0s autopkgtest [15:20:53]: starting date and time: 2024-12-02 15:20:53+0000 0s autopkgtest [15:20:53]: git checkout: be626eda Fix armhf LXD image generation for plucky 0s autopkgtest [15:20:53]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gdbu_dwp/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-hypothesis --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-hypothesis/6.122.1-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-7.secgroup --name adt-plucky-ppc64el-mdanalysis-20241202-152052-juju-7f2275-prod-proposed-migration-environment-15-069d8757-381a-4cd4-b5d1-99a9a32145cd --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/ 114s autopkgtest [15:22:47]: testbed dpkg architecture: ppc64el 114s autopkgtest [15:22:47]: testbed apt version: 2.9.14ubuntu1 114s autopkgtest [15:22:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 114s autopkgtest [15:22:47]: testbed release detected to be: None 115s autopkgtest [15:22:48]: updating testbed package index (apt update) 115s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 116s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 116s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 116s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 116s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [68.5 kB] 116s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 116s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB] 116s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [782 kB] 116s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [95.9 kB] 116s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [928 B] 116s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [671 kB] 116s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [11.0 kB] 116s Fetched 1728 kB in 1s (1785 kB/s) 117s Reading package lists... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s autopkgtest [15:22:52]: upgrading testbed (apt dist-upgrade and autopurge) 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 119s Starting 2 pkgProblemResolver with broken count: 0 119s Done 120s Entering ResolveByKeep 120s 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s autopkgtest [15:22:56]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 123s autopkgtest [15:22:56]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 127s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (dsc) [2885 B] 127s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (tar) [47.0 MB] 127s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (diff) [10.9 kB] 127s gpgv: Signature made Fri Nov 15 13:40:58 2024 UTC 127s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 127s gpgv: Can't check signature: No public key 127s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5build1.dsc: no acceptable signature found 129s autopkgtest [15:23:02]: testing package mdanalysis version 2.7.0-5build1 129s autopkgtest [15:23:02]: build not needed 135s autopkgtest [15:23:08]: test test-mdanalysis: preparing testbed 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s Starting pkgProblemResolver with broken count: 0 136s Starting 2 pkgProblemResolver with broken count: 0 136s Done 136s The following NEW packages will be installed: 136s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 136s cpp-14-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cython3 debhelper 136s debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common 136s dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 136s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 136s g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14 136s gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext 136s intltool-debian libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 136s libcc1-0 libdebhelper-perl libdeflate0 libexpat1-dev 136s libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libgcc-14-dev 136s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 136s libhdf5-hl-100t64 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 136s libjpeg8 libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc 136s libjs-underscore libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 136s liblsan0 liblzf1 libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 136s libpython3-all-dev libpython3-dev libpython3.12-dev libqhull-r8.0 136s libquadmath0 libraqm0 libsharpyuv0 libstdc++-14-dev libsz2 libtcl8.6 136s libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2 136s libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 136s libxss1 m4 po-debconf pybuild-plugin-pyproject python-matplotlib-data 136s python-mdanalysis-doc python3-alabaster python3-all python3-all-dev 136s python3-appdirs python3-biopython python3-brotli python3-build python3-cairo 136s python3-cftime python3-citeproc python3-contourpy python3-cycler 136s python3-dateutil python3-decorator python3-defusedxml python3-dev 136s python3-docutils python3-duecredit python3-fasteners python3-fonttools 136s python3-freetype python3-fs python3-griddataformats python3-gsd python3-h5py 136s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 136s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 136s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 136s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 136s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 136s python3-netcdf4 python3-networkx python3-numpy python3-packaging 136s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 136s python3-pluggy python3-pybtex python3-pybtex-docutils 136s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 136s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 136s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 136s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 136s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 136s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 136s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 136s python3.12-tk python3.13-tk sphinx-common sphinx-rtd-theme-common 136s tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 136s xfonts-utils zlib1g-dev 137s 0 upgraded, 200 newly installed, 0 to remove and 0 not upgraded. 137s Need to get 214 MB of archives. 137s After this operation, 1034 MB of additional disk space will be used. 137s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-lato all 2.015-1 [2781 kB] 138s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el m4 ppc64el 1.4.19-4build1 [278 kB] 138s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el autoconf all 2.72-3 [382 kB] 138s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el autotools-dev all 20220109.1 [44.9 kB] 138s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] 138s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el autopoint all 0.22.5-2 [616 kB] 138s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.15+dfsg-2 [1201 kB] 138s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 138s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 138s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 138s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 138s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 138s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 138s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 139s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB] 139s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB] 139s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 139s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 139s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 139s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.15-1 [942 kB] 139s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-7build1 [784 kB] 139s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el blt ppc64el 2.5.3+dfsg-7build1 [4840 B] 139s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libisl23 ppc64el 0.27-1 [882 kB] 139s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libmpc3 ppc64el 1.3.1-1build2 [62.1 kB] 139s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [10.5 MB] 139s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14 ppc64el 14.2.0-8ubuntu1 [1034 B] 139s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [5456 B] 139s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp ppc64el 4:14.1.0-2ubuntu1 [22.5 kB] 139s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcc1-0 ppc64el 14.2.0-8ubuntu1 [48.1 kB] 139s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 139s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libitm1 ppc64el 14.2.0-8ubuntu1 [31.9 kB] 139s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasan8 ppc64el 14.2.0-8ubuntu1 [2945 kB] 139s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsan0 ppc64el 14.2.0-8ubuntu1 [1322 kB] 139s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtsan2 ppc64el 14.2.0-8ubuntu1 [2695 kB] 140s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libubsan1 ppc64el 14.2.0-8ubuntu1 [1191 kB] 140s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libquadmath0 ppc64el 14.2.0-8ubuntu1 [158 kB] 140s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-14-dev ppc64el 14.2.0-8ubuntu1 [1619 kB] 140s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [20.6 MB] 141s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14 ppc64el 14.2.0-8ubuntu1 [528 kB] 141s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [1222 B] 141s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc ppc64el 4:14.1.0-2ubuntu1 [5006 B] 141s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++-14-dev ppc64el 14.2.0-8ubuntu1 [2673 kB] 141s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [12.0 MB] 141s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14 ppc64el 14.2.0-8ubuntu1 [19.9 kB] 141s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [968 B] 141s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++ ppc64el 4:14.1.0-2ubuntu1 [1090 B] 141s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 141s Get:48 http://ftpmaster.internal/ubuntu plucky/universe ppc64el cython3 ppc64el 3.0.11+dfsg-1ubuntu2 [3263 kB] 141s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 141s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtool all 2.4.7-8 [166 kB] 141s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-autoreconf all 20 [16.1 kB] 141s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 141s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 141s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-strip-nondeterminism all 1.14.0-1 [5058 B] 141s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el debugedit ppc64el 1:5.1-1 [52.1 kB] 142s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el dwz ppc64el 0.15-1build6 [142 kB] 142s Get:57 http://ftpmaster.internal/ubuntu plucky/main ppc64el gettext ppc64el 0.22.5-2 [1082 kB] 142s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] 142s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] 142s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el debhelper all 13.20ubuntu1 [893 kB] 142s Get:61 http://ftpmaster.internal/ubuntu plucky/universe ppc64el dh-python all 6.20241024 [112 kB] 142s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el docutils-common all 0.21.2+dfsg-2 [131 kB] 142s Get:63 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 142s Get:64 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-lyx all 2.4.2.1-1 [171 kB] 142s Get:65 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 142s Get:66 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 142s Get:67 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-4 [222 kB] 142s Get:68 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 142s Get:69 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 142s Get:70 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 142s Get:71 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 142s Get:72 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 142s Get:73 