0s autopkgtest [11:18:41]: starting date and time: 2024-11-15 11:18:41+0000
  0s autopkgtest [11:18:41]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [11:18:41]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.84c_js26/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu4-ram8-disk100 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-5.secgroup --name adt-plucky-amd64-mdanalysis-20241115-111841-juju-7f2275-prod-proposed-migration-environment-15-be7b4769-633a-4687-a1dc-f604b282a2e1 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 39s autopkgtest [11:19:20]: testbed dpkg architecture: amd64
 39s autopkgtest [11:19:20]: testbed apt version: 2.9.8
 39s autopkgtest [11:19:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 40s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 40s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1056 kB]
 40s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB]
 40s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 40s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [94.5 kB]
 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [109 kB]
 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [176 kB]
 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [297 kB]
 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [833 kB]
 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [740 B]
 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9416 B]
 40s Fetched 2704 kB in 1s (3231 kB/s)
 40s Reading package lists...
 43s Reading package lists...
 43s Building dependency tree...
 43s Reading state information...
 43s Calculating upgrade...
 44s The following packages will be upgraded:
 44s   firmware-sof-signed grub-common grub-pc grub-pc-bin grub2-common libcap-ng0
 44s   libexpat1 lxd-installer man-db pastebinit python3-systemd xfsprogs
 44s 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 44s Need to get 13.6 MB of archives.
 44s After this operation, 477 kB of additional disk space will be used.
 44s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB]
 44s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-3build1 [15.6 kB]
 44s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1 amd64 2.6.4-1 [94.9 kB]
 44s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 man-db amd64 2.13.0-1 [1352 kB]
 44s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 grub2-common amd64 2.12-5ubuntu7 [672 kB]
 45s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc amd64 2.12-5ubuntu7 [137 kB]
 45s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-pc-bin amd64 2.12-5ubuntu7 [1127 kB]
 45s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 grub-common amd64 2.12-5ubuntu7 [2110 kB]
 45s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 9 [5084 B]
 45s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB]
 45s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build5 [45.7 kB]
 45s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfsprogs amd64 6.8.0-2.2ubuntu2 [926 kB]
 45s Preconfiguring packages ...
 45s Fetched 13.6 MB in 1s (13.0 MB/s)
 45s (Reading database ... 
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(Reading database ... 75542 files and directories currently installed.)
 45s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ...
 45s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ...
 45s Preparing to unpack .../libcap-ng0_0.8.5-3build1_amd64.deb ...
 45s Unpacking libcap-ng0:amd64 (0.8.5-3build1) over (0.8.5-1) ...
 45s Setting up libcap-ng0:amd64 (0.8.5-3build1) ...
 45s (Reading database ... 
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(Reading database ... 75568 files and directories currently installed.)
 45s Preparing to unpack .../0-libexpat1_2.6.4-1_amd64.deb ...
 45s Unpacking libexpat1:amd64 (2.6.4-1) over (2.6.2-2) ...
 45s Preparing to unpack .../1-man-db_2.13.0-1_amd64.deb ...
 45s Unpacking man-db (2.13.0-1) over (2.12.1-3) ...
 46s Preparing to unpack .../2-grub2-common_2.12-5ubuntu7_amd64.deb ...
 46s Unpacking grub2-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 46s Preparing to unpack .../3-grub-pc_2.12-5ubuntu7_amd64.deb ...
 46s Unpacking grub-pc (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 46s Preparing to unpack .../4-grub-pc-bin_2.12-5ubuntu7_amd64.deb ...
 46s Unpacking grub-pc-bin (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 46s Preparing to unpack .../5-grub-common_2.12-5ubuntu7_amd64.deb ...
 46s Unpacking grub-common (2.12-5ubuntu7) over (2.12-5ubuntu5.1) ...
 46s Preparing to unpack .../6-lxd-installer_9_all.deb ...
 46s Unpacking lxd-installer (9) over (8) ...
 46s Preparing to unpack .../7-pastebinit_1.7.1-1_all.deb ...
 46s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
 46s Preparing to unpack .../8-python3-systemd_235-1build5_amd64.deb ...
 46s Unpacking python3-systemd (235-1build5) over (235-1build4) ...
 46s Preparing to unpack .../9-xfsprogs_6.8.0-2.2ubuntu2_amd64.deb ...
 46s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ...
 46s Setting up libexpat1:amd64 (2.6.4-1) ...
 46s Setting up firmware-sof-signed (2024.06-1ubuntu2) ...
 46s Setting up pastebinit (1.7.1-1) ...
 46s Setting up man-db (2.13.0-1) ...
 46s Updating database of manual pages ...
 48s man-db.service is a disabled or a static unit not running, not starting it.
 48s Setting up grub-common (2.12-5ubuntu7) ...
 48s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
 49s Setting up xfsprogs (6.8.0-2.2ubuntu2) ...
 49s update-initramfs: deferring update (trigger activated)
 49s Setting up lxd-installer (9) ...
 50s Setting up python3-systemd (235-1build5) ...
 50s Setting up grub2-common (2.12-5ubuntu7) ...
 50s Setting up grub-pc-bin (2.12-5ubuntu7) ...
 50s Setting up grub-pc (2.12-5ubuntu7) ...
 50s Installing for i386-pc platform.
 50s Installation finished. No error reported.
 51s Sourcing file `/etc/default/grub'
 51s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
 51s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
 51s Generating grub configuration file ...
 51s Found linux image: /boot/vmlinuz-6.11.0-8-generic
 51s Found initrd image: /boot/initrd.img-6.11.0-8-generic
 51s Warning: os-prober will not be executed to detect other bootable partitions.
 51s Systems on them will not be added to the GRUB boot configuration.
 51s Check GRUB_DISABLE_OS_PROBER documentation entry.
 51s Adding boot menu entry for UEFI Firmware Settings ...
 51s done
 51s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 51s Processing triggers for install-info (7.1.1-1) ...
 51s Processing triggers for initramfs-tools (0.142ubuntu34) ...
 51s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic
 51s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
 60s Reading package lists...
 60s Building dependency tree...
 60s Reading state information...
 60s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 60s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 60s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 61s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 61s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 61s Reading package lists...
 61s Reading package lists...
 62s Building dependency tree...
 62s Reading state information...
 62s Calculating upgrade...
 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 62s Reading package lists...
 62s Building dependency tree...
 62s Reading state information...
 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 63s autopkgtest [11:19:44]: rebooting testbed after setup commands that affected boot
 66s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
 81s autopkgtest [11:20:02]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 83s autopkgtest [11:20:04]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis
 87s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B]
 87s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB]
 87s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB]
 87s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC
 87s gpgv:                using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA
 87s gpgv:                issuer "dparsons@debian.org"
 87s gpgv: Can't check signature: No public key
 87s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found
 88s autopkgtest [11:20:09]: testing package mdanalysis version 2.7.0-5
 89s autopkgtest [11:20:10]: build not needed
 93s autopkgtest [11:20:14]: test test-mdanalysis: preparing testbed
 95s Reading package lists...
 95s Building dependency tree...
 95s Reading state information...
