0s autopkgtest [03:42:38]: starting date and time: 2024-11-15 03:42:38+0000 0s autopkgtest [03:42:38]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [03:42:38]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0b8m9q52/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:matplotlib --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=matplotlib/3.8.3-3ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-17.secgroup --name adt-plucky-ppc64el-mdanalysis-20241115-034238-juju-7f2275-prod-proposed-migration-environment-15-57d586e8-fc89-41f5-8c61-6444bb04c9e3 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/ 82s autopkgtest [03:44:00]: testbed dpkg architecture: ppc64el 82s autopkgtest [03:44:00]: testbed apt version: 2.9.8 82s autopkgtest [03:44:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 83s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 83s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.5 kB] 83s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 83s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 83s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1030 kB] 83s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [147 kB] 83s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [765 kB] 83s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8632 B] 84s Fetched 2148 kB in 1s (1926 kB/s) 84s Reading package lists... 86s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Calculating upgrade... 87s The following packages will be upgraded: 87s bpfcc-tools bpftrace firmware-sof-signed libbpfcc libcap-ng0 libexpat1 87s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 87s libutempter0 lxd-installer man-db pastebinit python3-bpfcc python3-newt 87s python3-systemd whiptail xfsprogs 87s 19 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Need to get 14.2 MB of archives. 87s After this operation, 623 kB of additional disk space will be used. 87s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el firmware-sof-signed all 2024.06-1ubuntu2 [7083 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcap-ng0 ppc64el 0.8.5-3build1 [16.3 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libexpat1 ppc64el 2.6.4-1 [98.1 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 89s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 89s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 89s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el man-db ppc64el 2.13.0-1 [1361 kB] 89s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 89s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 89s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 89s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 89s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 89s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 89s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 89s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el lxd-installer all 9 [5084 B] 89s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el pastebinit all 1.7.1-1 [14.9 kB] 89s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-systemd ppc64el 235-1build5 [48.7 kB] 89s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfsprogs ppc64el 6.8.0-2.2ubuntu2 [995 kB] 89s Preconfiguring packages ... 90s Fetched 14.2 MB in 2s (7390 kB/s) 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 90s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu2_all.deb ... 90s Unpacking firmware-sof-signed (2024.06-1ubuntu2) over (2024.06-1ubuntu1) ... 90s Preparing to unpack .../libcap-ng0_0.8.5-3build1_ppc64el.deb ... 90s Unpacking libcap-ng0:ppc64el (0.8.5-3build1) over (0.8.5-1) ... 90s Setting up libcap-ng0:ppc64el (0.8.5-3build1) ... 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73793 files and directories currently installed.) 90s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 90s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 90s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73793 files and directories currently installed.) 90s Preparing to unpack .../00-libexpat1_2.6.4-1_ppc64el.deb ... 90s Unpacking libexpat1:ppc64el (2.6.4-1) over (2.6.2-2) ... 90s Preparing to unpack .../01-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 90s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 91s Preparing to unpack .../02-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 91s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 91s Preparing to unpack .../03-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 91s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 91s Preparing to unpack .../04-man-db_2.13.0-1_ppc64el.deb ... 91s Unpacking man-db (2.13.0-1) over (2.12.1-3) ... 91s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 91s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 91s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 91s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 91s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 91s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 91s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 91s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 91s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 91s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 91s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 91s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 91s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ... 91s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 91s Preparing to unpack .../12-lxd-installer_9_all.deb ... 91s Unpacking lxd-installer (9) over (8) ... 91s Preparing to unpack .../13-pastebinit_1.7.1-1_all.deb ... 91s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 91s Preparing to unpack .../14-python3-systemd_235-1build5_ppc64el.deb ... 91s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 91s Preparing to unpack .../15-xfsprogs_6.8.0-2.2ubuntu2_ppc64el.deb ... 91s Unpacking xfsprogs (6.8.0-2.2ubuntu2) over (6.8.0-2.2ubuntu1) ... 92s Setting up libexpat1:ppc64el (2.6.4-1) ... 92s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 92s Setting up firmware-sof-signed (2024.06-1ubuntu2) ... 92s Setting up pastebinit (1.7.1-1) ... 92s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 92s Setting up man-db (2.13.0-1) ... 92s Updating database of manual pages ... 95s man-db.service is a disabled or a static unit not running, not starting it. 95s Setting up xfsprogs (6.8.0-2.2ubuntu2) ... 95s update-initramfs: deferring update (trigger activated) 96s Setting up lxd-installer (9) ... 97s Setting up libutempter0:ppc64el (1.2.1-4) ... 97s Setting up whiptail (0.52.24-2ubuntu4) ... 97s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 97s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 97s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 97s Setting up python3-systemd (235-1build5) ... 97s Setting up bpftrace (0.21.2-2ubuntu2) ... 97s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 97s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 97s Processing triggers for libc-bin (2.40-1ubuntu3) ... 97s Processing triggers for initramfs-tools (0.142ubuntu34) ... 97s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 97s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 109s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 109s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 110s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 111s Reading package lists... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Calculating upgrade... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [03:44:30]: rebooting testbed after setup commands that affected boot 116s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 148s autopkgtest [03:45:06]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 151s autopkgtest [03:45:09]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 160s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B] 160s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB] 160s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB] 160s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC 160s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 160s gpgv: issuer "dparsons@debian.org" 160s gpgv: Can't check signature: No public key 160s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found 163s autopkgtest [03:45:21]: testing package mdanalysis version 2.7.0-5 163s autopkgtest [03:45:21]: build not needed 167s autopkgtest [03:45:25]: test test-mdanalysis: preparing testbed 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s Starting pkgProblemResolver with broken count: 0 170s Starting 2 pkgProblemResolver with broken count: 0 170s Done 170s The following additional packages will be installed: 170s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 170s cpp-14-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cython3 debhelper 170s debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common 170s dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 170s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 170s g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14 170s gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext 170s intltool-debian libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 170s libcc1-0 libdebhelper-perl libdeflate0 libexpat1-dev 170s libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libgcc-14-dev 170s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 170s libhdf5-hl-100t64 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 170s libjpeg8 libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc 170s libjs-underscore libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 170s liblsan0 liblzf1 libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 170s libpython3-all-dev libpython3-dev libpython3.12-dev libqhull-r8.0 170s libquadmath0 libraqm0 libsharpyuv0 libstdc++-14-dev libsz2 libtcl8.6 170s libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2 170s libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 170s libxss1 m4 po-debconf pybuild-plugin-pyproject python-matplotlib-data 170s python-mdanalysis-doc python3-alabaster python3-all python3-all-dev 170s python3-appdirs python3-biopython python3-brotli python3-build python3-cairo 170s python3-cftime python3-citeproc python3-contourpy python3-cycler 170s python3-dateutil python3-decorator python3-defusedxml python3-dev 170s python3-docutils python3-duecredit python3-fasteners python3-fonttools 170s python3-freetype python3-fs python3-griddataformats python3-gsd python3-h5py 170s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 170s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 170s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 170s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 170s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 170s python3-netcdf4 python3-networkx python3-numpy python3-packaging 170s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 170s python3-pluggy python3-pybtex python3-pybtex-docutils 170s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 170s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 170s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 170s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 170s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 170s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 170s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 170s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 170s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 170s zlib1g-dev 170s Suggested packages: 170s autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales 170s cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf 170s fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 170s gdb-powerpc64le-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 170s libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc 170s liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran 170s | fortran95-compiler gcj-jdk m4-doc libmail-box-perl bwa clustalo clustalw 170s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 170s python3-mysqldb python3-rdflib python3-psycopg2 raxml samtools t-coffee wise 170s python3-pip python3-venv python-build-doc python-cycler-doc docutils-doc 170s fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 170s texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc 170s python-hypothesis-doc python-installer-doc python-joblib-doc 170s python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 170s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 170s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 170s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 170s texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal 170s python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc 170s python3-statsmodels python-pil-doc python-pybtex-doc 170s python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools 170s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 170s python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm 170s fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre 170s texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic 170s python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg 170s python3.13-tk sgml-base-doc 170s Recommended packages: 170s libarchive-cpio-perl javascript-common libjson-xs-perl libltdl-dev 170s libmail-sendmail-perl python-biopython-doc ncbi-blast+ libpaper-utils 170s python3-click python3-simplejson python3-psutil python3-bs4 170s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 170s python3-odf python3-openpyxl python3-tables python3-olefile 170s fonts-dejavu-extra isympy-common 170s The following NEW packages will be installed: 170s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 170s build-essential cpp cpp-14 cpp-14-powerpc64le-linux-gnu 170s cpp-powerpc64le-linux-gnu cython3 debhelper debugedit dh-autoreconf 170s dh-python dh-strip-nondeterminism docutils-common dwz fontconfig-config 170s fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx 170s fonts-mathjax fonts-urw-base35 g++ g++-14 g++-14-powerpc64le-linux-gnu 170s g++-powerpc64le-linux-gnu gcc gcc-14 gcc-14-powerpc64le-linux-gnu 170s gcc-powerpc64le-linux-gnu gettext intltool-debian libaec0 170s libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdebhelper-perl 170s libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 170s libfontenc1 libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 170s libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libisl23 libitm1 libjbig0 170s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-mathjax 170s libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0 170s liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libnetcdf19t64 libopenjp2-7 170s libpixman-1-0 libpython3-all-dev libpython3-dev libpython3.12-dev 170s libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 libstdc++-14-dev libsz2 170s libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 170s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 170s libxslt1.1 libxss1 m4 po-debconf pybuild-plugin-pyproject 170s python-matplotlib-data python-mdanalysis-doc python3-alabaster python3-all 170s python3-all-dev python3-appdirs python3-biopython python3-brotli 170s python3-build python3-cairo python3-cftime python3-citeproc 170s python3-contourpy python3-cycler python3-dateutil python3-decorator 170s python3-defusedxml python3-dev python3-docutils python3-duecredit 170s python3-fasteners python3-fonttools python3-freetype python3-fs 170s python3-griddataformats python3-gsd python3-h5py python3-h5py-serial 170s python3-hypothesis python3-imagesize python3-iniconfig python3-installer 170s python3-joblib python3-kiwisolver python3-latexcodec python3-looseversion 170s python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib 170s python3-mdanalysis python3-mmtf python3-monotonic python3-mpmath 170s python3-mrcfile python3-msgpack python3-msmb-theme python3-netcdf4 170s python3-networkx python3-numpy python3-packaging python3-pandas 170s python3-pandas-lib python3-pil python3-pil.imagetk python3-pluggy 170s python3-pybtex python3-pybtex-docutils python3-pyproject-hooks 170s python3-pytest python3-reportlab python3-rlpycairo python3-roman 170s python3-scipy python3-seaborn python3-six python3-sklearn 170s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 170s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 170s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 170s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 170s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 170s python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5 170s unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 170s zlib1g-dev 170s 0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded. 170s Need to get 203 MB/203 MB of archives. 