0s autopkgtest [15:20:34]: starting date and time: 2024-12-02 15:20:34+0000 0s autopkgtest [15:20:34]: git checkout: be626eda Fix armhf LXD image generation for plucky 0s autopkgtest [15:20:34]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.i2ujrabu/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@lcy02-2.secgroup --name adt-plucky-amd64-mdanalysis-20241202-152034-juju-7f2275-prod-proposed-migration-environment-20-71342017-8f27-4c90-bc28-0987fa7b0db3 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -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/ 50s autopkgtest [15:21:24]: testbed dpkg architecture: amd64 50s autopkgtest [15:21:24]: testbed apt version: 2.9.14ubuntu1 50s autopkgtest [15:21:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s autopkgtest [15:21:24]: testbed release detected to be: None 50s autopkgtest [15:21:24]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 51s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [782 kB] 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [68.5 kB] 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB] 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [126 kB] 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [85.1 kB] 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2572 B] 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.6 kB] 51s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [285 kB] 51s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [714 kB] 51s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [6364 B] 51s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [21.9 kB] 51s Fetched 2230 kB in 0s (7548 kB/s) 52s Reading package lists... 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 53s Calculating upgrade... 53s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s autopkgtest [15:21:28]: upgrading testbed (apt dist-upgrade and autopurge) 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 54s Starting 2 pkgProblemResolver with broken count: 0 54s Done 55s Entering ResolveByKeep 55s 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Starting pkgProblemResolver with broken count: 0 56s Starting 2 pkgProblemResolver with broken count: 0 56s Done 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s autopkgtest [15:21:31]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 58s autopkgtest [15:21:32]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 59s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (dsc) [2885 B] 59s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (tar) [47.0 MB] 59s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (diff) [10.9 kB] 60s gpgv: Signature made Fri Nov 15 13:40:58 2024 UTC 60s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 60s gpgv: Can't check signature: No public key 60s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5build1.dsc: no acceptable signature found 61s autopkgtest [15:21:35]: testing package mdanalysis version 2.7.0-5build1 61s autopkgtest [15:21:35]: build not needed 62s autopkgtest [15:21:36]: test test-mdanalysis: preparing testbed 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 63s Starting pkgProblemResolver with broken count: 0 63s Starting 2 pkgProblemResolver with broken count: 0 63s Done 63s The following NEW packages will be installed: 63s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 63s cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cython3 debhelper debugedit 63s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 63s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 63s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 63s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 63s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian libaec0 63s libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdebhelper-perl 63s libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 63s libfontenc1 libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 63s libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libimagequant0 libisl23 63s libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui 63s libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 63s liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libnetcdf19t64 63s libopenjp2-7 libpixman-1-0 libpython3-all-dev libpython3-dev 63s libpython3.12-dev libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 63s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 63s libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 63s libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 63s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 63s python3-alabaster python3-all python3-all-dev python3-appdirs 63s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 63s python3-citeproc python3-contourpy python3-cycler python3-dateutil 63s python3-decorator python3-defusedxml python3-dev python3-docutils 63s python3-duecredit python3-fasteners python3-fonttools python3-freetype 63s python3-fs python3-griddataformats python3-gsd python3-h5py 63s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 63s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 63s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 63s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 63s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 63s python3-netcdf4 python3-networkx python3-numpy python3-packaging 63s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 63s python3-pluggy python3-pybtex python3-pybtex-docutils 63s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 63s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 63s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 63s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 63s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 63s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 63s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 63s python3.12-tk python3.13-tk sphinx-common sphinx-rtd-theme-common 63s tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 63s xfonts-utils zlib1g-dev 63s 0 upgraded, 201 newly installed, 0 to remove and 0 not upgraded. 63s Need to get 223 MB of archives. 