 95s Starting pkgProblemResolver with broken count: 0
 95s Starting 2 pkgProblemResolver with broken count: 0
 95s Done
 96s The following additional packages will be installed:
 96s   autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14
 96s   cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cython3 debhelper debugedit
 96s   dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz
 96s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome
 96s   fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14
 96s   g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
 96s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian libaec0
 96s   libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdebhelper-perl
 96s   libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1
 96s   libfontenc1 libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
 96s   libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libimagequant0 libisl23
 96s   libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui
 96s   libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl liblapack3
 96s   liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libnetcdf19t64
 96s   libopenjp2-7 libpixman-1-0 libpython3-all-dev libpython3-dev
 96s   libpython3.12-dev libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0
 96s   libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2
 96s   libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0
 96s   libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf
 96s   pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc
 96s   python3-alabaster python3-all python3-all-dev python3-appdirs
 96s   python3-biopython python3-brotli python3-build python3-cairo python3-cftime
 96s   python3-citeproc python3-contourpy python3-cycler python3-dateutil
 96s   python3-decorator python3-defusedxml python3-dev python3-docutils
 96s   python3-duecredit python3-fasteners python3-fonttools python3-freetype
 96s   python3-fs python3-griddataformats python3-gsd python3-h5py
 96s   python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig
 96s   python3-installer python3-joblib python3-kiwisolver python3-latexcodec
 96s   python3-looseversion python3-lxml python3-lz4 python3-matplotlib
 96s   python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic
 96s   python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme
 96s   python3-netcdf4 python3-networkx python3-numpy python3-packaging
 96s   python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk
 96s   python3-pluggy python3-pybtex python3-pybtex-docutils
 96s   python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo
 96s   python3-roman python3-scipy python3-seaborn python3-six python3-sklearn
 96s   python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
 96s   python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap
 96s   python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy
 96s   python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz
 96s   python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev
 96s   python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5
 96s   unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
 96s   zlib1g-dev
 96s Suggested packages:
 96s   autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales
 96s   cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf
 96s   fonts-texgyre g++-multilib g++-14-multilib gcc-14-doc gcc-multilib
 96s   manpages-dev flex bison gdb gcc-doc gcc-14-multilib gdb-x86-64-linux-gnu
 96s   gettext-doc libasprintf-dev libgettextpo-dev libjs-jquery-ui-docs
 96s   fonts-mathjax-extras fonts-stix libjs-mathjax-doc liblcms2-utils
 96s   libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler
 96s   gcj-jdk m4-doc libmail-box-perl bwa clustalo clustalw dialign dssp emboss
 96s   fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb
 96s   python3-rdflib python3-psycopg2 raxml samtools t-coffee wise python3-pip
 96s   python3-venv python-build-doc python-cycler-doc docutils-doc
 96s   fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
 96s   texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc
 96s   python-hypothesis-doc python-installer-doc python-joblib-doc
 96s   python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg
 96s   fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common
 96s   python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject
 96s   python3-pyqt5 python3-sip python3-tornado texlive-extra-utils
 96s   texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal
 96s   python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc
 96s   python3-statsmodels python-pil-doc python-pybtex-doc
 96s   python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools
 96s   python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap
 96s   python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm
 96s   fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre
 96s   texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic
 96s   python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg
 96s   python3.13-tk sgml-base-doc
 96s Recommended packages:
 96s   libarchive-cpio-perl javascript-common libjson-xs-perl libltdl-dev
 96s   libmail-sendmail-perl python-biopython-doc ncbi-blast+ libpaper-utils
 96s   python3-click python3-simplejson python3-psutil python3-bs4
 96s   python3-cssselect python3-html5lib python3-bottleneck python3-numexpr
 96s   python3-odf python3-openpyxl python3-tables python3-numba python3-olefile
 96s   fonts-dejavu-extra isympy-common
 96s The following NEW packages will be installed:
 96s   autoconf automake autopkgtest-satdep autopoint autotools-dev blt
 96s   build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu
 96s   cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism
 96s   docutils-common dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono
 96s   fonts-font-awesome fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++
 96s   g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
 96s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian libaec0
 96s   libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdebhelper-perl
 96s   libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1
 96s   libfontenc1 libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
 96s   libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libimagequant0 libisl23
 96s   libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui
 96s   libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl liblapack3
 96s   liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libnetcdf19t64
 96s   libopenjp2-7 libpixman-1-0 libpython3-all-dev libpython3-dev
 96s   libpython3.12-dev libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0
 96s   libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2
 96s   libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0
 96s   libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf
 96s   pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc
 96s   python3-alabaster python3-all python3-all-dev python3-appdirs
 96s   python3-biopython python3-brotli python3-build python3-cairo python3-cftime
 96s   python3-citeproc python3-contourpy python3-cycler python3-dateutil
 96s   python3-decorator python3-defusedxml python3-dev python3-docutils
 96s   python3-duecredit python3-fasteners python3-fonttools python3-freetype
 96s   python3-fs python3-griddataformats python3-gsd python3-h5py
 96s   python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig
 96s   python3-installer python3-joblib python3-kiwisolver python3-latexcodec
 96s   python3-looseversion python3-lxml python3-lz4 python3-matplotlib
 96s   python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic
 96s   python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme
 96s   python3-netcdf4 python3-networkx python3-numpy python3-packaging
 96s   python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk
 96s   python3-pluggy python3-pybtex python3-pybtex-docutils
 96s   python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo
 96s   python3-roman python3-scipy python3-seaborn python3-six python3-sklearn
 96s   python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
 96s   python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap
 96s   python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy
 96s   python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz
 96s   python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev
 96s   python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5
 96s   unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
 96s   zlib1g-dev
 96s 0 upgraded, 203 newly installed, 0 to remove and 0 not upgraded.
 96s Need to get 210 MB/210 MB of archives.
 96s After this operation, 894 MB of additional disk space will be used.