170s After this operation, 898 MB of additional disk space will be used. 170s Get:1 /tmp/autopkgtest.fEu9Gl/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [1016 B] 170s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-lato all 2.015-1 [2781 kB] 171s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB] 171s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el m4 ppc64el 1.4.19-4build1 [278 kB] 171s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el autoconf all 2.72-3 [382 kB] 171s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el autotools-dev all 20220109.1 [44.9 kB] 171s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] 171s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el autopoint all 0.22.5-2 [616 kB] 171s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.15+dfsg-2 [1201 kB] 171s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 171s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 171s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 171s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 171s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 172s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 172s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 172s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB] 172s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB] 172s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 172s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 172s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 172s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.15-1 [942 kB] 172s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-7build1 [784 kB] 172s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el blt ppc64el 2.5.3+dfsg-7build1 [4840 B] 172s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libisl23 ppc64el 0.27-1 [882 kB] 172s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libmpc3 ppc64el 1.3.1-1build2 [62.1 kB] 172s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [10.5 MB] 173s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14 ppc64el 14.2.0-8ubuntu1 [1034 B] 173s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [5456 B] 173s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp ppc64el 4:14.1.0-2ubuntu1 [22.5 kB] 173s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcc1-0 ppc64el 14.2.0-8ubuntu1 [48.1 kB] 173s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 173s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libitm1 ppc64el 14.2.0-8ubuntu1 [31.9 kB] 173s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasan8 ppc64el 14.2.0-8ubuntu1 [2945 kB] 173s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsan0 ppc64el 14.2.0-8ubuntu1 [1322 kB] 173s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtsan2 ppc64el 14.2.0-8ubuntu1 [2695 kB] 173s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libubsan1 ppc64el 14.2.0-8ubuntu1 [1191 kB] 173s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libquadmath0 ppc64el 14.2.0-8ubuntu1 [158 kB] 173s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-14-dev ppc64el 14.2.0-8ubuntu1 [1619 kB] 173s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [20.6 MB] 174s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14 ppc64el 14.2.0-8ubuntu1 [528 kB] 174s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [1222 B] 174s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc ppc64el 4:14.1.0-2ubuntu1 [5006 B] 174s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++-14-dev ppc64el 14.2.0-8ubuntu1 [2673 kB] 174s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [12.0 MB] 174s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14 ppc64el 14.2.0-8ubuntu1 [19.9 kB] 174s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [968 B] 174s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++ ppc64el 4:14.1.0-2ubuntu1 [1090 B] 174s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 174s Get:50 http://ftpmaster.internal/ubuntu plucky/universe ppc64el cython3 ppc64el 3.0.11+dfsg-1ubuntu2 [3263 kB] 174s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 174s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtool all 2.4.7-7build1 [166 kB] 174s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-autoreconf all 20 [16.1 kB] 174s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 174s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 174s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-strip-nondeterminism all 1.14.0-1 [5058 B] 174s Get:57 http://ftpmaster.internal/ubuntu plucky/main ppc64el debugedit ppc64el 1:5.1-1 [52.1 kB] 174s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el dwz ppc64el 0.15-1build6 [142 kB] 174s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el gettext ppc64el 0.22.5-2 [1082 kB] 174s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] 174s Get:61 http://ftpmaster.internal/ubuntu plucky/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] 174s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el debhelper all 13.20ubuntu1 [893 kB] 174s Get:63 http://ftpmaster.internal/ubuntu plucky/universe ppc64el dh-python all 6.20241024 [112 kB] 174s Get:64 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB] 174s Get:65 http://ftpmaster.internal/ubuntu plucky/main ppc64el docutils-common all 0.21.2+dfsg-2 [131 kB] 174s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 175s Get:67 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-lyx all 2.4.2.1-1 [171 kB] 175s Get:68 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 175s Get:69 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 175s Get:70 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 175s Get:71 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 175s Get:72 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 175s Get:73 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 175s Get:74 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 175s Get:75 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 175s Get:76 http://ftpmaster.internal/ubuntu plucky/main ppc64el libexpat1-dev ppc64el 2.6.4-1 [149 kB] 175s Get:77 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 175s Get:78 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 175s Get:79 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB] 175s Get:80 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 175s Get:81 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-4ubuntu3 [1387 kB] 175s Get:82 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-4ubuntu3 [71.2 kB] 175s Get:83 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 175s Get:84 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB] 175s Get:85 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 175s Get:86 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 175s Get:87 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 175s Get:88 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 175s Get:89 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-sphinxdoc all 7.4.7-4 [158 kB] 175s Get:90 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-perl all 4.10000-1 [81.9 kB] 175s Get:91 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 175s Get:92 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 175s Get:93 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 175s Get:94 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB] 175s Get:95 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 175s Get:96 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libnetcdf19t64 ppc64el 1:4.9.2-6ubuntu1 [596 kB] 175s Get:97 http://ftpmaster.internal/ubuntu plucky/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu1 [902 kB] 175s Get:98 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.12-dev ppc64el 3.12.7-3 [6136 kB] 175s Get:99 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3-dev ppc64el 3.12.6-0ubuntu1 [10.2 kB] 175s Get:100 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3-all-dev ppc64el 3.12.6-0ubuntu1 [916 B] 175s Get:101 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6build1 [225 kB] 175s Get:102 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB] 175s Get:103 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB] 175s Get:104 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 175s Get:105 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB] 176s Get:106 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 176s Get:107 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 176s Get:108 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 176s Get:109 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu1 [191 kB] 176s Get:110 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 176s Get:111 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 176s Get:112 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-toml all 0.10.2-1 [16.5 kB] 176s Get:113 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-wheel all 0.44.0-1 [54.2 kB] 176s Get:114 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-build all 1.2.2-1 [31.0 kB] 176s Get:115 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 176s Get:116 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pybuild-plugin-pyproject all 6.20241024 [1728 B] 176s Get:117 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 176s Get:118 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 176s Get:119 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-mdanalysis-doc all 2.7.0-5 [2323 kB] 176s Get:120 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all ppc64el 3.12.6-0ubuntu1 [888 B] 176s Get:121 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-dev ppc64el 3.12.7-3 [505 kB] 176s Get:122 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dev ppc64el 3.12.6-0ubuntu1 [26.7 kB] 176s Get:123 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all-dev ppc64el 3.12.6-0ubuntu1 [908 B] 176s Get:124 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 176s Get:125 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 176s Get:126 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-tk ppc64el 3.12.7-3 [116 kB] 176s Get:127 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tk ppc64el 3.12.6-1ubuntu1 [9806 B] 176s Get:128 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pil.imagetk ppc64el 10.4.0-1ubuntu1 [9810 B] 176s Get:129 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB] 176s Get:130 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB] 176s Get:131 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB] 176s Get:132 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 176s Get:133 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 176s Get:134 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB] 177s Get:135 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 177s Get:136 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4 [1738 kB] 177s Get:137 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-brotli ppc64el 1.1.0-2build2 [413 kB] 177s Get:138 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cftime ppc64el 1.6.4-1 [224 kB] 177s Get:139 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.0-1 [1354 kB] 177s Get:140 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-citeproc all 0.6.0-3 [98.4 kB] 177s Get:141 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-contourpy ppc64el 1.3.0-2 [217 kB] 177s Get:142 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cycler all 0.12.1-1 [9716 B] 177s Get:143 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-six all 1.16.0-7 [13.1 kB] 177s Get:144 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-2 [80.3 kB] 177s Get:145 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 177s Get:146 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-defusedxml all 0.7.1-2 [42.0 kB] 177s Get:147 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-roman all 4.2-1 [10.0 kB] 177s Get:148 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-docutils all 0.21.2+dfsg-2 [409 kB] 177s Get:149 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-looseversion all 1.3.0-3 [8354 B] 177s Get:150 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-duecredit all 0.10.2-2 [66.0 kB] 177s Get:151 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-monotonic all 1.6-2 [5732 B] 177s Get:152 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-fasteners all 0.18-2 [12.5 kB] 177s Get:153 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB] 178s Get:154 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 178s Get:155 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mpmath all 1.3.0-1 [425 kB] 178s Get:156 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sympy all 1.13.3-1 [4228 kB] 178s Get:157 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB] 178s Get:158 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fs all 2.4.16-4 [91.3 kB] 178s Get:159 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1build4 [27.8 kB] 178s Get:160 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-unicodedata2 ppc64el 15.1.0+ds-1build2 [361 kB] 178s Get:161 http://ftpmaster.internal/ubuntu plucky/universe ppc64el unicode-data all 15.1.0-1 [8878 kB] 178s Get:162 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fonttools ppc64el 4.46.0-1build2 [1473 kB] 178s Get:163 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 178s Get:164 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mrcfile all 1.5.3-3 [114 kB] 178s Get:165 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-griddataformats all 1.0.2-2 [2107 kB] 178s Get:166 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-gsd ppc64el 3.3.0-1 [211 kB] 178s Get:167 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.11.0-5ubuntu1 [1159 kB] 178s Get:168 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.11.0-5ubuntu1 [7974 B] 178s Get:169 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-sortedcontainers all 2.4.0-2 [27.6 kB] 178s Get:170 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-hypothesis all 6.116.0-1 [326 kB] 178s Get:171 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-imagesize all 1.4.1-1 [6844 B] 178s Get:172 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 178s Get:173 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-joblib all 1.3.2-5 [206 kB] 178s Get:174 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-kiwisolver ppc64el 1.4.7-2build1 [72.9 kB] 179s Get:175 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-latexcodec all 3.0.0-1 [16.6 kB] 179s Get:176 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python3-matplotlib ppc64el 3.8.3-3ubuntu1 [4704 kB] 179s Get:177 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 179s Get:178 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-msgpack ppc64el 1.0.3-3build2 [86.9 kB] 179s Get:179 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mmtf all 1.1.3-1 [16.2 kB] 179s Get:180 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-threadpoolctl all 3.1.0-1 [21.3 kB] 179s Get:181 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-tqdm all 4.67.0-1 [91.6 kB] 179s Get:182 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mdanalysis ppc64el 2.7.0-5 [2103 kB] 179s Get:183 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-common all 7.4.7-4 [775 kB] 179s Get:184 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-alabaster all 0.7.16-0.1 [18.5 kB] 179s Get:185 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 179s Get:186 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-sphinx all 7.4.7-4 [593 kB] 179s Get:187 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 179s Get:188 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 179s Get:189 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-msmb-theme all 1.2.0-4 [35.4 kB] 179s Get:190 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-netcdf4 ppc64el 1.7.2-1 [635 kB] 179s Get:191 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 179s Get:192 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5 [4761 kB] 180s Get:193 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5 [3112 kB] 180s Get:194 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 180s Get:195 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pybtex all 0.24.0-4 [70.0 kB] 180s Get:196 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pybtex-docutils all 1.0.2-1 [7176 B] 180s Get:197 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB] 180s Get:198 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-seaborn all 0.13.2-4 [225 kB] 180s Get:199 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn-lib ppc64el 1.4.2+dfsg-6 [3838 kB] 180s Get:200 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 180s Get:201 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinx-sitemap all 2.6.0-1 [6674 B] 180s Get:202 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 181s Fetched 203 MB in 10s (20.2 MB/s) 181s Selecting previously unselected package fonts-lato. 181s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73800 files and directories currently installed.) 181s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 181s Unpacking fonts-lato (2.015-1) ... 182s Selecting previously unselected package sgml-base. 182s Preparing to unpack .../001-sgml-base_1.31_all.deb ... 182s Unpacking sgml-base (1.31) ... 182s Selecting previously unselected package m4. 182s Preparing to unpack .../002-m4_1.4.19-4build1_ppc64el.deb ... 182s Unpacking m4 (1.4.19-4build1) ... 182s Selecting previously unselected package autoconf. 182s Preparing to unpack .../003-autoconf_2.72-3_all.deb ... 182s Unpacking autoconf (2.72-3) ... 182s Selecting previously unselected package autotools-dev. 182s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ... 182s Unpacking autotools-dev (20220109.1) ... 182s Selecting previously unselected package automake. 182s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 182s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 182s Selecting previously unselected package autopoint. 182s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ... 182s Unpacking autopoint (0.22.5-2) ... 182s Selecting previously unselected package libtcl8.6:ppc64el. 182s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_ppc64el.deb ... 182s Unpacking libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 182s Selecting previously unselected package fonts-dejavu-mono. 182s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8_all.deb ... 182s Unpacking fonts-dejavu-mono (2.37-8) ... 182s Selecting previously unselected package fonts-dejavu-core. 182s Preparing to unpack .../009-fonts-dejavu-core_2.37-8_all.deb ... 182s Unpacking fonts-dejavu-core (2.37-8) ... 182s Selecting previously unselected package libfontenc1:ppc64el. 182s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 182s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 182s Selecting previously unselected package x11-common. 182s Preparing to unpack .../011-x11-common_1%3a7.7+23ubuntu3_all.deb ... 182s Unpacking x11-common (1:7.7+23ubuntu3) ... 182s Selecting previously unselected package xfonts-encodings. 182s Preparing to unpack .../012-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 182s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 182s Selecting previously unselected package xfonts-utils. 182s Preparing to unpack .../013-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 182s Unpacking xfonts-utils (1:7.7+7) ... 182s Selecting previously unselected package fonts-urw-base35. 182s Preparing to unpack .../014-fonts-urw-base35_20200910-8_all.deb ... 182s Unpacking fonts-urw-base35 (20200910-8) ... 182s Selecting previously unselected package fontconfig-config. 182s Preparing to unpack .../015-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ... 183s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 183s Selecting previously unselected package libfontconfig1:ppc64el. 183s Preparing to unpack .../016-libfontconfig1_2.15.0-1.1ubuntu2_ppc64el.deb ... 183s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 183s Selecting previously unselected package libxrender1:ppc64el. 183s Preparing to unpack .../017-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 183s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 183s Selecting previously unselected package libxft2:ppc64el. 183s Preparing to unpack .../018-libxft2_2.3.6-1build1_ppc64el.deb ... 183s Unpacking libxft2:ppc64el (2.3.6-1build1) ... 183s Selecting previously unselected package libxss1:ppc64el. 183s Preparing to unpack .../019-libxss1_1%3a1.2.3-1build3_ppc64el.deb ... 183s Unpacking libxss1:ppc64el (1:1.2.3-1build3) ... 183s Selecting previously unselected package libtk8.6:ppc64el. 183s Preparing to unpack .../020-libtk8.6_8.6.15-1_ppc64el.deb ... 183s Unpacking libtk8.6:ppc64el (8.6.15-1) ... 183s Selecting previously unselected package tk8.6-blt2.5. 183s Preparing to unpack .../021-tk8.6-blt2.5_2.5.3+dfsg-7build1_ppc64el.deb ... 183s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 183s Selecting previously unselected package blt. 183s Preparing to unpack .../022-blt_2.5.3+dfsg-7build1_ppc64el.deb ... 183s Unpacking blt (2.5.3+dfsg-7build1) ... 183s Selecting previously unselected package libisl23:ppc64el. 183s Preparing to unpack .../023-libisl23_0.27-1_ppc64el.deb ... 183s Unpacking libisl23:ppc64el (0.27-1) ... 183s Selecting previously unselected package libmpc3:ppc64el. 183s Preparing to unpack .../024-libmpc3_1.3.1-1build2_ppc64el.deb ... 