http://ftpmaster.internal/ubuntu plucky/main ppc64el libexpat1-dev ppc64el 2.6.4-1 [149 kB] 142s Get:74 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 142s Get:75 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 142s Get:76 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB] 142s Get:77 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 142s Get:78 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-4ubuntu3 [1387 kB] 142s Get:79 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-4ubuntu3 [71.2 kB] 142s Get:80 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 142s Get:81 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-3ubuntu2 [215 kB] 142s Get:82 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 142s Get:83 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 142s Get:84 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 142s Get:85 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 142s Get:86 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-sphinxdoc all 7.4.7-4 [158 kB] 142s Get:87 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-perl all 4.10000-1 [81.9 kB] 142s Get:88 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-4 [2814 kB] 142s Get:89 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 142s Get:90 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 142s Get:91 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu1 [298 kB] 142s Get:92 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 142s Get:93 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libnetcdf19t64 ppc64el 1:4.9.2-6ubuntu1 [596 kB] 142s Get:94 http://ftpmaster.internal/ubuntu plucky/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu1 [902 kB] 142s Get:95 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.12-dev ppc64el 3.12.7-3 [6136 kB] 143s Get:96 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3-dev ppc64el 3.12.6-0ubuntu1 [10.2 kB] 143s Get:97 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3-all-dev ppc64el 3.12.6-0ubuntu1 [916 B] 143s Get:98 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6build1 [225 kB] 143s Get:99 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB] 143s Get:100 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB] 143s Get:101 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 143s Get:102 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB] 143s Get:103 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 143s Get:104 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 143s Get:105 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 143s Get:106 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu1 [191 kB] 143s Get:107 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.2-1 [51.5 kB] 143s Get:108 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 143s Get:109 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-toml all 0.10.2-1 [16.5 kB] 143s Get:110 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-wheel all 0.45.1-1 [57.7 kB] 143s Get:111 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-build all 1.2.2-1 [31.0 kB] 143s Get:112 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 143s Get:113 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pybuild-plugin-pyproject all 6.20241024 [1728 B] 143s Get:114 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 143s Get:115 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 144s Get:116 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-mdanalysis-doc all 2.7.0-5build1 [2323 kB] 144s Get:117 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all ppc64el 3.12.6-0ubuntu1 [888 B] 144s Get:118 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-dev ppc64el 3.12.7-3 [505 kB] 144s Get:119 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dev ppc64el 3.12.6-0ubuntu1 [26.7 kB] 144s Get:120 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all-dev ppc64el 3.12.6-0ubuntu1 [908 B] 144s Get:121 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 144s Get:122 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11ubuntu1 [5148 kB] 144s Get:123 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-tk ppc64el 3.12.7-3 [116 kB] 144s Get:124 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-tk ppc64el 3.13.0-2 [107 kB] 144s Get:125 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tk ppc64el 3.12.7-1 [9752 B] 144s Get:126 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pil.imagetk ppc64el 10.4.0-1ubuntu2 [9872 B] 144s Get:127 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB] 144s Get:128 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu2 [606 kB] 144s Get:129 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2build1 [150 kB] 144s Get:130 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 144s Get:131 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 144s Get:132 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB] 144s Get:133 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 144s Get:134 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4build1 [1745 kB] 145s Get:135 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-brotli ppc64el 1.1.0-2build3 [423 kB] 145s Get:136 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cftime ppc64el 1.6.4-1build1 [327 kB] 145s Get:137 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.0-1build1 [1751 kB] 145s Get:138 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-citeproc all 0.6.0-3 [98.4 kB] 145s Get:139 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-contourpy ppc64el 1.3.0-2build1 [261 kB] 145s Get:140 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cycler all 0.12.1-1 [9716 B] 145s Get:141 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-3 [80.2 kB] 145s Get:142 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 145s Get:143 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-defusedxml all 0.7.1-2 [42.0 kB] 145s Get:144 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-roman all 4.2-1 [10.0 kB] 145s Get:145 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-docutils all 0.21.2+dfsg-2 [409 kB] 145s Get:146 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-looseversion all 1.3.0-3 [8354 B] 145s Get:147 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-duecredit all 0.10.2-2 [66.0 kB] 145s Get:148 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-monotonic all 1.6-2 [5732 B] 145s Get:149 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-fasteners all 0.18-2 [12.5 kB] 145s Get:150 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB] 145s Get:151 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fs all 2.4.16-5 [90.7 kB] 145s Get:152 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1build5 [28.4 kB] 145s Get:153 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5ubuntu1 [21.5 MB] 146s Get:154 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mpmath all 1.3.0-1 [425 kB] 146s Get:155 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sympy all 1.13.3-1 [4228 kB] 146s Get:156 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 146s Get:157 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-unicodedata2 ppc64el 15.1.0+ds-1build2 [361 kB] 147s Get:158 http://ftpmaster.internal/ubuntu plucky/universe ppc64el unicode-data all 15.1.0-1 [8878 kB] 147s Get:159 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fonttools ppc64el 4.55.0-3 [1727 kB] 147s Get:160 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1014 kB] 147s Get:161 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mrcfile all 1.5.3-3 [114 kB] 147s Get:162 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-griddataformats all 1.0.2-2 [2107 kB] 147s Get:163 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-gsd ppc64el 3.3.0-1build1 [234 kB] 147s Get:164 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.11.0-5ubuntu1 [1159 kB] 147s Get:165 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.11.0-5ubuntu1 [7974 B] 147s Get:166 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-sortedcontainers all 2.4.0-2 [27.6 kB] 147s Get:167 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python3-hypothesis all 6.122.1-1 [330 kB] 147s Get:168 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-imagesize all 1.4.1-1 [6844 B] 147s Get:169 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 147s Get:170 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-joblib all 1.3.2-5 [206 kB] 147s Get:171 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-kiwisolver ppc64el 1.4.7-2build1 [72.9 kB] 147s Get:172 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-latexcodec all 3.0.0-1 [16.6 kB] 148s Get:173 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-matplotlib ppc64el 3.8.3-3ubuntu1 [4704 kB] 148s Get:174 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 148s Get:175 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-msgpack ppc64el 1.0.3-3build3 [110 kB] 148s Get:176 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mmtf all 1.1.3-1 [16.2 kB] 148s Get:177 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-threadpoolctl all 3.1.0-1 [21.3 kB] 148s Get:178 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-tqdm all 4.67.1-1 [92.5 kB] 148s Get:179 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mdanalysis ppc64el 2.7.0-5build1 [2697 kB] 148s Get:180 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-common all 7.4.7-4 [775 kB] 148s Get:181 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-alabaster all 0.7.16-0.1 [18.5 kB] 148s Get:182 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 148s Get:183 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-sphinx all 7.4.7-4 [593 kB] 148s Get:184 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 148s Get:185 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [23.5 kB] 148s Get:186 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-msmb-theme all 1.2.0-4 [35.4 kB] 148s Get:187 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-netcdf4 ppc64el 1.7.2-1build1 [896 kB] 148s Get:188 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 149s Get:189 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5ubuntu1 [7350 kB] 149s Get:190 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 150s Get:191 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 150s Get:192 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-six all 1.16.0-7 [13.1 kB] 150s Get:193 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pybtex all 0.24.0-4 [70.0 kB] 150s Get:194 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pybtex-docutils all 1.0.2-1 [7176 B] 150s Get:195 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB] 150s Get:196 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-seaborn all 0.13.2-4 [225 kB] 150s Get:197 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn-lib ppc64el 1.4.2+dfsg-6build1 [6462 kB] 150s Get:198 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn all 1.4.2+dfsg-6build1 [2257 kB] 150s Get:199 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinx-sitemap all 2.6.0-1 [6674 B] 150s Get:200 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 151s Fetched 214 MB in 14s (15.4 MB/s) 151s Selecting previously unselected package fonts-lato. 151s (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 ... 74178 files and directories currently installed.) 151s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 151s Unpacking fonts-lato (2.015-1) ... 151s Selecting previously unselected package m4. 151s Preparing to unpack .../001-m4_1.4.19-4build1_ppc64el.deb ... 151s Unpacking m4 (1.4.19-4build1) ... 151s Selecting previously unselected package autoconf. 151s Preparing to unpack .../002-autoconf_2.72-3_all.deb ... 151s Unpacking autoconf (2.72-3) ... 151s Selecting previously unselected package autotools-dev. 151s Preparing to unpack .../003-autotools-dev_20220109.1_all.deb ... 151s Unpacking autotools-dev (20220109.1) ... 