0s autopkgtest [20:17:54]: starting date and time: 2024-11-15 20:17:54+0000
  0s autopkgtest [20:17:54]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [20:17:54]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1ebx_r_r/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:scikit-learn --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-6build1 -- lxd -r lxd-armhf-10.145.243.240 lxd-armhf-10.145.243.240:autopkgtest/ubuntu/plucky/armhf
 52s autopkgtest [20:18:46]: testbed dpkg architecture: armhf
 54s autopkgtest [20:18:48]: testbed apt version: 2.9.8
 54s autopkgtest [20:18:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 62s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 62s 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/universe Sources [1043 kB]
 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [92.2 kB]
 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [143 kB]
 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [747 kB]
 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4428 B]
 63s Fetched 2126 kB in 1s (1833 kB/s)
 63s Reading package lists...
 80s tee: /proc/self/fd/2: Permission denied
103s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
105s Reading package lists...
105s Reading package lists...
106s Building dependency tree...
106s Reading state information...
106s Calculating upgrade...
107s The following NEW packages will be installed:
107s   libassuan9
107s The following packages will be upgraded:
107s   libgpgme11t64 libseccomp2 python3-cffi-backend python3-markupsafe
107s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
107s Need to get 297 kB of archives.
107s After this operation, 224 kB of additional disk space will be used.
107s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libseccomp2 armhf 2.5.5-1ubuntu5 [49.3 kB]
107s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cffi-backend armhf 1.17.1-2build1 [75.9 kB]
107s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libassuan9 armhf 3.0.1-2 [34.3 kB]
107s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgpgme11t64 armhf 1.24.0-2ubuntu1 [125 kB]
108s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-markupsafe armhf 2.1.5-1build3 [12.5 kB]
108s Fetched 297 kB in 1s (592 kB/s)
108s (Reading database ... 
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(Reading database ... 59566 files and directories currently installed.)
108s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu5_armhf.deb ...
108s Unpacking libseccomp2:armhf (2.5.5-1ubuntu5) over (2.5.5-1ubuntu4) ...
108s Setting up libseccomp2:armhf (2.5.5-1ubuntu5) ...
108s (Reading database ... 
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(Reading database ... 59566 files and directories currently installed.)
108s Preparing to unpack .../python3-cffi-backend_1.17.1-2build1_armhf.deb ...
108s Unpacking python3-cffi-backend:armhf (1.17.1-2build1) over (1.17.1-2) ...
108s Selecting previously unselected package libassuan9:armhf.
108s Preparing to unpack .../libassuan9_3.0.1-2_armhf.deb ...
108s Unpacking libassuan9:armhf (3.0.1-2) ...
108s Preparing to unpack .../libgpgme11t64_1.24.0-2ubuntu1_armhf.deb ...
108s Unpacking libgpgme11t64:armhf (1.24.0-2ubuntu1) over (1.23.2-5ubuntu4) ...
108s Preparing to unpack .../python3-markupsafe_2.1.5-1build3_armhf.deb ...
109s Unpacking python3-markupsafe (2.1.5-1build3) over (2.1.5-1build2) ...
109s Setting up python3-markupsafe (2.1.5-1build3) ...
109s Setting up libassuan9:armhf (3.0.1-2) ...
109s Setting up libgpgme11t64:armhf (1.24.0-2ubuntu1) ...
109s Setting up python3-cffi-backend:armhf (1.17.1-2build1) ...
109s Processing triggers for libc-bin (2.40-1ubuntu3) ...
109s Reading package lists...
110s Building dependency tree...
110s Reading state information...
111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
113s autopkgtest [20:19:47]: rebooting testbed after setup commands that affected boot
182s autopkgtest [20:20:56]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct  7 11:49:53 UTC 2
208s autopkgtest [20:21:22]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis
223s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B]
223s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB]
223s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB]
223s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC
223s gpgv:                using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA
223s gpgv:                issuer "dparsons@debian.org"
223s gpgv: Can't check signature: No public key
223s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found
225s autopkgtest [20:21:39]: testing package mdanalysis version 2.7.0-5
227s autopkgtest [20:21:41]: build not needed
232s autopkgtest [20:21:46]: test test-mdanalysis: preparing testbed
242s Reading package lists...
243s Building dependency tree...
243s Reading state information...
243s Starting pkgProblemResolver with broken count: 0
243s Starting 2 pkgProblemResolver with broken count: 0
243s Done
244s The following additional packages will be installed:
244s   autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14
244s   cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cython3 debhelper
244s   debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
244s   dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome
244s   fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14
244s   g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14
244s   gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian
244s   libaec0 libarchive-zip-perl libasan8 libblas3 libc-dev-bin libc6-dev
244s   libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl libdeflate0 libexpat1-dev
244s   libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6
244s   libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
244s   libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libisl23 libjbig0
244s   libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-mathjax
244s   libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0
244s   liblcms2-2 liblerc4 liblzf1 libmpc3 libnetcdf19t64 libopenjp2-7
244s   libpixman-1-0 libpython3-all-dev libpython3-dev libpython3.12-dev
244s   libpython3.12t64 libqhull-r8.0 libraqm0 libsharpyuv0 libstdc++-14-dev libsz2
244s   libtcl8.6 libtiff6 libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2
244s   libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1
244s   libxss1 linux-libc-dev m4 po-debconf pybuild-plugin-pyproject
244s   python-matplotlib-data python-mdanalysis-doc python3-alabaster python3-all
244s   python3-all-dev python3-appdirs python3-biopython python3-brotli
244s   python3-build python3-cairo python3-cftime python3-citeproc
244s   python3-contourpy python3-cycler python3-dateutil python3-decorator
244s   python3-defusedxml python3-dev python3-docutils python3-duecredit
244s   python3-fasteners python3-fonttools python3-freetype python3-fs
244s   python3-griddataformats python3-gsd python3-h5py python3-h5py-serial
244s   python3-hypothesis python3-imagesize python3-iniconfig python3-installer
244s   python3-joblib python3-kiwisolver python3-latexcodec python3-looseversion
244s   python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib
244s   python3-mdanalysis python3-mmtf python3-monotonic python3-mpmath
244s   python3-mrcfile python3-msgpack python3-msmb-theme python3-netcdf4
244s   python3-networkx python3-numpy python3-packaging python3-pandas
244s   python3-pandas-lib python3-pil python3-pil.imagetk python3-pluggy
244s   python3-pybtex python3-pybtex-docutils python3-pyproject-hooks
244s   python3-pytest python3-reportlab python3-rlpycairo python3-roman
244s   python3-scipy python3-seaborn python3-six python3-sklearn
244s   python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
244s   python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap
244s   python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy
244s   python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz
244s   python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev
244s   python3.12-tk rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common
244s   tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings
244s   xfonts-utils xml-core zlib1g-dev
244s Suggested packages:
244s   autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales
244s   cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf
244s   fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
244s   gdb-arm-linux-gnueabihf gettext-doc libasprintf-dev libgettextpo-dev
244s   libc-devtools glibc-doc libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix
244s   libjs-mathjax-doc liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc
244s   gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl bwa clustalo
244s   clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank
244s   probcons python3-mysqldb python3-rdflib python3-psycopg2 raxml samtools
244s   t-coffee wise python3-pip python3-venv python-build-doc python-cycler-doc
244s   docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
244s   texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc
244s   python-hypothesis-doc python-installer-doc python-joblib-doc
244s   python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg
244s   fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common
244s   python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject
244s   python3-pyqt5 python3-sip python3-tornado texlive-extra-utils
244s   texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal
244s   python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc
244s   python3-statsmodels python-pil-doc python-pybtex-doc
244s   python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools
244s   python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap
244s   python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm
244s   fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre
244s   texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic
244s   python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg
244s   python3.13-tk sgml-base-doc
244s Recommended packages:
244s   manpages manpages-dev libarchive-cpio-perl javascript-common libjson-xs-perl
244s   libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+
244s   libpaper-utils python3-click python3-simplejson python3-psutil python3-bs4
244s   python3-cssselect python3-html5lib python3-bottleneck python3-numexpr
244s   python3-odf python3-openpyxl python3-tables python3-olefile
244s   fonts-dejavu-extra isympy-common
245s The following NEW packages will be installed:
245s   autoconf automake autopkgtest-satdep autopoint autotools-dev blt
245s   build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf
245s   cpp-arm-linux-gnueabihf cython3 debhelper debugedit dh-autoreconf dh-python
245s   dh-strip-nondeterminism docutils-common dwz fontconfig-config
245s   fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx
245s   fonts-mathjax fonts-urw-base35 g++ g++-14 g++-14-arm-linux-gnueabihf
245s   g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf
245s   gcc-arm-linux-gnueabihf gettext intltool-debian libaec0 libarchive-zip-perl
245s   libasan8 libblas3 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev
245s   libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl
245s   libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev libgfortran5 libgomp1
245s   libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64
245s   libimagequant0 libisl23 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery
245s   libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl
245s   liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblzf1 libmpc3 libnetcdf19t64
245s   libopenjp2-7 libpixman-1-0 libpython3-all-dev libpython3-dev
245s   libpython3.12-dev libpython3.12t64 libqhull-r8.0 libraqm0 libsharpyuv0
245s   libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libubsan1
245s   libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2
245s   libxrender1 libxslt1.1 libxss1 linux-libc-dev m4 po-debconf
245s   pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc
245s   python3-alabaster python3-all python3-all-dev python3-appdirs
245s   python3-biopython python3-brotli python3-build python3-cairo python3-cftime
245s   python3-citeproc python3-contourpy python3-cycler python3-dateutil
245s   python3-decorator python3-defusedxml python3-dev python3-docutils
245s   python3-duecredit python3-fasteners python3-fonttools python3-freetype
245s   python3-fs python3-griddataformats python3-gsd python3-h5py
245s   python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig
245s   python3-installer python3-joblib python3-kiwisolver python3-latexcodec
245s   python3-looseversion python3-lxml python3-lz4 python3-matplotlib
245s   python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic
245s   python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme
245s   python3-netcdf4 python3-networkx python3-numpy python3-packaging
245s   python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk
245s   python3-pluggy python3-pybtex python3-pybtex-docutils
245s   python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo
245s   python3-roman python3-scipy python3-seaborn python3-six python3-sklearn
245s   python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
245s   python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap
245s   python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy
245s   python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz
245s   python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev
245s   python3.12-tk rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common
245s   tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings
245s   xfonts-utils xml-core zlib1g-dev
245s 0 upgraded, 205 newly installed, 0 to remove and 0 not upgraded.