 96s Get:1 /tmp/autopkgtest.pgcwp3/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [1012 B]
 96s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB]
 96s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB]
 96s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB]
 96s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB]
 96s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB]
 96s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB]
 97s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB]
 97s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB]
 97s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
 97s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
 97s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB]
 97s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
 97s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
 97s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB]
 97s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB]
 97s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
 97s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
 97s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
 97s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
 97s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
 97s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB]
 97s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB]
 97s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B]
 97s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB]
 97s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB]
 98s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB]
 98s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B]
 98s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B]
 98s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB]
 98s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB]
 98s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
 98s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB]
 98s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB]
 98s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB]
 98s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB]
 98s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB]
 98s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB]
 98s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB]
 98s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB]
 98s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB]
 99s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB]
 99s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B]
 99s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B]
 99s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB]
 99s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB]
 99s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB]
 99s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B]
 99s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B]
 99s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
 99s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-1ubuntu2 [3368 kB]
 99s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB]
 99s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB]
 99s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB]
 99s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB]
 99s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB]
 99s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B]
 99s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB]
 99s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB]
 99s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB]
 99s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB]
 99s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB]
 99s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB]
 99s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB]
 99s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB]
 99s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB]
 99s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
 99s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB]
 99s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
100s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB]
100s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
100s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
100s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
100s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
100s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
100s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
100s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB]
100s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
100s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
100s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB]
100s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B]
100s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB]
100s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB]
100s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
100s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB]
100s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
100s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
100s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
100s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
100s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
100s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-perl all 4.10000-1 [81.9 kB]
100s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
100s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB]
100s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB]
100s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB]
100s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B]
100s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf19t64 amd64 1:4.9.2-6ubuntu1 [472 kB]
100s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB]
100s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.7-3 [5699 kB]
100s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.12.6-0ubuntu1 [10.2 kB]
100s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-all-dev amd64 3.12.6-0ubuntu1 [916 B]
100s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB]
100s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB]
100s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
100s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
100s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
101s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
101s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB]
101s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB]
101s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB]
101s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB]
101s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB]
101s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-toml all 0.10.2-1 [16.5 kB]
101s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wheel all 0.44.0-1 [54.2 kB]
101s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-build all 1.2.2-1 [31.0 kB]
101s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB]
101s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-pyproject all 6.20241024 [1728 B]
101s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB]
101s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
101s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-mdanalysis-doc all 2.7.0-5 [2323 kB]
101s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B]
101s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB]
101s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.12.6-0ubuntu1 [26.7 kB]
101s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all-dev amd64 3.12.6-0ubuntu1 [908 B]
101s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB]
101s Get:126 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB]
101s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB]
101s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.6-1ubuntu1 [9806 B]
101s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B]
101s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB]
101s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB]
101s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB]
101s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB]
101s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B]
101s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB]
101s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB]
102s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB]
102s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB]
102s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cftime amd64 1.6.4-1 [214 kB]
102s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB]
102s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-citeproc all 0.6.0-3 [98.4 kB]
102s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB]
102s Get:143 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B]
102s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB]
102s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB]
102s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB]
102s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-defusedxml all 0.7.1-2 [42.0 kB]
102s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-roman all 4.2-1 [10.0 kB]
102s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB]
102s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-looseversion all 1.3.0-3 [8354 B]
102s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-duecredit all 0.10.2-2 [66.0 kB]
102s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-monotonic all 1.6-2 [5732 B]
102s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-fasteners all 0.18-2 [12.5 kB]
102s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB]
103s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB]
103s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB]
103s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB]
103s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB]
103s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB]
103s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB]
103s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB]
103s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB]
103s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB]
104s Get:164 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB]
104s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mrcfile all 1.5.3-3 [114 kB]
104s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-griddataformats all 1.0.2-2 [2107 kB]
104s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-gsd amd64 3.3.0-1 [203 kB]
104s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB]
104s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B]
104s Get:170 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sortedcontainers all 2.4.0-2 [27.6 kB]
104s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-hypothesis all 6.116.0-1 [326 kB]
104s Get:172 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-imagesize all 1.4.1-1 [6844 B]
104s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B]
104s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB]
104s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB]
104s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-latexcodec all 3.0.0-1 [16.6 kB]
104s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB]
104s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mda-xdrlib all 0.2.0-3 [11.4 kB]
104s Get:179 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-msgpack amd64 1.0.3-3build2 [80.1 kB]
104s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mmtf all 1.1.3-1 [16.2 kB]
104s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB]
104s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.0-1 [91.6 kB]
104s Get:183 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mdanalysis amd64 2.7.0-5 [1992 kB]
104s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-common all 7.4.7-4 [775 kB]
104s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-alabaster all 0.7.16-0.1 [18.5 kB]
104s Get:186 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB]
104s Get:187 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sphinx all 7.4.7-4 [593 kB]
104s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B]
104s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB]
104s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-msmb-theme all 1.2.0-4 [35.4 kB]
104s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-netcdf4 amd64 1.7.2-1 [645 kB]
104s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB]
105s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB]
105s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB]
106s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB]
106s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pybtex all 0.24.0-4 [70.0 kB]
106s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pybtex-docutils all 1.0.2-1 [7176 B]
106s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB]
106s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-seaborn all 0.13.2-4 [225 kB]
106s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB]
106s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB]
106s Get:202 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinx-sitemap all 2.6.0-1 [6674 B]
106s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB]
106s Fetched 210 MB in 10s (20.5 MB/s)
106s Selecting previously unselected package fonts-lato.
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107s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ...
107s Unpacking fonts-lato (2.015-1) ...
107s Selecting previously unselected package sgml-base.
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107s Unpacking sgml-base (1.31) ...
107s Selecting previously unselected package m4.
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107s Selecting previously unselected package autoconf.
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107s Selecting previously unselected package autotools-dev.
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107s Selecting previously unselected package autopoint.
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107s Selecting previously unselected package libtcl8.6:amd64.
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107s Selecting previously unselected package fonts-dejavu-mono.
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107s Selecting previously unselected package fonts-dejavu-core.
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107s Unpacking fonts-dejavu-core (2.37-8) ...
107s Selecting previously unselected package libfontenc1:amd64.
107s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build1_amd64.deb ...
107s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ...
107s Selecting previously unselected package x11-common.
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107s Selecting previously unselected package xfonts-encodings.
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107s Selecting previously unselected package fonts-urw-base35.
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108s Selecting previously unselected package libfontconfig1:amd64.
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108s Selecting previously unselected package libxrender1:amd64.
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108s Selecting previously unselected package libxft2:amd64.
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108s Selecting previously unselected package libxss1:amd64.
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108s Unpacking libxss1:amd64 (1:1.2.3-1build3) ...
108s Selecting previously unselected package libtk8.6:amd64.
108s Preparing to unpack .../020-libtk8.6_8.6.15-1_amd64.deb ...
108s Unpacking libtk8.6:amd64 (8.6.15-1) ...
108s Selecting previously unselected package tk8.6-blt2.5.
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108s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
108s Selecting previously unselected package blt.
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108s Unpacking blt (2.5.3+dfsg-7build1) ...
108s Selecting previously unselected package libisl23:amd64.
108s Preparing to unpack .../023-libisl23_0.27-1_amd64.deb ...
108s Unpacking libisl23:amd64 (0.27-1) ...
108s Selecting previously unselected package libmpc3:amd64.
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108s Unpacking libmpc3:amd64 (1.3.1-1build2) ...
108s Selecting previously unselected package cpp-14-x86-64-linux-gnu.
108s Preparing to unpack .../025-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ...
108s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ...
108s Selecting previously unselected package cpp-14.
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108s Unpacking cpp-14 (14.2.0-8ubuntu1) ...
108s Selecting previously unselected package cpp-x86-64-linux-gnu.
108s Preparing to unpack .../027-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ...
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108s Selecting previously unselected package cpp.
108s Preparing to unpack .../028-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ...
108s Unpacking cpp (4:14.1.0-2ubuntu1) ...
108s Selecting previously unselected package libcc1-0:amd64.
108s Preparing to unpack .../029-libcc1-0_14.2.0-8ubuntu1_amd64.deb ...
108s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ...
108s Selecting previously unselected package libgomp1:amd64.
108s Preparing to unpack .../030-libgomp1_14.2.0-8ubuntu1_amd64.deb ...
108s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ...
108s Selecting previously unselected package libitm1:amd64.
108s Preparing to unpack .../031-libitm1_14.2.0-8ubuntu1_amd64.deb ...
108s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ...
108s Selecting previously unselected package libasan8:amd64.
108s Preparing to unpack .../032-libasan8_14.2.0-8ubuntu1_amd64.deb ...
108s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ...
108s Selecting previously unselected package liblsan0:amd64.
108s Preparing to unpack .../033-liblsan0_14.2.0-8ubuntu1_amd64.deb ...