151s Selecting previously unselected package automake. 151s Preparing to unpack .../004-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 151s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 151s Selecting previously unselected package autopoint. 151s Preparing to unpack .../005-autopoint_0.22.5-2_all.deb ... 151s Unpacking autopoint (0.22.5-2) ... 151s Selecting previously unselected package libtcl8.6:ppc64el. 151s Preparing to unpack .../006-libtcl8.6_8.6.15+dfsg-2_ppc64el.deb ... 151s Unpacking libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 152s Selecting previously unselected package fonts-dejavu-mono. 152s Preparing to unpack .../007-fonts-dejavu-mono_2.37-8_all.deb ... 152s Unpacking fonts-dejavu-mono (2.37-8) ... 152s Selecting previously unselected package fonts-dejavu-core. 152s Preparing to unpack .../008-fonts-dejavu-core_2.37-8_all.deb ... 152s Unpacking fonts-dejavu-core (2.37-8) ... 152s Selecting previously unselected package libfontenc1:ppc64el. 152s Preparing to unpack .../009-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 152s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 152s Selecting previously unselected package x11-common. 152s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 152s Unpacking x11-common (1:7.7+23ubuntu3) ... 152s Selecting previously unselected package xfonts-encodings. 152s Preparing to unpack .../011-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 152s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 152s Selecting previously unselected package xfonts-utils. 152s Preparing to unpack .../012-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 152s Unpacking xfonts-utils (1:7.7+7) ... 152s Selecting previously unselected package fonts-urw-base35. 152s Preparing to unpack .../013-fonts-urw-base35_20200910-8_all.deb ... 152s Unpacking fonts-urw-base35 (20200910-8) ... 152s Selecting previously unselected package fontconfig-config. 152s Preparing to unpack .../014-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ... 152s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 152s Selecting previously unselected package libfontconfig1:ppc64el. 152s Preparing to unpack .../015-libfontconfig1_2.15.0-1.1ubuntu2_ppc64el.deb ... 152s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 152s Selecting previously unselected package libxrender1:ppc64el. 152s Preparing to unpack .../016-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 152s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 152s Selecting previously unselected package libxft2:ppc64el. 152s Preparing to unpack .../017-libxft2_2.3.6-1build1_ppc64el.deb ... 152s Unpacking libxft2:ppc64el (2.3.6-1build1) ... 152s Selecting previously unselected package libxss1:ppc64el. 152s Preparing to unpack .../018-libxss1_1%3a1.2.3-1build3_ppc64el.deb ... 152s Unpacking libxss1:ppc64el (1:1.2.3-1build3) ... 152s Selecting previously unselected package libtk8.6:ppc64el. 152s Preparing to unpack .../019-libtk8.6_8.6.15-1_ppc64el.deb ... 152s Unpacking libtk8.6:ppc64el (8.6.15-1) ... 152s Selecting previously unselected package tk8.6-blt2.5. 152s Preparing to unpack .../020-tk8.6-blt2.5_2.5.3+dfsg-7build1_ppc64el.deb ... 152s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 152s Selecting previously unselected package blt. 152s Preparing to unpack .../021-blt_2.5.3+dfsg-7build1_ppc64el.deb ... 152s Unpacking blt (2.5.3+dfsg-7build1) ... 152s Selecting previously unselected package libisl23:ppc64el. 152s Preparing to unpack .../022-libisl23_0.27-1_ppc64el.deb ... 152s Unpacking libisl23:ppc64el (0.27-1) ... 152s Selecting previously unselected package libmpc3:ppc64el. 152s Preparing to unpack .../023-libmpc3_1.3.1-1build2_ppc64el.deb ... 152s Unpacking libmpc3:ppc64el (1.3.1-1build2) ... 152s Selecting previously unselected package cpp-14-powerpc64le-linux-gnu. 152s Preparing to unpack .../024-cpp-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 152s Unpacking cpp-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 152s Selecting previously unselected package cpp-14. 152s Preparing to unpack .../025-cpp-14_14.2.0-8ubuntu1_ppc64el.deb ... 152s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 152s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 152s Preparing to unpack .../026-cpp-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 152s Unpacking cpp-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 152s Selecting previously unselected package cpp. 152s Preparing to unpack .../027-cpp_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 152s Unpacking cpp (4:14.1.0-2ubuntu1) ... 152s Selecting previously unselected package libcc1-0:ppc64el. 152s Preparing to unpack .../028-libcc1-0_14.2.0-8ubuntu1_ppc64el.deb ... 152s Unpacking libcc1-0:ppc64el (14.2.0-8ubuntu1) ... 152s Selecting previously unselected package libgomp1:ppc64el. 152s Preparing to unpack .../029-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 152s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 152s Selecting previously unselected package libitm1:ppc64el. 152s Preparing to unpack .../030-libitm1_14.2.0-8ubuntu1_ppc64el.deb ... 152s Unpacking libitm1:ppc64el (14.2.0-8ubuntu1) ... 152s Selecting previously unselected package libasan8:ppc64el. 152s Preparing to unpack .../031-libasan8_14.2.0-8ubuntu1_ppc64el.deb ... 152s Unpacking libasan8:ppc64el (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package liblsan0:ppc64el. 153s Preparing to unpack .../032-liblsan0_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking liblsan0:ppc64el (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package libtsan2:ppc64el. 153s Preparing to unpack .../033-libtsan2_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking libtsan2:ppc64el (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package libubsan1:ppc64el. 153s Preparing to unpack .../034-libubsan1_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking libubsan1:ppc64el (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package libquadmath0:ppc64el. 153s Preparing to unpack .../035-libquadmath0_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking libquadmath0:ppc64el (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package libgcc-14-dev:ppc64el. 153s Preparing to unpack .../036-libgcc-14-dev_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking libgcc-14-dev:ppc64el (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package gcc-14-powerpc64le-linux-gnu. 153s Preparing to unpack .../037-gcc-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking gcc-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package gcc-14. 153s Preparing to unpack .../038-gcc-14_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 153s Preparing to unpack .../039-gcc-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 153s Unpacking gcc-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 153s Selecting previously unselected package gcc. 153s Preparing to unpack .../040-gcc_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 153s Unpacking gcc (4:14.1.0-2ubuntu1) ... 153s Selecting previously unselected package libstdc++-14-dev:ppc64el. 153s Preparing to unpack .../041-libstdc++-14-dev_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking libstdc++-14-dev:ppc64el (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package g++-14-powerpc64le-linux-gnu. 153s Preparing to unpack .../042-g++-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking g++-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package g++-14. 153s Preparing to unpack .../043-g++-14_14.2.0-8ubuntu1_ppc64el.deb ... 153s Unpacking g++-14 (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package g++-powerpc64le-linux-gnu. 153s Preparing to unpack .../044-g++-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 153s Unpacking g++-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 153s Selecting previously unselected package g++. 153s Preparing to unpack .../045-g++_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 153s Unpacking g++ (4:14.1.0-2ubuntu1) ... 153s Selecting previously unselected package build-essential. 153s Preparing to unpack .../046-build-essential_12.10ubuntu1_ppc64el.deb ... 153s Unpacking build-essential (12.10ubuntu1) ... 153s Selecting previously unselected package cython3. 153s Preparing to unpack .../047-cython3_3.0.11+dfsg-1ubuntu2_ppc64el.deb ... 153s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ... 154s Selecting previously unselected package libdebhelper-perl. 154s Preparing to unpack .../048-libdebhelper-perl_13.20ubuntu1_all.deb ... 154s Unpacking libdebhelper-perl (13.20ubuntu1) ... 154s Selecting previously unselected package libtool. 154s Preparing to unpack .../049-libtool_2.4.7-8_all.deb ... 154s Unpacking libtool (2.4.7-8) ... 154s Selecting previously unselected package dh-autoreconf. 154s Preparing to unpack .../050-dh-autoreconf_20_all.deb ... 154s Unpacking dh-autoreconf (20) ... 154s Selecting previously unselected package libarchive-zip-perl. 154s Preparing to unpack .../051-libarchive-zip-perl_1.68-1_all.deb ... 154s Unpacking libarchive-zip-perl (1.68-1) ... 154s Selecting previously unselected package libfile-stripnondeterminism-perl. 154s Preparing to unpack .../052-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 154s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 154s Selecting previously unselected package dh-strip-nondeterminism. 154s Preparing to unpack .../053-dh-strip-nondeterminism_1.14.0-1_all.deb ... 154s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 154s Selecting previously unselected package debugedit. 154s Preparing to unpack .../054-debugedit_1%3a5.1-1_ppc64el.deb ... 154s Unpacking debugedit (1:5.1-1) ... 154s Selecting previously unselected package dwz. 154s Preparing to unpack .../055-dwz_0.15-1build6_ppc64el.deb ... 154s Unpacking dwz (0.15-1build6) ... 154s Selecting previously unselected package gettext. 154s Preparing to unpack .../056-gettext_0.22.5-2_ppc64el.deb ... 154s Unpacking gettext (0.22.5-2) ... 154s Selecting previously unselected package intltool-debian. 154s Preparing to unpack .../057-intltool-debian_0.35.0+20060710.6_all.deb ... 154s Unpacking intltool-debian (0.35.0+20060710.6) ... 154s Selecting previously unselected package po-debconf. 154s Preparing to unpack .../058-po-debconf_1.0.21+nmu1_all.deb ... 154s Unpacking po-debconf (1.0.21+nmu1) ... 154s Selecting previously unselected package debhelper. 154s Preparing to unpack .../059-debhelper_13.20ubuntu1_all.deb ... 154s Unpacking debhelper (13.20ubuntu1) ... 154s Selecting previously unselected package dh-python. 154s Preparing to unpack .../060-dh-python_6.20241024_all.deb ... 154s Unpacking dh-python (6.20241024) ... 154s Selecting previously unselected package docutils-common. 154s Preparing to unpack .../061-docutils-common_0.21.2+dfsg-2_all.deb ... 154s Unpacking docutils-common (0.21.2+dfsg-2) ... 154s Selecting previously unselected package fonts-font-awesome. 154s Preparing to unpack .../062-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 154s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 154s Selecting previously unselected package fonts-lyx. 154s Preparing to unpack .../063-fonts-lyx_2.4.2.1-1_all.deb ... 154s Unpacking fonts-lyx (2.4.2.1-1) ... 154s Selecting previously unselected package fonts-mathjax. 154s Preparing to unpack .../064-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 154s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 154s Selecting previously unselected package libaec0:ppc64el. 154s Preparing to unpack .../065-libaec0_1.1.3-1_ppc64el.deb ... 154s Unpacking libaec0:ppc64el (1.1.3-1) ... 154s Selecting previously unselected package libblas3:ppc64el. 154s Preparing to unpack .../066-libblas3_3.12.0-4_ppc64el.deb ... 154s Unpacking libblas3:ppc64el (3.12.0-4) ... 154s Selecting previously unselected package libpixman-1-0:ppc64el. 154s Preparing to unpack .../067-libpixman-1-0_0.44.0-3_ppc64el.deb ... 