63s After this operation, 1008 MB of additional disk space will be used. 63s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-lato all 2.015-1 [2781 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 63s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 63s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 63s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 63s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 63s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 63s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 64s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 64s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 64s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 64s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 64s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 64s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 64s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 64s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 64s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 64s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 64s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 64s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 64s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 64s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 64s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 64s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 64s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 64s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 64s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 64s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 64s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 64s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 64s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 64s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 64s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 64s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 64s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 64s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 64s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 64s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 64s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 64s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 64s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 64s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 64s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 64s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 64s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-1ubuntu2 [3368 kB] 64s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 64s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-8 [166 kB] 64s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 64s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 64s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 64s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 64s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 64s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 64s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 64s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 64s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 64s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 64s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB] 64s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 64s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 64s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 64s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 64s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 64s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 64s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 64s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 64s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 64s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 64s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 64s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libexpat1-dev amd64 2.6.4-1 [148 kB] 64s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 64s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 64s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 64s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 64s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 64s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 64s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 64s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 64s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 64s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 64s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 64s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 64s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 64s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libjson-perl all 4.10000-1 [81.9 kB] 64s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 64s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 64s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 64s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 64s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 64s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf19t64 amd64 1:4.9.2-6ubuntu1 [472 kB] 64s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 64s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.12-dev amd64 3.12.7-3 [5699 kB] 64s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-dev amd64 3.12.6-0ubuntu1 [10.2 kB] 64s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-all-dev amd64 3.12.6-0ubuntu1 [916 B] 64s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 64s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 64s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 64s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 64s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 64s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 64s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 64s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 64s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 64s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 64s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 64s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] 64s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wheel