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108s Selecting previously unselected package libtsan2:amd64.
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108s Selecting previously unselected package libubsan1:amd64.
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108s Selecting previously unselected package libhwasan0:amd64.
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108s Selecting previously unselected package libquadmath0:amd64.
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108s Selecting previously unselected package libgcc-14-dev:amd64.
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109s Selecting previously unselected package gcc-14-x86-64-linux-gnu.
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109s Selecting previously unselected package gcc-14.
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109s Selecting previously unselected package gcc-x86-64-linux-gnu.
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109s Unpacking gcc (4:14.1.0-2ubuntu1) ...
109s Selecting previously unselected package libstdc++-14-dev:amd64.
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109s Selecting previously unselected package g++-14-x86-64-linux-gnu.
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109s Selecting previously unselected package g++-14.
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109s Unpacking g++-14 (14.2.0-8ubuntu1) ...
109s Selecting previously unselected package g++-x86-64-linux-gnu.
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109s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
109s Selecting previously unselected package g++.
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109s Selecting previously unselected package build-essential.
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109s Selecting previously unselected package cython3.
109s Preparing to unpack .../049-cython3_3.0.11+dfsg-1ubuntu2_amd64.deb ...
109s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ...
109s Selecting previously unselected package libdebhelper-perl.
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109s Unpacking libdebhelper-perl (13.20ubuntu1) ...
110s Selecting previously unselected package libtool.
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110s Unpacking libtool (2.4.7-7build1) ...
110s Selecting previously unselected package dh-autoreconf.
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110s Selecting previously unselected package libarchive-zip-perl.
110s Preparing to unpack .../053-libarchive-zip-perl_1.68-1_all.deb ...
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110s Selecting previously unselected package libfile-stripnondeterminism-perl.
110s Preparing to unpack .../054-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
110s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
110s Selecting previously unselected package dh-strip-nondeterminism.
110s Preparing to unpack .../055-dh-strip-nondeterminism_1.14.0-1_all.deb ...
110s Unpacking dh-strip-nondeterminism (1.14.0-1) ...
110s Selecting previously unselected package debugedit.
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110s Selecting previously unselected package dwz.
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110s Selecting previously unselected package gettext.
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110s Selecting previously unselected package intltool-debian.
110s Preparing to unpack .../059-intltool-debian_0.35.0+20060710.6_all.deb ...
110s Unpacking intltool-debian (0.35.0+20060710.6) ...
110s Selecting previously unselected package po-debconf.
110s Preparing to unpack .../060-po-debconf_1.0.21+nmu1_all.deb ...
110s Unpacking po-debconf (1.0.21+nmu1) ...
110s Selecting previously unselected package debhelper.
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110s Unpacking debhelper (13.20ubuntu1) ...
110s Selecting previously unselected package dh-python.
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110s Unpacking dh-python (6.20241024) ...
110s Selecting previously unselected package xml-core.
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110s Unpacking xml-core (0.19) ...
110s Selecting previously unselected package docutils-common.
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110s Unpacking docutils-common (0.21.2+dfsg-2) ...
110s Selecting previously unselected package fonts-font-awesome.
110s Preparing to unpack .../065-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
110s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
110s Selecting previously unselected package fonts-lyx.
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110s Unpacking fonts-lyx (2.4.2.1-1) ...
110s Selecting previously unselected package fonts-mathjax.
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110s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
110s Selecting previously unselected package libaec0:amd64.
110s Preparing to unpack .../068-libaec0_1.1.3-1_amd64.deb ...
110s Unpacking libaec0:amd64 (1.1.3-1) ...
110s Selecting previously unselected package libblas3:amd64.
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110s Unpacking libblas3:amd64 (3.12.0-3build2) ...
110s Selecting previously unselected package libpixman-1-0:amd64.
110s Preparing to unpack .../070-libpixman-1-0_0.44.0-3_amd64.deb ...
110s Unpacking libpixman-1-0:amd64 (0.44.0-3) ...
110s Selecting previously unselected package libxcb-render0:amd64.
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110s Unpacking libxcb-render0:amd64 (1.17.0-2) ...
110s Selecting previously unselected package libxcb-shm0:amd64.
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110s Unpacking libxcb-shm0:amd64 (1.17.0-2) ...
110s Selecting previously unselected package libcairo2:amd64.
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110s Unpacking libcairo2:amd64 (1.18.2-2) ...
110s Selecting previously unselected package libdeflate0:amd64.
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110s Unpacking libdeflate0:amd64 (1.22-1) ...
110s Selecting previously unselected package libexpat1-dev:amd64.
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110s Unpacking libexpat1-dev:amd64 (2.6.4-1) ...
110s Selecting previously unselected package libgfortran5:amd64.
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110s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ...
110s Selecting previously unselected package libgraphite2-3:amd64.
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111s Selecting previously unselected package libjpeg-turbo8:amd64.
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111s Selecting previously unselected package libjs-jquery-ui.
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111s Selecting previously unselected package libjs-sphinxdoc.
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111s Selecting previously unselected package libjson-perl.
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111s Unpacking libjson-perl (4.10000-1) ...
111s Selecting previously unselected package liblapack3:amd64.
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112s Selecting previously unselected package python-matplotlib-data.
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112s Selecting previously unselected package libjs-mathjax.
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112s Selecting previously unselected package python-mdanalysis-doc.
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112s Selecting previously unselected package python3-all.
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112s Selecting previously unselected package python3.12-dev.
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112s Selecting previously unselected package python3-all-dev.
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112s Selecting previously unselected package python3-numpy.
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113s Selecting previously unselected package python3-pil.imagetk:amd64.
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113s Selecting previously unselected package libopenjp2-7:amd64.
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113s Selecting previously unselected package python3-pil:amd64.
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113s Selecting previously unselected package python3-cairo.
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113s Selecting previously unselected package python3-freetype.
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113s Selecting previously unselected package python3-rlpycairo.
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113s Selecting previously unselected package python3-reportlab.
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113s Selecting previously unselected package w3c-sgml-lib.
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113s Selecting previously unselected package python3-biopython.
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113s Selecting previously unselected package python3-brotli.
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113s Selecting previously unselected package python3-cftime.
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113s Selecting previously unselected package python3-lxml:amd64.
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113s Selecting previously unselected package python3-citeproc.
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113s Selecting previously unselected package python3-contourpy.
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113s Selecting previously unselected package python3-cycler.
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113s Selecting previously unselected package python3-six.
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113s Selecting previously unselected package python3-dateutil.
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113s Selecting previously unselected package python3-decorator.
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113s Selecting previously unselected package python3-defusedxml.
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113s Selecting previously unselected package python3-roman.
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113s Selecting previously unselected package python3-docutils.
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114s Selecting previously unselected package python3-looseversion.
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114s Selecting previously unselected package python3-duecredit.
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114s Selecting previously unselected package python3-monotonic.
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114s Selecting previously unselected package python3-fasteners.
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114s Selecting previously unselected package python3-scipy.
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114s Selecting previously unselected package python3-ufolib2.
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114s Selecting previously unselected package python3-mpmath.
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114s Selecting previously unselected package python3-sympy.
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114s Selecting previously unselected package python3-tz.
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114s Selecting previously unselected package python3-fs.
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114s Selecting previously unselected package python3-lz4.
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114s Selecting previously unselected package python3-unicodedata2.
