues]
1263s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments]
1263s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce
1263s     return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
1263s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
1263s   /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.
1263s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings
1263s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings
1263s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings
1263s   /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.
1263s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
1263s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
1263s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide
1263s     return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum()
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings
1263s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide
1263s     _centers /= _weights.sum(axis=1)[:, None]
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
1263s   /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`.
1263s     warnings.warn(msg, category=SelectionWarning)
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
1263s   /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`.
1263s     warnings.warn(msg, category=SelectionWarning)
1263s 
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12]
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13]
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15]
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16]
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17]
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18]
1263s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19]
1263s   /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`.
1263s     warnings.warn(msg, category=SelectionWarning)
1263s 
1263s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments]
1263s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules]
1263s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues]
1263s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group]
1263s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments]
1263s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc
1263s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc
1263s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options
1263s   /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
1263s     warnings.warn("The 'pbc' kwarg has been deprecated and will be "
1263s 
1263s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel
1263s   /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`.
1263s     warnings.warn(msg, category=SelectionWarning)
1263s 
1263s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial]
1263s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp]
1263s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial]
1263s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp]
1263s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide
1263s     x = np.dot(a, b) / (norm(a) * norm(b))
1263s 
1263s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt
1263s     ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2)
1263s 
1263s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt
1263s     box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 -
1263s 
1263s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide
1263s     a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z)))
1263s 
1263s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide
1263s     b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z)))
1263s 
1263s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide
1263s     c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y)))
1263s 
1263s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide
1263s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
1263s 
1263s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide
1263s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
1263s 
1263s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2]
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3]
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4]
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5]
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6]
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7]
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10]
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11]
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14]
1263s   /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     cls(buf, protocol).dump(obj)
1263s 
1263s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     ps = pickle.dumps(ref_reader)
1263s 
1263s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0]
1263s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd
1263s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd
1263s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset
1263s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific
1263s   /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset.
1263s     warnings.warn('Cannot average position for non sequential'
1263s 
1263s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name]
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname]
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type]
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid]
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information.  Defaulted to '1'
1263s     warnings.warn("PDB file is missing resid information.  "
1263s 
1263s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX
1263s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1263s 
1263s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2]
1263s   /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.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2]
1263s   /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.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2]
1263s   /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.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2]
1263s   /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.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
1263s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings
1263s   /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.
1263s     warnings.warn(msg)
1263s 
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts
1263s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr]
1263s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file.
1263s     warnings.warn('No coordinate reader found for {}. Skipping '
1263s 
1263s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses
1263s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses.
1263s     warnings.warn(msg, category=SelectionWarning)
1263s 
1263s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2
1263s   /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.
1263s     warnings.warn(
1263s 
1263s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
1263s 
1263s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
1263s 
1263s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL)
1263s 
1263s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL)
1263s 
1263s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL)
1263s 
1263s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL)
1263s 
1263s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag
1263s   /tmp/autopkgtest.dci7le/build.glK/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps
1263s     pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL)
1263s 
1263s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings
1263s   /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream
1263s     warnings.warn("Constructed NamedStream from a NamedStream",
1263s 
1263s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159]
1263s   /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.
1263s     warnings.warn(wmsg, DeprecationWarning)
1263s 
1263s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
1263s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8130 warnings in 875.24s (0:14:35) =
1287s 
1287s DueCredit Report:
1287s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2]
1287s   - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3]
1287s   - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4]
1287s   - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5]
1287s   - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8]
1287s   - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9]
1287s   - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10]
1287s   - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2]
1287s   - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.7.0) [11, 12]
1287s   - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13]
1287s   - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14]
1287s   - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 1.1, 2.7.0) [15, 16]
1287s   - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17]
1287s   - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18]
1287s   - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20]
1287s   - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17]
1287s   - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21]
1287s - Scientific tools library / numpy (v 1.26.4) [22]
1287s 
1287s 2 packages cited
1287s 16 modules cited
1287s 0 functions cited
1287s 
1287s References
1287s ----------
1287s 
1287s [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.
1287s [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.
1287s [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.
1287s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858.
1287s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415.
1287s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460.
1287s [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.
1287s [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.
1287s [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.
1287s [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).
1287s [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.
1287s [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.
1287s [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.
1287s [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.
1287s [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.
1287s [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.
1287s [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.
1287s [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.
1287s [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.
1287s [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.
1287s [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.
1287s [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.
1291s autopkgtest [16:17:57]: test test-mdanalysis: -----------------------]
1296s test-mdanalysis      PASS
1296s autopkgtest [16:18:02]: test test-mdanalysis:  - - - - - - - - - - results - - - - - - - - - -
1300s autopkgtest [16:18:06]: @@@@@@@@@@@@@@@@@@@@ summary
1300s test-mdanalysis      PASS