183s Unpacking libmpc3:ppc64el (1.3.1-1build2) ... 183s Selecting previously unselected package cpp-14-powerpc64le-linux-gnu. 183s Preparing to unpack .../025-cpp-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking cpp-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package cpp-14. 183s Preparing to unpack .../026-cpp-14_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 183s Preparing to unpack .../027-cpp-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 183s Unpacking cpp-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 183s Selecting previously unselected package cpp. 183s Preparing to unpack .../028-cpp_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 183s Unpacking cpp (4:14.1.0-2ubuntu1) ... 183s Selecting previously unselected package libcc1-0:ppc64el. 183s Preparing to unpack .../029-libcc1-0_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking libcc1-0:ppc64el (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libgomp1:ppc64el. 183s Preparing to unpack .../030-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libitm1:ppc64el. 183s Preparing to unpack .../031-libitm1_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking libitm1:ppc64el (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libasan8:ppc64el. 183s Preparing to unpack .../032-libasan8_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking libasan8:ppc64el (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package liblsan0:ppc64el. 183s Preparing to unpack .../033-liblsan0_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking liblsan0:ppc64el (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libtsan2:ppc64el. 183s Preparing to unpack .../034-libtsan2_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking libtsan2:ppc64el (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libubsan1:ppc64el. 183s Preparing to unpack .../035-libubsan1_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking libubsan1:ppc64el (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libquadmath0:ppc64el. 183s Preparing to unpack .../036-libquadmath0_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking libquadmath0:ppc64el (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libgcc-14-dev:ppc64el. 183s Preparing to unpack .../037-libgcc-14-dev_14.2.0-8ubuntu1_ppc64el.deb ... 183s Unpacking libgcc-14-dev:ppc64el (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package gcc-14-powerpc64le-linux-gnu. 184s Preparing to unpack .../038-gcc-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 184s Unpacking gcc-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package gcc-14. 184s Preparing to unpack .../039-gcc-14_14.2.0-8ubuntu1_ppc64el.deb ... 184s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 184s Preparing to unpack .../040-gcc-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 184s Unpacking gcc-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 184s Selecting previously unselected package gcc. 184s Preparing to unpack .../041-gcc_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 184s Unpacking gcc (4:14.1.0-2ubuntu1) ... 184s Selecting previously unselected package libstdc++-14-dev:ppc64el. 184s Preparing to unpack .../042-libstdc++-14-dev_14.2.0-8ubuntu1_ppc64el.deb ... 184s Unpacking libstdc++-14-dev:ppc64el (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package g++-14-powerpc64le-linux-gnu. 184s Preparing to unpack .../043-g++-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 184s Unpacking g++-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package g++-14. 184s Preparing to unpack .../044-g++-14_14.2.0-8ubuntu1_ppc64el.deb ... 184s Unpacking g++-14 (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package g++-powerpc64le-linux-gnu. 184s Preparing to unpack .../045-g++-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 184s Unpacking g++-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 184s Selecting previously unselected package g++. 184s Preparing to unpack .../046-g++_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 184s Unpacking g++ (4:14.1.0-2ubuntu1) ... 184s Selecting previously unselected package build-essential. 184s Preparing to unpack .../047-build-essential_12.10ubuntu1_ppc64el.deb ... 184s Unpacking build-essential (12.10ubuntu1) ... 184s Selecting previously unselected package cython3. 184s Preparing to unpack .../048-cython3_3.0.11+dfsg-1ubuntu2_ppc64el.deb ... 184s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ... 185s Selecting previously unselected package libdebhelper-perl. 185s Preparing to unpack .../049-libdebhelper-perl_13.20ubuntu1_all.deb ... 185s Unpacking libdebhelper-perl (13.20ubuntu1) ... 185s Selecting previously unselected package libtool. 185s Preparing to unpack .../050-libtool_2.4.7-7build1_all.deb ... 185s Unpacking libtool (2.4.7-7build1) ... 185s Selecting previously unselected package dh-autoreconf. 185s Preparing to unpack .../051-dh-autoreconf_20_all.deb ... 185s Unpacking dh-autoreconf (20) ... 185s Selecting previously unselected package libarchive-zip-perl. 185s Preparing to unpack .../052-libarchive-zip-perl_1.68-1_all.deb ... 185s Unpacking libarchive-zip-perl (1.68-1) ... 185s Selecting previously unselected package libfile-stripnondeterminism-perl. 185s Preparing to unpack .../053-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 185s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 185s Selecting previously unselected package dh-strip-nondeterminism. 185s Preparing to unpack .../054-dh-strip-nondeterminism_1.14.0-1_all.deb ... 185s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 185s Selecting previously unselected package debugedit. 185s Preparing to unpack .../055-debugedit_1%3a5.1-1_ppc64el.deb ... 185s Unpacking debugedit (1:5.1-1) ... 185s Selecting previously unselected package dwz. 185s Preparing to unpack .../056-dwz_0.15-1build6_ppc64el.deb ... 185s Unpacking dwz (0.15-1build6) ... 185s Selecting previously unselected package gettext. 185s Preparing to unpack .../057-gettext_0.22.5-2_ppc64el.deb ... 185s Unpacking gettext (0.22.5-2) ... 185s Selecting previously unselected package intltool-debian. 185s Preparing to unpack .../058-intltool-debian_0.35.0+20060710.6_all.deb ... 185s Unpacking intltool-debian (0.35.0+20060710.6) ... 185s Selecting previously unselected package po-debconf. 185s Preparing to unpack .../059-po-debconf_1.0.21+nmu1_all.deb ... 185s Unpacking po-debconf (1.0.21+nmu1) ... 185s Selecting previously unselected package debhelper. 185s Preparing to unpack .../060-debhelper_13.20ubuntu1_all.deb ... 185s Unpacking debhelper (13.20ubuntu1) ... 185s Selecting previously unselected package dh-python. 185s Preparing to unpack .../061-dh-python_6.20241024_all.deb ... 185s Unpacking dh-python (6.20241024) ... 185s Selecting previously unselected package xml-core. 185s Preparing to unpack .../062-xml-core_0.19_all.deb ... 185s Unpacking xml-core (0.19) ... 185s Selecting previously unselected package docutils-common. 185s Preparing to unpack .../063-docutils-common_0.21.2+dfsg-2_all.deb ... 185s Unpacking docutils-common (0.21.2+dfsg-2) ... 185s Selecting previously unselected package fonts-font-awesome. 185s Preparing to unpack .../064-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 185s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 185s Selecting previously unselected package fonts-lyx. 185s Preparing to unpack .../065-fonts-lyx_2.4.2.1-1_all.deb ... 185s Unpacking fonts-lyx (2.4.2.1-1) ... 185s Selecting previously unselected package fonts-mathjax. 185s Preparing to unpack .../066-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 185s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 185s Selecting previously unselected package libaec0:ppc64el. 185s Preparing to unpack .../067-libaec0_1.1.3-1_ppc64el.deb ... 185s Unpacking libaec0:ppc64el (1.1.3-1) ... 185s Selecting previously unselected package libblas3:ppc64el. 185s Preparing to unpack .../068-libblas3_3.12.0-3build2_ppc64el.deb ... 185s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 185s Selecting previously unselected package libpixman-1-0:ppc64el. 185s Preparing to unpack .../069-libpixman-1-0_0.44.0-3_ppc64el.deb ... 185s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 185s Selecting previously unselected package libxcb-render0:ppc64el. 185s Preparing to unpack .../070-libxcb-render0_1.17.0-2_ppc64el.deb ... 185s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 185s Selecting previously unselected package libxcb-shm0:ppc64el. 185s Preparing to unpack .../071-libxcb-shm0_1.17.0-2_ppc64el.deb ... 185s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 185s Selecting previously unselected package libcairo2:ppc64el. 185s Preparing to unpack .../072-libcairo2_1.18.2-2_ppc64el.deb ... 185s Unpacking libcairo2:ppc64el (1.18.2-2) ... 186s Selecting previously unselected package libdeflate0:ppc64el. 186s Preparing to unpack .../073-libdeflate0_1.22-1_ppc64el.deb ... 186s Unpacking libdeflate0:ppc64el (1.22-1) ... 186s Selecting previously unselected package libexpat1-dev:ppc64el. 186s Preparing to unpack .../074-libexpat1-dev_2.6.4-1_ppc64el.deb ... 186s Unpacking libexpat1-dev:ppc64el (2.6.4-1) ... 186s Selecting previously unselected package libgfortran5:ppc64el. 186s Preparing to unpack .../075-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 186s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 186s Selecting previously unselected package libgraphite2-3:ppc64el. 186s Preparing to unpack .../076-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 186s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 186s Selecting previously unselected package libharfbuzz0b:ppc64el. 186s Preparing to unpack .../077-libharfbuzz0b_10.0.1-1_ppc64el.deb ... 186s Unpacking libharfbuzz0b:ppc64el (10.0.1-1) ... 186s Selecting previously unselected package libsz2:ppc64el. 186s Preparing to unpack .../078-libsz2_1.1.3-1_ppc64el.deb ... 186s Unpacking libsz2:ppc64el (1.1.3-1) ... 186s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 186s Preparing to unpack .../079-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 186s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ... 186s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 186s Preparing to unpack .../080-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 186s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ... 186s Selecting previously unselected package libimagequant0:ppc64el. 186s Preparing to unpack .../081-libimagequant0_2.18.0-1build1_ppc64el.deb ... 186s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 186s Selecting previously unselected package libjpeg-turbo8:ppc64el. 186s Preparing to unpack .../082-libjpeg-turbo8_2.1.5-2ubuntu2_ppc64el.deb ... 186s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 186s Selecting previously unselected package libjpeg8:ppc64el. 186s Preparing to unpack .../083-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 186s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 186s Selecting previously unselected package libjs-jquery. 186s Preparing to unpack .../084-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 186s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 186s Selecting previously unselected package libjs-jquery-ui. 186s Preparing to unpack .../085-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 186s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 186s Selecting previously unselected package libjs-underscore. 186s Preparing to unpack .../086-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 186s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 186s Selecting previously unselected package libjs-sphinxdoc. 186s Preparing to unpack .../087-libjs-sphinxdoc_7.4.7-4_all.deb ... 186s Unpacking libjs-sphinxdoc (7.4.7-4) ... 186s Selecting previously unselected package libjson-perl. 186s Preparing to unpack .../088-libjson-perl_4.10000-1_all.deb ... 186s Unpacking libjson-perl (4.10000-1) ... 186s Selecting previously unselected package liblapack3:ppc64el. 186s Preparing to unpack .../089-liblapack3_3.12.0-3build2_ppc64el.deb ... 186s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 186s Selecting previously unselected package liblbfgsb0:ppc64el. 186s Preparing to unpack .../090-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 186s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 186s Selecting previously unselected package liblcms2-2:ppc64el. 186s Preparing to unpack .../091-liblcms2-2_2.16-2_ppc64el.deb ... 186s Unpacking liblcms2-2:ppc64el (2.16-2) ... 186s Selecting previously unselected package liblerc4:ppc64el. 186s Preparing to unpack .../092-liblerc4_4.0.0+ds-4ubuntu2_ppc64el.deb ... 186s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 186s Selecting previously unselected package liblzf1:ppc64el. 186s Preparing to unpack .../093-liblzf1_3.6-4_ppc64el.deb ... 186s Unpacking liblzf1:ppc64el (3.6-4) ... 186s Selecting previously unselected package libnetcdf19t64:ppc64el. 186s Preparing to unpack .../094-libnetcdf19t64_1%3a4.9.2-6ubuntu1_ppc64el.deb ... 186s Unpacking libnetcdf19t64:ppc64el (1:4.9.2-6ubuntu1) ... 186s Selecting previously unselected package zlib1g-dev:ppc64el. 186s Preparing to unpack .../095-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_ppc64el.deb ... 186s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 186s Selecting previously unselected package libpython3.12-dev:ppc64el. 186s Preparing to unpack .../096-libpython3.12-dev_3.12.7-3_ppc64el.deb ... 186s Unpacking libpython3.12-dev:ppc64el (3.12.7-3) ... 186s Selecting previously unselected package libpython3-dev:ppc64el. 186s Preparing to unpack .../097-libpython3-dev_3.12.6-0ubuntu1_ppc64el.deb ... 186s Unpacking libpython3-dev:ppc64el (3.12.6-0ubuntu1) ... 186s Selecting previously unselected package libpython3-all-dev:ppc64el. 186s Preparing to unpack .../098-libpython3-all-dev_3.12.6-0ubuntu1_ppc64el.deb ... 186s Unpacking libpython3-all-dev:ppc64el (3.12.6-0ubuntu1) ... 186s Selecting previously unselected package libqhull-r8.0:ppc64el. 186s Preparing to unpack .../099-libqhull-r8.0_2020.2-6build1_ppc64el.deb ... 186s Unpacking libqhull-r8.0:ppc64el (2020.2-6build1) ... 186s Selecting previously unselected package libraqm0:ppc64el. 186s Preparing to unpack .../100-libraqm0_0.10.1-1build1_ppc64el.deb ... 186s Unpacking libraqm0:ppc64el (0.10.1-1build1) ... 187s Selecting previously unselected package libsharpyuv0:ppc64el. 187s Preparing to unpack .../101-libsharpyuv0_1.4.0-0.1_ppc64el.deb ... 187s Unpacking libsharpyuv0:ppc64el (1.4.0-0.1) ... 187s Selecting previously unselected package libjbig0:ppc64el. 187s Preparing to unpack .../102-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 187s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 187s Selecting previously unselected package libwebp7:ppc64el. 187s Preparing to unpack .../103-libwebp7_1.4.0-0.1_ppc64el.deb ... 187s Unpacking libwebp7:ppc64el (1.4.0-0.1) ... 187s Selecting previously unselected package libtiff6:ppc64el. 187s Preparing to unpack .../104-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ... 187s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 187s Selecting previously unselected package libwebpdemux2:ppc64el. 187s Preparing to unpack .../105-libwebpdemux2_1.4.0-0.1_ppc64el.deb ... 187s Unpacking libwebpdemux2:ppc64el (1.4.0-0.1) ... 187s Selecting previously unselected package libwebpmux3:ppc64el. 187s Preparing to unpack .../106-libwebpmux3_1.4.0-0.1_ppc64el.deb ... 187s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ... 187s Selecting previously unselected package libxslt1.1:ppc64el. 187s Preparing to unpack .../107-libxslt1.1_1.1.39-0exp1ubuntu1_ppc64el.deb ... 187s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 187s Selecting previously unselected package python3-packaging. 187s Preparing to unpack .../108-python3-packaging_24.1-1_all.deb ... 187s Unpacking python3-packaging (24.1-1) ... 187s Selecting previously unselected package python3-pyproject-hooks. 187s Preparing to unpack .../109-python3-pyproject-hooks_1.2.0-1_all.deb ... 187s Unpacking python3-pyproject-hooks (1.2.0-1) ... 187s Selecting previously unselected package python3-toml. 187s Preparing to unpack .../110-python3-toml_0.10.2-1_all.deb ... 187s Unpacking python3-toml (0.10.2-1) ... 187s Selecting previously unselected package python3-wheel. 187s Preparing to unpack .../111-python3-wheel_0.44.0-1_all.deb ... 187s Unpacking python3-wheel (0.44.0-1) ... 187s Selecting previously unselected package python3-build. 187s Preparing to unpack .../112-python3-build_1.2.2-1_all.deb ... 187s Unpacking python3-build (1.2.2-1) ... 187s Selecting previously unselected package python3-installer. 187s Preparing to unpack .../113-python3-installer_0.7.0+dfsg1-3_all.deb ... 187s Unpacking python3-installer (0.7.0+dfsg1-3) ... 187s Selecting previously unselected package pybuild-plugin-pyproject. 187s Preparing to unpack .../114-pybuild-plugin-pyproject_6.20241024_all.deb ... 187s Unpacking pybuild-plugin-pyproject (6.20241024) ... 187s Selecting previously unselected package python-matplotlib-data. 187s Preparing to unpack .../115-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ... 187s Unpacking python-matplotlib-data (3.8.3-3ubuntu1) ... 187s Selecting previously unselected package libjs-mathjax. 187s Preparing to unpack .../116-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 187s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 188s Selecting previously unselected package python-mdanalysis-doc. 188s Preparing to unpack .../117-python-mdanalysis-doc_2.7.0-5_all.deb ... 188s Unpacking python-mdanalysis-doc (2.7.0-5) ... 188s Selecting previously unselected package python3-all. 188s Preparing to unpack .../118-python3-all_3.12.6-0ubuntu1_ppc64el.deb ... 188s Unpacking python3-all (3.12.6-0ubuntu1) ... 188s Selecting previously unselected package python3.12-dev. 188s Preparing to unpack .../119-python3.12-dev_3.12.7-3_ppc64el.deb ... 188s Unpacking python3.12-dev (3.12.7-3) ... 188s Selecting previously unselected package python3-dev. 188s Preparing to unpack .../120-python3-dev_3.12.6-0ubuntu1_ppc64el.deb ... 188s Unpacking python3-dev (3.12.6-0ubuntu1) ... 188s Selecting previously unselected package python3-all-dev. 188s Preparing to unpack .../121-python3-all-dev_3.12.6-0ubuntu1_ppc64el.deb ... 188s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 188s Selecting previously unselected package python3-appdirs. 188s Preparing to unpack .../122-python3-appdirs_1.4.4-4_all.deb ... 188s Unpacking python3-appdirs (1.4.4-4) ... 188s Selecting previously unselected package python3-numpy. 188s Preparing to unpack .../123-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 188s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 188s Selecting previously unselected package python3.12-tk. 188s Preparing to unpack .../124-python3.12-tk_3.12.7-3_ppc64el.deb ... 188s Unpacking python3.12-tk (3.12.7-3) ... 188s Selecting previously unselected package python3-tk:ppc64el. 188s Preparing to unpack .../125-python3-tk_3.12.6-1ubuntu1_ppc64el.deb ... 188s Unpacking python3-tk:ppc64el (3.12.6-1ubuntu1) ... 