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114s Selecting previously unselected package unicode-data.
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115s Selecting previously unselected package sphinx-rtd-theme-common.
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115s Selecting previously unselected package python3-griddataformats.
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115s Selecting previously unselected package python3-h5py-serial.
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115s Selecting previously unselected package python3-sortedcontainers.
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115s Selecting previously unselected package python3-hypothesis.
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115s Selecting previously unselected package python3-imagesize.
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115s Selecting previously unselected package python3-iniconfig.
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115s Selecting previously unselected package python3-joblib.
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115s Selecting previously unselected package python3-kiwisolver.
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115s Selecting previously unselected package python3-latexcodec.
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115s Selecting previously unselected package python3-matplotlib.
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115s Selecting previously unselected package python3-mda-xdrlib.
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115s Selecting previously unselected package python3-msgpack.
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115s Selecting previously unselected package python3-mmtf.
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115s Selecting previously unselected package python3-threadpoolctl.
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115s Selecting previously unselected package python3-tqdm.
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115s Selecting previously unselected package python3-mdanalysis.
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116s Selecting previously unselected package sphinx-common.
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116s Selecting previously unselected package python3-alabaster.
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116s Selecting previously unselected package python3-snowballstemmer.
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116s Selecting previously unselected package python3-sphinx.
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116s Selecting previously unselected package python3-sphinxcontrib.jquery.
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116s Selecting previously unselected package python3-sphinx-rtd-theme.
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116s Selecting previously unselected package python3-msmb-theme.
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116s Selecting previously unselected package python3-netcdf4.
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116s Selecting previously unselected package python3-networkx.
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116s Selecting previously unselected package python3-pandas-lib:amd64.
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117s Selecting previously unselected package python3-pluggy.
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117s Selecting previously unselected package python3-pybtex.
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117s Selecting previously unselected package python3-pybtex-docutils.
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117s Selecting previously unselected package python3-pytest.
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117s Selecting previously unselected package python3-seaborn.
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117s Selecting previously unselected package python3-sklearn-lib:amd64.
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141s Setting up python3-fonttools (4.46.0-1build2) ...
142s Setting up python3-matplotlib (3.8.3-3) ...
143s Setting up python3-mdanalysis (2.7.0-5) ...
143s Setting up python3-seaborn (0.13.2-4) ...
144s Processing triggers for man-db (2.13.0-1) ...
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145s Setting up docutils-common (0.21.2+dfsg-2) ...
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169s Processing triggers for sgml-base (1.31) ...
169s Setting up python3-docutils (0.21.2+dfsg-2) ...
169s Setting up python3-pybtex-docutils (1.0.2-1) ...
169s Setting up python3-sphinx (7.4.7-4) ...
170s Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ...
170s Setting up python3-sphinx-sitemap (2.6.0-1) ...
170s Setting up python3-sphinxcontrib.jquery (4.1-5) ...
170s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ...
170s Setting up python3-msmb-theme (1.2.0-4) ...
170s Setting up autopkgtest-satdep (0) ...
175s (Reading database ... 101418 files and directories currently installed.)
175s Removing autopkgtest-satdep (0) ...
176s autopkgtest [11:21:37]: test test-mdanalysis: [-----------------------
176s skipping tests with SKIP_TEST_LIST=
183s ============================= test session starts ==============================
183s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
183s rootdir: /tmp/autopkgtest.pgcwp3/build.yjm/src
183s plugins: typeguard-4.4.1, hypothesis-6.116.0
183s collected 19229 items / 6 skipped
183s 
186s testsuite/MDAnalysisTests/analysis/test_align.py ....................... [  0%]
192s ....................s.ss.s...                                            [  0%]
192s testsuite/MDAnalysisTests/analysis/test_atomicdistances.py ...           [  0%]
192s testsuite/MDAnalysisTests/analysis/test_base.py ........................ [  0%]
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199s testsuite/MDAnalysisTests/analysis/test_data.py .                        [  1%]
199s testsuite/MDAnalysisTests/analysis/test_density.py ..................... [  1%]
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204s testsuite/MDAnalysisTests/analysis/test_dielectric.py ......             [  1%]
205s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py ..........       [  1%]
210s testsuite/MDAnalysisTests/analysis/test_dihedrals.py ................... [  1%]
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214s testsuite/MDAnalysisTests/analysis/test_distances.py ............        [  1%]
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249s testsuite/MDAnalysisTests/analysis/test_gnm.py ......                    [  2%]
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251s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py ...... [  2%]
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251s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py . [  2%]
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252s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py ...... [  2%]
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256s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py ................ [  3%]
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256s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py .................... [  3%]
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258s testsuite/MDAnalysisTests/analysis/test_pca.py ......................... [  3%]
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260s testsuite/MDAnalysisTests/analysis/test_persistencelength.py ........... [  4%]
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276s testsuite/MDAnalysisTests/analysis/test_psa.py ......................... [  4%]
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276s testsuite/MDAnalysisTests/analysis/test_rdf.py ....................      [  4%]
277s testsuite/MDAnalysisTests/analysis/test_rdf_s.py .....................   [  4%]
278s testsuite/MDAnalysisTests/analysis/test_rms.py ......................... [  4%]
280s ................                                                         [  4%]
280s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py ............... [  4%]
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280s testsuite/MDAnalysisTests/analysis/test_wbridge.py ..................... [  5%]
280s ...........................                                              [  5%]
280s testsuite/MDAnalysisTests/auxiliary/test_core.py .....                   [  5%]
280s testsuite/MDAnalysisTests/auxiliary/test_edr.py .sssssssssssssssssssssss [  5%]
281s ssssssssssssssssssssssssssssssssssssssssssss                             [  5%]
281s testsuite/MDAnalysisTests/auxiliary/test_xvg.py ........................ [  5%]
281s ........................................................................ [  6%]
281s ....                                                                     [  6%]
281s testsuite/MDAnalysisTests/converters/test_base.py ..                     [  6%]
281s testsuite/MDAnalysisTests/converters/test_rdkit.py .ssssssssssssssssssss [  6%]
281s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [  6%]
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281s ssssssssssssssssssssssssssssss                                           [  7%]
281s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py ...           [  7%]
283s testsuite/MDAnalysisTests/coordinates/test_chainreader.py .............. [  7%]
290s .......................................................                  [  7%]
291s testsuite/MDAnalysisTests/coordinates/test_copying.py .................. [  7%]
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307s testsuite/MDAnalysisTests/coordinates/test_crd.py ..............         [  8%]
307s testsuite/MDAnalysisTests/coordinates/test_dcd.py ...................... [  8%]
308s .......x.......ss....................................................... [  9%]
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309s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py ................... [  9%]
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310s testsuite/MDAnalysisTests/coordinates/test_dms.py .........              [  9%]
310s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py .................. [  9%]
310s .......                                                                  [  9%]
310s testsuite/MDAnalysisTests/coordinates/test_gms.py ..................     [  9%]
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331s testsuite/MDAnalysisTests/coordinates/test_gsd.py ss....                 [ 11%]
331s testsuite/MDAnalysisTests/coordinates/test_h5md.py ..................... [ 11%]
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379s testsuite/MDAnalysisTests/coordinates/test_mmtf.py ...........           [ 13%]
380s testsuite/MDAnalysisTests/coordinates/test_mol2.py ..................... [ 13%]
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380s testsuite/MDAnalysisTests/coordinates/test_namdbin.py .................. [ 13%]
380s .....                                                                    [ 13%]
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386s testsuite/MDAnalysisTests/coordinates/test_null.py .                     [ 14%]
386s testsuite/MDAnalysisTests/coordinates/test_pdb.py ...................... [ 14%]
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594s ....                                                                     [ 85%]
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600s .....                                                                    [ 86%]
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602s ......                                                                   [ 86%]
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607s .......                                                                  [ 89%]
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661s testsuite/MDAnalysisTests/transformations/test_boxdimensions.py ........ [ 96%]
661s ......                                                                   [ 96%]
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662s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py .... [ 96%]
662s .                                                                        [ 96%]
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668s testsuite/MDAnalysisTests/transformations/test_wrap.py ................. [ 97%]
668s .......                                                                  [ 97%]
668s testsuite/MDAnalysisTests/utils/test_authors.py .                        [ 97%]
668s testsuite/MDAnalysisTests/utils/test_datafiles.py ....                   [ 97%]
668s testsuite/MDAnalysisTests/utils/test_duecredit.py ..............         [ 97%]
668s testsuite/MDAnalysisTests/utils/test_failure.py .                        [ 97%]
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669s testsuite/MDAnalysisTests/utils/test_modelling.py .............          [ 98%]
670s testsuite/MDAnalysisTests/utils/test_persistence.py .......              [ 98%]
681s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%]
681s ..............ss..                                                       [ 98%]
681s testsuite/MDAnalysisTests/utils/test_qcprot.py ......                    [ 98%]
683s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%]
683s                                                                          [ 98%]
683s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 98%]
683s ...............                                                          [ 99%]
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683s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%]
683s .......                                                                  [ 99%]
683s testsuite/MDAnalysisTests/visualization/test_streamlines.py ...          [100%]
683s 
683s =============================== warnings summary ===============================
683s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39
683s   /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
683s   
683s   Due to the on going maintenance burden of keeping command line application
683s   wrappers up to date, we have decided to deprecate and eventually remove these
683s   modules.