154s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 154s Selecting previously unselected package libxcb-render0:ppc64el. 154s Preparing to unpack .../068-libxcb-render0_1.17.0-2_ppc64el.deb ... 154s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 154s Selecting previously unselected package libxcb-shm0:ppc64el. 154s Preparing to unpack .../069-libxcb-shm0_1.17.0-2_ppc64el.deb ... 154s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 154s Selecting previously unselected package libcairo2:ppc64el. 154s Preparing to unpack .../070-libcairo2_1.18.2-2_ppc64el.deb ... 154s Unpacking libcairo2:ppc64el (1.18.2-2) ... 154s Selecting previously unselected package libdeflate0:ppc64el. 154s Preparing to unpack .../071-libdeflate0_1.22-1_ppc64el.deb ... 154s Unpacking libdeflate0:ppc64el (1.22-1) ... 154s Selecting previously unselected package libexpat1-dev:ppc64el. 154s Preparing to unpack .../072-libexpat1-dev_2.6.4-1_ppc64el.deb ... 154s Unpacking libexpat1-dev:ppc64el (2.6.4-1) ... 154s Selecting previously unselected package libgfortran5:ppc64el. 154s Preparing to unpack .../073-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 154s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 154s Selecting previously unselected package libgraphite2-3:ppc64el. 154s Preparing to unpack .../074-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 154s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 154s Selecting previously unselected package libharfbuzz0b:ppc64el. 154s Preparing to unpack .../075-libharfbuzz0b_10.0.1-1_ppc64el.deb ... 154s Unpacking libharfbuzz0b:ppc64el (10.0.1-1) ... 154s Selecting previously unselected package libsz2:ppc64el. 154s Preparing to unpack .../076-libsz2_1.1.3-1_ppc64el.deb ... 154s Unpacking libsz2:ppc64el (1.1.3-1) ... 154s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 154s Preparing to unpack .../077-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 154s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ... 154s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 154s Preparing to unpack .../078-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 154s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ... 154s Selecting previously unselected package libimagequant0:ppc64el. 154s Preparing to unpack .../079-libimagequant0_2.18.0-1build1_ppc64el.deb ... 154s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 154s Selecting previously unselected package libjpeg-turbo8:ppc64el. 154s Preparing to unpack .../080-libjpeg-turbo8_2.1.5-3ubuntu2_ppc64el.deb ... 154s Unpacking libjpeg-turbo8:ppc64el (2.1.5-3ubuntu2) ... 155s Selecting previously unselected package libjpeg8:ppc64el. 155s Preparing to unpack .../081-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 155s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 155s Selecting previously unselected package libjs-jquery. 155s Preparing to unpack .../082-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 155s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 155s Selecting previously unselected package libjs-jquery-ui. 155s Preparing to unpack .../083-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 155s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 155s Selecting previously unselected package libjs-underscore. 155s Preparing to unpack .../084-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 155s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 155s Selecting previously unselected package libjs-sphinxdoc. 155s Preparing to unpack .../085-libjs-sphinxdoc_7.4.7-4_all.deb ... 155s Unpacking libjs-sphinxdoc (7.4.7-4) ... 155s Selecting previously unselected package libjson-perl. 155s Preparing to unpack .../086-libjson-perl_4.10000-1_all.deb ... 155s Unpacking libjson-perl (4.10000-1) ... 155s Selecting previously unselected package liblapack3:ppc64el. 155s Preparing to unpack .../087-liblapack3_3.12.0-4_ppc64el.deb ... 155s Unpacking liblapack3:ppc64el (3.12.0-4) ... 155s Selecting previously unselected package liblbfgsb0:ppc64el. 155s Preparing to unpack .../088-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 155s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 155s Selecting previously unselected package liblcms2-2:ppc64el. 155s Preparing to unpack .../089-liblcms2-2_2.16-2_ppc64el.deb ... 155s Unpacking liblcms2-2:ppc64el (2.16-2) ... 155s Selecting previously unselected package liblerc4:ppc64el. 155s Preparing to unpack .../090-liblerc4_4.0.0+ds-5ubuntu1_ppc64el.deb ... 155s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ... 155s Selecting previously unselected package liblzf1:ppc64el. 155s Preparing to unpack .../091-liblzf1_3.6-4_ppc64el.deb ... 155s Unpacking liblzf1:ppc64el (3.6-4) ... 155s Selecting previously unselected package libnetcdf19t64:ppc64el. 155s Preparing to unpack .../092-libnetcdf19t64_1%3a4.9.2-6ubuntu1_ppc64el.deb ... 155s Unpacking libnetcdf19t64:ppc64el (1:4.9.2-6ubuntu1) ... 155s Selecting previously unselected package zlib1g-dev:ppc64el. 155s Preparing to unpack .../093-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_ppc64el.deb ... 155s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 155s Selecting previously unselected package libpython3.12-dev:ppc64el. 155s Preparing to unpack .../094-libpython3.12-dev_3.12.7-3_ppc64el.deb ... 155s Unpacking libpython3.12-dev:ppc64el (3.12.7-3) ... 155s Selecting previously unselected package libpython3-dev:ppc64el. 155s Preparing to unpack .../095-libpython3-dev_3.12.6-0ubuntu1_ppc64el.deb ... 155s Unpacking libpython3-dev:ppc64el (3.12.6-0ubuntu1) ... 155s Selecting previously unselected package libpython3-all-dev:ppc64el. 155s Preparing to unpack .../096-libpython3-all-dev_3.12.6-0ubuntu1_ppc64el.deb ... 155s Unpacking libpython3-all-dev:ppc64el (3.12.6-0ubuntu1) ... 155s Selecting previously unselected package libqhull-r8.0:ppc64el. 155s Preparing to unpack .../097-libqhull-r8.0_2020.2-6build1_ppc64el.deb ... 155s Unpacking libqhull-r8.0:ppc64el (2020.2-6build1) ... 155s Selecting previously unselected package libraqm0:ppc64el. 155s Preparing to unpack .../098-libraqm0_0.10.1-1build1_ppc64el.deb ... 155s Unpacking libraqm0:ppc64el (0.10.1-1build1) ... 155s Selecting previously unselected package libsharpyuv0:ppc64el. 155s Preparing to unpack .../099-libsharpyuv0_1.4.0-0.1_ppc64el.deb ... 155s Unpacking libsharpyuv0:ppc64el (1.4.0-0.1) ... 155s Selecting previously unselected package libjbig0:ppc64el. 155s Preparing to unpack .../100-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 155s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 155s Selecting previously unselected package libwebp7:ppc64el. 155s Preparing to unpack .../101-libwebp7_1.4.0-0.1_ppc64el.deb ... 155s Unpacking libwebp7:ppc64el (1.4.0-0.1) ... 155s Selecting previously unselected package libtiff6:ppc64el. 155s Preparing to unpack .../102-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ... 155s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 155s Selecting previously unselected package libwebpdemux2:ppc64el. 155s Preparing to unpack .../103-libwebpdemux2_1.4.0-0.1_ppc64el.deb ... 155s Unpacking libwebpdemux2:ppc64el (1.4.0-0.1) ... 155s Selecting previously unselected package libwebpmux3:ppc64el. 155s Preparing to unpack .../104-libwebpmux3_1.4.0-0.1_ppc64el.deb ... 155s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ... 155s Selecting previously unselected package libxslt1.1:ppc64el. 155s Preparing to unpack .../105-libxslt1.1_1.1.39-0exp1ubuntu1_ppc64el.deb ... 155s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 155s Selecting previously unselected package python3-packaging. 155s Preparing to unpack .../106-python3-packaging_24.2-1_all.deb ... 155s Unpacking python3-packaging (24.2-1) ... 155s Selecting previously unselected package python3-pyproject-hooks. 155s Preparing to unpack .../107-python3-pyproject-hooks_1.2.0-1_all.deb ... 155s Unpacking python3-pyproject-hooks (1.2.0-1) ... 155s Selecting previously unselected package python3-toml. 155s Preparing to unpack .../108-python3-toml_0.10.2-1_all.deb ... 155s Unpacking python3-toml (0.10.2-1) ... 155s Selecting previously unselected package python3-wheel. 155s Preparing to unpack .../109-python3-wheel_0.45.1-1_all.deb ... 155s Unpacking python3-wheel (0.45.1-1) ... 155s Selecting previously unselected package python3-build. 155s Preparing to unpack .../110-python3-build_1.2.2-1_all.deb ... 155s Unpacking python3-build (1.2.2-1) ... 155s Selecting previously unselected package python3-installer. 155s Preparing to unpack .../111-python3-installer_0.7.0+dfsg1-3_all.deb ... 155s Unpacking python3-installer (0.7.0+dfsg1-3) ... 155s Selecting previously unselected package pybuild-plugin-pyproject. 155s Preparing to unpack .../112-pybuild-plugin-pyproject_6.20241024_all.deb ... 155s Unpacking pybuild-plugin-pyproject (6.20241024) ... 155s Selecting previously unselected package python-matplotlib-data. 155s Preparing to unpack .../113-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ... 155s Unpacking python-matplotlib-data (3.8.3-3ubuntu1) ... 155s Selecting previously unselected package libjs-mathjax. 155s Preparing to unpack .../114-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 155s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 156s Selecting previously unselected package python-mdanalysis-doc. 156s Preparing to unpack .../115-python-mdanalysis-doc_2.7.0-5build1_all.deb ... 156s Unpacking python-mdanalysis-doc (2.7.0-5build1) ... 156s Selecting previously unselected package python3-all. 156s Preparing to unpack .../116-python3-all_3.12.6-0ubuntu1_ppc64el.deb ... 156s Unpacking python3-all (3.12.6-0ubuntu1) ... 156s Selecting previously unselected package python3.12-dev. 156s Preparing to unpack .../117-python3.12-dev_3.12.7-3_ppc64el.deb ... 156s Unpacking python3.12-dev (3.12.7-3) ... 156s Selecting previously unselected package python3-dev. 156s Preparing to unpack .../118-python3-dev_3.12.6-0ubuntu1_ppc64el.deb ... 156s Unpacking python3-dev (3.12.6-0ubuntu1) ... 156s Selecting previously unselected package python3-all-dev. 156s Preparing to unpack .../119-python3-all-dev_3.12.6-0ubuntu1_ppc64el.deb ... 156s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 156s Selecting previously unselected package python3-appdirs. 156s Preparing to unpack .../120-python3-appdirs_1.4.4-4_all.deb ... 156s Unpacking python3-appdirs (1.4.4-4) ... 156s Selecting previously unselected package python3-numpy. 156s Preparing to unpack .../121-python3-numpy_1%3a1.26.4+ds-11ubuntu1_ppc64el.deb ... 156s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 156s Selecting previously unselected package python3.12-tk. 156s Preparing to unpack .../122-python3.12-tk_3.12.7-3_ppc64el.deb ... 156s Unpacking python3.12-tk (3.12.7-3) ... 156s Selecting previously unselected package python3.13-tk. 156s Preparing to unpack .../123-python3.13-tk_3.13.0-2_ppc64el.deb ... 156s Unpacking python3.13-tk (3.13.0-2) ... 156s Selecting previously unselected package python3-tk:ppc64el. 156s Preparing to unpack .../124-python3-tk_3.12.7-1_ppc64el.deb ... 156s Unpacking python3-tk:ppc64el (3.12.7-1) ... 156s Selecting previously unselected package python3-pil.imagetk:ppc64el. 156s Preparing to unpack .../125-python3-pil.imagetk_10.4.0-1ubuntu2_ppc64el.deb ... 156s Unpacking python3-pil.imagetk:ppc64el (10.4.0-1ubuntu2) ... 156s Selecting previously unselected package libopenjp2-7:ppc64el. 156s Preparing to unpack .../126-libopenjp2-7_2.5.0-2ubuntu1_ppc64el.deb ... 156s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 156s Selecting previously unselected package python3-pil:ppc64el. 157s Preparing to unpack .../127-python3-pil_10.4.0-1ubuntu2_ppc64el.deb ... 157s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu2) ... 157s Selecting previously unselected package python3-cairo. 