all 0.45.1-1 [57.7 kB] 64s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-build all 1.2.2-1 [31.0 kB] 64s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 64s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-pyproject all 6.20241024 [1728 B] 64s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 64s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 64s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-mdanalysis-doc all 2.7.0-5build1 [2323 kB] 64s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 64s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] 64s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dev amd64 3.12.6-0ubuntu1 [26.7 kB] 64s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all-dev amd64 3.12.6-0ubuntu1 [908 B] 64s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 64s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 65s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 65s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 65s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 65s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu2 [9568 B] 65s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 65s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu2 [580 kB] 65s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build1 [143 kB] 65s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 65s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 65s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 65s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 65s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4build1 [1719 kB] 65s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build3 [368 kB] 65s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cftime amd64 1.6.4-1build1 [346 kB] 65s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1build1 [1834 kB] 65s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-citeproc all 0.6.0-3 [98.4 kB] 65s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2build1 [271 kB] 65s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 65s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 65s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 65s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-defusedxml all 0.7.1-2 [42.0 kB] 65s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-roman all 4.2-1 [10.0 kB] 65s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 65s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-looseversion all 1.3.0-3 [8354 B] 65s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-duecredit all 0.10.2-2 [66.0 kB] 65s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-monotonic all 1.6-2 [5732 B] 65s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-fasteners all 0.18-2 [12.5 kB] 65s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 65s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-5 [90.7 kB] 65s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build5 [27.5 kB] 65s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5ubuntu1 [21.7 MB] 65s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 65s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 65s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 65s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB] 65s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 65s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.0-3 [1759 kB] 65s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1014 kB] 65s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mrcfile all 1.5.3-3 [114 kB] 65s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-griddataformats all 1.0.2-2 [2107 kB] 65s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-gsd amd64 3.3.0-1build1 [233 kB] 65s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB] 65s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 65s Get:167 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 65s Get:168 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-hypothesis all 6.122.1-1 [330 kB] 65s Get:169 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-imagesize all 1.4.1-1 [6844 B] 65s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 65s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 65s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2build1 [70.3 kB] 65s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-latexcodec all 3.0.0-1 [16.6 kB] 65s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu1 [4691 kB] 65s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 65s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-msgpack amd64 1.0.3-3build3 [113 kB] 65s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mmtf all 1.1.3-1 [16.2 kB] 65s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 65s Get:179 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.1-1 [92.5 kB] 65s Get:180 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mdanalysis amd64 2.7.0-5build1 [2560 kB] 65s Get:181 http://ftpmaster.internal/ubuntu plucky/main amd64 sphinx-common all 7.4.7-4 [775 kB] 65s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 65s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 65s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-sphinx all 7.4.7-4 [593 kB] 65s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 65s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [23.5 kB] 65s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-msmb-theme all 1.2.0-4 [35.4 kB] 65s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-netcdf4 amd64 1.7.2-1build1 [942 kB] 65s Get:189 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 65s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5ubuntu1 [8271 kB] 66s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 66s Get:192 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 66s Get:193 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 66s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pybtex all 0.24.0-4 [70.0 kB] 66s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pybtex-docutils all 1.0.2-1 [7176 B] 66s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 66s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-seaborn all 0.13.2-4 [225 kB] 66s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6build1 [6868 kB] 66s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6build1 [2257 kB] 66s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinx-sitemap all 2.6.0-1 [6674 B] 66s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 66s Fetched 223 MB in 2s (96.3 MB/s) 66s Selecting previously unselected package fonts-lato. 67s (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 ... 