683s   
683s   We instead now recommend building your command line and invoking it directly
683s   with the subprocess module.
683s     warnings.warn(
683s 
683s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings
683s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings
683s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings
683s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings
683s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings
683s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings
683s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings
683s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings
683s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings
683s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings
683s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings
683s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings
683s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings
683s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings
683s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings
683s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
683s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings
683s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings
683s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings
683s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings
683s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings
683s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings
683s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings
683s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings
683s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings
683s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings
683s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings
683s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings
683s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings
683s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
683s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings
683s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
683s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings
683s   /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.
683s     warnings.warn("DCDReader currently makes independent timesteps"
683s 
683s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52
683s   /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.
683s     warnings.warn(wmsg, category=DeprecationWarning)
683s 
683s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter]
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles'
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings
683s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings
683s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written
683s     warnings.warn(wmsg)
683s 
683s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings
683s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings
683s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings
683s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings
683s   /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
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings
683s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
683s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings
683s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning
683s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
683s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'c3', 'h1', 'hc', 'oh', 'ho'}. These have been given an empty element record.
683s     warnings.warn("Unknown elements found for some "
683s 
683s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
683s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning
683s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings
683s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings
683s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
683s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings
683s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings
683s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps
683s     self.times[i] = ts.time
683s 
683s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings
683s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning
683s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings
683s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
683s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings
683s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings
683s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings
683s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded
683s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps
683s     results.append((ts.time, x.sum() / mask.sum()))
683s 
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue
683s   /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.
683s     warnings.warn(msg)
683s 
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
683s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding
683s   /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
683s     warnings.warn(msg)
683s 
683s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
683s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
683s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings
683s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
683s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
683s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings
683s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning
683s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings
683s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings
683s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings
683s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
683s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings
683s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings
683s   /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.
683s     warnings.warn("Element information is missing, elements attribute "
683s 
683s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran
683s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame
683s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections
683s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues
683s     warnings.warn("Cannot determine phi and psi angles for the first "
683s 
683s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin
683s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr
683s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame
683s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot
683s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning
683s   /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.
683s     warnings.warn(f"All residues selected with '{select_remove}' "
683s 
683s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings
683s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings
683s   /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=5752) is multi-threaded, use of fork() may lead to deadlocks in the child.
683s     self.pid = os.fork()
683s 
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes
683s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide
683s     cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms
683s 
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide
683s     local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T  # (n_res-3, 3)
683s 
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
683s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice
683s     ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
683s 
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
683s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide
683s     ret = um.true_divide(
683s 
683s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
683s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide
683s     ret = ret.dtype.type(ret / rcount)
683s 
683s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
683s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning
683s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning
683s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
683s   /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.
683s     warnings.warn("1 A^3 CRYST1 record,"
683s 
683s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values.
683s     warnings.warn("Unit cell dimensions not found. "
683s 
683s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' '
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings
683s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings
683s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings
683s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
683s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings
683s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
683s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning
683s   /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
683s     warnings.warn(wmsg, DeprecationWarning)
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6
683s     warnings.warn("Desired number of sample points too high, using {0}"
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbond = HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbond = HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbond = HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbond = HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbond = HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbond = HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbond = HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbond = HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     HBAC(
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
683s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
683s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbond = HBAC(u,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated!
683s   `find_hydrogen_donors` will be removed in release 3.0.0.
683s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     D = hbonds.find_hydrogen_donors(H)
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated!
683s   `find_hydrogen_donors` will be removed in release 3.0.0.
683s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
683s     hbonds.find_hydrogen_donors(u.atoms)
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
683s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
683s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
683s     return _methods._mean(a, axis=axis, dtype=dtype,
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
683s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
683s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
683s     ret = ret.dtype.type(ret / rcount)
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
683s   /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.
683s     warnings.warn(msg.format(sel))
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
683s   /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.
683s     warnings.warn(msg.format(sel))
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
683s   /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.
683s     warnings.warn(msg.format(sel))
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned.
683s     warnings.warn("Empty string to select atoms, empty group returned.",
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
683s   /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, .
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
683s   /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, .
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
683s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
683s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
683s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
683s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
683s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
683s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple
683s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content
683s   /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.
683s     warnings.warn(wmsg)
683s 
683s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning
683s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning
683s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
683s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
683s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
683s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
683s   /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.)
683s     phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi
683s 
683s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j
683s   /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
683s     warnings.warn("Column index entered (j = {:d} is smaller than row "
683s 
683s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps
683s     dt=self.trajectory.ts.dt * step,
683s 
683s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8]
683s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0]
683s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8]
683s   /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
683s     warnings.warn(wmsg, DeprecationWarning)
683s 
683s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
683s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings
683s   /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.
683s     warnings.warn("The `u` attribute is superflous and will be removed "
683s 
683s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267]
683s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm
683s   /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.
683s     warnings.warn("The `density` attribute was deprecated in "
683s 
683s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata
683s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first.