245s Need to get 190 MB/190 MB of archives.
245s After this operation, 740 MB of additional disk space will be used.
245s Get:1 /tmp/autopkgtest.nyWww9/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [1016 B]
245s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB]
245s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB]
245s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB]
245s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB]
245s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB]
245s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB]
245s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB]
245s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.15+dfsg-2 [909 kB]
245s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB]
245s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB]
245s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB]
245s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB]
245s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB]
245s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
245s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB]
245s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB]
246s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB]
246s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB]
246s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB]
246s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB]
246s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B]
246s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.15-1 [685 kB]
246s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7build1 [525 kB]
246s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf blt armhf 2.5.3+dfsg-7build1 [4840 B]
246s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB]
246s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB]
246s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB]
246s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB]
246s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB]
246s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB]
246s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB]
246s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [9219 kB]
246s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-8ubuntu1 [1032 B]
246s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B]
246s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB]
246s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-8ubuntu1 [43.3 kB]
246s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB]
246s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-8ubuntu1 [2901 kB]
246s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-8ubuntu1 [1150 kB]
246s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-8ubuntu1 [897 kB]
246s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [18.0 MB]
247s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-8ubuntu1 [498 kB]
247s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B]
247s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B]
247s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-8ubuntu1 [2569 kB]
247s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [10.5 MB]
247s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-8ubuntu1 [19.9 kB]
247s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B]
247s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B]
247s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B]
247s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf cython3 armhf 3.0.11+dfsg-1ubuntu2 [3061 kB]
247s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB]
247s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-7build1 [166 kB]
247s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB]
247s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB]
247s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB]
247s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B]
247s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB]
247s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB]
247s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB]
247s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB]
247s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB]
247s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB]
247s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20241024 [112 kB]
247s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB]
247s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB]
247s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
247s Get:69 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lyx all 2.4.2.1-1 [171 kB]
247s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
247s Get:71 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB]
247s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB]
247s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB]
247s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB]
247s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B]
247s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB]
247s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB]
247s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.4-1 [121 kB]
247s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB]
248s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB]
248s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB]
248s Get:82 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B]
248s Get:83 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB]
248s Get:84 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB]
248s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB]
248s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB]
248s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B]
248s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
248s Get:89 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
248s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
248s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB]
248s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-perl all 4.10000-1 [81.9 kB]
248s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB]
248s Get:94 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB]
248s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB]
248s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB]
248s Get:97 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B]
248s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf libnetcdf19t64 armhf 1:4.9.2-6ubuntu1 [419 kB]
248s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.7-3 [2075 kB]
248s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB]
248s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.7-3 [4344 kB]
248s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-dev armhf 3.12.6-0ubuntu1 [10.2 kB]
248s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-all-dev armhf 3.12.6-0ubuntu1 [914 B]
248s Get:104 http://ftpmaster.internal/ubuntu plucky/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB]
248s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB]
248s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB]
248s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB]
248s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB]
249s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB]
249s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB]
249s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB]
249s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu1 [150 kB]
249s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB]
249s Get:114 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyproject-hooks all 1.2.0-1 [10.2 kB]
249s Get:115 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-toml all 0.10.2-1 [16.5 kB]
249s Get:116 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-wheel all 0.44.0-1 [54.2 kB]
249s Get:117 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-build all 1.2.2-1 [31.0 kB]
249s Get:118 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-installer all 0.7.0+dfsg1-3 [17.4 kB]
249s Get:119 http://ftpmaster.internal/ubuntu plucky/universe armhf pybuild-plugin-pyproject all 6.20241024 [1728 B]
249s Get:120 http://ftpmaster.internal/ubuntu plucky/universe armhf python-matplotlib-data all 3.8.3-3 [2928 kB]
250s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
250s Get:122 http://ftpmaster.internal/ubuntu plucky/universe armhf python-mdanalysis-doc all 2.7.0-5 [2323 kB]
251s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B]
251s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.7-3 [505 kB]
251s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dev armhf 3.12.6-0ubuntu1 [26.7 kB]
251s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all-dev armhf 3.12.6-0ubuntu1 [908 B]
251s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf python3-appdirs all 1.4.4-4 [10.9 kB]
251s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB]
251s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-tk armhf 3.12.7-3 [112 kB]
251s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tk armhf 3.12.6-1ubuntu1 [9806 B]
251s Get:131 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pil.imagetk armhf 10.4.0-1ubuntu1 [8848 B]
251s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB]
251s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB]
251s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB]
251s Get:135 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB]
251s Get:136 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B]
251s Get:137 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB]
251s Get:138 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB]
251s Get:139 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB]
251s Get:140 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-brotli armhf 1.1.0-2build2 [321 kB]
251s Get:141 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cftime armhf 1.6.4-1 [202 kB]
251s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lxml armhf 5.3.0-1 [1234 kB]
251s Get:143 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-citeproc all 0.6.0-3 [98.4 kB]
251s Get:144 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-contourpy armhf 1.3.0-2build1 [238 kB]
251s Get:145 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cycler all 0.12.1-1 [9716 B]
251s Get:146 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB]
251s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-2 [80.3 kB]
251s Get:148 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB]
251s Get:149 http://ftpmaster.internal/ubuntu plucky/main armhf python3-defusedxml all 0.7.1-2 [42.0 kB]
251s Get:150 http://ftpmaster.internal/ubuntu plucky/main armhf python3-roman all 4.2-1 [10.0 kB]
251s Get:151 http://ftpmaster.internal/ubuntu plucky/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB]
252s Get:152 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-looseversion all 1.3.0-3 [8354 B]
252s Get:153 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-duecredit all 0.10.2-2 [66.0 kB]
252s Get:154 http://ftpmaster.internal/ubuntu plucky/main armhf python3-monotonic all 1.6-2 [5732 B]
252s Get:155 http://ftpmaster.internal/ubuntu plucky/main armhf python3-fasteners all 0.18-2 [12.5 kB]
252s Get:156 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB]
252s Get:157 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB]
252s Get:158 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mpmath all 1.3.0-1 [425 kB]
252s Get:159 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sympy all 1.13.3-1 [4228 kB]
252s Get:160 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB]
252s Get:161 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fs all 2.4.16-4 [91.3 kB]
252s Get:162 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-lz4 armhf 4.0.2+dfsg-1build4 [24.8 kB]
252s Get:163 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-unicodedata2 armhf 15.1.0+ds-1build2 [357 kB]
252s Get:164 http://ftpmaster.internal/ubuntu plucky/universe armhf unicode-data all 15.1.0-1 [8878 kB]
253s Get:165 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fonttools armhf 4.46.0-1build2 [1402 kB]
253s Get:166 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB]
253s Get:167 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mrcfile all 1.5.3-3 [114 kB]
253s Get:168 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-griddataformats all 1.0.2-2 [2107 kB]
253s Get:169 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-gsd armhf 3.3.0-1 [197 kB]
253s Get:170 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-5ubuntu1 [1061 kB]
253s Get:171 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-5ubuntu1 [7974 B]
253s Get:172 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sortedcontainers all 2.4.0-2 [27.6 kB]
253s Get:173 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-hypothesis all 6.116.0-1 [326 kB]
253s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf python3-imagesize all 1.4.1-1 [6844 B]
253s Get:175 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B]
253s Get:176 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.3.2-5 [206 kB]
253s Get:177 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-kiwisolver armhf 1.4.7-2build1 [71.1 kB]
253s Get:178 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-latexcodec all 3.0.0-1 [16.6 kB]
253s Get:179 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-matplotlib armhf 3.8.3-3 [4500 kB]
253s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mda-xdrlib all 0.2.0-3 [11.4 kB]
253s Get:181 http://ftpmaster.internal/ubuntu plucky/main armhf python3-msgpack armhf 1.0.3-3build2 [76.1 kB]
253s Get:182 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB]
253s Get:183 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-threadpoolctl all 3.1.0-1 [21.3 kB]
253s Get:184 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.0-1 [91.6 kB]
253s Get:185 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mdanalysis armhf 2.7.0-5 [1882 kB]
253s Get:186 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-common all 7.4.7-4 [775 kB]
253s Get:187 http://ftpmaster.internal/ubuntu plucky/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB]
253s Get:188 http://ftpmaster.internal/ubuntu plucky/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB]
253s Get:189 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sphinx all 7.4.7-4 [593 kB]
253s Get:190 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B]
253s Get:191 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB]
253s Get:192 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-msmb-theme all 1.2.0-4 [35.4 kB]
253s Get:193 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-netcdf4 armhf 1.7.2-1 [589 kB]
253s Get:194 http://ftpmaster.internal/ubuntu plucky/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB]
254s Get:195 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5 [4728 kB]
254s Get:196 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5 [3112 kB]
254s Get:197 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB]
254s Get:198 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex all 0.24.0-4 [70.0 kB]
254s Get:199 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex-docutils all 1.0.2-1 [7176 B]
254s Get:200 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.3-1 [251 kB]
254s Get:201 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-seaborn all 0.13.2-4 [225 kB]
254s Get:202 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-sklearn-lib armhf 1.4.2+dfsg-6build1 [6321 kB]
254s Get:203 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-sklearn all 1.4.2+dfsg-6build1 [2257 kB]
254s Get:204 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-sitemap all 2.6.0-1 [6674 B]
254s Get:205 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB]
255s Fetched 190 MB in 10s (19.8 MB/s)
255s Selecting previously unselected package fonts-lato.
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255s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ...
255s Unpacking fonts-lato (2.015-1) ...
255s Selecting previously unselected package sgml-base.
255s Preparing to unpack .../001-sgml-base_1.31_all.deb ...
255s Unpacking sgml-base (1.31) ...
255s Selecting previously unselected package m4.
255s Preparing to unpack .../002-m4_1.4.19-4build1_armhf.deb ...
255s Unpacking m4 (1.4.19-4build1) ...
255s Selecting previously unselected package autoconf.
255s Preparing to unpack .../003-autoconf_2.72-3_all.deb ...
255s Unpacking autoconf (2.72-3) ...
256s Selecting previously unselected package autotools-dev.
256s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ...
256s Unpacking autotools-dev (20220109.1) ...
256s Selecting previously unselected package automake.
256s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ...
256s Unpacking automake (1:1.16.5-1.3ubuntu1) ...
256s Selecting previously unselected package autopoint.
256s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ...
256s Unpacking autopoint (0.22.5-2) ...
256s Selecting previously unselected package libtcl8.6:armhf.
256s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_armhf.deb ...