75952 files and directories currently installed.) 67s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 67s Unpacking fonts-lato (2.015-1) ... 67s Selecting previously unselected package m4. 67s Preparing to unpack .../001-m4_1.4.19-4build1_amd64.deb ... 67s Unpacking m4 (1.4.19-4build1) ... 67s Selecting previously unselected package autoconf. 67s Preparing to unpack .../002-autoconf_2.72-3_all.deb ... 67s Unpacking autoconf (2.72-3) ... 67s Selecting previously unselected package autotools-dev. 67s Preparing to unpack .../003-autotools-dev_20220109.1_all.deb ... 67s Unpacking autotools-dev (20220109.1) ... 67s Selecting previously unselected package automake. 67s Preparing to unpack .../004-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 67s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 67s Selecting previously unselected package autopoint. 67s Preparing to unpack .../005-autopoint_0.22.5-2_all.deb ... 67s Unpacking autopoint (0.22.5-2) ... 67s Selecting previously unselected package libtcl8.6:amd64. 67s Preparing to unpack .../006-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 67s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 67s Selecting previously unselected package fonts-dejavu-mono. 67s Preparing to unpack .../007-fonts-dejavu-mono_2.37-8_all.deb ... 67s Unpacking fonts-dejavu-mono (2.37-8) ... 67s Selecting previously unselected package fonts-dejavu-core. 67s Preparing to unpack .../008-fonts-dejavu-core_2.37-8_all.deb ... 67s Unpacking fonts-dejavu-core (2.37-8) ... 67s Selecting previously unselected package libfontenc1:amd64. 67s Preparing to unpack .../009-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 67s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 67s Selecting previously unselected package x11-common. 67s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 67s Unpacking x11-common (1:7.7+23ubuntu3) ... 67s Selecting previously unselected package xfonts-encodings. 67s Preparing to unpack .../011-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 67s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 67s Selecting previously unselected package xfonts-utils. 67s Preparing to unpack .../012-xfonts-utils_1%3a7.7+7_amd64.deb ... 67s Unpacking xfonts-utils (1:7.7+7) ... 67s Selecting previously unselected package fonts-urw-base35. 67s Preparing to unpack .../013-fonts-urw-base35_20200910-8_all.deb ... 67s Unpacking fonts-urw-base35 (20200910-8) ... 67s Selecting previously unselected package fontconfig-config. 67s Preparing to unpack .../014-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 68s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 68s Selecting previously unselected package libfontconfig1:amd64. 68s Preparing to unpack .../015-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 68s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 68s Selecting previously unselected package libxrender1:amd64. 68s Preparing to unpack .../016-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 68s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 68s Selecting previously unselected package libxft2:amd64. 68s Preparing to unpack .../017-libxft2_2.3.6-1build1_amd64.deb ... 68s Unpacking libxft2:amd64 (2.3.6-1build1) ... 68s Selecting previously unselected package libxss1:amd64. 68s Preparing to unpack .../018-libxss1_1%3a1.2.3-1build3_amd64.deb ... 68s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 68s Selecting previously unselected package libtk8.6:amd64. 68s Preparing to unpack .../019-libtk8.6_8.6.15-1_amd64.deb ... 68s Unpacking libtk8.6:amd64 (8.6.15-1) ... 68s Selecting previously unselected package tk8.6-blt2.5. 68s Preparing to unpack .../020-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 68s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 68s Selecting previously unselected package blt. 68s Preparing to unpack .../021-blt_2.5.3+dfsg-7build1_amd64.deb ... 68s Unpacking blt (2.5.3+dfsg-7build1) ... 68s Selecting previously unselected package libisl23:amd64. 68s Preparing to unpack .../022-libisl23_0.27-1_amd64.deb ... 68s Unpacking libisl23:amd64 (0.27-1) ... 68s Selecting previously unselected package libmpc3:amd64. 68s Preparing to unpack .../023-libmpc3_1.3.1-1build2_amd64.deb ... 68s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 68s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 68s Preparing to unpack .../024-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package cpp-14. 68s Preparing to unpack .../025-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package cpp-x86-64-linux-gnu. 68s Preparing to unpack .../026-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 68s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 68s Selecting previously unselected package cpp. 68s Preparing to unpack .../027-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 68s Unpacking cpp (4:14.1.0-2ubuntu1) ... 68s Selecting previously unselected package libcc1-0:amd64. 68s Preparing to unpack .../028-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package libgomp1:amd64. 68s Preparing to unpack .../029-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package libitm1:amd64. 68s Preparing to unpack .../030-libitm1_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 68s Selecting previously unselected package libasan8:amd64. 68s Preparing to unpack .../031-libasan8_14.2.0-8ubuntu1_amd64.deb ... 68s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package liblsan0:amd64. 69s Preparing to unpack .../032-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package libtsan2:amd64. 69s Preparing to unpack .../033-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package libubsan1:amd64. 69s Preparing to unpack .../034-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package libhwasan0:amd64. 69s Preparing to unpack .../035-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package libquadmath0:amd64. 