157s Preparing to unpack .../128-python3-cairo_1.26.1-2build1_ppc64el.deb ... 157s Unpacking python3-cairo (1.26.1-2build1) ... 157s Selecting previously unselected package python3-freetype. 157s Preparing to unpack .../129-python3-freetype_2.5.1-1_all.deb ... 157s Unpacking python3-freetype (2.5.1-1) ... 157s Selecting previously unselected package python3-rlpycairo. 157s Preparing to unpack .../130-python3-rlpycairo_0.3.0-3_all.deb ... 157s Unpacking python3-rlpycairo (0.3.0-3) ... 157s Selecting previously unselected package python3-reportlab. 157s Preparing to unpack .../131-python3-reportlab_4.2.5-1_all.deb ... 157s Unpacking python3-reportlab (4.2.5-1) ... 157s Selecting previously unselected package w3c-sgml-lib. 157s Preparing to unpack .../132-w3c-sgml-lib_1.3-3_all.deb ... 157s Unpacking w3c-sgml-lib (1.3-3) ... 157s Selecting previously unselected package python3-biopython. 157s Preparing to unpack .../133-python3-biopython_1.84+dfsg-4build1_ppc64el.deb ... 157s Unpacking python3-biopython (1.84+dfsg-4build1) ... 157s Selecting previously unselected package python3-brotli. 157s Preparing to unpack .../134-python3-brotli_1.1.0-2build3_ppc64el.deb ... 157s Unpacking python3-brotli (1.1.0-2build3) ... 157s Selecting previously unselected package python3-cftime. 157s Preparing to unpack .../135-python3-cftime_1.6.4-1build1_ppc64el.deb ... 157s Unpacking python3-cftime (1.6.4-1build1) ... 157s Selecting previously unselected package python3-lxml:ppc64el. 157s Preparing to unpack .../136-python3-lxml_5.3.0-1build1_ppc64el.deb ... 157s Unpacking python3-lxml:ppc64el (5.3.0-1build1) ... 157s Selecting previously unselected package python3-citeproc. 157s Preparing to unpack .../137-python3-citeproc_0.6.0-3_all.deb ... 157s Unpacking python3-citeproc (0.6.0-3) ... 157s Selecting previously unselected package python3-contourpy. 157s Preparing to unpack .../138-python3-contourpy_1.3.0-2build1_ppc64el.deb ... 157s Unpacking python3-contourpy (1.3.0-2build1) ... 157s Selecting previously unselected package python3-cycler. 157s Preparing to unpack .../139-python3-cycler_0.12.1-1_all.deb ... 157s Unpacking python3-cycler (0.12.1-1) ... 157s Selecting previously unselected package python3-dateutil. 157s Preparing to unpack .../140-python3-dateutil_2.9.0-3_all.deb ... 157s Unpacking python3-dateutil (2.9.0-3) ... 157s Selecting previously unselected package python3-decorator. 157s Preparing to unpack .../141-python3-decorator_5.1.1-5_all.deb ... 157s Unpacking python3-decorator (5.1.1-5) ... 157s Selecting previously unselected package python3-defusedxml. 157s Preparing to unpack .../142-python3-defusedxml_0.7.1-2_all.deb ... 157s Unpacking python3-defusedxml (0.7.1-2) ... 157s Selecting previously unselected package python3-roman. 157s Preparing to unpack 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159s Preparing to unpack .../170-python3-kiwisolver_1.4.7-2build1_ppc64el.deb ... 159s Unpacking python3-kiwisolver (1.4.7-2build1) ... 159s Selecting previously unselected package python3-latexcodec. 159s Preparing to unpack .../171-python3-latexcodec_3.0.0-1_all.deb ... 159s Unpacking python3-latexcodec (3.0.0-1) ... 159s Selecting previously unselected package python3-matplotlib. 159s Preparing to unpack .../172-python3-matplotlib_3.8.3-3ubuntu1_ppc64el.deb ... 159s Unpacking python3-matplotlib (3.8.3-3ubuntu1) ... 159s Selecting previously unselected package python3-mda-xdrlib. 159s Preparing to unpack .../173-python3-mda-xdrlib_0.2.0-3_all.deb ... 159s Unpacking python3-mda-xdrlib (0.2.0-3) ... 159s Selecting previously unselected package python3-msgpack. 159s Preparing to unpack .../174-python3-msgpack_1.0.3-3build3_ppc64el.deb ... 159s Unpacking python3-msgpack (1.0.3-3build3) ... 159s Selecting previously unselected package python3-mmtf. 159s Preparing to unpack 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160s Selecting previously unselected package python3-netcdf4. 160s Preparing to unpack .../186-python3-netcdf4_1.7.2-1build1_ppc64el.deb ... 160s Unpacking python3-netcdf4 (1.7.2-1build1) ... 160s Selecting previously unselected package python3-networkx. 160s Preparing to unpack .../187-python3-networkx_3.2.1-4ubuntu1_all.deb ... 160s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 160s Selecting previously unselected package python3-pandas-lib:ppc64el. 160s Preparing to unpack .../188-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_ppc64el.deb ... 160s Unpacking python3-pandas-lib:ppc64el (2.2.3+dfsg-5ubuntu1) ... 160s Selecting previously unselected package python3-pandas. 160s Preparing to unpack .../189-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 160s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 161s Selecting previously unselected package python3-pluggy. 161s Preparing to unpack .../190-python3-pluggy_1.5.0-1_all.deb ... 161s Unpacking python3-pluggy (1.5.0-1) ... 161s Selecting 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Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ... 161s Setting up w3c-sgml-lib (1.3-3) ... 193s Setting up fonts-lato (2.015-1) ... 193s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 193s Setting up liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ... 193s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 193s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ... 193s Setting up python3-joblib (1.3.2-5) ... 193s Setting up python3-lz4 (4.0.2+dfsg-1build5) ... 193s Setting up libxcb-render0:ppc64el (1.17.0-2) ... 193s Setting up python3-defusedxml (0.7.1-2) ... 193s Setting up libarchive-zip-perl (1.68-1) ... 193s Setting up python3-alabaster (0.7.16-0.1) ... 193s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 193s Setting up fonts-lyx (2.4.2.1-1) ... 193s Setting up libdebhelper-perl (13.20ubuntu1) ... 193s Setting up python3-tqdm (4.67.1-1) ... 193s Setting up python3-threadpoolctl (3.1.0-1) ... 194s Setting up x11-common (1:7.7+23ubuntu3) ... 194s Setting up libdeflate0:ppc64el (1.22-1) ... 194s Setting up m4 (1.4.19-4build1) ... 194s Setting up python3-latexcodec (3.0.0-1) ... 194s Setting up libqhull-r8.0:ppc64el (2020.2-6build1) ... 194s Setting up python3-all (3.12.6-0ubuntu1) ... 194s Setting up libxcb-shm0:ppc64el (1.17.0-2) ... 194s Setting up python3-sortedcontainers (2.4.0-2) ... 194s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ... 194s Setting up python3-freetype (2.5.1-1) ... 194s Setting up python3-networkx (3.2.1-4ubuntu1) ... 196s Setting up python3-wheel (0.45.1-1) ... 196s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ... 196s Setting up python3-mda-xdrlib (0.2.0-3) ... 196s Setting up libaec0:ppc64el (1.1.3-1) ... 196s Setting up python3-tz (2024.1-2) ... 196s Setting up python3-monotonic (1.6-2) ... 196s Setting up unicode-data (15.1.0-1) ... 196s Setting up python3-six (1.16.0-7) ... 196s Setting up python3-roman (4.2-1) ... 196s Setting up python3-decorator (5.1.1-5) ... 197s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ... 197s Setting up autotools-dev (20220109.1) ... 197s Setting up libblas3:ppc64el (3.12.0-4) ... 197s 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 197s Setting up python3-packaging (24.2-1) ... 197s Setting up libexpat1-dev:ppc64el (2.6.4-1) ... 197s Setting up python3-pyproject-hooks (1.2.0-1) ... 197s Setting up python3-snowballstemmer (2.2.0-4build1) ... 197s Setting up python3-brotli (1.1.0-2build3) ... 197s Setting up liblzf1:ppc64el (3.6-4) ... 197s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 197s Setting up libquadmath0:ppc64el (14.2.0-8ubuntu1) ... 197s Setting up python3-cycler (0.12.1-1) ... 197s Setting up libimagequant0:ppc64el (2.18.0-1build1) ... 197s Setting up fonts-dejavu-mono (2.37-8) ... 197s Setting up python3-kiwisolver (1.4.7-2build1) ... 197s Setting up libmpc3:ppc64el (1.3.1-1build2) ... 197s Setting up cython3 (3.0.11+dfsg-1ubuntu2) ... 198s Setting up libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 198s Setting up autopoint (0.22.5-2) ... 198s Setting up fonts-dejavu-core (2.37-8) ... 198s Setting up python3-fasteners (0.18-2) ... 198s Setting up libjpeg-turbo8:ppc64el (2.1.5-3ubuntu2) ... 198s Setting up python3-toml (0.10.2-1) ... 199s Setting up python3-installer (0.7.0+dfsg1-3) ... 199s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 199s Setting up autoconf (2.72-3) ... 199s Setting up python3-pluggy (1.5.0-1) ... 199s Setting up libwebp7:ppc64el (1.4.0-0.1) ... 199s Setting up python3-pybtex (0.24.0-4) ... 199s Setting up libubsan1:ppc64el (14.2.0-8ubuntu1) ... 199s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 199s Setting up dwz (0.15-1build6) ... 199s Setting up python3-looseversion (1.3.0-3) ... 199s Setting up libasan8:ppc64el (14.2.0-8ubuntu1) ... 199s Setting up docutils-common (0.21.2+dfsg-2) ... 199s Setting up libjson-perl (4.10000-1) ... 199s Setting up libxslt1.1:ppc64el 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libsz2:ppc64el (1.1.3-1) ... 200s Setting up libitm1:ppc64el (14.2.0-8ubuntu1) ... 200s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 200s Setting up python3-imagesize (1.4.1-1) ... 200s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 200s Setting up automake (1:1.16.5-1.3ubuntu1) ... 200s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 200s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 200s Setting up python3-sympy (1.13.3-1) ... 207s Setting up liblapack3:ppc64el (3.12.0-4) ... 207s 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 207s Setting up gettext (0.22.5-2) ... 207s Setting up pybuild-plugin-pyproject (6.20241024) ... 207s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 208s Setting up python3-pytest (8.3.3-1) ... 208s Setting up libwebpdemux2:ppc64el 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Processing triggers for libc-bin (2.40-1ubuntu3) ... 235s autopkgtest [15:24:48]: test test-mdanalysis: [----------------------- 236s skipping tests with SKIP_TEST_LIST= 245s ============================= test session starts ============================== 245s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 245s rootdir: /tmp/autopkgtest.ap6EeH/build.KOR/src 245s plugins: typeguard-4.4.1, hypothesis-6.122.1 245s collected 19229 items / 6 skipped 245s 251s testsuite/MDAnalysisTests/analysis/test_align.py ....................... 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[100%] 1097s 1097s =============================== warnings summary =============================== 1097s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39 1097s /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. 1097s 1097s Due to the on going maintenance burden of keeping command line application 1097s wrappers up to date, we have decided to deprecate and eventually remove these 1097s modules. 1097s 1097s We instead now recommend building your command line and invoking it directly 1097s with the subprocess module. 1097s warnings.warn( 1097s 1097s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings 1097s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings 1097s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings 1097s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings 1097s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings 1097s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings 1097s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings 1097s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings 1097s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings 1097s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings 1097s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings 1097s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings 1097s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1097s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings 1097s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings 1097s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings 1097s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings 1097s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings 1097s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings 1097s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings 1097s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings 1097s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings 1097s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings 1097s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings 1097s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings 1097s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings 1097s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1097s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings 1097s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1097s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings 1097s /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. 