256s Unpacking libtcl8.6:armhf (8.6.15+dfsg-2) ...
256s Selecting previously unselected package libfreetype6:armhf.
256s Preparing to unpack .../008-libfreetype6_2.13.3+dfsg-1_armhf.deb ...
256s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ...
256s Selecting previously unselected package fonts-dejavu-mono.
256s Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ...
256s Unpacking fonts-dejavu-mono (2.37-8) ...
256s Selecting previously unselected package fonts-dejavu-core.
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256s Unpacking fonts-dejavu-core (2.37-8) ...
256s Selecting previously unselected package libfontenc1:armhf.
256s Preparing to unpack .../011-libfontenc1_1%3a1.1.8-1build1_armhf.deb ...
256s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ...
256s Selecting previously unselected package x11-common.
256s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ...
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256s Selecting previously unselected package xfonts-encodings.
256s Preparing to unpack .../013-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
256s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
256s Selecting previously unselected package xfonts-utils.
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256s Selecting previously unselected package fonts-urw-base35.
256s Preparing to unpack .../015-fonts-urw-base35_20200910-8_all.deb ...
256s Unpacking fonts-urw-base35 (20200910-8) ...
257s Selecting previously unselected package fontconfig-config.
257s Preparing to unpack .../016-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ...
257s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
257s Selecting previously unselected package libfontconfig1:armhf.
257s Preparing to unpack .../017-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ...
257s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ...
257s Selecting previously unselected package libxrender1:armhf.
257s Preparing to unpack .../018-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ...
257s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ...
257s Selecting previously unselected package libxft2:armhf.
257s Preparing to unpack .../019-libxft2_2.3.6-1build1_armhf.deb ...
257s Unpacking libxft2:armhf (2.3.6-1build1) ...
257s Selecting previously unselected package libxss1:armhf.
257s Preparing to unpack .../020-libxss1_1%3a1.2.3-1build3_armhf.deb ...
257s Unpacking libxss1:armhf (1:1.2.3-1build3) ...
257s Selecting previously unselected package libtk8.6:armhf.
257s Preparing to unpack .../021-libtk8.6_8.6.15-1_armhf.deb ...
257s Unpacking libtk8.6:armhf (8.6.15-1) ...
257s Selecting previously unselected package tk8.6-blt2.5.
257s Preparing to unpack .../022-tk8.6-blt2.5_2.5.3+dfsg-7build1_armhf.deb ...
257s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
257s Selecting previously unselected package blt.
257s Preparing to unpack .../023-blt_2.5.3+dfsg-7build1_armhf.deb ...
257s Unpacking blt (2.5.3+dfsg-7build1) ...
257s Selecting previously unselected package libc-dev-bin.
257s Preparing to unpack .../024-libc-dev-bin_2.40-1ubuntu3_armhf.deb ...
257s Unpacking libc-dev-bin (2.40-1ubuntu3) ...
257s Selecting previously unselected package linux-libc-dev:armhf.
257s Preparing to unpack .../025-linux-libc-dev_6.11.0-8.8_armhf.deb ...
257s Unpacking linux-libc-dev:armhf (6.11.0-8.8) ...
258s Selecting previously unselected package libcrypt-dev:armhf.
258s Preparing to unpack .../026-libcrypt-dev_1%3a4.4.36-4build1_armhf.deb ...
258s Unpacking libcrypt-dev:armhf (1:4.4.36-4build1) ...
258s Selecting previously unselected package rpcsvc-proto.
258s Preparing to unpack .../027-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ...
258s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ...
258s Selecting previously unselected package libc6-dev:armhf.
258s Preparing to unpack .../028-libc6-dev_2.40-1ubuntu3_armhf.deb ...
258s Unpacking libc6-dev:armhf (2.40-1ubuntu3) ...
258s Selecting previously unselected package libisl23:armhf.
258s Preparing to unpack .../029-libisl23_0.27-1_armhf.deb ...
258s Unpacking libisl23:armhf (0.27-1) ...
258s Selecting previously unselected package libmpc3:armhf.
258s Preparing to unpack .../030-libmpc3_1.3.1-1build2_armhf.deb ...
258s Unpacking libmpc3:armhf (1.3.1-1build2) ...
258s Selecting previously unselected package cpp-14-arm-linux-gnueabihf.
258s Preparing to unpack .../031-cpp-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ...
258s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ...
258s Selecting previously unselected package cpp-14.
258s Preparing to unpack .../032-cpp-14_14.2.0-8ubuntu1_armhf.deb ...
258s Unpacking cpp-14 (14.2.0-8ubuntu1) ...
258s Selecting previously unselected package cpp-arm-linux-gnueabihf.
259s Preparing to unpack .../033-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ...
259s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ...
259s Selecting previously unselected package cpp.
259s Preparing to unpack .../034-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ...
259s Unpacking cpp (4:14.1.0-2ubuntu1) ...
259s Selecting previously unselected package libcc1-0:armhf.
259s Preparing to unpack .../035-libcc1-0_14.2.0-8ubuntu1_armhf.deb ...
259s Unpacking libcc1-0:armhf (14.2.0-8ubuntu1) ...
259s Selecting previously unselected package libgomp1:armhf.
259s Preparing to unpack .../036-libgomp1_14.2.0-8ubuntu1_armhf.deb ...
259s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ...
259s Selecting previously unselected package libasan8:armhf.
259s Preparing to unpack .../037-libasan8_14.2.0-8ubuntu1_armhf.deb ...
259s Unpacking libasan8:armhf (14.2.0-8ubuntu1) ...
259s Selecting previously unselected package libubsan1:armhf.
259s Preparing to unpack .../038-libubsan1_14.2.0-8ubuntu1_armhf.deb ...
259s Unpacking libubsan1:armhf (14.2.0-8ubuntu1) ...
259s Selecting previously unselected package libgcc-14-dev:armhf.
259s Preparing to unpack .../039-libgcc-14-dev_14.2.0-8ubuntu1_armhf.deb ...
259s Unpacking libgcc-14-dev:armhf (14.2.0-8ubuntu1) ...
259s Selecting previously unselected package gcc-14-arm-linux-gnueabihf.
259s Preparing to unpack .../040-gcc-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ...
259s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ...
260s Selecting previously unselected package gcc-14.
260s Preparing to unpack .../041-gcc-14_14.2.0-8ubuntu1_armhf.deb ...
260s Unpacking gcc-14 (14.2.0-8ubuntu1) ...
260s Selecting previously unselected package gcc-arm-linux-gnueabihf.
260s Preparing to unpack .../042-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ...
260s Unpacking gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ...
260s Selecting previously unselected package gcc.
260s Preparing to unpack .../043-gcc_4%3a14.1.0-2ubuntu1_armhf.deb ...
260s Unpacking gcc (4:14.1.0-2ubuntu1) ...
260s Selecting previously unselected package libstdc++-14-dev:armhf.
260s Preparing to unpack .../044-libstdc++-14-dev_14.2.0-8ubuntu1_armhf.deb ...
260s Unpacking libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ...
260s Selecting previously unselected package g++-14-arm-linux-gnueabihf.
260s Preparing to unpack .../045-g++-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ...
260s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ...
261s Selecting previously unselected package g++-14.
261s Preparing to unpack .../046-g++-14_14.2.0-8ubuntu1_armhf.deb ...
261s Unpacking g++-14 (14.2.0-8ubuntu1) ...
261s Selecting previously unselected package g++-arm-linux-gnueabihf.
261s Preparing to unpack .../047-g++-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ...
261s Unpacking g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ...
261s Selecting previously unselected package g++.
261s Preparing to unpack .../048-g++_4%3a14.1.0-2ubuntu1_armhf.deb ...
261s Unpacking g++ (4:14.1.0-2ubuntu1) ...
261s Selecting previously unselected package build-essential.
261s Preparing to unpack .../049-build-essential_12.10ubuntu1_armhf.deb ...
261s Unpacking build-essential (12.10ubuntu1) ...
261s Selecting previously unselected package cython3.
261s Preparing to unpack .../050-cython3_3.0.11+dfsg-1ubuntu2_armhf.deb ...
261s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ...
261s Selecting previously unselected package libdebhelper-perl.
261s Preparing to unpack .../051-libdebhelper-perl_13.20ubuntu1_all.deb ...
261s Unpacking libdebhelper-perl (13.20ubuntu1) ...
261s Selecting previously unselected package libtool.
261s Preparing to unpack .../052-libtool_2.4.7-7build1_all.deb ...
261s Unpacking libtool (2.4.7-7build1) ...
261s Selecting previously unselected package dh-autoreconf.
261s Preparing to unpack .../053-dh-autoreconf_20_all.deb ...
261s Unpacking dh-autoreconf (20) ...
261s Selecting previously unselected package libarchive-zip-perl.
261s Preparing to unpack .../054-libarchive-zip-perl_1.68-1_all.deb ...
261s Unpacking libarchive-zip-perl (1.68-1) ...
261s Selecting previously unselected package libfile-stripnondeterminism-perl.
261s Preparing to unpack .../055-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
261s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
261s Selecting previously unselected package dh-strip-nondeterminism.
261s Preparing to unpack .../056-dh-strip-nondeterminism_1.14.0-1_all.deb ...
261s Unpacking dh-strip-nondeterminism (1.14.0-1) ...
261s Selecting previously unselected package debugedit.
261s Preparing to unpack .../057-debugedit_1%3a5.1-1_armhf.deb ...
261s Unpacking debugedit (1:5.1-1) ...
261s Selecting previously unselected package dwz.
261s Preparing to unpack .../058-dwz_0.15-1build6_armhf.deb ...
261s Unpacking dwz (0.15-1build6) ...
261s Selecting previously unselected package gettext.
261s Preparing to unpack .../059-gettext_0.22.5-2_armhf.deb ...
261s Unpacking gettext (0.22.5-2) ...
261s Selecting previously unselected package intltool-debian.
262s Preparing to unpack .../060-intltool-debian_0.35.0+20060710.6_all.deb ...
262s Unpacking intltool-debian (0.35.0+20060710.6) ...
262s Selecting previously unselected package po-debconf.
262s Preparing to unpack .../061-po-debconf_1.0.21+nmu1_all.deb ...
262s Unpacking po-debconf (1.0.21+nmu1) ...
262s Selecting previously unselected package debhelper.
262s Preparing to unpack .../062-debhelper_13.20ubuntu1_all.deb ...
262s Unpacking debhelper (13.20ubuntu1) ...
262s Selecting previously unselected package dh-python.
262s Preparing to unpack .../063-dh-python_6.20241024_all.deb ...
262s Unpacking dh-python (6.20241024) ...