69s Preparing to unpack .../036-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package libgcc-14-dev:amd64. 69s Preparing to unpack .../037-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 69s Preparing to unpack .../038-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package gcc-14. 69s Preparing to unpack .../039-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 69s Selecting previously unselected package gcc-x86-64-linux-gnu. 69s Preparing to unpack .../040-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 69s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 69s Selecting previously unselected package gcc. 69s Preparing to unpack .../041-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 69s Unpacking gcc (4:14.1.0-2ubuntu1) ... 69s Selecting previously unselected package libstdc++-14-dev:amd64. 69s Preparing to unpack .../042-libstdc++-14-dev_14.2.0-8ubuntu1_amd64.deb ... 69s Unpacking libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 70s Selecting previously unselected package g++-14-x86-64-linux-gnu. 70s Preparing to unpack .../043-g++-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 70s Unpacking g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 70s Selecting previously unselected package g++-14. 70s Preparing to unpack .../044-g++-14_14.2.0-8ubuntu1_amd64.deb ... 70s Unpacking g++-14 (14.2.0-8ubuntu1) ... 70s Selecting previously unselected package g++-x86-64-linux-gnu. 70s Preparing to unpack .../045-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 70s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 70s Selecting previously unselected package g++. 70s Preparing to unpack .../046-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 70s Unpacking g++ (4:14.1.0-2ubuntu1) ... 70s Selecting previously unselected package build-essential. 70s Preparing to unpack .../047-build-essential_12.10ubuntu1_amd64.deb ... 70s Unpacking build-essential (12.10ubuntu1) ... 70s Selecting previously unselected package cython3. 70s Preparing to unpack .../048-cython3_3.0.11+dfsg-1ubuntu2_amd64.deb ... 70s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ... 70s Selecting previously unselected package libdebhelper-perl. 70s Preparing to unpack .../049-libdebhelper-perl_13.20ubuntu1_all.deb ... 70s Unpacking libdebhelper-perl (13.20ubuntu1) ... 70s Selecting previously unselected package libtool. 70s Preparing to unpack .../050-libtool_2.4.7-8_all.deb ... 70s Unpacking libtool (2.4.7-8) ... 70s Selecting previously unselected package dh-autoreconf. 70s Preparing to unpack .../051-dh-autoreconf_20_all.deb ... 70s Unpacking dh-autoreconf (20) ... 70s Selecting previously unselected package libarchive-zip-perl. 70s Preparing to unpack .../052-libarchive-zip-perl_1.68-1_all.deb ... 70s Unpacking libarchive-zip-perl (1.68-1) ... 70s Selecting previously unselected package libfile-stripnondeterminism-perl. 70s Preparing to unpack .../053-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 70s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 70s Selecting previously unselected package dh-strip-nondeterminism. 70s Preparing to unpack .../054-dh-strip-nondeterminism_1.14.0-1_all.deb ... 70s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 70s Selecting previously unselected package debugedit. 70s Preparing to unpack .../055-debugedit_1%3a5.1-1_amd64.deb ... 70s Unpacking debugedit (1:5.1-1) ... 70s Selecting previously unselected package dwz. 70s Preparing to unpack .../056-dwz_0.15-1build6_amd64.deb ... 70s Unpacking dwz (0.15-1build6) ... 70s Selecting previously unselected package gettext. 70s Preparing to unpack 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fonts-font-awesome. 71s Preparing to unpack .../063-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 71s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 71s Selecting previously unselected package fonts-lyx. 71s Preparing to unpack .../064-fonts-lyx_2.4.2.1-1_all.deb ... 71s Unpacking fonts-lyx (2.4.2.1-1) ... 71s Selecting previously unselected package fonts-mathjax. 71s Preparing to unpack .../065-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 71s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 71s Selecting previously unselected package libaec0:amd64. 71s Preparing to unpack .../066-libaec0_1.1.3-1_amd64.deb ... 71s Unpacking libaec0:amd64 (1.1.3-1) ... 71s Selecting previously unselected package libblas3:amd64. 71s Preparing to unpack .../067-libblas3_3.12.0-4_amd64.deb ... 71s Unpacking libblas3:amd64 (3.12.0-4) ... 71s Selecting previously unselected package libpixman-1-0:amd64. 71s Preparing to unpack .../068-libpixman-1-0_0.44.0-3_amd64.deb ... 71s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 71s Selecting previously unselected package libxcb-render0:amd64. 71s Preparing to unpack .../069-libxcb-render0_1.17.0-2_amd64.deb ... 71s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 71s Selecting previously unselected package libxcb-shm0:amd64. 71s Preparing to unpack .../070-libxcb-shm0_1.17.0-2_amd64.deb ... 71s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 71s Selecting previously unselected package libcairo2:amd64. 71s Preparing to unpack .../071-libcairo2_1.18.2-2_amd64.deb ... 71s Unpacking libcairo2:amd64 (1.18.2-2) ... 71s Selecting previously unselected package libdeflate0:amd64. 71s Preparing to unpack .../072-libdeflate0_1.22-1_amd64.deb ... 71s Unpacking libdeflate0:amd64 (1.22-1) ... 71s Selecting previously unselected package libexpat1-dev:amd64. 71s Preparing to unpack .../073-libexpat1-dev_2.6.4-1_amd64.deb ... 71s Unpacking libexpat1-dev:amd64 (2.6.4-1) ... 71s Selecting previously unselected package libgfortran5:amd64. 71s Preparing 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unselected package libpython3.12-dev:amd64. 72s Preparing to unpack .../095-libpython3.12-dev_3.12.7-3_amd64.deb ... 72s Unpacking libpython3.12-dev:amd64 (3.12.7-3) ... 72s Selecting previously unselected package libpython3-dev:amd64. 72s Preparing to unpack .../096-libpython3-dev_3.12.6-0ubuntu1_amd64.deb ... 72s Unpacking libpython3-dev:amd64 (3.12.6-0ubuntu1) ... 72s Selecting previously unselected package libpython3-all-dev:amd64. 72s Preparing to unpack .../097-libpython3-all-dev_3.12.6-0ubuntu1_amd64.deb ... 