1097s warnings.warn("DCDReader currently makes independent timesteps" 1097s 1097s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 1097s /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. 1097s warnings.warn(wmsg, category=DeprecationWarning) 1097s 1097s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings 1097s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written 1097s warnings.warn(wmsg) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings 1097s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings 1097s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings 1097s /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 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings 1097s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1097s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings 1097s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning 1097s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'c3', 'hc', 'oh', 'h1', 'ho'}. These have been given an empty element record. 1097s warnings.warn("Unknown elements found for some " 1097s 1097s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning 1097s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings 1097s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings 1097s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1097s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings 1097s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings 1097s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps 1097s self.times[i] = ts.time 1097s 1097s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning 1097s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings 1097s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1097s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings 1097s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings 1097s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings 1097s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded 1097s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps 1097s results.append((ts.time, x.sum() / mask.sum())) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue 1097s /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. 1097s warnings.warn(msg) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1097s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding 1097s /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 1097s warnings.warn(msg) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1097s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1097s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1097s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings 1097s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning 1097s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings 1097s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings 1097s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings 1097s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1097s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings 1097s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings 1097s /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. 1097s warnings.warn("Element information is missing, elements attribute " 1097s 1097s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran 1097s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame 1097s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections 1097s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues 1097s warnings.warn("Cannot determine phi and psi angles for the first " 1097s 1097s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin 1097s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr 1097s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame 1097s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot 1097s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning 1097s /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. 1097s warnings.warn(f"All residues selected with '{select_remove}' " 1097s 1097s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings 1097s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings 1097s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=6140) is multi-threaded, use of fork() may lead to deadlocks in the child. 1097s self.pid = os.fork() 1097s 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes 1097s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide 1097s cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms 1097s 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide 1097s local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1097s /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice 1097s ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1097s /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide 1097s ret = um.true_divide( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1097s /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide 1097s ret = ret.dtype.type(ret / rcount) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1097s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning 1097s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning 1097s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1097s /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. 1097s warnings.warn("1 A^3 CRYST1 record," 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. 1097s warnings.warn("Unit cell dimensions not found. " 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings 1097s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings 1097s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings 1097s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1097s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings 1097s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1097s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning 1097s /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 1097s warnings.warn(wmsg, DeprecationWarning) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 1097s warnings.warn("Desired number of sample points too high, using {0}" 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbond = HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbond = HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbond = HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbond = HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbond = HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbond = HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbond = HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbond = HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s HBAC( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1097s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1097s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbond = HBAC(u, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1097s `find_hydrogen_donors` will be removed in release 3.0.0. 1097s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s D = hbonds.find_hydrogen_donors(H) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1097s `find_hydrogen_donors` will be removed in release 3.0.0. 1097s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1097s hbonds.find_hydrogen_donors(u.atoms) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1097s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1097s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. 1097s return _methods._mean(a, axis=axis, dtype=dtype, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1097s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1097s /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide 1097s ret = ret.dtype.type(ret / rcount) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1097s /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. 1097s warnings.warn(msg.format(sel)) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1097s /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. 1097s warnings.warn(msg.format(sel)) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1097s /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. 1097s warnings.warn(msg.format(sel)) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. 1097s warnings.warn("Empty string to select atoms, empty group returned.", 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1097s /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, . 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1097s /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, . 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1097s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1097s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1097s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1097s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1097s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1097s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple 1097s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content 1097s /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. 1097s warnings.warn(wmsg) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning 1097s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning 1097s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1097s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1097s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1097s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1097s /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.) 1097s phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi 1097s 1097s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j 1097s /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 1097s warnings.warn("Column index entered (j = {:d} is smaller than row " 1097s 1097s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps 1097s dt=self.trajectory.ts.dt * step, 1097s 1097s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] 1097s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] 1097s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] 1097s /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 1097s warnings.warn(wmsg, DeprecationWarning) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1097s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings 1097s /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. 1097s warnings.warn("The `u` attribute is superflous and will be removed " 1097s 1097s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] 1097s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm 1097s /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. 1097s warnings.warn("The `density` attribute was deprecated in " 1097s 1097s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata 1097s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. 