262s Selecting previously unselected package xml-core.
262s Preparing to unpack .../064-xml-core_0.19_all.deb ...
262s Unpacking xml-core (0.19) ...
262s Selecting previously unselected package docutils-common.
262s Preparing to unpack .../065-docutils-common_0.21.2+dfsg-2_all.deb ...
262s Unpacking docutils-common (0.21.2+dfsg-2) ...
262s Selecting previously unselected package fonts-font-awesome.
262s Preparing to unpack .../066-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
262s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
262s Selecting previously unselected package fonts-lyx.
262s Preparing to unpack .../067-fonts-lyx_2.4.2.1-1_all.deb ...
262s Unpacking fonts-lyx (2.4.2.1-1) ...
262s Selecting previously unselected package fonts-mathjax.
262s Preparing to unpack .../068-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
262s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
262s Selecting previously unselected package libaec0:armhf.
262s Preparing to unpack .../069-libaec0_1.1.3-1_armhf.deb ...
262s Unpacking libaec0:armhf (1.1.3-1) ...
262s Selecting previously unselected package libblas3:armhf.
262s Preparing to unpack .../070-libblas3_3.12.0-3build2_armhf.deb ...
262s Unpacking libblas3:armhf (3.12.0-3build2) ...
262s Selecting previously unselected package libpixman-1-0:armhf.
262s Preparing to unpack .../071-libpixman-1-0_0.44.0-3_armhf.deb ...
262s Unpacking libpixman-1-0:armhf (0.44.0-3) ...
262s Selecting previously unselected package libxcb-render0:armhf.
262s Preparing to unpack .../072-libxcb-render0_1.17.0-2_armhf.deb ...
262s Unpacking libxcb-render0:armhf (1.17.0-2) ...
262s Selecting previously unselected package libxcb-shm0:armhf.
262s Preparing to unpack .../073-libxcb-shm0_1.17.0-2_armhf.deb ...
262s Unpacking libxcb-shm0:armhf (1.17.0-2) ...
262s Selecting previously unselected package libcairo2:armhf.
262s Preparing to unpack .../074-libcairo2_1.18.2-2_armhf.deb ...
262s Unpacking libcairo2:armhf (1.18.2-2) ...
263s Selecting previously unselected package libdeflate0:armhf.
263s Preparing to unpack .../075-libdeflate0_1.22-1_armhf.deb ...
263s Unpacking libdeflate0:armhf (1.22-1) ...
263s Selecting previously unselected package libexpat1-dev:armhf.
263s Preparing to unpack .../076-libexpat1-dev_2.6.4-1_armhf.deb ...
263s Unpacking libexpat1-dev:armhf (2.6.4-1) ...
263s Selecting previously unselected package libgfortran5:armhf.
263s Preparing to unpack .../077-libgfortran5_14.2.0-8ubuntu1_armhf.deb ...
263s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ...
263s Selecting previously unselected package libgraphite2-3:armhf.
263s Preparing to unpack .../078-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ...
263s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ...
263s Selecting previously unselected package libharfbuzz0b:armhf.
263s Preparing to unpack .../079-libharfbuzz0b_10.0.1-1_armhf.deb ...
263s Unpacking libharfbuzz0b:armhf (10.0.1-1) ...
263s Selecting previously unselected package libsz2:armhf.
263s Preparing to unpack .../080-libsz2_1.1.3-1_armhf.deb ...
263s Unpacking libsz2:armhf (1.1.3-1) ...
263s Selecting previously unselected package libhdf5-103-1t64:armhf.
263s Preparing to unpack .../081-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ...
263s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ...
263s Selecting previously unselected package libhdf5-hl-100t64:armhf.
263s Preparing to unpack .../082-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ...
263s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ...
263s Selecting previously unselected package libimagequant0:armhf.
263s Preparing to unpack .../083-libimagequant0_2.18.0-1build1_armhf.deb ...
263s Unpacking libimagequant0:armhf (2.18.0-1build1) ...
263s Selecting previously unselected package libjpeg-turbo8:armhf.
263s Preparing to unpack .../084-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ...
263s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ...
263s Selecting previously unselected package libjpeg8:armhf.
263s Preparing to unpack .../085-libjpeg8_8c-2ubuntu11_armhf.deb ...
263s Unpacking libjpeg8:armhf (8c-2ubuntu11) ...
263s Selecting previously unselected package libjs-jquery.
263s Preparing to unpack .../086-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
263s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
263s Selecting previously unselected package libjs-jquery-ui.
263s Preparing to unpack .../087-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
263s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
263s Selecting previously unselected package libjs-underscore.
263s Preparing to unpack .../088-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
263s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
263s Selecting previously unselected package libjs-sphinxdoc.
263s Preparing to unpack .../089-libjs-sphinxdoc_7.4.7-4_all.deb ...
263s Unpacking libjs-sphinxdoc (7.4.7-4) ...
263s Selecting previously unselected package libjson-perl.
264s Preparing to unpack .../090-libjson-perl_4.10000-1_all.deb ...
264s Unpacking libjson-perl (4.10000-1) ...
264s Selecting previously unselected package liblapack3:armhf.
264s Preparing to unpack .../091-liblapack3_3.12.0-3build2_armhf.deb ...
264s Unpacking liblapack3:armhf (3.12.0-3build2) ...
264s Selecting previously unselected package liblbfgsb0:armhf.
264s Preparing to unpack .../092-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ...
264s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ...
264s Selecting previously unselected package liblcms2-2:armhf.
264s Preparing to unpack .../093-liblcms2-2_2.16-2_armhf.deb ...
264s Unpacking liblcms2-2:armhf (2.16-2) ...
264s Selecting previously unselected package liblerc4:armhf.
264s Preparing to unpack .../094-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ...
264s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ...
264s Selecting previously unselected package liblzf1:armhf.
264s Preparing to unpack .../095-liblzf1_3.6-4_armhf.deb ...
264s Unpacking liblzf1:armhf (3.6-4) ...
264s Selecting previously unselected package libnetcdf19t64:armhf.
264s Preparing to unpack .../096-libnetcdf19t64_1%3a4.9.2-6ubuntu1_armhf.deb ...
264s Unpacking libnetcdf19t64:armhf (1:4.9.2-6ubuntu1) ...
264s Selecting previously unselected package libpython3.12t64:armhf.
264s Preparing to unpack .../097-libpython3.12t64_3.12.7-3_armhf.deb ...
264s Unpacking libpython3.12t64:armhf (3.12.7-3) ...
264s Selecting previously unselected package zlib1g-dev:armhf.
264s Preparing to unpack .../098-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ...
264s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
264s Selecting previously unselected package libpython3.12-dev:armhf.
264s Preparing to unpack .../099-libpython3.12-dev_3.12.7-3_armhf.deb ...
264s Unpacking libpython3.12-dev:armhf (3.12.7-3) ...
264s Selecting previously unselected package libpython3-dev:armhf.
264s Preparing to unpack .../100-libpython3-dev_3.12.6-0ubuntu1_armhf.deb ...
264s Unpacking libpython3-dev:armhf (3.12.6-0ubuntu1) ...
264s Selecting previously unselected package libpython3-all-dev:armhf.
264s Preparing to unpack .../101-libpython3-all-dev_3.12.6-0ubuntu1_armhf.deb ...
264s Unpacking libpython3-all-dev:armhf (3.12.6-0ubuntu1) ...
264s Selecting previously unselected package libqhull-r8.0:armhf.
265s Preparing to unpack .../102-libqhull-r8.0_2020.2-6build1_armhf.deb ...
265s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ...
265s Selecting previously unselected package libraqm0:armhf.
265s Preparing to unpack .../103-libraqm0_0.10.1-1build1_armhf.deb ...
265s Unpacking libraqm0:armhf (0.10.1-1build1) ...
265s Selecting previously unselected package libsharpyuv0:armhf.
265s Preparing to unpack .../104-libsharpyuv0_1.4.0-0.1_armhf.deb ...
265s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ...
265s Selecting previously unselected package libjbig0:armhf.
265s Preparing to unpack .../105-libjbig0_2.1-6.1ubuntu2_armhf.deb ...
265s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ...
265s Selecting previously unselected package libwebp7:armhf.
265s Preparing to unpack .../106-libwebp7_1.4.0-0.1_armhf.deb ...
265s Unpacking libwebp7:armhf (1.4.0-0.1) ...
265s Selecting previously unselected package libtiff6:armhf.
265s Preparing to unpack .../107-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ...
265s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ...
265s Selecting previously unselected package libwebpdemux2:armhf.
265s Preparing to unpack .../108-libwebpdemux2_1.4.0-0.1_armhf.deb ...
265s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ...
265s Selecting previously unselected package libwebpmux3:armhf.
265s Preparing to unpack .../109-libwebpmux3_1.4.0-0.1_armhf.deb ...
265s Unpacking libwebpmux3:armhf (1.4.0-0.1) ...
265s Selecting previously unselected package libxslt1.1:armhf.
265s Preparing to unpack .../110-libxslt1.1_1.1.39-0exp1ubuntu1_armhf.deb ...
265s Unpacking libxslt1.1:armhf (1.1.39-0exp1ubuntu1) ...
265s Selecting previously unselected package python3-packaging.
265s Preparing to unpack .../111-python3-packaging_24.1-1_all.deb ...
265s Unpacking python3-packaging (24.1-1) ...
265s Selecting previously unselected package python3-pyproject-hooks.
265s Preparing to unpack .../112-python3-pyproject-hooks_1.2.0-1_all.deb ...
265s Unpacking python3-pyproject-hooks (1.2.0-1) ...
265s Selecting previously unselected package python3-toml.
265s Preparing to unpack .../113-python3-toml_0.10.2-1_all.deb ...
265s Unpacking python3-toml (0.10.2-1) ...
265s Selecting previously unselected package python3-wheel.
265s Preparing to unpack .../114-python3-wheel_0.44.0-1_all.deb ...
265s Unpacking python3-wheel (0.44.0-1) ...
265s Selecting previously unselected package python3-build.
265s Preparing to unpack .../115-python3-build_1.2.2-1_all.deb ...
265s Unpacking python3-build (1.2.2-1) ...
265s Selecting previously unselected package python3-installer.
265s Preparing to unpack .../116-python3-installer_0.7.0+dfsg1-3_all.deb ...
265s Unpacking python3-installer (0.7.0+dfsg1-3) ...
265s Selecting previously unselected package pybuild-plugin-pyproject.
265s Preparing to unpack .../117-pybuild-plugin-pyproject_6.20241024_all.deb ...
265s Unpacking pybuild-plugin-pyproject (6.20241024) ...