188s Selecting previously unselected package python3-pil.imagetk:ppc64el. 188s Preparing to unpack .../126-python3-pil.imagetk_10.4.0-1ubuntu1_ppc64el.deb ... 188s Unpacking python3-pil.imagetk:ppc64el (10.4.0-1ubuntu1) ... 188s Selecting previously unselected package libopenjp2-7:ppc64el. 188s Preparing to unpack .../127-libopenjp2-7_2.5.0-2ubuntu1_ppc64el.deb ... 188s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 188s Selecting previously unselected package python3-pil:ppc64el. 188s Preparing to unpack .../128-python3-pil_10.4.0-1ubuntu1_ppc64el.deb ... 188s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu1) ... 188s Selecting previously unselected package python3-cairo. 188s Preparing to unpack .../129-python3-cairo_1.26.1-2_ppc64el.deb ... 188s Unpacking python3-cairo (1.26.1-2) ... 188s Selecting previously unselected package python3-freetype. 188s Preparing to unpack .../130-python3-freetype_2.5.1-1_all.deb ... 188s Unpacking python3-freetype (2.5.1-1) ... 188s Selecting previously unselected package python3-rlpycairo. 188s Preparing to unpack .../131-python3-rlpycairo_0.3.0-3_all.deb ... 188s Unpacking python3-rlpycairo (0.3.0-3) ... 188s Selecting previously unselected package python3-reportlab. 188s Preparing to unpack .../132-python3-reportlab_4.2.5-1_all.deb ... 188s Unpacking python3-reportlab (4.2.5-1) ... 188s Selecting previously unselected package w3c-sgml-lib. 188s Preparing to unpack .../133-w3c-sgml-lib_1.3-3_all.deb ... 188s Unpacking w3c-sgml-lib (1.3-3) ... 188s Selecting previously unselected package python3-biopython. 188s Preparing to unpack .../134-python3-biopython_1.84+dfsg-4_ppc64el.deb ... 188s Unpacking python3-biopython (1.84+dfsg-4) ... 189s Selecting previously unselected package python3-brotli. 189s Preparing to unpack .../135-python3-brotli_1.1.0-2build2_ppc64el.deb ... 189s Unpacking python3-brotli (1.1.0-2build2) ... 189s Selecting previously unselected package python3-cftime. 189s Preparing to unpack .../136-python3-cftime_1.6.4-1_ppc64el.deb ... 189s Unpacking python3-cftime (1.6.4-1) ... 189s Selecting previously unselected package python3-lxml:ppc64el. 189s Preparing to unpack .../137-python3-lxml_5.3.0-1_ppc64el.deb ... 189s Unpacking python3-lxml:ppc64el (5.3.0-1) ... 189s Selecting previously unselected package python3-citeproc. 189s Preparing to unpack .../138-python3-citeproc_0.6.0-3_all.deb ... 189s Unpacking python3-citeproc (0.6.0-3) ... 189s Selecting previously unselected package python3-contourpy. 189s Preparing to unpack .../139-python3-contourpy_1.3.0-2_ppc64el.deb ... 189s Unpacking python3-contourpy (1.3.0-2) ... 189s Selecting previously unselected package python3-cycler. 189s Preparing to unpack .../140-python3-cycler_0.12.1-1_all.deb ... 189s Unpacking python3-cycler (0.12.1-1) ... 189s Selecting previously unselected package python3-six. 189s Preparing to unpack .../141-python3-six_1.16.0-7_all.deb ... 189s Unpacking python3-six (1.16.0-7) ... 189s Selecting previously unselected package python3-dateutil. 189s Preparing to unpack .../142-python3-dateutil_2.9.0-2_all.deb ... 189s Unpacking python3-dateutil (2.9.0-2) ... 189s Selecting previously unselected package python3-decorator. 189s Preparing to unpack .../143-python3-decorator_5.1.1-5_all.deb ... 189s Unpacking python3-decorator (5.1.1-5) ... 189s Selecting previously unselected package python3-defusedxml. 189s Preparing to unpack .../144-python3-defusedxml_0.7.1-2_all.deb ... 189s Unpacking python3-defusedxml (0.7.1-2) ... 189s Selecting previously unselected package python3-roman. 189s Preparing to unpack .../145-python3-roman_4.2-1_all.deb ... 189s Unpacking python3-roman (4.2-1) ... 189s Selecting previously unselected package python3-docutils. 189s Preparing to unpack .../146-python3-docutils_0.21.2+dfsg-2_all.deb ... 189s Unpacking python3-docutils (0.21.2+dfsg-2) ... 189s Selecting previously unselected package python3-looseversion. 189s Preparing to unpack .../147-python3-looseversion_1.3.0-3_all.deb ... 189s Unpacking python3-looseversion (1.3.0-3) ... 189s Selecting previously unselected package python3-duecredit. 189s Preparing to unpack .../148-python3-duecredit_0.10.2-2_all.deb ... 189s Unpacking python3-duecredit (0.10.2-2) ... 189s Selecting previously unselected package python3-monotonic. 189s Preparing to unpack .../149-python3-monotonic_1.6-2_all.deb ... 189s Unpacking python3-monotonic (1.6-2) ... 189s Selecting previously unselected package python3-fasteners. 189s Preparing to unpack .../150-python3-fasteners_0.18-2_all.deb ... 189s Unpacking python3-fasteners (0.18-2) ... 189s Selecting previously unselected package python3-scipy. 189s Preparing to unpack .../151-python3-scipy_1.13.1-5_ppc64el.deb ... 189s Unpacking python3-scipy (1.13.1-5) ... 190s Selecting previously unselected package python3-ufolib2. 190s Preparing to unpack .../152-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 190s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 190s Selecting previously unselected package python3-mpmath. 190s Preparing to unpack .../153-python3-mpmath_1.3.0-1_all.deb ... 190s Unpacking python3-mpmath (1.3.0-1) ... 190s Selecting previously unselected package python3-sympy. 190s Preparing to unpack .../154-python3-sympy_1.13.3-1_all.deb ... 190s Unpacking python3-sympy (1.13.3-1) ... 190s Selecting previously unselected package python3-tz. 190s Preparing to unpack .../155-python3-tz_2024.1-2_all.deb ... 190s Unpacking python3-tz (2024.1-2) ... 190s Selecting previously unselected package python3-fs. 190s Preparing to unpack .../156-python3-fs_2.4.16-4_all.deb ... 190s Unpacking python3-fs (2.4.16-4) ... 190s Selecting previously unselected package python3-lz4. 190s Preparing to unpack .../157-python3-lz4_4.0.2+dfsg-1build4_ppc64el.deb ... 190s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 190s Selecting previously unselected package python3-unicodedata2. 190s Preparing to unpack .../158-python3-unicodedata2_15.1.0+ds-1build2_ppc64el.deb ... 190s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 190s Selecting previously unselected package unicode-data. 190s Preparing to unpack .../159-unicode-data_15.1.0-1_all.deb ... 190s Unpacking unicode-data (15.1.0-1) ... 190s Selecting previously unselected package python3-fonttools. 190s Preparing to unpack .../160-python3-fonttools_4.46.0-1build2_ppc64el.deb ... 190s Unpacking python3-fonttools (4.46.0-1build2) ... 191s Selecting previously unselected package sphinx-rtd-theme-common. 191s Preparing to unpack .../161-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 191s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 191s Selecting previously unselected package python3-mrcfile. 191s Preparing to unpack .../162-python3-mrcfile_1.5.3-3_all.deb ... 191s Unpacking python3-mrcfile (1.5.3-3) ... 191s Selecting previously unselected package python3-griddataformats. 191s Preparing to unpack .../163-python3-griddataformats_1.0.2-2_all.deb ... 191s Unpacking python3-griddataformats (1.0.2-2) ... 191s Selecting previously unselected package python3-gsd. 191s Preparing to unpack .../164-python3-gsd_3.3.0-1_ppc64el.deb ... 191s Unpacking python3-gsd (3.3.0-1) ... 191s Selecting previously unselected package python3-h5py-serial. 191s Preparing to unpack .../165-python3-h5py-serial_3.11.0-5ubuntu1_ppc64el.deb ... 191s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 191s Selecting previously unselected package python3-h5py. 191s Preparing to unpack .../166-python3-h5py_3.11.0-5ubuntu1_all.deb ... 191s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 191s Selecting previously unselected package python3-sortedcontainers. 191s Preparing to unpack .../167-python3-sortedcontainers_2.4.0-2_all.deb ... 191s Unpacking python3-sortedcontainers (2.4.0-2) ... 191s Selecting previously unselected package python3-hypothesis. 191s Preparing to unpack .../168-python3-hypothesis_6.116.0-1_all.deb ... 191s Unpacking python3-hypothesis (6.116.0-1) ... 191s Selecting previously unselected package python3-imagesize. 191s Preparing to unpack .../169-python3-imagesize_1.4.1-1_all.deb ... 191s Unpacking python3-imagesize (1.4.1-1) ... 191s Selecting previously unselected package python3-iniconfig. 191s Preparing to unpack .../170-python3-iniconfig_1.1.1-2_all.deb ... 191s Unpacking python3-iniconfig (1.1.1-2) ... 191s Selecting previously unselected package python3-joblib. 191s Preparing to unpack .../171-python3-joblib_1.3.2-5_all.deb ... 191s Unpacking python3-joblib (1.3.2-5) ... 191s Selecting previously unselected package python3-kiwisolver. 191s Preparing to unpack .../172-python3-kiwisolver_1.4.7-2build1_ppc64el.deb ... 191s Unpacking python3-kiwisolver (1.4.7-2build1) ... 191s Selecting previously unselected package python3-latexcodec. 191s Preparing to unpack .../173-python3-latexcodec_3.0.0-1_all.deb ... 191s Unpacking python3-latexcodec (3.0.0-1) ... 191s Selecting previously unselected package python3-matplotlib. 191s Preparing to unpack .../174-python3-matplotlib_3.8.3-3ubuntu1_ppc64el.deb ... 191s Unpacking python3-matplotlib (3.8.3-3ubuntu1) ... 191s Selecting previously unselected package python3-mda-xdrlib. 191s Preparing to unpack .../175-python3-mda-xdrlib_0.2.0-3_all.deb ... 191s Unpacking python3-mda-xdrlib (0.2.0-3) ... 191s Selecting previously unselected package python3-msgpack. 191s Preparing to unpack .../176-python3-msgpack_1.0.3-3build2_ppc64el.deb ... 191s Unpacking python3-msgpack (1.0.3-3build2) ... 191s Selecting previously unselected package python3-mmtf. 191s Preparing to unpack .../177-python3-mmtf_1.1.3-1_all.deb ... 191s Unpacking python3-mmtf (1.1.3-1) ... 191s Selecting previously unselected package python3-threadpoolctl. 191s Preparing to unpack .../178-python3-threadpoolctl_3.1.0-1_all.deb ... 191s Unpacking python3-threadpoolctl (3.1.0-1) ... 191s Selecting previously unselected package python3-tqdm. 191s Preparing to unpack .../179-python3-tqdm_4.67.0-1_all.deb ... 191s Unpacking python3-tqdm (4.67.0-1) ... 191s Selecting previously unselected package python3-mdanalysis. 191s Preparing to unpack .../180-python3-mdanalysis_2.7.0-5_ppc64el.deb ... 191s Unpacking python3-mdanalysis (2.7.0-5) ... 191s Selecting previously unselected package sphinx-common. 191s Preparing to unpack .../181-sphinx-common_7.4.7-4_all.deb ... 191s Unpacking sphinx-common (7.4.7-4) ... 192s Selecting previously unselected package python3-alabaster. 192s Preparing to unpack .../182-python3-alabaster_0.7.16-0.1_all.deb ... 192s Unpacking python3-alabaster (0.7.16-0.1) ... 192s Selecting previously unselected package python3-snowballstemmer. 192s Preparing to unpack .../183-python3-snowballstemmer_2.2.0-4build1_all.deb ... 192s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 192s Selecting previously unselected package python3-sphinx. 192s Preparing to unpack .../184-python3-sphinx_7.4.7-4_all.deb ... 192s Unpacking python3-sphinx (7.4.7-4) ... 192s Selecting previously unselected package python3-sphinxcontrib.jquery. 192s Preparing to unpack .../185-python3-sphinxcontrib.jquery_4.1-5_all.deb ... 192s Unpacking python3-sphinxcontrib.jquery (4.1-5) ... 192s Selecting previously unselected package python3-sphinx-rtd-theme. 192s Preparing to unpack .../186-python3-sphinx-rtd-theme_3.0.1+dfsg-1_all.deb ... 192s Unpacking python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 192s Selecting previously unselected package python3-msmb-theme. 192s Preparing to unpack .../187-python3-msmb-theme_1.2.0-4_all.deb ... 192s Unpacking python3-msmb-theme (1.2.0-4) ... 192s Selecting previously unselected package python3-netcdf4. 192s Preparing to unpack .../188-python3-netcdf4_1.7.2-1_ppc64el.deb ... 192s Unpacking python3-netcdf4 (1.7.2-1) ... 192s Selecting previously unselected package python3-networkx. 192s Preparing to unpack .../189-python3-networkx_3.2.1-4ubuntu1_all.deb ... 192s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 192s Selecting previously unselected package python3-pandas-lib:ppc64el. 192s Preparing to unpack .../190-python3-pandas-lib_2.2.3+dfsg-5_ppc64el.deb ... 192s Unpacking python3-pandas-lib:ppc64el (2.2.3+dfsg-5) ... 193s Selecting previously unselected package python3-pandas. 193s Preparing to unpack .../191-python3-pandas_2.2.3+dfsg-5_all.deb ... 193s Unpacking python3-pandas (2.2.3+dfsg-5) ... 193s Selecting previously unselected package python3-pluggy. 193s Preparing to unpack .../192-python3-pluggy_1.5.0-1_all.deb ... 193s Unpacking python3-pluggy (1.5.0-1) ... 193s Selecting previously unselected package python3-pybtex. 193s Preparing to unpack .../193-python3-pybtex_0.24.0-4_all.deb ... 193s Unpacking python3-pybtex (0.24.0-4) ... 193s Selecting previously unselected package python3-pybtex-docutils. 193s Preparing to unpack .../194-python3-pybtex-docutils_1.0.2-1_all.deb ... 193s Unpacking python3-pybtex-docutils (1.0.2-1) ... 193s Selecting previously unselected package python3-pytest. 193s Preparing to unpack .../195-python3-pytest_8.3.3-1_all.deb ... 193s Unpacking python3-pytest (8.3.3-1) ... 193s Selecting previously unselected package python3-seaborn. 193s Preparing to unpack .../196-python3-seaborn_0.13.2-4_all.deb ... 193s Unpacking python3-seaborn (0.13.2-4) ... 193s Selecting previously unselected package python3-sklearn-lib:ppc64el. 193s Preparing to unpack .../197-python3-sklearn-lib_1.4.2+dfsg-6_ppc64el.deb ... 193s Unpacking python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ... 193s Selecting previously unselected package python3-sklearn. 193s Preparing to unpack .../198-python3-sklearn_1.4.2+dfsg-6_all.deb ... 193s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 193s Selecting previously unselected package python3-sphinx-sitemap. 193s Preparing to unpack .../199-python3-sphinx-sitemap_2.6.0-1_all.deb ... 193s Unpacking python3-sphinx-sitemap (2.6.0-1) ... 193s Selecting previously unselected package python3-sphinxcontrib.bibtex. 193s Preparing to unpack .../200-python3-sphinxcontrib.bibtex_2.6.2-1_all.deb ... 193s Unpacking python3-sphinxcontrib.bibtex (2.6.2-1) ... 193s Selecting previously unselected package autopkgtest-satdep. 193s Preparing to unpack .../201-1-autopkgtest-satdep.deb ... 193s Unpacking autopkgtest-satdep (0) ... 193s Setting up dh-python (6.20241024) ... 194s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 194s Setting up liblcms2-2:ppc64el (2.16-2) ... 194s Setting up python3-iniconfig (1.1.1-2) ... 194s Setting up libpixman-1-0:ppc64el (0.44.0-3) ... 194s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ... 194s Setting up fonts-lato (2.015-1) ... 194s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 194s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 194s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 194s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ... 194s Setting up python3-joblib (1.3.2-5) ... 194s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 194s Setting up libxcb-render0:ppc64el (1.17.0-2) ... 194s Setting up python3-defusedxml (0.7.1-2) ... 194s Setting up libarchive-zip-perl (1.68-1) ... 194s Setting up python3-alabaster (0.7.16-0.1) ... 194s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 194s Setting up fonts-lyx (2.4.2.1-1) ... 194s Setting up libdebhelper-perl (13.20ubuntu1) ... 194s Setting up python3-tqdm (4.67.0-1) ... 195s Setting up python3-threadpoolctl (3.1.0-1) ... 195s Setting up x11-common (1:7.7+23ubuntu3) ... 195s Setting up libdeflate0:ppc64el (1.22-1) ... 195s Setting up m4 (1.4.19-4build1) ... 195s Setting up python3-latexcodec (3.0.0-1) ... 195s Setting up libqhull-r8.0:ppc64el (2020.2-6build1) ... 195s Setting up python3-all (3.12.6-0ubuntu1) ... 195s Setting up libxcb-shm0:ppc64el (1.17.0-2) ... 195s Setting up python3-sortedcontainers (2.4.0-2) ... 196s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ... 196s Setting up python3-freetype (2.5.1-1) ... 196s Setting up python3-networkx (3.2.1-4ubuntu1) ... 197s Setting up python3-wheel (0.44.0-1) ... 198s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ... 198s Setting up python3-mda-xdrlib (0.2.0-3) ... 198s Setting up libaec0:ppc64el (1.1.3-1) ... 198s Setting up python3-tz (2024.1-2) ... 198s Setting up python3-monotonic (1.6-2) ... 198s Setting up unicode-data (15.1.0-1) ... 198s Setting up python3-six (1.16.0-7) ... 198s Setting up python3-roman (4.2-1) ... 198s Setting up python3-decorator (5.1.1-5) ... 199s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ... 199s Setting up autotools-dev (20220109.1) ... 199s Setting up libblas3:ppc64el (3.12.0-3build2) ... 199s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 199s Setting up python3-packaging (24.1-1) ... 199s Setting up libexpat1-dev:ppc64el (2.6.4-1) ... 199s Setting up python3-pyproject-hooks (1.2.0-1) ... 199s Setting up python3-snowballstemmer (2.2.0-4build1) ... 199s Setting up python3-brotli (1.1.0-2build2) ... 199s Setting up liblzf1:ppc64el (3.6-4) ... 199s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 199s Setting up libquadmath0:ppc64el (14.2.0-8ubuntu1) ... 199s Setting up python3-cycler (0.12.1-1) ... 200s Setting up libimagequant0:ppc64el (2.18.0-1build1) ... 200s Setting up fonts-dejavu-mono (2.37-8) ... 200s Setting up python3-kiwisolver (1.4.7-2build1) ... 200s Setting up libmpc3:ppc64el (1.3.1-1build2) ... 200s Setting up cython3 (3.0.11+dfsg-1ubuntu2) ... 201s Setting up libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 201s Setting up autopoint (0.22.5-2) ... 201s Setting up fonts-dejavu-core (2.37-8) ... 201s Setting up python3-fasteners (0.18-2) ... 201s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 201s Setting up python3-toml (0.10.2-1) ... 201s Setting up python3-installer (0.7.0+dfsg1-3) ... 201s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 201s Setting up autoconf (2.72-3) ... 201s Setting up python3-pluggy (1.5.0-1) ... 201s Setting up libwebp7:ppc64el (1.4.0-0.1) ... 201s Setting up python3-pybtex (0.24.0-4) ... 202s Setting up libubsan1:ppc64el (14.2.0-8ubuntu1) ... 202s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 202s Setting up dwz (0.15-1build6) ... 202s Setting up python3-looseversion (1.3.0-3) ... 202s Setting up libasan8:ppc64el (14.2.0-8ubuntu1) ... 202s Setting up libjson-perl (4.10000-1) ... 202s Setting up libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 202s Setting up debugedit (1:5.1-1) ... 202s Setting up libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 202s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ... 202s Setting up python3-dateutil (2.9.0-2) ... 202s Setting up sgml-base (1.31) ... 202s Setting up python3-msgpack (1.0.3-3build2) ... 202s Setting up libxss1:ppc64el (1:1.2.3-1build3) ... 202s Setting up libtsan2:ppc64el (14.2.0-8ubuntu1) ... 202s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 202s Setting up python3-mpmath (1.3.0-1) ... 203s Setting up libisl23:ppc64el (0.27-1) ... 203s Setting up python3-build (1.2.2-1) ... 203s Setting up python-matplotlib-data (3.8.3-3ubuntu1) ... 203s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ... 203s Setting up python3-appdirs (1.4.4-4) ... 203s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 203s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 203s Setting up libcc1-0:ppc64el (14.2.0-8ubuntu1) ... 