683s     warnings.warn(msg, category=MissingDataWarning)
683s 
683s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps
683s     self.timesteps.append(self._ts.time)
683s 
683s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning
683s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default
683s     warnings.warn("{} does not support time selection. Reverting to "
683s 
683s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default
683s     warnings.warn("{} does not support data selection. Reverting to "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings
683s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings
683s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
683s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings
683s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps
683s     return self.ts.dt
683s 
683s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings
683s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
683s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps
683s     ts.data['time'] = step_num * ts.dt
683s 
683s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats
683s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_unsupported_filetypes
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x7f555b93b880>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
683s       self.close()
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close
683s       self._apply('close')
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply
683s       return [reader.__getattribute__(method)(**kwargs) for reader in self.readers]
683s                                                                       ^^^^^^^^^^^^
683s   AttributeError: 'ChainReader' object has no attribute 'readers'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing
683s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain
683s     warnings.warn("Missing frame in continuous chain", UserWarning)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps
683s     time_frame_0 = ts.time - ts.frame*ts.dt  # assumes ts.dt is constant
683s 
683s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps
683s     frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps
683s     step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps
683s     self._add_step_to_frame_data(ts.time)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames]
683s   /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. 
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids]
683s   /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. 
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names]
683s   /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. 
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors]
683s   /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. 
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings
683s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
683s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps
683s     if not np.allclose(A.time, B.time):
683s 
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1]
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2]
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3]
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0]
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1]
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2]
683s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array
683s   /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
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x7f555b93b880>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
683s       self.close()
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close
683s       self._file.close()
683s       ^^^^^^^^^^
683s   AttributeError: 'DCDReader' object has no attribute '_file'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms
683s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit
683s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function DCDWriter.__del__ at 0x7f555b962200>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__
683s       self.close()
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close
683s       self._file.close()
683s       ^^^^^^^^^^
683s   AttributeError: 'DCDWriter' object has no attribute '_file'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings
683s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings
683s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
683s   /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.
683s     warnings.warn(msg)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps
683s     return self.ts.time
683s 
683s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter]
683s   /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. 
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps
683s     assert_equal(reader.ts.dt, reader.dt)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps
683s     time_frame = time_frame_0 + frame_index*ts.dt
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps
683s     reader_p = pickle.loads(pickle.dumps(reader))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings
683s   /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
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.]
683s     warnings.warn(wmsg)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
683s   /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`.
683s     warnings.warn(wmsg)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present.  Unset velocities set to zero.
683s     warnings.warn("Not all velocities were present.  "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps
683s     reader_p = pickle.loads(pickle.dumps(reader))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader
683s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps
683s     reader_p = pickle.loads(pickle.dumps(reader))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x7f555b93b880>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
683s       self.close()
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close
683s       self._file.close()
683s       ^^^^^^^^^^
683s   AttributeError: 'H5MDReader' object has no attribute '_file'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM'
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x7f555b93b880>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
683s       for aux in self.aux_list:
683s                  ^^^^^^^^^^^^^
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
683s       return self._auxs.keys()
683s              ^^^^^^^^^^
683s   AttributeError: 'H5MDReader' object has no attribute '_auxs'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings
683s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
683s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0
683s     warnings.warn('Guessed all Masses to 1.0')
683s 
683s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit
683s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x7f555b93b880>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
683s       for aux in self.aux_list:
683s                  ^^^^^^^^^^^^^
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
683s       return self._auxs.keys()
683s              ^^^^^^^^^^
683s   AttributeError: 'DCDReader' object has no attribute '_auxs'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view
683s   /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
683s     warnings.warn("MemoryReader.timeseries inclusive `stop` "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader
683s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps
683s     reader_p = pickle.loads(pickle.dumps(reader))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
683s   /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
683s     warnings.warn(wmsg)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps
683s     ts.time)  # in-place ! (hope this works...)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps
683s     time_list = [ts.time for ts in u.trajectory]
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps
683s     assert u.trajectory.ts.dt == pytest.approx(ref)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4
683s   /tmp/autopkgtest.pgcwp3/build.yjm/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.)
683s     return self._test_write_trajectory(universe, outfile)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0]
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0]
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0]
683s   /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.
683s     warnings.warn(wmsg)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
683s   /tmp/autopkgtest.pgcwp3/build.yjm/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.)
683s     return self._test_write_trajectory(universe, outfile)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of ''
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings
683s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'
683s     warnings.warn("Found missing chainIDs."
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom]
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond]
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom]
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree]
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond]
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom]
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps
683s     time = ts.time
683s 
683s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0x7f555b93bba0>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
683s       self.close()
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close
683s       if self.trjfile is not None:
683s          ^^^^^^^^^^^^
683s   AttributeError: 'NCDFWriter' object has no attribute 'trjfile'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
683s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK'
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' '
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
683s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1'
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
683s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X'
683s     warnings.warn("Found no information for attr: '{}'"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@]
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X'
683s     warnings.warn("Found chainIDs using unnaccepted character."
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA]
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X'
683s     warnings.warn("Found chainIDs with invalid length."
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000.  Higher serials have been guessed
683s     warnings.warn("Serial numbers went over 100,000.  "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed
683s     warnings.warn("Invalid atom serials were present, bonds will not"
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed
683s     warnings.warn("Invalid atom serials were present, "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment
683s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
683s   /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.
683s     warnings.warn(wmsg)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
683s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
683s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
683s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
683s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges
683s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
683s   /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. 
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps
683s     assert_equal(ts.dt, 1.0)  # default value
683s 
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps
683s     assert_equal(ts.time, 0.0)  # default to 1.0 (dt) * 0 (frame)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps
683s     assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x7f555b93b880>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
683s       for aux in self.aux_list:
683s                  ^^^^^^^^^^^^^
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
683s       return self._auxs.keys()
683s              ^^^^^^^^^^
683s   AttributeError: 'TNGReader' object has no attribute '_auxs'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms
683s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe
683s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe
683s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks!
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x7f555b93b880>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
683s       self.close()
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close
683s       if self.trjfile is None:
683s          ^^^^^^^^^^^^
683s   AttributeError: 'TRJReader' object has no attribute 'trjfile'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps
683s     data['time'] = ts.time
683s 
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
683s   /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
683s     warnings.warn("Timestep didn't have the following attributes: '{0}', "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
683s   /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. 
683s     warnings.warn("Timestep didn't have velocity information, "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
683s   /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
683s     warnings.warn("Timestep didn't have dimensions information, "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0x7f555b93bba0>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
683s       self.close()
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close
683s       if self.trzfile is None:
683s          ^^^^^^^^^^^^
683s   AttributeError: 'TRZWriter' object has no attribute 'trzfile'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
683s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
683s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
683s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
683s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
683s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
683s   /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.
683s     warnings.warn("Element information is missing, elements attribute "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
683s   /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
683s     warnings.warn(wmsg, DeprecationWarning)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter]
683s   /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. 
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter]
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter]
683s   /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. 
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter]
683s   /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. 