265s Selecting previously unselected package python-matplotlib-data.
265s Preparing to unpack .../118-python-matplotlib-data_3.8.3-3_all.deb ...
265s Unpacking python-matplotlib-data (3.8.3-3) ...
265s Selecting previously unselected package libjs-mathjax.
266s Preparing to unpack .../119-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
266s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
267s Selecting previously unselected package python-mdanalysis-doc.
267s Preparing to unpack .../120-python-mdanalysis-doc_2.7.0-5_all.deb ...
267s Unpacking python-mdanalysis-doc (2.7.0-5) ...
267s Selecting previously unselected package python3-all.
267s Preparing to unpack .../121-python3-all_3.12.6-0ubuntu1_armhf.deb ...
267s Unpacking python3-all (3.12.6-0ubuntu1) ...
267s Selecting previously unselected package python3.12-dev.
267s Preparing to unpack .../122-python3.12-dev_3.12.7-3_armhf.deb ...
267s Unpacking python3.12-dev (3.12.7-3) ...
267s Selecting previously unselected package python3-dev.
267s Preparing to unpack .../123-python3-dev_3.12.6-0ubuntu1_armhf.deb ...
267s Unpacking python3-dev (3.12.6-0ubuntu1) ...
267s Selecting previously unselected package python3-all-dev.
267s Preparing to unpack .../124-python3-all-dev_3.12.6-0ubuntu1_armhf.deb ...
267s Unpacking python3-all-dev (3.12.6-0ubuntu1) ...
267s Selecting previously unselected package python3-appdirs.
267s Preparing to unpack .../125-python3-appdirs_1.4.4-4_all.deb ...
267s Unpacking python3-appdirs (1.4.4-4) ...
267s Selecting previously unselected package python3-numpy.
267s Preparing to unpack .../126-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ...
267s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
267s Selecting previously unselected package python3.12-tk.
267s Preparing to unpack .../127-python3.12-tk_3.12.7-3_armhf.deb ...
267s Unpacking python3.12-tk (3.12.7-3) ...
267s Selecting previously unselected package python3-tk:armhf.
267s Preparing to unpack .../128-python3-tk_3.12.6-1ubuntu1_armhf.deb ...
267s Unpacking python3-tk:armhf (3.12.6-1ubuntu1) ...
267s Selecting previously unselected package python3-pil.imagetk:armhf.
268s Preparing to unpack .../129-python3-pil.imagetk_10.4.0-1ubuntu1_armhf.deb ...
268s Unpacking python3-pil.imagetk:armhf (10.4.0-1ubuntu1) ...
268s Selecting previously unselected package libopenjp2-7:armhf.
268s Preparing to unpack .../130-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ...
268s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ...
268s Selecting previously unselected package python3-pil:armhf.
268s Preparing to unpack .../131-python3-pil_10.4.0-1ubuntu1_armhf.deb ...
268s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ...
268s Selecting previously unselected package python3-cairo.
268s Preparing to unpack .../132-python3-cairo_1.26.1-2_armhf.deb ...
268s Unpacking python3-cairo (1.26.1-2) ...
268s Selecting previously unselected package python3-freetype.
268s Preparing to unpack .../133-python3-freetype_2.5.1-1_all.deb ...
268s Unpacking python3-freetype (2.5.1-1) ...
268s Selecting previously unselected package python3-rlpycairo.
268s Preparing to unpack .../134-python3-rlpycairo_0.3.0-3_all.deb ...
268s Unpacking python3-rlpycairo (0.3.0-3) ...
268s Selecting previously unselected package python3-reportlab.
268s Preparing to unpack .../135-python3-reportlab_4.2.5-1_all.deb ...
268s Unpacking python3-reportlab (4.2.5-1) ...
268s Selecting previously unselected package w3c-sgml-lib.
268s Preparing to unpack .../136-w3c-sgml-lib_1.3-3_all.deb ...
268s Unpacking w3c-sgml-lib (1.3-3) ...
268s Selecting previously unselected package python3-biopython.
268s Preparing to unpack .../137-python3-biopython_1.84+dfsg-4_armhf.deb ...
268s Unpacking python3-biopython (1.84+dfsg-4) ...
269s Selecting previously unselected package python3-brotli.
269s Preparing to unpack .../138-python3-brotli_1.1.0-2build2_armhf.deb ...
269s Unpacking python3-brotli (1.1.0-2build2) ...
269s Selecting previously unselected package python3-cftime.
269s Preparing to unpack .../139-python3-cftime_1.6.4-1_armhf.deb ...
269s Unpacking python3-cftime (1.6.4-1) ...
269s Selecting previously unselected package python3-lxml:armhf.
269s Preparing to unpack .../140-python3-lxml_5.3.0-1_armhf.deb ...
269s Unpacking python3-lxml:armhf (5.3.0-1) ...
269s Selecting previously unselected package python3-citeproc.
269s Preparing to unpack .../141-python3-citeproc_0.6.0-3_all.deb ...
269s Unpacking python3-citeproc (0.6.0-3) ...
269s Selecting previously unselected package python3-contourpy.
269s Preparing to unpack .../142-python3-contourpy_1.3.0-2build1_armhf.deb ...
269s Unpacking python3-contourpy (1.3.0-2build1) ...
269s Selecting previously unselected package python3-cycler.
269s Preparing to unpack .../143-python3-cycler_0.12.1-1_all.deb ...
269s Unpacking python3-cycler (0.12.1-1) ...
269s Selecting previously unselected package python3-six.
269s Preparing to unpack .../144-python3-six_1.16.0-7_all.deb ...
269s Unpacking python3-six (1.16.0-7) ...
269s Selecting previously unselected package python3-dateutil.
269s Preparing to unpack .../145-python3-dateutil_2.9.0-2_all.deb ...
269s Unpacking python3-dateutil (2.9.0-2) ...
269s Selecting previously unselected package python3-decorator.
269s Preparing to unpack .../146-python3-decorator_5.1.1-5_all.deb ...
269s Unpacking python3-decorator (5.1.1-5) ...
269s Selecting previously unselected package python3-defusedxml.
269s Preparing to unpack .../147-python3-defusedxml_0.7.1-2_all.deb ...
269s Unpacking python3-defusedxml (0.7.1-2) ...
269s Selecting previously unselected package python3-roman.
269s Preparing to unpack .../148-python3-roman_4.2-1_all.deb ...
269s Unpacking python3-roman (4.2-1) ...
269s Selecting previously unselected package python3-docutils.
269s Preparing to unpack .../149-python3-docutils_0.21.2+dfsg-2_all.deb ...
269s Unpacking python3-docutils (0.21.2+dfsg-2) ...
269s Selecting previously unselected package python3-looseversion.
269s Preparing to unpack .../150-python3-looseversion_1.3.0-3_all.deb ...
269s Unpacking python3-looseversion (1.3.0-3) ...
269s Selecting previously unselected package python3-duecredit.
270s Preparing to unpack .../151-python3-duecredit_0.10.2-2_all.deb ...
270s Unpacking python3-duecredit (0.10.2-2) ...
270s Selecting previously unselected package python3-monotonic.
270s Preparing to unpack .../152-python3-monotonic_1.6-2_all.deb ...
270s Unpacking python3-monotonic (1.6-2) ...
270s Selecting previously unselected package python3-fasteners.
270s Preparing to unpack .../153-python3-fasteners_0.18-2_all.deb ...
270s Unpacking python3-fasteners (0.18-2) ...
270s Selecting previously unselected package python3-scipy.
270s Preparing to unpack .../154-python3-scipy_1.13.1-5_armhf.deb ...
270s Unpacking python3-scipy (1.13.1-5) ...
270s Selecting previously unselected package python3-ufolib2.
270s Preparing to unpack .../155-python3-ufolib2_0.16.1+dfsg1-1_all.deb ...
270s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ...
270s Selecting previously unselected package python3-mpmath.
270s Preparing to unpack .../156-python3-mpmath_1.3.0-1_all.deb ...
270s Unpacking python3-mpmath (1.3.0-1) ...
271s Selecting previously unselected package python3-sympy.
271s Preparing to unpack .../157-python3-sympy_1.13.3-1_all.deb ...
271s Unpacking python3-sympy (1.13.3-1) ...
271s Selecting previously unselected package python3-tz.
271s Preparing to unpack .../158-python3-tz_2024.1-2_all.deb ...
271s Unpacking python3-tz (2024.1-2) ...
271s Selecting previously unselected package python3-fs.
271s Preparing to unpack .../159-python3-fs_2.4.16-4_all.deb ...
271s Unpacking python3-fs (2.4.16-4) ...
271s Selecting previously unselected package python3-lz4.
271s Preparing to unpack .../160-python3-lz4_4.0.2+dfsg-1build4_armhf.deb ...
271s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ...
271s Selecting previously unselected package python3-unicodedata2.
271s Preparing to unpack .../161-python3-unicodedata2_15.1.0+ds-1build2_armhf.deb ...
271s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ...
271s Selecting previously unselected package unicode-data.
271s Preparing to unpack .../162-unicode-data_15.1.0-1_all.deb ...
271s Unpacking unicode-data (15.1.0-1) ...
272s Selecting previously unselected package python3-fonttools.
272s Preparing to unpack .../163-python3-fonttools_4.46.0-1build2_armhf.deb ...
272s Unpacking python3-fonttools (4.46.0-1build2) ...
272s Selecting previously unselected package sphinx-rtd-theme-common.
272s Preparing to unpack .../164-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ...
272s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ...
272s Selecting previously unselected package python3-mrcfile.
272s Preparing to unpack .../165-python3-mrcfile_1.5.3-3_all.deb ...
272s Unpacking python3-mrcfile (1.5.3-3) ...
272s Selecting previously unselected package python3-griddataformats.
272s Preparing to unpack .../166-python3-griddataformats_1.0.2-2_all.deb ...
272s Unpacking python3-griddataformats (1.0.2-2) ...
272s Selecting previously unselected package python3-gsd.
272s Preparing to unpack .../167-python3-gsd_3.3.0-1_armhf.deb ...
272s Unpacking python3-gsd (3.3.0-1) ...
272s Selecting previously unselected package python3-h5py-serial.
272s Preparing to unpack .../168-python3-h5py-serial_3.11.0-5ubuntu1_armhf.deb ...
272s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ...
272s Selecting previously unselected package python3-h5py.
272s Preparing to unpack .../169-python3-h5py_3.11.0-5ubuntu1_all.deb ...
272s Unpacking python3-h5py (3.11.0-5ubuntu1) ...
272s Selecting previously unselected package python3-sortedcontainers.