203s Setting up liblsan0:ppc64el (14.2.0-8ubuntu1) ... 203s Setting up libsz2:ppc64el (1.1.3-1) ... 203s Setting up libitm1:ppc64el (14.2.0-8ubuntu1) ... 203s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 203s Setting up python3-imagesize (1.4.1-1) ... 203s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 203s Setting up automake (1:1.16.5-1.3ubuntu1) ... 203s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 203s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 203s Setting up python3-sympy (1.13.3-1) ... 212s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 212s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 212s Setting up gettext (0.22.5-2) ... 212s Setting up pybuild-plugin-pyproject (6.20241024) ... 212s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 212s Setting up python3-pytest (8.3.3-1) ... 212s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ... 212s Setting up python3-hypothesis (6.116.0-1) ... 213s Setting up libpython3.12-dev:ppc64el (3.12.7-3) ... 213s Setting up xfonts-utils (1:7.7+7) ... 213s Setting up intltool-debian (0.35.0+20060710.6) ... 213s Setting up python3-fs (2.4.16-4) ... 213s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 213s Setting up libraqm0:ppc64el (0.10.1-1build1) ... 213s Setting up python3.12-dev (3.12.7-3) ... 213s Setting up cpp-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 213s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 215s Setting up libjs-sphinxdoc (7.4.7-4) ... 215s Setting up cpp-14 (14.2.0-8ubuntu1) ... 215s Setting up dh-strip-nondeterminism (1.14.0-1) ... 215s Setting up python3-lxml:ppc64el (5.3.0-1) ... 216s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 216s Setting up xml-core (0.19) ... 216s Setting up python3-contourpy (1.3.0-2) ... 216s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 216s Setting up libgcc-14-dev:ppc64el (14.2.0-8ubuntu1) ... 216s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ... 216s Setting up libstdc++-14-dev:ppc64el (14.2.0-8ubuntu1) ... 216s Setting up cpp-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 216s Setting up gcc-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 216s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 216s Setting up python3-mrcfile (1.5.3-3) ... 216s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ... 216s Setting up libnetcdf19t64:ppc64el (1:4.9.2-6ubuntu1) ... 216s Setting up libxft2:ppc64el (2.3.6-1build1) ... 216s Setting up python3-scipy (1.13.1-5) ... 221s Setting up libpython3-dev:ppc64el (3.12.6-0ubuntu1) ... 221s Setting up g++-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 221s Setting up python3-citeproc (0.6.0-3) ... 221s Setting up po-debconf (1.0.21+nmu1) ... 221s Setting up libtk8.6:ppc64el (8.6.15-1) ... 221s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-5) ... 221s Setting up python3.12-tk (3.12.7-3) ... 221s Setting up python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ... 221s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 221s Setting up python3-gsd (3.3.0-1) ... 221s Setting up python3-mmtf (1.1.3-1) ... 222s Setting up fonts-urw-base35 (20200910-8) ... 222s Setting up libcairo2:ppc64el (1.18.2-2) ... 222s Setting up python-mdanalysis-doc (2.7.0-5) ... 222s Setting up gcc-14 (14.2.0-8ubuntu1) ... 222s Setting up python3-pil:ppc64el (10.4.0-1ubuntu1) ... 222s Setting up python3-griddataformats (1.0.2-2) ... 222s Setting up python3-pandas (2.2.3+dfsg-5) ... 229s Setting up gcc-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 229s Setting up libpython3-all-dev:ppc64el (3.12.6-0ubuntu1) ... 229s Setting up sphinx-common (7.4.7-4) ... 229s Setting up python3-dev (3.12.6-0ubuntu1) ... 229s Setting up python3-h5py (3.11.0-5ubuntu1) ... 229s Setting up python3-sklearn (1.4.2+dfsg-6) ... 232s Setting up python3-cftime (1.6.4-1) ... 232s Setting up cpp (4:14.1.0-2ubuntu1) ... 232s Setting up g++-14 (14.2.0-8ubuntu1) ... 232s Setting up python3-netcdf4 (1.7.2-1) ... 232s Setting up g++-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 232s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 232s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 232s Setting up python3-cairo (1.26.1-2) ... 232s Setting up python3-duecredit (0.10.2-2) ... 232s Setting up libtool (2.4.7-7build1) ... 232s Setting up blt (2.5.3+dfsg-7build1) ... 232s Setting up python3-tk:ppc64el (3.12.6-1ubuntu1) ... 232s Setting up gcc (4:14.1.0-2ubuntu1) ... 232s Setting up dh-autoreconf (20) ... 232s Setting up python3-pil.imagetk:ppc64el (10.4.0-1ubuntu1) ... 232s Setting up python3-rlpycairo (0.3.0-3) ... 232s Setting up python3-reportlab (4.2.5-1) ... 233s Setting up g++ (4:14.1.0-2ubuntu1) ... 233s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 233s Setting up build-essential (12.10ubuntu1) ... 234s Setting up debhelper (13.20ubuntu1) ... 234s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 234s Setting up python3-fonttools (4.46.0-1build2) ... 235s Setting up python3-matplotlib (3.8.3-3ubuntu1) ... 237s Setting up python3-mdanalysis (2.7.0-5) ... 237s Setting up python3-seaborn (0.13.2-4) ... 238s Processing triggers for man-db (2.13.0-1) ... 240s Processing triggers for install-info (7.1.1-1) ... 240s Processing triggers for libc-bin (2.40-1ubuntu3) ... 241s Processing triggers for sgml-base (1.31) ... 241s Setting up docutils-common (0.21.2+dfsg-2) ... 241s Setting up w3c-sgml-lib (1.3-3) ... 280s Setting up python3-biopython (1.84+dfsg-4) ... 282s Processing triggers for sgml-base (1.31) ... 282s Setting up python3-docutils (0.21.2+dfsg-2) ... 282s Setting up python3-pybtex-docutils (1.0.2-1) ... 282s Setting up python3-sphinx (7.4.7-4) ... 283s Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ... 283s Setting up python3-sphinx-sitemap (2.6.0-1) ... 283s Setting up python3-sphinxcontrib.jquery (4.1-5) ... 284s Setting up python3-sphinx-rtd-theme (3.0.1+dfsg-1) ... 284s Setting up python3-msmb-theme (1.2.0-4) ... 284s Setting up autopkgtest-satdep (0) ... 291s (Reading database ... 99538 files and directories currently installed.) 291s Removing autopkgtest-satdep (0) ... 291s autopkgtest [03:47:29]: test test-mdanalysis: [----------------------- 291s skipping tests with SKIP_TEST_LIST= 303s ============================= test session starts ============================== 303s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 303s rootdir: /tmp/autopkgtest.fEu9Gl/build.v4n/src 303s plugins: typeguard-4.4.1, hypothesis-6.116.0 303s collected 19229 items / 6 skipped 303s 309s testsuite/MDAnalysisTests/analysis/test_align.py ....................... [ 0%] 323s ....................s.ss.s... [ 0%] 323s testsuite/MDAnalysisTests/analysis/test_atomicdistances.py ... [ 0%] 323s testsuite/MDAnalysisTests/analysis/test_base.py ........................ [ 0%] 323s ........................................................................ [ 0%] 327s ....................................................................... [ 1%] 330s testsuite/MDAnalysisTests/analysis/test_bat.py ............ [ 1%] 332s testsuite/MDAnalysisTests/analysis/test_contacts.py .................... [ 1%] 336s .............. [ 1%] 336s testsuite/MDAnalysisTests/analysis/test_data.py . [ 1%] 336s testsuite/MDAnalysisTests/analysis/test_density.py ..................... [ 1%] 344s ...................... [ 1%] 345s testsuite/MDAnalysisTests/analysis/test_dielectric.py ...... [ 1%] 347s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py .......... [ 1%] 357s testsuite/MDAnalysisTests/analysis/test_dihedrals.py ................... [ 1%] 358s .... [ 1%] 368s testsuite/MDAnalysisTests/analysis/test_distances.py ............ [ 1%] 400s testsuite/MDAnalysisTests/analysis/test_encore.py .................X..X. [ 2%] 424s ..................................... [ 2%] 443s testsuite/MDAnalysisTests/analysis/test_gnm.py ...... [ 2%] 443s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py .............. [ 2%] 445s ................................ [ 2%] 445s testsuite/MDAnalysisTests/analysis/test_hole2.py ....sssssssssssssssssss [ 2%] 445s ssssssssssssssssssssssssssssssss [ 2%] 446s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py ...... [ 2%] 446s ......... [ 2%] 446s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py . [ 2%] 448s ................. [ 2%] 448s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py ...... [ 2%] 448s ...................................... [ 3%] 451s testsuite/MDAnalysisTests/analysis/test_leaflet.py s............ [ 3%] 451s testsuite/MDAnalysisTests/analysis/test_lineardensity.py ........ [ 3%] 455s testsuite/MDAnalysisTests/analysis/test_msd.py .......................ss [ 3%] 455s sssssssssssssssssssssssssssss [ 3%] 456s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py ................ [ 3%] 456s [ 3%] 457s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py .................... [ 3%] 457s .............. [ 3%] 460s testsuite/MDAnalysisTests/analysis/test_pca.py ......................... [ 3%] 461s ...................... [ 4%] 466s testsuite/MDAnalysisTests/analysis/test_persistencelength.py ........... [ 4%] 467s ....... [ 4%] 498s testsuite/MDAnalysisTests/analysis/test_psa.py ......................... [ 4%] 498s .................... [ 4%] 498s testsuite/MDAnalysisTests/analysis/test_rdf.py .................... [ 4%] 500s testsuite/MDAnalysisTests/analysis/test_rdf_s.py ..................... [ 4%] 503s testsuite/MDAnalysisTests/analysis/test_rms.py ......................... [ 4%] 508s ................ [ 4%] 508s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py ............... [ 4%] 508s ........... [ 4%] 508s testsuite/MDAnalysisTests/analysis/test_wbridge.py ..................... [ 5%] 509s ........................... [ 5%] 509s testsuite/MDAnalysisTests/auxiliary/test_core.py ..... [ 5%] 509s testsuite/MDAnalysisTests/auxiliary/test_edr.py .sssssssssssssssssssssss [ 5%] 509s ssssssssssssssssssssssssssssssssssssssssssss [ 5%] 509s testsuite/MDAnalysisTests/auxiliary/test_xvg.py ........................ [ 5%] 509s ........................................................................ [ 6%] 509s .... [ 6%] 509s testsuite/MDAnalysisTests/converters/test_base.py .. [ 6%] 509s testsuite/MDAnalysisTests/converters/test_rdkit.py .ssssssssssssssssssss [ 6%] 509s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 6%] 509s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 6%] 509s ssssssssssssssssssssssssssssss [ 7%] 509s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py ... [ 7%] 514s testsuite/MDAnalysisTests/coordinates/test_chainreader.py .............. [ 7%] 529s ....................................................... [ 7%] 530s testsuite/MDAnalysisTests/coordinates/test_copying.py .................. [ 7%] 543s ...............................................................ss.ss.s.s [ 7%] 560s s.sss....ss...s.ssss.ss.s.ss.sss....ss...s.ssss.ss.s.ss.sss....ss.s.ssss [ 8%] 570s .......................................................s [ 8%] 571s testsuite/MDAnalysisTests/coordinates/test_crd.py .............. [ 8%] 571s testsuite/MDAnalysisTests/coordinates/test_dcd.py ...................... [ 8%] 574s .......x.......ss....................................................... [ 9%] 577s ..........................................s [ 9%] 577s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py ................... [ 9%] 578s .................................... [ 9%] 579s testsuite/MDAnalysisTests/coordinates/test_dms.py ......... [ 9%] 579s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py .................. [ 9%] 579s ....... [ 9%] 579s testsuite/MDAnalysisTests/coordinates/test_gms.py .................. [ 9%] 581s testsuite/MDAnalysisTests/coordinates/test_gro.py ...................... [ 10%] 584s .......................sss.............................................. [ 10%] 584s ..............sss...................................................sss. [ 10%] 613s ..................................................sss................... [ 11%] 630s .................... [ 11%] 630s testsuite/MDAnalysisTests/coordinates/test_gsd.py ss.... [ 11%] 631s testsuite/MDAnalysisTests/coordinates/test_h5md.py ..................... [ 11%] 637s ..............ss........................................................ [ 11%] 654s .......x................................................... [ 12%] 655s testsuite/MDAnalysisTests/coordinates/test_lammps.py ................... [ 12%] 668s ........................................................................ [ 12%] 696s ............................................................ [ 12%] 700s testsuite/MDAnalysisTests/coordinates/test_memory.py ................... [ 13%] 715s ........x......xxx...................................................... [ 13%] 715s .......................... [ 13%] 715s testsuite/MDAnalysisTests/coordinates/test_mmtf.py ........... [ 13%] 717s testsuite/MDAnalysisTests/coordinates/test_mol2.py ..................... [ 13%] 717s [ 13%] 718s testsuite/MDAnalysisTests/coordinates/test_namdbin.py .................. [ 13%] 718s ..... [ 13%] 719s testsuite/MDAnalysisTests/coordinates/test_netcdf.py ................... [ 13%] 722s ........................................................................ [ 14%] 727s ........................................................................ [ 14%] 728s .................. [ 14%] 728s testsuite/MDAnalysisTests/coordinates/test_null.py . [ 14%] 730s testsuite/MDAnalysisTests/coordinates/test_pdb.py ...................... [ 14%] 770s ........................................................................ [ 15%] 776s ........................................................................ [ 15%] 777s ................ [ 15%] 777s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py ............... [ 15%] 779s testsuite/MDAnalysisTests/coordinates/test_pqr.py ...................... [ 15%] 779s ........ [ 15%] 779s testsuite/MDAnalysisTests/coordinates/test_reader_api.py ............... [ 16%] 779s ........................................................................ [ 16%] 780s ........................................................................ [ 16%] 780s ............................. [ 16%] 780s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py ............. [ 16%] 780s ........................................................................ [ 17%] 785s ........................................................................ [ 17%] 787s ................. [ 17%] 787s testsuite/MDAnalysisTests/coordinates/test_tng.py ..ssssssssssssssssssss [ 17%] 787s ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 18%] 787s s [ 18%] 788s testsuite/MDAnalysisTests/coordinates/test_trc.py ...................... [ 18%] 788s .......... [ 18%] 788s testsuite/MDAnalysisTests/coordinates/test_trj.py ...................... [ 18%] 789s .............. [ 18%] 790s testsuite/MDAnalysisTests/coordinates/test_trz.py ...................... [ 18%] 791s .. [ 18%] 791s testsuite/MDAnalysisTests/coordinates/test_txyz.py ...... [ 18%] 791s testsuite/MDAnalysisTests/coordinates/test_windows.py .................. [ 18%] 792s ................................................. [ 19%] 792s testsuite/MDAnalysisTests/coordinates/test_writer_api.py .ss............ [ 19%] 792s ......ss.....s............ss.....s........... [ 19%] 792s testsuite/MDAnalysisTests/coordinates/test_writer_registration.py .... [ 19%] 795s testsuite/MDAnalysisTests/coordinates/test_xdr.py ...................... [ 19%] 815s ........................................................................ [ 19%] 816s ....ss.................................................................. [ 20%] 817s .ss......................................................... [ 20%] 817s testsuite/MDAnalysisTests/coordinates/test_xyz.py ...................... [ 20%] 818s ...............ss....................................................... [ 21%] 819s .................ss....................................... [ 21%] 819s testsuite/MDAnalysisTests/core/test_accessors.py ssss..s [ 21%] 820s testsuite/MDAnalysisTests/core/test_accumulate.py ...................... [ 21%] 832s ................................................................... [ 21%] 836s testsuite/MDAnalysisTests/core/test_atom.py ................... [ 22%] 844s testsuite/MDAnalysisTests/core/test_atomgroup.py ....................... [ 22%] 863s ........................................................................ [ 22%] 865s ........................................................................ [ 22%] 884s ........................................................................ [ 23%] 914s ........................................................................ [ 23%] 932s ........................................................................ [ 24%] 939s .................................................... [ 24%] 940s testsuite/MDAnalysisTests/core/test_atomselections.py .................. [ 24%] 940s ........................................................................ [ 24%] 941s ........................................................................ [ 25%] 966s ..................sssssssssssssssssss................................... [ 25%] 968s ........................................................................ [ 25%] 968s ........................................................................ [ 26%] 970s ........................................................................ [ 26%] 981s .....................................sssss...........ssssss.... [ 26%] 981s testsuite/MDAnalysisTests/core/test_copying.py ......................... [ 27%] 981s .................... [ 27%] 984s testsuite/MDAnalysisTests/core/test_fragments.py ................ [ 27%] 984s testsuite/MDAnalysisTests/core/test_group_traj_access.py ............... [ 27%] 989s ................................................. [ 27%] 989s testsuite/MDAnalysisTests/core/test_groups.py .......................... [ 27%] 989s ........................................................................ [ 28%] 989s ........................................................................ [ 28%] 989s ........................................................................ [ 28%] 991s ........................................................................ [ 29%] 991s ........................................................................ [ 29%] 992s ........................................................................ [ 30%] 992s ........................................................................ [ 30%] 1013s ....................................................................... [ 30%] 1013s testsuite/MDAnalysisTests/core/test_index_dtype.py ............... [ 30%] 1013s testsuite/MDAnalysisTests/core/test_requires.py .... [ 30%] 1014s testsuite/MDAnalysisTests/core/test_residue.py .... [ 30%] 1017s testsuite/MDAnalysisTests/core/test_residuegroup.py s..................s [ 30%] 1018s ssss..... [ 31%] 1018s testsuite/MDAnalysisTests/core/test_segment.py ....... [ 31%] 1019s testsuite/MDAnalysisTests/core/test_segmentgroup.py ........... [ 31%] 1020s testsuite/MDAnalysisTests/core/test_topology.py ........................ [ 31%] 1020s ........................................ [ 31%] 1020s testsuite/MDAnalysisTests/core/test_topologyattrs.py ................... [ 31%] 1020s ................................................................x....... [ 31%] 1022s ..................................................... [ 32%] 1022s testsuite/MDAnalysisTests/core/test_topologyobjects.py ................. [ 32%] 1028s ...................................................................... [ 32%] 1030s testsuite/MDAnalysisTests/core/test_universe.py .................sssssss [ 32%] 1037s s....................................................................... [ 33%] 1044s ........................................................................ [ 33%] 1046s ........................................................................ [ 33%] 1049s .................. [ 34%] 1050s testsuite/MDAnalysisTests/core/test_unwrap.py .......................... [ 34%] 1050s ........................................................................ [ 34%] 1051s ........................................................................ [ 34%] 1051s ........................................................................ [ 35%] 1052s ........................................................................ [ 35%] 1052s ........................................................................ [ 36%] 1052s ........................................................................ [ 36%] 1053s ................................................... [ 36%] 1057s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py .............. [ 36%] 1057s . [ 36%] 1057s testsuite/MDAnalysisTests/core/test_wrap.py ............................ [ 36%] 1057s ........................................................................ [ 37%] 1058s ........................................................................ [ 37%] 1058s ........................................................................ [ 37%] 1059s ........................................................................ [ 38%] 1059s ........................................................................ [ 38%] 1059s ........................................................................ [ 39%] 1061s ......................................................... [ 39%] 1061s testsuite/MDAnalysisTests/formats/test_libdcd.py ....................... [ 39%] 1062s ........................................................................ [ 39%] 1062s ...... [ 39%] 1062s testsuite/MDAnalysisTests/formats/test_libmdaxdr.py .................... [ 40%] 1063s ........................................................................ [ 40%] 1063s ... [ 40%] 1066s testsuite/MDAnalysisTests/import/test_import.py .. [ 40%] 1066s testsuite/MDAnalysisTests/lib/test_augment.py .......................... [ 40%] 1066s .......... [ 40%] 1066s testsuite/MDAnalysisTests/lib/test_cutil.py ............. [ 40%] 1066s testsuite/MDAnalysisTests/lib/test_distances.py ........................ [ 40%] 1067s ........................................................................ [ 41%] 1067s ........................................................................ [ 41%] 1067s ........................................................................ [ 41%] 1068s ........................................................................ [ 42%] 1068s ........................................................................ [ 42%] 1068s ........................................................................ [ 43%] 1077s ........................................................................ [ 43%] 1080s ........................................................................ [ 43%] 1080s ........................................................................ [ 44%] 1081s ........................................................................ [ 44%] 1082s ........................................................................ [ 44%] 1082s ........................................................................ [ 45%] 1082s ........................................................................ [ 45%] 1082s ........................................................................ [ 46%] 1082s ........................................................................ [ 46%] 1082s ........................................................................ [ 46%] 1082s ........................................................................ [ 47%] 1083s ........................................................................ [ 47%] 1083s ........................................................................ [ 47%] 1083s ........................................................................ [ 48%] 1083s ........................................................................ [ 48%] 1083s ........................................................................ [ 49%] 1083s ........................................................................ [ 49%] 1083s ........................................................................ [ 49%] 1083s ........................................................................ [ 50%] 1084s ........................................................................ [ 50%] 1084s ........................................................................ [ 50%] 1084s ........................................................................ [ 51%] 1084s ........................................................................ [ 51%] 1084s ........................................................................ [ 52%] 1084s ........................................................................ [ 52%] 1084s ........................................................................ [ 52%] 1085s ........................................................................ [ 53%] 1085s ........................................................................ [ 53%] 1085s .............................................. [ 53%] 1085s testsuite/MDAnalysisTests/lib/test_log.py ... [ 53%] 1086s testsuite/MDAnalysisTests/lib/test_neighborsearch.py .. [ 53%] 1093s testsuite/MDAnalysisTests/lib/test_nsgrid.py ........................... [ 53%] 1094s ..s [ 53%] 1094s testsuite/MDAnalysisTests/lib/test_pkdtree.py ................. [ 54%] 1094s testsuite/MDAnalysisTests/lib/test_qcprot.py .... [ 54%] 1094s testsuite/MDAnalysisTests/lib/test_util.py ............................. [ 54%] 1095s ........................................................................ [ 54%] 1095s ........................................................................ [ 54%] 1095s ........................................................................ [ 55%] 1095s ........................................................................ [ 55%] 1095s ........................................................................ [ 56%] 1095s ........................................................................ [ 56%] 1095s ........................................................................ [ 56%] 1095s ........................................................................ [ 57%] 1096s ........................................................................ [ 57%] 1096s ........................................................................ [ 57%] 1096s ........................................................................ [ 58%] 1096s ........................................................................ [ 58%] 1096s ........................................................................ [ 59%] 1096s ........................................................................ [ 59%] 1096s ........................................................................ [ 59%] 1096s ........................................................................ [ 60%] 1096s ........................................................................ [ 60%] 1096s ........................................................................ [ 60%] 1096s ........................................................................ [ 61%] 1097s ........................................................................ [ 61%] 1097s ........................................................................ [ 62%] 1097s ........................................................................ [ 62%] 1097s ........................................................................ [ 62%] 1097s ........................................................................ [ 63%] 1097s ........................................................................ [ 63%] 1097s ........................................................................ [ 63%] 1097s ........................................................................ [ 64%] 1097s ........................................................................ [ 64%] 1098s ........................................................................ [ 65%] 1098s ........................................................................ [ 65%] 1098s ........................................................................ [ 65%] 1098s ........................................................................ [ 66%] 1098s ........................................................................ [ 66%] 1098s ........................................................................ [ 66%] 1098s ........................................................................ [ 67%] 1098s ........................................................................ [ 67%] 1098s ........................................................................ [ 68%] 1098s ........................................................................ [ 68%] 1099s ........................................................................ [ 68%] 1099s ........................................................................ [ 69%] 1099s ........................................................................ [ 69%] 1099s ........................................................................ [ 69%] 1099s ........................................................................ [ 70%] 1099s ........................................................................ [ 70%] 1099s ........................................................................ [ 71%] 1099s ........................................................................ [ 71%] 1099s ........................................................................ [ 71%] 1099s ........................................................................ [ 72%] 1100s ........................................................................ [ 72%] 1100s ........................................................................ [ 72%] 1100s ........................................................................ [ 73%] 1100s ........................................................................ [ 73%] 1100s ........................................................................ [ 74%] 1100s ........................................................................ [ 74%] 1100s ........................................................................ [ 74%] 1100s ........................................................................ [ 75%] 1100s ........................................................................ [ 75%] 1100s ........................................................................ [ 75%] 1100s ........................................................................ [ 76%] 1100s ........................................................................ [ 76%] 1101s ........................................................................ [ 77%] 1101s ........................................................................ [ 77%] 1101s ........................................................................ [ 77%] 1101s ........................................................................ [ 78%] 1101s ........................................................................ [ 78%] 1101s ........................................................................ [ 78%] 1101s ........................................................................ [ 79%] 1101s ........................................................................ [ 79%] 1101s ........................................................................ [ 80%] 1101s ........................................................................ [ 80%] 1102s ........................................................................ [ 80%] 1103s ........................................................................ [ 81%] 1103s ........................................................................ [ 81%] 1103s ........................................................................ [ 81%] 1103s ........................................................................ [ 82%] 1103s ........................................................................ [ 82%] 1103s ........................................................................ [ 83%] 1103s ........................................................................ [ 83%] 1103s ........................................................................ [ 83%] 1104s .........................................s.............................. [ 84%] 1104s ........................................................................ [ 84%] 1105s .............s.......................................................... [ 84%] 1114s ........................................................................ [ 85%] 1114s .................................................. [ 85%] 1117s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py .......... [ 85%] 1149s ....................................... [ 85%] 1150s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py .... [ 85%] 1150s .... [ 85%] 1150s testsuite/MDAnalysisTests/test_api.py ............................ [ 86%] 1161s testsuite/MDAnalysisTests/topology/test_altloc.py ... [ 86%] 1161s testsuite/MDAnalysisTests/topology/test_crd.py ........ [ 86%] 1162s testsuite/MDAnalysisTests/topology/test_dlpoly.py ...................... [ 86%] 1162s .......................................... [ 86%] 1164s testsuite/MDAnalysisTests/topology/test_dms.py .................... [ 86%] 1164s testsuite/MDAnalysisTests/topology/test_fhiaims.py ............ [ 86%] 1164s testsuite/MDAnalysisTests/topology/test_gms.py ......................... [ 86%] 1164s ..... [ 86%] 1168s testsuite/MDAnalysisTests/topology/test_gro.py ............... [ 86%] 1168s testsuite/MDAnalysisTests/topology/test_gsd.py ......................... [ 86%] 1169s ...... [ 86%] 1169s testsuite/MDAnalysisTests/topology/test_guessers.py .................... [ 87%] 1169s ..............ssssssssss [ 87%] 1169s testsuite/MDAnalysisTests/topology/test_hoomdxml.py .................. [ 87%] 1170s testsuite/MDAnalysisTests/topology/test_itp.py ......................... [ 87%] 1170s ........................................................................ [ 87%] 1170s .......................... [ 87%] 1175s testsuite/MDAnalysisTests/topology/test_lammpsdata.py .................. [ 88%] 1176s ........................................................................ [ 88%] 1177s ....................................................... [ 88%] 1177s testsuite/MDAnalysisTests/topology/test_minimal.py ..................... [ 88%] 1177s ........... [ 88%] 1177s testsuite/MDAnalysisTests/topology/test_mmtf.py ........................ [ 88%] 1178s ...................................................... [ 89%] 1178s testsuite/MDAnalysisTests/topology/test_mol2.py ........................ [ 89%] 1178s ....... [ 89%] 1184s testsuite/MDAnalysisTests/topology/test_pdb.py ......................... [ 89%] 1184s .......................... [ 89%] 1184s testsuite/MDAnalysisTests/topology/test_pdbqt.py ......... [ 89%] 1185s testsuite/MDAnalysisTests/topology/test_pqr.py .................... [ 89%] 1193s testsuite/MDAnalysisTests/topology/test_psf.py ......................... [ 89%] 1196s ....................................... [ 90%] 1197s testsuite/MDAnalysisTests/topology/test_top.py ......................... [ 90%] 1202s ........................................................................ [ 90%] 1203s ........................................................................ [ 91%] 1203s ........... [ 91%] 1203s testsuite/MDAnalysisTests/topology/test_topology_base.py ... [ 91%] 1204s testsuite/MDAnalysisTests/topology/test_topology_str_types.py .......... [ 91%] 1214s ........................................................................ [ 91%] 1215s .................. [ 91%] 1220s testsuite/MDAnalysisTests/topology/test_tprparser.py ................... [ 91%] 1228s ........................................................................ [ 92%] 1237s ........................................................................ [ 92%] 1245s ........................................................................ [ 92%] 1254s ........................................................................ [ 93%] 1261s ........................................................................ [ 93%] 1261s ........................................................................ [ 93%] 1261s ........................................................................ [ 94%] 1261s ........................................................................ [ 94%] 1262s ........................................................................ [ 95%] 1262s ........................................................................ [ 95%] 1263s ........................................................................ [ 95%] 1265s ...................................... [ 96%] 1265s testsuite/MDAnalysisTests/topology/test_txyz.py ...................... [ 96%] 1265s testsuite/MDAnalysisTests/topology/test_xpdb.py ........ [ 96%] 1266s testsuite/MDAnalysisTests/topology/test_xyz.py ........................ [ 96%] 1266s testsuite/MDAnalysisTests/transformations/test_base.py ..... [ 96%] 1266s testsuite/MDAnalysisTests/transformations/test_boxdimensions.py ........ [ 96%] 1266s ...... [ 96%] 1266s testsuite/MDAnalysisTests/transformations/test_fit.py .................. [ 96%] 1266s ......................................... [ 96%] 1269s testsuite/MDAnalysisTests/transformations/test_nojump.py ............ [ 96%] 1269s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py .... [ 96%] 1269s . [ 96%] 1269s testsuite/MDAnalysisTests/transformations/test_rotate.py ............... [ 96%] 1269s ............................ [ 97%] 1269s testsuite/MDAnalysisTests/transformations/test_translate.py ............ [ 97%] 1269s ............ [ 97%] 1280s testsuite/MDAnalysisTests/transformations/test_wrap.py ................. [ 97%] 1280s ....... [ 97%] 1280s testsuite/MDAnalysisTests/utils/test_authors.py . [ 97%] 1280s testsuite/MDAnalysisTests/utils/test_datafiles.py .... [ 97%] 1280s testsuite/MDAnalysisTests/utils/test_duecredit.py .............. [ 97%] 1280s testsuite/MDAnalysisTests/utils/test_failure.py . [ 97%] 1280s testsuite/MDAnalysisTests/utils/test_imports.py ........................ [ 97%] 1281s ........................................................................ [ 97%] 1281s ........................................................................ [ 98%] 1281s ................... [ 98%] 1281s testsuite/MDAnalysisTests/utils/test_log.py . [ 98%] 1281s testsuite/MDAnalysisTests/utils/test_meta.py .... [ 98%] 1282s testsuite/MDAnalysisTests/utils/test_modelling.py ............. [ 98%] 1283s testsuite/MDAnalysisTests/utils/test_persistence.py ....... [ 98%] 1307s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%] 1307s ..............ss.. [ 98%] 1307s testsuite/MDAnalysisTests/utils/test_qcprot.py ...... [ 98%] 1310s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%] 1310s [ 98%] 1311s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 98%] 1311s ............... [ 99%] 1311s testsuite/MDAnalysisTests/utils/test_transformations.py ................ [ 99%] 1311s ........................................................................ [ 99%] 1311s ........................................................ [ 99%] 1311s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%] 1311s ....... [ 99%] 1312s testsuite/MDAnalysisTests/visualization/test_streamlines.py ... [100%] 1312s 1312s =============================== warnings summary =============================== 1312s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39 1312s /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. 1312s 1312s Due to the on going maintenance burden of keeping command line application 1312s wrappers up to date, we have decided to deprecate and eventually remove these 1312s modules. 1312s 1312s We instead now recommend building your command line and invoking it directly 1312s with the subprocess module. 1312s warnings.warn( 1312s 1312s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings 1312s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings 1312s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings 1312s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings 1312s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings 1312s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings 1312s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings 1312s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings 1312s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings 1312s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings 1312s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings 1312s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings 1312s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1312s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings 1312s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings 1312s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings 1312s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings 1312s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings 1312s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings 1312s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings 1312s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings 1312s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings 1312s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings 1312s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings 1312s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings 1312s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings 1312s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1312s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings 1312s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1312s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings 1312s /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. 1312s warnings.warn("DCDReader currently makes independent timesteps" 1312s 1312s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 1312s /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. 1312s warnings.warn(wmsg, category=DeprecationWarning) 1312s 1312s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings 1312s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written 1312s warnings.warn(wmsg) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings 1312s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings 1312s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings 1312s /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 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings 1312s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1312s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings 1312s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning 1312s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'hc', 'oh', 'h1', 'c3', 'ho'}. These have been given an empty element record. 1312s warnings.warn("Unknown elements found for some " 1312s 1312s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning 1312s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings 1312s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings 1312s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1312s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings 1312s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings 1312s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps 1312s self.times[i] = ts.time 1312s 1312s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning 1312s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings 1312s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1312s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings 1312s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings 1312s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings 1312s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded 1312s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps 1312s results.append((ts.time, x.sum() / mask.sum())) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue 1312s /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. 1312s warnings.warn(msg) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1312s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding 1312s /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 1312s warnings.warn(msg) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1312s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1312s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1312s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings 1312s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning 1312s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings 1312s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings 1312s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings 1312s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1312s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings 1312s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings 1312s /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. 1312s warnings.warn("Element information is missing, elements attribute " 1312s 1312s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran 1312s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame 1312s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections 1312s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues 1312s warnings.warn("Cannot determine phi and psi angles for the first " 1312s 1312s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin 1312s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr 1312s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame 1312s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot 1312s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning 1312s /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. 1312s warnings.warn(f"All residues selected with '{select_remove}' " 1312s 1312s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings 1312s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings 1312s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=5896) is multi-threaded, use of fork() may lead to deadlocks in the child. 1312s self.pid = os.fork() 1312s 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes 1312s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide 1312s cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms 1312s 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide 1312s local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1312s /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice 1312s ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1312s /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide 1312s ret = um.true_divide( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1312s /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide 1312s ret = ret.dtype.type(ret / rcount) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1312s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning 1312s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning 1312s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1312s /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. 1312s warnings.warn("1 A^3 CRYST1 record," 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. 1312s warnings.warn("Unit cell dimensions not found. " 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings 1312s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings 1312s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings 1312s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1312s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings 1312s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1312s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning 1312s /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 1312s warnings.warn(wmsg, DeprecationWarning) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 1312s warnings.warn("Desired number of sample points too high, using {0}" 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbond = HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbond = HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbond = HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbond = HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbond = HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbond = HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbond = HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbond = HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s HBAC( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1312s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1312s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbond = HBAC(u, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1312s `find_hydrogen_donors` will be removed in release 3.0.0. 1312s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s D = hbonds.find_hydrogen_donors(H) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1312s `find_hydrogen_donors` will be removed in release 3.0.0. 1312s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1312s hbonds.find_hydrogen_donors(u.atoms) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1312s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1312s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. 1312s return _methods._mean(a, axis=axis, dtype=dtype, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1312s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1312s /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide 1312s ret = ret.dtype.type(ret / rcount) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1312s /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. 1312s warnings.warn(msg.format(sel)) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1312s /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. 1312s warnings.warn(msg.format(sel)) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1312s /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. 1312s warnings.warn(msg.format(sel)) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. 1312s warnings.warn("Empty string to select atoms, empty group returned.", 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1312s /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, . 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1312s /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, . 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1312s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1312s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1312s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1312s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1312s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1312s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple 1312s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content 1312s /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. 1312s warnings.warn(wmsg) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning 1312s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning 1312s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1312s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1312s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1312s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1312s /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.) 1312s phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi 1312s 1312s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j 1312s /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 1312s warnings.warn("Column index entered (j = {:d} is smaller than row " 1312s 1312s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps 1312s dt=self.trajectory.ts.dt * step, 1312s 1312s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] 1312s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] 1312s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] 1312s /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 1312s warnings.warn(wmsg, DeprecationWarning) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1312s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings 1312s /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. 1312s warnings.warn("The `u` attribute is superflous and will be removed " 1312s 1312s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] 1312s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm 1312s /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. 1312s warnings.warn("The `density` attribute was deprecated in " 1312s 1312s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata 1312s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. 1312s warnings.warn(msg, category=MissingDataWarning) 1312s 1312s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps 1312s self.timesteps.append(self._ts.time) 1312s 1312s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning 1312s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default 1312s warnings.warn("{} does not support time selection. Reverting to " 1312s 1312s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default 1312s warnings.warn("{} does not support data selection. Reverting to " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1312s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings 1312s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps 1312s return self.ts.dt 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1312s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps 1312s ts.data['time'] = step_num * ts.dt 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_istart[2] 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDWriterWithRealTrajectory::test_write_trajectory[True-False-False] 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1312s self.close() 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close 1312s self._apply('close') 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply 1312s return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] 1312s ^^^^^^^^^^^^ 1312s AttributeError: 'ChainReader' object has no attribute 'readers' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing 1312s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain 1312s warnings.warn("Missing frame in continuous chain", UserWarning) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps 1312s time_frame_0 = ts.time - ts.frame*ts.dt # assumes ts.dt is constant 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps 1312s frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps 1312s step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps 1312s self._add_step_to_frame_data(ts.time) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps 1312s if not np.allclose(A.time, B.time): 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] 1312s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array 1312s /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 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1312s self.close() 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close 1312s self._file.close() 1312s ^^^^^^^^^^ 1312s AttributeError: 'DCDReader' object has no attribute '_file' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms 1312s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit 1312s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__ 1312s self.close() 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close 1312s self._file.close() 1312s ^^^^^^^^^^ 1312s AttributeError: 'DCDWriter' object has no attribute '_file' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings 1312s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings 1312s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1312s /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. 1312s warnings.warn(msg) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps 1312s return self.ts.time 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps 1312s assert_equal(reader.ts.dt, reader.dt) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps 1312s time_frame = time_frame_0 + frame_index*ts.dt 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps 1312s reader_p = pickle.loads(pickle.dumps(reader)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings 1312s /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 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] 1312s warnings.warn(wmsg) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1312s /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`. 1312s warnings.warn(wmsg) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. 