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter]
683s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter]
683s   /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'
683s     warnings.warn(wmsg)
683s 
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD
683s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps
683s     time = ts.time
683s 
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD
683s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps
683s     time = ts.time
683s 
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0x7f555b3705e0>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
683s       self.close()
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
683s       self._xdr.close()
683s       ^^^^^^^^^
683s   AttributeError: 'XTCWriter' object has no attribute '_xdr'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container
683s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0x7f555b3705e0>
683s   
683s   Traceback (most recent call last):
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
683s       self.close()
683s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
683s       self._xdr.close()
683s       ^^^^^^^^^
683s   AttributeError: 'TRRWriter' object has no attribute '_xdr'
683s   
683s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
683s 
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
683s   /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.
683s   Consider setting 'refresh_offsets=True' when loading your Universe.
683s     warnings.warn(f"Reading offsets from {fname} failed, "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly
683s   /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.
683s     warnings.warn(f"Cannot write lock/offset file in same location as "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
683s   /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.
683s   Consider setting 'refresh_offsets=True' when loading your Universe.
683s     warnings.warn(f"Reading offsets from {fname} failed, "
683s 
683s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly
683s   /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.
683s     warnings.warn(f"Cannot write lock/offset file in same location as "
683s 
683s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms]
683s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues]
683s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments]
683s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce
683s     return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
683s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
683s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
683s   /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.
683s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings
683s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings
683s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings
683s   /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.
683s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
683s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
683s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
683s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide
683s     return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum()
683s 
683s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings
683s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide
683s     _centers /= _weights.sum(axis=1)[:, None]
683s 
683s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
683s   /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`.
683s     warnings.warn(msg, category=SelectionWarning)
683s 
683s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
683s   /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`.
683s     warnings.warn(msg, category=SelectionWarning)
683s 
683s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12]
683s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13]
683s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15]
683s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16]
683s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17]
683s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18]
683s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19]
683s   /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`.
683s     warnings.warn(msg, category=SelectionWarning)
683s 
683s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments]
683s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules]
683s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues]
683s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group]
683s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments]
683s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc
683s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc
683s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options
683s   /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
683s     warnings.warn("The 'pbc' kwarg has been deprecated and will be "
683s 
683s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel
683s   /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`.
683s     warnings.warn(msg, category=SelectionWarning)
683s 
683s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial]
683s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp]
683s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial]
683s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp]
683s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan]
683s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide
683s     x = np.dot(a, b) / (norm(a) * norm(b))
683s 
683s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt
683s     ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2)
683s 
683s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt
683s     box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 -
683s 
683s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide
683s     a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z)))
683s 
683s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide
683s     b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z)))
683s 
683s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide
683s     c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y)))
683s 
683s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide
683s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
683s 
683s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide
683s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
683s 
683s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2]
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3]
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4]
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5]
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6]
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7]
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10]
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11]
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14]
683s   /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps
683s     cls(buf, protocol).dump(obj)
683s 
683s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps
683s     ps = pickle.dumps(ref_reader)
683s 
683s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0]
683s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd
683s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd
683s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset
683s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific
683s   /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset.
683s     warnings.warn('Cannot average position for non sequential'
683s 
683s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name]
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname]
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type]
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid]
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information.  Defaulted to '1'
683s     warnings.warn("PDB file is missing resid information.  "
683s 
683s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX
683s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
683s 
683s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2]
683s   /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.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2]
683s   /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.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2]
683s   /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.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2]
683s   /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.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
683s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings
683s   /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.
683s     warnings.warn(msg)
683s 
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts
683s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr]
683s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file.
683s     warnings.warn('No coordinate reader found for {}. Skipping '
683s 
683s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses
683s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses.
683s     warnings.warn(msg, category=SelectionWarning)
683s 
683s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2
683s   /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.
683s     warnings.warn(
683s 
683s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps
683s     return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
683s 
683s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps
683s     pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
683s 
683s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps
683s     return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL)
683s 
683s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps
683s     return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL)
683s 
683s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps
683s     return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL)
683s 
683s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps
683s     pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL)
683s 
683s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag
683s   /tmp/autopkgtest.pgcwp3/build.yjm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps
683s     pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL)
683s 
683s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings
683s   /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream
683s     warnings.warn("Constructed NamedStream from a NamedStream",
683s 
683s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159]
683s   /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.
683s     warnings.warn(wmsg, DeprecationWarning)
683s 
683s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
683s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8130 warnings in 507.02s (0:08:27) =
705s 
705s DueCredit Report:
705s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2]
705s   - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3]
705s   - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4]
705s   - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5]
705s   - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8]
705s   - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9]
705s   - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10]
705s   - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2]
705s   - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.7.0) [11, 12]
705s   - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13]
705s   - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14]
705s   - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 1.1, 2.7.0) [15, 16]
705s   - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17]
705s   - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18]
705s   - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20]
705s   - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17]
705s   - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21]
705s - Scientific tools library / numpy (v 1.26.4) [22]
705s 
705s 2 packages cited
705s 16 modules cited
705s 0 functions cited
705s 
705s References
705s ----------
705s 
705s [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.
705s [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.
705s [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.
705s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858.
705s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415.
705s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460.
705s [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.
705s [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.
705s [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.
705s [10] Gowers, R.J. & Carbone, P., 2015. A multiscale approach to model hydrogen bonding: The case of polyamide. The Journal of Chemical Physics, 142(22).
705s [11] de Buyl, P., 2018. tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3(28), p.877.
705s [12] Calandrini, V. et al., 2011. nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. École thématique de la Société Française de la Neutronique, 12, pp.201–232.
705s [13] Yang, L. et al., 2008. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure, 16(2), pp.321–330.
705s [14] Seyler, S.L. et al., 2015. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways E. Tajkhorshid, ed.. PLOS Computational Biology, 11(10), p.1004568.
705s [15] Jakupovic, E. & Beckstein, O., 2021. MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. In Proceedings of the 20th Python in Science Conference. SciPy.  SciPy, pp. 40–48.
705s [16] de Buyl, P., Colberg, P.H. & Höfling, F., 2014. H5MD: A structured, efficient, and portable file format for molecular data. Computer Physics Communications, 185(6), pp.1546–1553.
705s [17] Bradley, A.R. et al., 2017. MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures D. Schneidman, ed.. PLOS Computational Biology, 13(6), p.1005575.
705s [18] Lundborg, M. et al., 2013. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. Journal of Computational Chemistry, 35(3), pp.260–269.
705s [19] Theobald, D.L., 2005. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A Foundations of Crystallography, 61(4), pp.478–480.
705s [20] Liu, P., Agrafiotis, D.K. & Theobald, D.L., Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7), pp.1561–1563.
705s [21] Kulke, M. & Vermaas, J.V., 2022. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 18(10), pp.6161–6171.
705s [22] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30.
708s autopkgtest [11:30:29]: test test-mdanalysis: -----------------------]
708s autopkgtest [11:30:29]: test test-mdanalysis:  - - - - - - - - - - results - - - - - - - - - -
708s test-mdanalysis      PASS
709s autopkgtest [11:30:30]: @@@@@@@@@@@@@@@@@@@@ summary
709s test-mdanalysis      PASS
721s nova [W] Skipping flock for amd64
721s Creating nova instance adt-plucky-amd64-mdanalysis-20241115-111841-juju-7f2275-prod-proposed-migration-environment-15-be7b4769-633a-4687-a1dc-f604b282a2e1 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...