1097s warnings.warn(msg, category=MissingDataWarning) 1097s 1097s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps 1097s self.timesteps.append(self._ts.time) 1097s 1097s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning 1097s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default 1097s warnings.warn("{} does not support time selection. Reverting to " 1097s 1097s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default 1097s warnings.warn("{} does not support data selection. Reverting to " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1097s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings 1097s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps 1097s return self.ts.dt 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1097s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps 1097s ts.data['time'] = step_num * ts.dt 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats 1097s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_unsupported_filetypes 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1097s self.close() 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close 1097s self._apply('close') 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply 1097s return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] 1097s ^^^^^^^^^^^^ 1097s AttributeError: 'ChainReader' object has no attribute 'readers' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing 1097s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain 1097s warnings.warn("Missing frame in continuous chain", UserWarning) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps 1097s time_frame_0 = ts.time - ts.frame*ts.dt # assumes ts.dt is constant 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps 1097s frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps 1097s step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps 1097s self._add_step_to_frame_data(ts.time) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps 1097s if not np.allclose(A.time, B.time): 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] 1097s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array 1097s /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 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1097s self.close() 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close 1097s self._file.close() 1097s ^^^^^^^^^^ 1097s AttributeError: 'DCDReader' object has no attribute '_file' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms 1097s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit 1097s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__ 1097s self.close() 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close 1097s self._file.close() 1097s ^^^^^^^^^^ 1097s AttributeError: 'DCDWriter' object has no attribute '_file' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings 1097s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings 1097s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1097s /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. 1097s warnings.warn(msg) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps 1097s return self.ts.time 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps 1097s assert_equal(reader.ts.dt, reader.dt) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps 1097s time_frame = time_frame_0 + frame_index*ts.dt 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps 1097s reader_p = pickle.loads(pickle.dumps(reader)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings 1097s /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 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] 1097s warnings.warn(wmsg) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1097s /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`. 1097s warnings.warn(wmsg) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. 1097s warnings.warn("Not all velocities were present. " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps 1097s reader_p = pickle.loads(pickle.dumps(reader)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader 1097s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps 1097s reader_p = pickle.loads(pickle.dumps(reader)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1097s self.close() 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close 1097s self._file.close() 1097s ^^^^^^^^^^ 1097s AttributeError: 'H5MDReader' object has no attribute '_file' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1097s for aux in self.aux_list: 1097s ^^^^^^^^^^^^^ 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1097s return self._auxs.keys() 1097s ^^^^^^^^^^ 1097s AttributeError: 'H5MDReader' object has no attribute '_auxs' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1097s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 1097s warnings.warn('Guessed all Masses to 1.0') 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit 1097s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1097s for aux in self.aux_list: 1097s ^^^^^^^^^^^^^ 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1097s return self._auxs.keys() 1097s ^^^^^^^^^^ 1097s AttributeError: 'DCDReader' object has no attribute '_auxs' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view 1097s /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 1097s warnings.warn("MemoryReader.timeseries inclusive `stop` " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader 1097s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps 1097s reader_p = pickle.loads(pickle.dumps(reader)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1097s /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 1097s warnings.warn(wmsg) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps 1097s ts.time) # in-place ! (hope this works...) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps 1097s time_list = [ts.time for ts in u.trajectory] 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps 1097s assert u.trajectory.ts.dt == pytest.approx(ref) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 1097s /tmp/autopkgtest.ap6EeH/build.KOR/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.) 1097s return self._test_write_trajectory(universe, outfile) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] 1097s /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. 1097s warnings.warn(wmsg) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1097s /tmp/autopkgtest.ap6EeH/build.KOR/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.) 1097s return self._test_write_trajectory(universe, outfile) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 1097s warnings.warn("Found missing chainIDs." 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom] 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond] 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom] 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree] 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond] 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom] 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps 1097s time = ts.time 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1097s self.close() 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close 1097s if self.trjfile is not None: 1097s ^^^^^^^^^^^^ 1097s AttributeError: 'NCDFWriter' object has no attribute 'trjfile' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' 1097s warnings.warn("Found no information for attr: '{}'" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' 1097s warnings.warn("Found chainIDs using unnaccepted character." 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' 1097s warnings.warn("Found chainIDs with invalid length." 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed 1097s warnings.warn("Serial numbers went over 100,000. " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed 1097s warnings.warn("Invalid atom serials were present, bonds will not" 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed 1097s warnings.warn("Invalid atom serials were present, " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment 1097s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1097s /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. 1097s warnings.warn(wmsg) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1097s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1097s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1097s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1097s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges 1097s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps 1097s assert_equal(ts.dt, 1.0) # default value 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps 1097s assert_equal(ts.time, 0.0) # default to 1.0 (dt) * 0 (frame) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps 1097s assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1097s for aux in self.aux_list: 1097s ^^^^^^^^^^^^^ 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1097s return self._auxs.keys() 1097s ^^^^^^^^^^ 1097s AttributeError: 'TNGReader' object has no attribute '_auxs' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms 1097s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe 1097s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe 1097s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1097s self.close() 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close 1097s if self.trjfile is None: 1097s ^^^^^^^^^^^^ 1097s AttributeError: 'TRJReader' object has no attribute 'trjfile' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps 1097s data['time'] = ts.time 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1097s /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 1097s warnings.warn("Timestep didn't have the following attributes: '{0}', " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1097s /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. 1097s warnings.warn("Timestep didn't have velocity information, " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1097s /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 1097s warnings.warn("Timestep didn't have dimensions information, " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1097s self.close() 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close 1097s if self.trzfile is None: 1097s ^^^^^^^^^^^^ 1097s AttributeError: 'TRZWriter' object has no attribute 'trzfile' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1097s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1097s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1097s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1097s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1097s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1097s /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. 1097s warnings.warn("Element information is missing, elements attribute " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1097s /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 1097s warnings.warn(wmsg, DeprecationWarning) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] 1097s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] 1097s /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' 1097s warnings.warn(wmsg) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD 1097s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps 1097s time = ts.time 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD 1097s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps 1097s time = ts.time 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1097s self.close() 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1097s self._xdr.close() 1097s ^^^^^^^^^ 1097s AttributeError: 'XTCWriter' object has no attribute '_xdr' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container 1097s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1097s 1097s Traceback (most recent call last): 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1097s self.close() 1097s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1097s self._xdr.close() 1097s ^^^^^^^^^ 1097s AttributeError: 'TRRWriter' object has no attribute '_xdr' 1097s 1097s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1097s /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. 