1312s warnings.warn("Not all velocities were present. " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps 1312s reader_p = pickle.loads(pickle.dumps(reader)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader 1312s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps 1312s reader_p = pickle.loads(pickle.dumps(reader)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1312s self.close() 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close 1312s self._file.close() 1312s ^^^^^^^^^^ 1312s AttributeError: 'H5MDReader' object has no attribute '_file' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1312s for aux in self.aux_list: 1312s ^^^^^^^^^^^^^ 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1312s return self._auxs.keys() 1312s ^^^^^^^^^^ 1312s AttributeError: 'H5MDReader' object has no attribute '_auxs' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1312s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 1312s warnings.warn('Guessed all Masses to 1.0') 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit 1312s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1312s for aux in self.aux_list: 1312s ^^^^^^^^^^^^^ 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1312s return self._auxs.keys() 1312s ^^^^^^^^^^ 1312s AttributeError: 'DCDReader' object has no attribute '_auxs' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view 1312s /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 1312s warnings.warn("MemoryReader.timeseries inclusive `stop` " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader 1312s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps 1312s reader_p = pickle.loads(pickle.dumps(reader)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1312s /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 1312s warnings.warn(wmsg) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps 1312s ts.time) # in-place ! (hope this works...) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps 1312s time_list = [ts.time for ts in u.trajectory] 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps 1312s assert u.trajectory.ts.dt == pytest.approx(ref) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/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.) 1312s return self._test_write_trajectory(universe, outfile) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] 1312s /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. 1312s warnings.warn(wmsg) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/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.) 1312s return self._test_write_trajectory(universe, outfile) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 1312s warnings.warn("Found missing chainIDs." 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom] 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond] 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom] 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree] 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond] 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom] 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps 1312s time = ts.time 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1312s self.close() 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close 1312s if self.trjfile is not None: 1312s ^^^^^^^^^^^^ 1312s AttributeError: 'NCDFWriter' object has no attribute 'trjfile' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' 1312s warnings.warn("Found no information for attr: '{}'" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' 1312s warnings.warn("Found chainIDs using unnaccepted character." 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' 1312s warnings.warn("Found chainIDs with invalid length." 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed 1312s warnings.warn("Serial numbers went over 100,000. " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed 1312s warnings.warn("Invalid atom serials were present, bonds will not" 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed 1312s warnings.warn("Invalid atom serials were present, " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment 1312s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1312s /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. 1312s warnings.warn(wmsg) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1312s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1312s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1312s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1312s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges 1312s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps 1312s assert_equal(ts.dt, 1.0) # default value 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps 1312s assert_equal(ts.time, 0.0) # default to 1.0 (dt) * 0 (frame) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps 1312s assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1312s for aux in self.aux_list: 1312s ^^^^^^^^^^^^^ 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1312s return self._auxs.keys() 1312s ^^^^^^^^^^ 1312s AttributeError: 'TNGReader' object has no attribute '_auxs' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms 1312s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe 1312s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe 1312s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1312s self.close() 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close 1312s if self.trjfile is None: 1312s ^^^^^^^^^^^^ 1312s AttributeError: 'TRJReader' object has no attribute 'trjfile' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps 1312s data['time'] = ts.time 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1312s /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 1312s warnings.warn("Timestep didn't have the following attributes: '{0}', " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1312s /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. 1312s warnings.warn("Timestep didn't have velocity information, " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1312s /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 1312s warnings.warn("Timestep didn't have dimensions information, " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1312s self.close() 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close 1312s if self.trzfile is None: 1312s ^^^^^^^^^^^^ 1312s AttributeError: 'TRZWriter' object has no attribute 'trzfile' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1312s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1312s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1312s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1312s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1312s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1312s /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. 1312s warnings.warn("Element information is missing, elements attribute " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1312s /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 1312s warnings.warn(wmsg, DeprecationWarning) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] 1312s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] 1312s /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' 1312s warnings.warn(wmsg) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD 1312s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps 1312s time = ts.time 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD 1312s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps 1312s time = ts.time 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1312s self.close() 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1312s self._xdr.close() 1312s ^^^^^^^^^ 1312s AttributeError: 'XTCWriter' object has no attribute '_xdr' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container 1312s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1312s 1312s Traceback (most recent call last): 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1312s self.close() 1312s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1312s self._xdr.close() 1312s ^^^^^^^^^ 1312s AttributeError: 'TRRWriter' object has no attribute '_xdr' 1312s 1312s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1312s /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. 1312s Consider setting 'refresh_offsets=True' when loading your Universe. 1312s warnings.warn(f"Reading offsets from {fname} failed, " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly 1312s /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. 1312s warnings.warn(f"Cannot write lock/offset file in same location as " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1312s /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. 1312s Consider setting 'refresh_offsets=True' when loading your Universe. 1312s warnings.warn(f"Reading offsets from {fname} failed, " 1312s 1312s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly 1312s /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. 1312s warnings.warn(f"Cannot write lock/offset file in same location as " 1312s 1312s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] 1312s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] 1312s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] 1312s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce 1312s return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1312s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1312s /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. 1312s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings 1312s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings 1312s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings 1312s /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. 1312s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1312s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1312s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide 1312s return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() 1312s 1312s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings 1312s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide 1312s _centers /= _weights.sum(axis=1)[:, None] 1312s 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1312s /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`. 1312s warnings.warn(msg, category=SelectionWarning) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1312s /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`. 1312s warnings.warn(msg, category=SelectionWarning) 1312s 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] 1312s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] 1312s /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`. 1312s warnings.warn(msg, category=SelectionWarning) 1312s 1312s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] 1312s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] 1312s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] 1312s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] 1312s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] 1312s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc 1312s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc 1312s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options 1312s /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 1312s warnings.warn("The 'pbc' kwarg has been deprecated and will be " 1312s 1312s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel 1312s /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`. 1312s warnings.warn(msg, category=SelectionWarning) 1312s 1312s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] 1312s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] 1312s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] 1312s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] 1312s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] 1312s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide 1312s x = np.dot(a, b) / (norm(a) * norm(b)) 1312s 1312s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt 1312s ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) 1312s 1312s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt 1312s box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - 1312s 1312s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide 1312s a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) 1312s 1312s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide 1312s b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) 1312s 1312s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide 1312s c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) 1312s 1312s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide 1312s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1312s 1312s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide 1312s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1312s 1312s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 1312s /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps 1312s cls(buf, protocol).dump(obj) 1312s 1312s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps 1312s ps = pickle.dumps(ref_reader) 1312s 1312s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] 1312s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd 1312s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd 1312s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset 1312s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific 1312s /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. 1312s warnings.warn('Cannot average position for non sequential' 1312s 1312s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name] 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname] 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type] 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid] 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' 1312s warnings.warn("PDB file is missing resid information. " 1312s 1312s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX 1312s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1312s 1312s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2] 1312s /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. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2] 1312s /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. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2] 1312s /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. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2] 1312s /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. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1312s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings 1312s /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. 1312s warnings.warn(msg) 1312s 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts 1312s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr] 1312s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file. 1312s warnings.warn('No coordinate reader found for {}. Skipping ' 1312s 1312s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses 1312s /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. 1312s warnings.warn(msg, category=SelectionWarning) 1312s 1312s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 1312s /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. 1312s warnings.warn( 1312s 1312s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps 1312s return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1312s 1312s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps 1312s pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1312s 1312s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps 1312s return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL) 1312s 1312s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps 1312s return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL) 1312s 1312s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps 1312s return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL) 1312s 1312s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps 1312s pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL) 1312s 1312s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag 1312s /tmp/autopkgtest.fEu9Gl/build.v4n/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps 1312s pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL) 1312s 1312s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings 1312s /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream 1312s warnings.warn("Constructed NamedStream from a NamedStream", 1312s 1312s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] 1312s /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. 1312s warnings.warn(wmsg, DeprecationWarning) 1312s 1312s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1312s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8131 warnings in 1020.21s (0:17:00) = 1334s 1334s DueCredit Report: 1334s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] 1334s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] 1334s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] 1334s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] 1334s - HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] 1334s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] 1334s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] 1334s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] 1334s - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] 1334s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] 1334s - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] 1334s - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 2.7.0, 1.1) [15, 16] 1334s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] 1334s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] 1334s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] 1334s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] 1334s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] 1334s - Scientific tools library / numpy (v 1.26.4) [22] 1334s 1334s 2 packages cited 1334s 16 modules cited 1334s 0 functions cited 1334s 1334s References 1334s ---------- 1334s 1334s [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. 1334s [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. 1334s [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. 1334s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 1334s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 1334s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460. 1334s [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. 1334s [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. 1334s [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. 1334s [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). 1334s [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. 1334s [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. 1334s [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. 1334s [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. 1334s [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. 1334s [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. 1334s [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. 1334s [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. 1334s [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. 1334s [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. 1334s [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. 1334s [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. 1337s autopkgtest [04:04:55]: test test-mdanalysis: -----------------------] 1337s test-mdanalysis PASS 1337s autopkgtest [04:04:55]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 1338s autopkgtest [04:04:56]: @@@@@@@@@@@@@@@@@@@@ summary 1338s test-mdanalysis PASS 1342s nova [W] Using flock in prodstack6-ppc64el 1342s Creating nova instance adt-plucky-ppc64el-mdanalysis-20241115-034238-juju-7f2275-prod-proposed-migration-environment-15-57d586e8-fc89-41f5-8c61-6444bb04c9e3 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...