272s Preparing to unpack .../170-python3-sortedcontainers_2.4.0-2_all.deb ...
272s Unpacking python3-sortedcontainers (2.4.0-2) ...
272s Selecting previously unselected package python3-hypothesis.
272s Preparing to unpack .../171-python3-hypothesis_6.116.0-1_all.deb ...
272s Unpacking python3-hypothesis (6.116.0-1) ...
273s Selecting previously unselected package python3-imagesize.
273s Preparing to unpack .../172-python3-imagesize_1.4.1-1_all.deb ...
273s Unpacking python3-imagesize (1.4.1-1) ...
273s Selecting previously unselected package python3-iniconfig.
273s Preparing to unpack .../173-python3-iniconfig_1.1.1-2_all.deb ...
273s Unpacking python3-iniconfig (1.1.1-2) ...
273s Selecting previously unselected package python3-joblib.
273s Preparing to unpack .../174-python3-joblib_1.3.2-5_all.deb ...
273s Unpacking python3-joblib (1.3.2-5) ...
273s Selecting previously unselected package python3-kiwisolver.
273s Preparing to unpack .../175-python3-kiwisolver_1.4.7-2build1_armhf.deb ...
273s Unpacking python3-kiwisolver (1.4.7-2build1) ...
273s Selecting previously unselected package python3-latexcodec.
273s Preparing to unpack .../176-python3-latexcodec_3.0.0-1_all.deb ...
273s Unpacking python3-latexcodec (3.0.0-1) ...
273s Selecting previously unselected package python3-matplotlib.
273s Preparing to unpack .../177-python3-matplotlib_3.8.3-3_armhf.deb ...
273s Unpacking python3-matplotlib (3.8.3-3) ...
273s Selecting previously unselected package python3-mda-xdrlib.
273s Preparing to unpack .../178-python3-mda-xdrlib_0.2.0-3_all.deb ...
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273s Selecting previously unselected package python3-msgpack.
273s Preparing to unpack .../179-python3-msgpack_1.0.3-3build2_armhf.deb ...
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273s Selecting previously unselected package python3-mmtf.
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273s Unpacking python3-mmtf (1.1.3-1) ...
273s Selecting previously unselected package python3-threadpoolctl.
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273s Unpacking python3-threadpoolctl (3.1.0-1) ...
273s Selecting previously unselected package python3-tqdm.
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273s Selecting previously unselected package python3-mdanalysis.
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273s Unpacking python3-mdanalysis (2.7.0-5) ...
274s Selecting previously unselected package sphinx-common.
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274s Unpacking sphinx-common (7.4.7-4) ...
274s Selecting previously unselected package python3-alabaster.
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274s Unpacking python3-alabaster (0.7.16-0.1) ...
274s Selecting previously unselected package python3-snowballstemmer.
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274s Unpacking python3-snowballstemmer (2.2.0-4build1) ...
274s Selecting previously unselected package python3-sphinx.
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274s Unpacking python3-sphinx (7.4.7-4) ...
274s Selecting previously unselected package python3-sphinxcontrib.jquery.
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274s Unpacking python3-sphinxcontrib.jquery (4.1-5) ...
274s Selecting previously unselected package python3-sphinx-rtd-theme.
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274s Unpacking python3-sphinx-rtd-theme (3.0.1+dfsg-1) ...
274s Selecting previously unselected package python3-msmb-theme.
274s Preparing to unpack .../190-python3-msmb-theme_1.2.0-4_all.deb ...
274s Unpacking python3-msmb-theme (1.2.0-4) ...
274s Selecting previously unselected package python3-netcdf4.
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274s Selecting previously unselected package python3-networkx.
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275s Selecting previously unselected package python3-pandas-lib:armhf.
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275s Selecting previously unselected package python3-pandas.
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276s Selecting previously unselected package python3-pybtex.
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276s Selecting previously unselected package python3-pybtex-docutils.
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276s Selecting previously unselected package python3-pytest.
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276s Selecting previously unselected package python3-seaborn.
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276s Selecting previously unselected package python3-sklearn-lib:armhf.
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277s Selecting previously unselected package python3-sklearn.
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277s Unpacking python3-sklearn (1.4.2+dfsg-6build1) ...
277s Selecting previously unselected package python3-sphinx-sitemap.
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277s Selecting previously unselected package python3-sphinxcontrib.bibtex.
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277s Selecting previously unselected package autopkgtest-satdep.
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277s Setting up dh-python (6.20241024) ...
277s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ...
277s Setting up liblcms2-2:armhf (2.16-2) ...
277s Setting up python3-iniconfig (1.1.1-2) ...
277s Setting up libpixman-1-0:armhf (0.44.0-3) ...
277s Setting up libsharpyuv0:armhf (1.4.0-0.1) ...
277s Setting up fonts-lato (2.015-1) ...
277s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
277s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu2) ...
277s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
277s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ...
277s Setting up python3-joblib (1.3.2-5) ...
278s Setting up python3-lz4 (4.0.2+dfsg-1build4) ...
278s Setting up libxcb-render0:armhf (1.17.0-2) ...
278s Setting up python3-defusedxml (0.7.1-2) ...
278s Setting up libarchive-zip-perl (1.68-1) ...
278s Setting up python3-alabaster (0.7.16-0.1) ...
278s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ...
278s Setting up fonts-lyx (2.4.2.1-1) ...
278s Setting up libdebhelper-perl (13.20ubuntu1) ...
278s Setting up python3-tqdm (4.67.0-1) ...
278s Setting up python3-threadpoolctl (3.1.0-1) ...
278s Setting up x11-common (1:7.7+23ubuntu3) ...
279s Setting up libdeflate0:armhf (1.22-1) ...
279s Setting up linux-libc-dev:armhf (6.11.0-8.8) ...
279s Setting up m4 (1.4.19-4build1) ...
279s Setting up python3-latexcodec (3.0.0-1) ...
279s Setting up libqhull-r8.0:armhf (2020.2-6build1) ...
279s Setting up python3-all (3.12.6-0ubuntu1) ...
279s Setting up libxcb-shm0:armhf (1.17.0-2) ...
279s Setting up python3-sortedcontainers (2.4.0-2) ...
279s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ...
279s Setting up python3-networkx (3.2.1-4ubuntu1) ...
283s Setting up python3-wheel (0.44.0-1) ...
283s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ...
283s Setting up python3-mda-xdrlib (0.2.0-3) ...
283s Setting up libaec0:armhf (1.1.3-1) ...
283s Setting up python3-tz (2024.1-2) ...
283s Setting up python3-monotonic (1.6-2) ...
283s Setting up unicode-data (15.1.0-1) ...
283s Setting up python3-six (1.16.0-7) ...
283s Setting up libpython3.12t64:armhf (3.12.7-3) ...
283s Setting up python3-roman (4.2-1) ...
283s Setting up python3-decorator (5.1.1-5) ...
283s Setting up libfontenc1:armhf (1:1.1.8-1build1) ...
283s Setting up autotools-dev (20220109.1) ...
283s Setting up libblas3:armhf (3.12.0-3build2) ...
283s 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
283s Setting up python3-packaging (24.1-1) ...
283s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ...
283s Setting up python3-pyproject-hooks (1.2.0-1) ...
283s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ...
283s Setting up python3-snowballstemmer (2.2.0-4build1) ...
283s Setting up python3-brotli (1.1.0-2build2) ...
283s Setting up liblzf1:armhf (3.6-4) ...
283s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
283s Setting up python3-cycler (0.12.1-1) ...
283s Setting up libimagequant0:armhf (2.18.0-1build1) ...
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306s Setting up python-mdanalysis-doc (2.7.0-5) ...
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314s Setting up python3-sklearn (1.4.2+dfsg-6build1) ...
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317s Setting up python3-netcdf4 (1.7.2-1) ...
317s Setting up g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ...
317s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
317s Setting up python3-cairo (1.26.1-2) ...
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317s Setting up python3-tk:armhf (3.12.6-1ubuntu1) ...
317s Setting up libpython3.12-dev:armhf (3.12.7-3) ...
317s Setting up gcc (4:14.1.0-2ubuntu1) ...
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317s Setting up python3.12-dev (3.12.7-3) ...
317s Setting up python3-reportlab (4.2.5-1) ...
318s Setting up g++ (4:14.1.0-2ubuntu1) ...
318s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
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318s Setting up libpython3-dev:armhf (3.12.6-0ubuntu1) ...
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318s Setting up python3-fonttools (4.46.0-1build2) ...
319s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ...
320s Setting up python3-matplotlib (3.8.3-3) ...
322s Setting up python3-mdanalysis (2.7.0-5) ...
323s Setting up python3-seaborn (0.13.2-4) ...
323s Processing triggers for man-db (2.13.0-1) ...
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325s Processing triggers for sgml-base (1.31) ...
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363s Processing triggers for sgml-base (1.31) ...
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363s Setting up python3-pybtex-docutils (1.0.2-1) ...
363s Setting up python3-sphinx (7.4.7-4) ...
364s Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ...
365s Setting up python3-sphinx-sitemap (2.6.0-1) ...
365s Setting up python3-sphinxcontrib.jquery (4.1-5) ...
365s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ...
365s Setting up python3-msmb-theme (1.2.0-4) ...
365s Setting up autopkgtest-satdep (0) ...
398s (Reading database ... 86939 files and directories currently installed.)
398s Removing autopkgtest-satdep (0) ...