1097s Consider setting 'refresh_offsets=True' when loading your Universe. 1097s warnings.warn(f"Reading offsets from {fname} failed, " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly 1097s /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. 1097s warnings.warn(f"Cannot write lock/offset file in same location as " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1097s /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. 1097s Consider setting 'refresh_offsets=True' when loading your Universe. 1097s warnings.warn(f"Reading offsets from {fname} failed, " 1097s 1097s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly 1097s /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. 1097s warnings.warn(f"Cannot write lock/offset file in same location as " 1097s 1097s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] 1097s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] 1097s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] 1097s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce 1097s return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1097s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1097s /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. 1097s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings 1097s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings 1097s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings 1097s /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. 1097s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1097s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1097s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide 1097s return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() 1097s 1097s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings 1097s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide 1097s _centers /= _weights.sum(axis=1)[:, None] 1097s 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1097s /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`. 1097s warnings.warn(msg, category=SelectionWarning) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1097s /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`. 1097s warnings.warn(msg, category=SelectionWarning) 1097s 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] 1097s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] 1097s /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`. 1097s warnings.warn(msg, category=SelectionWarning) 1097s 1097s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] 1097s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] 1097s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] 1097s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] 1097s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] 1097s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc 1097s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc 1097s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options 1097s /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 1097s warnings.warn("The 'pbc' kwarg has been deprecated and will be " 1097s 1097s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel 1097s /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`. 1097s warnings.warn(msg, category=SelectionWarning) 1097s 1097s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] 1097s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] 1097s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] 1097s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] 1097s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] 1097s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide 1097s x = np.dot(a, b) / (norm(a) * norm(b)) 1097s 1097s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt 1097s ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) 1097s 1097s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt 1097s box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - 1097s 1097s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide 1097s a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) 1097s 1097s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide 1097s b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) 1097s 1097s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide 1097s c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) 1097s 1097s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide 1097s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1097s 1097s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide 1097s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1097s 1097s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 1097s /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps 1097s cls(buf, protocol).dump(obj) 1097s 1097s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps 1097s ps = pickle.dumps(ref_reader) 1097s 1097s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] 1097s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd 1097s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd 1097s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset 1097s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific 1097s /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. 1097s warnings.warn('Cannot average position for non sequential' 1097s 1097s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name] 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname] 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type] 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid] 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' 1097s warnings.warn("PDB file is missing resid information. " 1097s 1097s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX 1097s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1097s 1097s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2] 1097s /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. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2] 1097s /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. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2] 1097s /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. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2] 1097s /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. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1097s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings 1097s /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. 1097s warnings.warn(msg) 1097s 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts 1097s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr] 1097s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file. 1097s warnings.warn('No coordinate reader found for {}. Skipping ' 1097s 1097s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses 1097s /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. 1097s warnings.warn(msg, category=SelectionWarning) 1097s 1097s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 1097s /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. 1097s warnings.warn( 1097s 1097s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps 1097s return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1097s 1097s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps 1097s pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1097s 1097s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps 1097s return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL) 1097s 1097s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps 1097s return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL) 1097s 1097s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps 1097s return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL) 1097s 1097s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps 1097s pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL) 1097s 1097s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag 1097s /tmp/autopkgtest.ap6EeH/build.KOR/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps 1097s pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL) 1097s 1097s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings 1097s /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream 1097s warnings.warn("Constructed NamedStream from a NamedStream", 1097s 1097s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] 1097s /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. 1097s warnings.warn(wmsg, DeprecationWarning) 1097s 1097s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1097s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8130 warnings in 861.35s (0:14:21) = 1119s 1119s DueCredit Report: 1119s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] 1119s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] 1119s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] 1119s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] 1119s - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] 1119s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] 1119s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] 1119s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] 1119s - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] 1119s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] 1119s - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] 1119s - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 2.7.0, 1.1) [15, 16] 1119s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] 1119s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] 1119s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] 1119s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] 1119s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] 1119s - Scientific tools library / numpy (v 1.26.4) [22] 1119s 1119s 2 packages cited 1119s 16 modules cited 1119s 0 functions cited 1119s 1119s References 1119s ---------- 1119s 1119s [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. 1119s [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. 1119s [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. 1119s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 1119s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 1119s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460. 1119s [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. 1119s [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. 1119s [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. 1119s [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). 1119s [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. 1119s [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. 1119s [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. 1119s [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. 1119s [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. 1119s [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. 1119s [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. 1119s [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. 1119s [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. 1119s [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. 1119s [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. 1119s [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. 1121s autopkgtest [15:39:34]: test test-mdanalysis: -----------------------] 1122s test-mdanalysis PASS 1122s autopkgtest [15:39:35]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 1122s autopkgtest [15:39:35]: @@@@@@@@@@@@@@@@@@@@ summary 1122s test-mdanalysis PASS 1133s nova [W] Using flock in prodstack6-ppc64el 1133s flock: timeout while waiting to get lock 1133s Creating nova instance adt-plucky-ppc64el-mdanalysis-20241202-152052-juju-7f2275-prod-proposed-migration-environment-15-069d8757-381a-4cd4-b5d1-99a9a32145cd from image adt/ubuntu-plucky-ppc64el-server-20241202.img (UUID 1217a33d-4450-41fa-8048-44455666bd68)...