404s autopkgtest [20:24:38]: test test-mdanalysis: [-----------------------
406s skipping tests with SKIP_TEST_LIST=
418s ============================= test session starts ==============================
418s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
418s rootdir: /tmp/autopkgtest.nyWww9/build.wZv/src
418s plugins: typeguard-4.4.1, hypothesis-6.116.0
418s collected 19229 items / 6 skipped
418s 
423s testsuite/MDAnalysisTests/analysis/test_align.py ....................... [  0%]
434s ....................s.ss.s...                                            [  0%]
434s testsuite/MDAnalysisTests/analysis/test_atomicdistances.py ...           [  0%]
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468s testsuite/MDAnalysisTests/analysis/test_dihedrals.py ................... [  1%]
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552s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py . [  2%]
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607s ....                                                                     [  6%]
607s testsuite/MDAnalysisTests/converters/test_base.py ..                     [  6%]
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607s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py ...           [  7%]
611s testsuite/MDAnalysisTests/coordinates/test_chainreader.py .............. [  7%]
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625s testsuite/MDAnalysisTests/coordinates/test_copying.py .................. [  7%]
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650s testsuite/MDAnalysisTests/coordinates/test_crd.py ..............         [  8%]
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656s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py ................... [  9%]
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657s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py .................. [  9%]
657s .......                                                                  [  9%]
658s testsuite/MDAnalysisTests/coordinates/test_gms.py ..................     [  9%]
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804s testsuite/MDAnalysisTests/coordinates/test_mol2.py ..................... [ 13%]
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805s testsuite/MDAnalysisTests/coordinates/test_namdbin.py .................. [ 13%]
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814s testsuite/MDAnalysisTests/coordinates/test_null.py .                     [ 14%]
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850s testsuite/MDAnalysisTests/coordinates/test_pqr.py ...................... [ 15%]
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850s testsuite/MDAnalysisTests/coordinates/test_reader_api.py ............... [ 16%]
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860s ..                                                                       [ 18%]
860s testsuite/MDAnalysisTests/coordinates/test_txyz.py ......                [ 18%]
860s testsuite/MDAnalysisTests/coordinates/test_windows.py .................. [ 18%]
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861s testsuite/MDAnalysisTests/coordinates/test_writer_registration.py ....   [ 19%]
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880s testsuite/MDAnalysisTests/core/test_accumulate.py ...................... [ 21%]
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1004s testsuite/MDAnalysisTests/core/test_group_traj_access.py ............... [ 27%]
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1039s testsuite/MDAnalysisTests/core/test_topology.py ........................ [ 31%]
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1153s ....                                                                     [ 85%]
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1158s testsuite/MDAnalysisTests/topology/test_altloc.py ...                    [ 86%]
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1160s .....                                                                    [ 86%]
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1164s ......                                                                   [ 86%]
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1172s .......                                                                  [ 89%]
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1177s ..........................                                               [ 89%]
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1194s ...........                                                              [ 91%]
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1204s ..................                                                       [ 91%]
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1262s testsuite/MDAnalysisTests/topology/test_xyz.py ........................  [ 96%]
1262s testsuite/MDAnalysisTests/transformations/test_base.py .....             [ 96%]
1262s testsuite/MDAnalysisTests/transformations/test_boxdimensions.py ........ [ 96%]
1262s ......                                                                   [ 96%]
1262s testsuite/MDAnalysisTests/transformations/test_fit.py .................. [ 96%]
1262s .........................................                                [ 96%]
1264s testsuite/MDAnalysisTests/transformations/test_nojump.py ............    [ 96%]
1264s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py .... [ 96%]
1264s .                                                                        [ 96%]
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1273s .......                                                                  [ 97%]
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1274s testsuite/MDAnalysisTests/utils/test_duecredit.py ..............         [ 97%]
1274s testsuite/MDAnalysisTests/utils/test_failure.py .                        [ 97%]
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1274s testsuite/MDAnalysisTests/utils/test_meta.py ....                        [ 98%]
1275s testsuite/MDAnalysisTests/utils/test_modelling.py .............          [ 98%]
1276s testsuite/MDAnalysisTests/utils/test_persistence.py .......              [ 98%]
1288s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%]
1288s ..............ss..                                                       [ 98%]
1288s testsuite/MDAnalysisTests/utils/test_qcprot.py ......                    [ 98%]
1291s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%]
1291s                                                                          [ 98%]
1291s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 98%]
1291s ...............                                                          [ 99%]
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1292s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%]
1292s .......                                                                  [ 99%]
1292s testsuite/MDAnalysisTests/visualization/test_streamlines.py ...          [100%]
1292s 
1292s =============================== warnings summary ===============================
1292s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39
1292s   /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
1292s   
1292s   Due to the on going maintenance burden of keeping command line application
1292s   wrappers up to date, we have decided to deprecate and eventually remove these
1292s   modules.
1292s   
1292s   We instead now recommend building your command line and invoking it directly
1292s   with the subprocess module.
1292s     warnings.warn(
1292s 
1292s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings
1292s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings
1292s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings
1292s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings
1292s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings
1292s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings
1292s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings
1292s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings
1292s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings
1292s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings
1292s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings
1292s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings
1292s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
1292s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings
1292s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings
1292s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings
1292s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings
1292s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings
1292s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings
1292s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings
1292s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings
1292s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings
1292s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings
1292s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings
1292s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings
1292s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings
1292s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
1292s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings
1292s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
1292s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings
1292s   /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.
1292s     warnings.warn("DCDReader currently makes independent timesteps"
1292s 
1292s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52
1292s   /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.
1292s     warnings.warn(wmsg, category=DeprecationWarning)
1292s 
1292s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles'
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings
1292s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written
1292s     warnings.warn(wmsg)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings
1292s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings
1292s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings
1292s   /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
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings
1292s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
1292s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings
1292s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning
1292s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'oh', 'c3', 'hc', 'ho', 'h1'}. These have been given an empty element record.
1292s     warnings.warn("Unknown elements found for some "
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning
1292s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings
1292s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings
1292s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
1292s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings
1292s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings
1292s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     self.times[i] = ts.time
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning
1292s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings
1292s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
1292s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings
1292s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings
1292s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings
1292s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded
1292s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     results.append((ts.time, x.sum() / mask.sum()))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue
1292s   /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.
1292s     warnings.warn(msg)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
1292s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding
1292s   /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
1292s     warnings.warn(msg)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
1292s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1292s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
1292s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings
1292s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning
1292s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings
1292s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings
1292s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings
1292s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
1292s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings
1292s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings
1292s   /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.
1292s     warnings.warn("Element information is missing, elements attribute "
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran
1292s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame
1292s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections
1292s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues
1292s     warnings.warn("Cannot determine phi and psi angles for the first "
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin
1292s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr
1292s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame
1292s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot
1292s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning
1292s   /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.
1292s     warnings.warn(f"All residues selected with '{select_remove}' "
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings
1292s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings
1292s   /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=5337) is multi-threaded, use of fork() may lead to deadlocks in the child.
1292s     self.pid = os.fork()
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes
1292s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide
1292s     cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide
1292s     local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T  # (n_res-3, 3)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
1292s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice
1292s     ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
1292s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide
1292s     ret = um.true_divide(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
1292s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide
1292s     ret = ret.dtype.type(ret / rcount)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
1292s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning
1292s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning
1292s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
1292s   /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.
1292s     warnings.warn("1 A^3 CRYST1 record,"
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values.
1292s     warnings.warn("Unit cell dimensions not found. "
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' '
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings
1292s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings
1292s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings
1292s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
1292s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings
1292s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
1292s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning
1292s   /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
1292s     warnings.warn(wmsg, DeprecationWarning)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6
1292s     warnings.warn("Desired number of sample points too high, using {0}"
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbond = HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbond = HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbond = HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbond = HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbond = HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbond = HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbond = HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbond = HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     HBAC(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
1292s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
1292s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbond = HBAC(u,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated!
1292s   `find_hydrogen_donors` will be removed in release 3.0.0.
1292s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     D = hbonds.find_hydrogen_donors(H)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated!
1292s   `find_hydrogen_donors` will be removed in release 3.0.0.
1292s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
1292s     hbonds.find_hydrogen_donors(u.atoms)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
1292s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
1292s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
1292s     return _methods._mean(a, axis=axis, dtype=dtype,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
1292s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
1292s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
1292s     ret = ret.dtype.type(ret / rcount)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1292s   /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.
1292s     warnings.warn(msg.format(sel))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1292s   /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.
1292s     warnings.warn(msg.format(sel))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1292s   /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.
1292s     warnings.warn(msg.format(sel))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned.
1292s     warnings.warn("Empty string to select atoms, empty group returned.",
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1292s   /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, .
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
1292s   /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, .
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
1292s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
1292s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
1292s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
1292s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
1292s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
1292s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple
1292s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content
1292s   /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.
1292s     warnings.warn(wmsg)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning
1292s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning
1292s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
1292s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
1292s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
1292s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
1292s   /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.)
1292s     phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j
1292s   /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
1292s     warnings.warn("Column index entered (j = {:d} is smaller than row "
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     dt=self.trajectory.ts.dt * step,
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8]
1292s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0]
1292s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8]
1292s   /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
1292s     warnings.warn(wmsg, DeprecationWarning)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
1292s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings
1292s   /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.
1292s     warnings.warn("The `u` attribute is superflous and will be removed "
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267]
1292s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm
1292s   /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.
1292s     warnings.warn("The `density` attribute was deprecated in "
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata
1292s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first.
1292s     warnings.warn(msg, category=MissingDataWarning)
1292s 
1292s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     self.timesteps.append(self._ts.time)
1292s 
1292s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning
1292s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default
1292s     warnings.warn("{} does not support time selection. Reverting to "
1292s 
1292s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default
1292s     warnings.warn("{} does not support data selection. Reverting to "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
1292s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings
1292s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     return self.ts.dt
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
1292s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     ts.data['time'] = step_num * ts.dt
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_unitcell_triclinic[RefNAMDtriclinicDCD]
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDWriterWithRealTrajectory::test_write_trajectory[True-True-False]
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf1d403e8>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
1292s       self.close()
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close
1292s       self._apply('close')
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply
1292s       return [reader.__getattribute__(method)(**kwargs) for reader in self.readers]
1292s                                                                       ^^^^^^^^^^^^
1292s   AttributeError: 'ChainReader' object has no attribute 'readers'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing
1292s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain
1292s     warnings.warn("Missing frame in continuous chain", UserWarning)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     time_frame_0 = ts.time - ts.frame*ts.dt  # assumes ts.dt is constant
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     self._add_step_to_frame_data(ts.time)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames]
1292s   /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. 
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids]
1292s   /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. 
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names]
1292s   /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. 
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors]
1292s   /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. 
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     if not np.allclose(A.time, B.time):
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1]
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2]
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3]
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0]
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1]
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2]
1292s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array
1292s   /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
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf1d403e8>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
1292s       self.close()
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close
1292s       self._file.close()
1292s       ^^^^^^^^^^
1292s   AttributeError: 'DCDReader' object has no attribute '_file'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms
1292s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit
1292s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function DCDWriter.__del__ at 0xf1cb8988>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__
1292s       self.close()
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close
1292s       self._file.close()
1292s       ^^^^^^^^^^
1292s   AttributeError: 'DCDWriter' object has no attribute '_file'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings
1292s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings
1292s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
1292s   /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.
1292s     warnings.warn(msg)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     return self.ts.time
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter]
1292s   /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. 
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     assert_equal(reader.ts.dt, reader.dt)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     time_frame = time_frame_0 + frame_index*ts.dt
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     reader_p = pickle.loads(pickle.dumps(reader))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings
1292s   /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
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.]
1292s     warnings.warn(wmsg)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
1292s   /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`.
1292s     warnings.warn(wmsg)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present.  Unset velocities set to zero.
1292s     warnings.warn("Not all velocities were present.  "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     reader_p = pickle.loads(pickle.dumps(reader))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader
1292s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     reader_p = pickle.loads(pickle.dumps(reader))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf1d403e8>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
1292s       self.close()
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close
1292s       self._file.close()
1292s       ^^^^^^^^^^
1292s   AttributeError: 'H5MDReader' object has no attribute '_file'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM'
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf1d403e8>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
1292s       for aux in self.aux_list:
1292s                  ^^^^^^^^^^^^^
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
1292s       return self._auxs.keys()
1292s              ^^^^^^^^^^
1292s   AttributeError: 'H5MDReader' object has no attribute '_auxs'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
1292s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0
1292s     warnings.warn('Guessed all Masses to 1.0')
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit
1292s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf1d403e8>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
1292s       for aux in self.aux_list:
1292s                  ^^^^^^^^^^^^^
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
1292s       return self._auxs.keys()
1292s              ^^^^^^^^^^
1292s   AttributeError: 'DCDReader' object has no attribute '_auxs'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view
1292s   /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
1292s     warnings.warn("MemoryReader.timeseries inclusive `stop` "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader
1292s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     reader_p = pickle.loads(pickle.dumps(reader))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
1292s   /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
1292s     warnings.warn(wmsg)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     ts.time)  # in-place ! (hope this works...)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     time_list = [ts.time for ts in u.trajectory]
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     assert u.trajectory.ts.dt == pytest.approx(ref)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4
1292s   /tmp/autopkgtest.nyWww9/build.wZv/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.)
1292s     return self._test_write_trajectory(universe, outfile)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0]
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0]
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0]
1292s   /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.
1292s     warnings.warn(wmsg)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
1292s   /tmp/autopkgtest.nyWww9/build.wZv/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.)
1292s     return self._test_write_trajectory(universe, outfile)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of ''
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'
1292s     warnings.warn("Found missing chainIDs."
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom]
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond]
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom]
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree]
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond]
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     time = ts.time
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0xf1d40528>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
1292s       self.close()
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close
1292s       if self.trjfile is not None:
1292s          ^^^^^^^^^^^^
1292s   AttributeError: 'NCDFWriter' object has no attribute 'trjfile'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK'
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' '
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1'
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X'
1292s     warnings.warn("Found no information for attr: '{}'"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X'
1292s     warnings.warn("Found chainIDs using unnaccepted character."
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X'
1292s     warnings.warn("Found chainIDs with invalid length."
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000.  Higher serials have been guessed
1292s     warnings.warn("Serial numbers went over 100,000.  "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed
1292s     warnings.warn("Invalid atom serials were present, bonds will not"
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed
1292s     warnings.warn("Invalid atom serials were present, "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment
1292s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
1292s   /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.
1292s     warnings.warn(wmsg)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
1292s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1292s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
1292s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1292s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges
1292s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
1292s   /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. 
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     assert_equal(ts.dt, 1.0)  # default value
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     assert_equal(ts.time, 0.0)  # default to 1.0 (dt) * 0 (frame)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf1d403e8>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
1292s       for aux in self.aux_list:
1292s                  ^^^^^^^^^^^^^
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
1292s       return self._auxs.keys()
1292s              ^^^^^^^^^^
1292s   AttributeError: 'TNGReader' object has no attribute '_auxs'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms
1292s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe
1292s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe
1292s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks!
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf1d403e8>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
1292s       self.close()
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close
1292s       if self.trjfile is None:
1292s          ^^^^^^^^^^^^
1292s   AttributeError: 'TRJReader' object has no attribute 'trjfile'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     data['time'] = ts.time
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
1292s   /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
1292s     warnings.warn("Timestep didn't have the following attributes: '{0}', "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
1292s   /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. 
1292s     warnings.warn("Timestep didn't have velocity information, "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
1292s   /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
1292s     warnings.warn("Timestep didn't have dimensions information, "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0xf1d40528>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
1292s       self.close()
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close
1292s       if self.trzfile is None:
1292s          ^^^^^^^^^^^^
1292s   AttributeError: 'TRZWriter' object has no attribute 'trzfile'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
1292s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
1292s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
1292s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
1292s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
1292s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
1292s   /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.
1292s     warnings.warn("Element information is missing, elements attribute "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
1292s   /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
1292s     warnings.warn(wmsg, DeprecationWarning)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter]
1292s   /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. 
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter]
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter]
1292s   /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. 
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter]
1292s   /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. 
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter]
1292s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter]
1292s   /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'
1292s     warnings.warn(wmsg)
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD
1292s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     time = ts.time
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD
1292s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     time = ts.time
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0xeeca8618>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
1292s       self.close()
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
1292s       self._xdr.close()
1292s       ^^^^^^^^^
1292s   AttributeError: 'XTCWriter' object has no attribute '_xdr'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container
1292s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0xeeca8618>
1292s   
1292s   Traceback (most recent call last):
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
1292s       self.close()
1292s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
1292s       self._xdr.close()
1292s       ^^^^^^^^^
1292s   AttributeError: 'TRRWriter' object has no attribute '_xdr'
1292s   
1292s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
1292s   /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.
1292s   Consider setting 'refresh_offsets=True' when loading your Universe.
1292s     warnings.warn(f"Reading offsets from {fname} failed, "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly
1292s   /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.
1292s     warnings.warn(f"Cannot write lock/offset file in same location as "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
1292s   /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.
1292s   Consider setting 'refresh_offsets=True' when loading your Universe.
1292s     warnings.warn(f"Reading offsets from {fname} failed, "
1292s 
1292s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly
1292s   /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.
1292s     warnings.warn(f"Cannot write lock/offset file in same location as "
1292s 
1292s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms]
1292s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues]
1292s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments]
1292s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce
1292s     return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
1292s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
1292s   /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.
1292s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings
1292s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings
1292s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings
1292s   /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.
1292s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
1292s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
1292s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide
1292s     return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum()
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings
1292s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide
1292s     _centers /= _weights.sum(axis=1)[:, None]
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
1292s   /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`.
1292s     warnings.warn(msg, category=SelectionWarning)
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
1292s   /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`.
1292s     warnings.warn(msg, category=SelectionWarning)
1292s 
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12]
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13]
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15]
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16]
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17]
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18]
1292s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19]
1292s   /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`.
1292s     warnings.warn(msg, category=SelectionWarning)
1292s 
1292s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments]
1292s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules]
1292s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues]
1292s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group]
1292s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments]
1292s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc
1292s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc
1292s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options
1292s   /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
1292s     warnings.warn("The 'pbc' kwarg has been deprecated and will be "
1292s 
1292s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel
1292s   /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`.
1292s     warnings.warn(msg, category=SelectionWarning)
1292s 
1292s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial]
1292s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp]
1292s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial]
1292s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp]
1292s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide
1292s     x = np.dot(a, b) / (norm(a) * norm(b))
1292s 
1292s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt
1292s     ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2)
1292s 
1292s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt
1292s     box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 -
1292s 
1292s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide
1292s     a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z)))
1292s 
1292s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide
1292s     b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z)))
1292s 
1292s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide
1292s     c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y)))
1292s 
1292s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide
1292s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
1292s 
1292s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide
1292s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
1292s 
1292s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2]
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3]
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4]
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5]
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6]
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7]
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10]
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11]
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14]
1292s   /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     cls(buf, protocol).dump(obj)
1292s 
1292s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     ps = pickle.dumps(ref_reader)
1292s 
1292s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0]
1292s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd
1292s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd
1292s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset
1292s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific
1292s   /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset.
1292s     warnings.warn('Cannot average position for non sequential'
1292s 
1292s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name]
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname]
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type]
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid]
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information.  Defaulted to '1'
1292s     warnings.warn("PDB file is missing resid information.  "
1292s 
1292s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX
1292s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
1292s 
1292s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2]
1292s   /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.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2]
1292s   /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.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2]
1292s   /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.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2]
1292s   /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.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
1292s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings
1292s   /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.
1292s     warnings.warn(msg)
1292s 
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts
1292s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr]
1292s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file.
1292s     warnings.warn('No coordinate reader found for {}. Skipping '
1292s 
1292s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses
1292s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses.
1292s     warnings.warn(msg, category=SelectionWarning)
1292s 
1292s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2
1292s   /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.
1292s     warnings.warn(
1292s 
1292s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
1292s 
1292s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
1292s 
1292s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL)
1292s 
1292s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL)
1292s 
1292s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL)
1292s 
1292s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL)
1292s 
1292s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag
1292s   /tmp/autopkgtest.nyWww9/build.wZv/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps
1292s     pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL)
1292s 
1292s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings
1292s   /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream
1292s     warnings.warn("Constructed NamedStream from a NamedStream",
1292s 
1292s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159]
1292s   /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.
1292s     warnings.warn(wmsg, DeprecationWarning)
1292s 
1292s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
1292s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8131 warnings in 886.10s (0:14:46) =
1315s 
1315s DueCredit Report:
1315s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2]
1315s   - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3]
1315s   - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4]
1315s   - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5]
1315s   - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8]
1315s   - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9]
1315s   - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10]
1315s   - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2]
1315s   - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12]
1315s   - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13]
1315s   - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14]
1315s   - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 1.1, 2.7.0) [15, 16]
1315s   - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17]
1315s   - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18]
1315s   - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20]
1315s   - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17]
1315s   - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21]
1315s - Scientific tools library / numpy (v 1.26.4) [22]
1315s 
1315s 2 packages cited
1315s 16 modules cited
1315s 0 functions cited
1315s 
1315s References
1315s ----------
1315s 
1315s [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.
1315s [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.
1315s [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.
1315s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858.
1315s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415.
1315s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460.
1315s [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.
1315s [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.
1315s [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.
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1318s autopkgtest [20:39:52]: test test-mdanalysis: -----------------------]
1323s autopkgtest [20:39:57]: test test-mdanalysis:  - - - - - - - - - - results - - - - - - - - - -
1323s test-mdanalysis      PASS
1326s autopkgtest [20:40:00]: @@@@@@@@@@@@@@@@@@@@ summary
1326s test-mdanalysis      PASS