72s Unpacking libpython3-all-dev:amd64 (3.12.6-0ubuntu1) ... 72s Selecting previously unselected package libqhull-r8.0:amd64. 72s Preparing to unpack .../098-libqhull-r8.0_2020.2-6build1_amd64.deb ... 72s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 72s Selecting previously unselected package libraqm0:amd64. 72s Preparing to unpack .../099-libraqm0_0.10.1-1build1_amd64.deb ... 72s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 72s Selecting previously unselected package libsharpyuv0:amd64. 72s Preparing to unpack .../100-libsharpyuv0_1.4.0-0.1_amd64.deb ... 72s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 72s Selecting previously unselected package libjbig0:amd64. 72s Preparing to unpack .../101-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 72s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 72s Selecting previously unselected package libwebp7:amd64. 72s Preparing to unpack .../102-libwebp7_1.4.0-0.1_amd64.deb ... 72s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 72s Selecting previously unselected package libtiff6:amd64. 72s Preparing to unpack .../103-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 72s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 73s Selecting previously unselected package libwebpdemux2:amd64. 73s Preparing to unpack .../104-libwebpdemux2_1.4.0-0.1_amd64.deb ... 73s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 73s Selecting previously unselected package libwebpmux3:amd64. 73s Preparing to unpack .../105-libwebpmux3_1.4.0-0.1_amd64.deb 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python3-build. 73s Preparing to unpack .../111-python3-build_1.2.2-1_all.deb ... 73s Unpacking python3-build (1.2.2-1) ... 73s Selecting previously unselected package python3-installer. 73s Preparing to unpack .../112-python3-installer_0.7.0+dfsg1-3_all.deb ... 73s Unpacking python3-installer (0.7.0+dfsg1-3) ... 73s Selecting previously unselected package pybuild-plugin-pyproject. 73s Preparing to unpack .../113-pybuild-plugin-pyproject_6.20241024_all.deb ... 73s Unpacking pybuild-plugin-pyproject (6.20241024) ... 73s Selecting previously unselected package python-matplotlib-data. 73s Preparing to unpack .../114-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ... 73s Unpacking python-matplotlib-data (3.8.3-3ubuntu1) ... 73s Selecting previously unselected package libjs-mathjax. 73s Preparing to unpack .../115-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 73s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 74s Selecting previously unselected package python-mdanalysis-doc. 74s Preparing to unpack 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libopenjp2-7:amd64. 74s Preparing to unpack .../127-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 74s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 74s Selecting previously unselected package python3-pil:amd64. 74s Preparing to unpack .../128-python3-pil_10.4.0-1ubuntu2_amd64.deb ... 74s Unpacking python3-pil:amd64 (10.4.0-1ubuntu2) ... 75s Selecting previously unselected package python3-cairo. 75s Preparing to unpack .../129-python3-cairo_1.26.1-2build1_amd64.deb ... 75s Unpacking python3-cairo (1.26.1-2build1) ... 75s Selecting previously unselected package python3-freetype. 75s Preparing to unpack .../130-python3-freetype_2.5.1-1_all.deb ... 75s Unpacking python3-freetype (2.5.1-1) ... 75s Selecting previously unselected package python3-rlpycairo. 75s Preparing to unpack .../131-python3-rlpycairo_0.3.0-3_all.deb ... 75s Unpacking python3-rlpycairo (0.3.0-3) ... 75s Selecting previously unselected package python3-reportlab. 75s Preparing to unpack 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(5.3.0-1build1) ... 75s Selecting previously unselected package python3-citeproc. 75s Preparing to unpack .../138-python3-citeproc_0.6.0-3_all.deb ... 75s Unpacking python3-citeproc (0.6.0-3) ... 75s Selecting previously unselected package python3-contourpy. 75s Preparing to unpack .../139-python3-contourpy_1.3.0-2build1_amd64.deb ... 75s Unpacking python3-contourpy (1.3.0-2build1) ... 75s Selecting previously unselected package python3-cycler. 75s Preparing to unpack .../140-python3-cycler_0.12.1-1_all.deb ... 75s Unpacking python3-cycler (0.12.1-1) ... 75s Selecting previously unselected package python3-dateutil. 75s Preparing to unpack .../141-python3-dateutil_2.9.0-3_all.deb ... 75s Unpacking python3-dateutil (2.9.0-3) ... 75s Selecting previously unselected package python3-decorator. 75s Preparing to unpack .../142-python3-decorator_5.1.1-5_all.deb ... 75s Unpacking python3-decorator (5.1.1-5) ... 75s Selecting previously unselected package python3-defusedxml. 75s Preparing to unpack .../143-python3-defusedxml_0.7.1-2_all.deb ... 75s Unpacking python3-defusedxml (0.7.1-2) ... 75s Selecting previously unselected package python3-roman. 75s Preparing to unpack .../144-python3-roman_4.2-1_all.deb ... 75s Unpacking python3-roman (4.2-1) ... 75s Selecting previously unselected package python3-docutils. 75s Preparing to unpack .../145-python3-docutils_0.21.2+dfsg-2_all.deb ... 75s Unpacking python3-docutils (0.21.2+dfsg-2) ... 75s Selecting previously unselected package python3-looseversion. 75s Preparing to unpack .../146-python3-looseversion_1.3.0-3_all.deb ... 75s Unpacking python3-looseversion (1.3.0-3) ... 76s Selecting previously unselected package python3-duecredit. 76s Preparing to unpack .../147-python3-duecredit_0.10.2-2_all.deb ... 76s Unpacking python3-duecredit (0.10.2-2) ... 76s Selecting previously unselected package python3-monotonic. 76s Preparing to unpack .../148-python3-monotonic_1.6-2_all.deb ... 76s Unpacking python3-monotonic (1.6-2) ... 76s Selecting previously unselected package python3-fasteners. 76s Preparing to unpack .../149-python3-fasteners_0.18-2_all.deb ... 76s Unpacking python3-fasteners (0.18-2) ... 76s Selecting previously unselected package python3-tz. 76s Preparing to unpack .../150-python3-tz_2024.1-2_all.deb ... 76s Unpacking python3-tz (2024.1-2) ... 76s Selecting previously unselected package python3-fs. 76s Preparing to unpack .../151-python3-fs_2.4.16-5_all.deb ... 76s Unpacking python3-fs (2.4.16-5) ... 76s Selecting previously unselected package python3-lz4. 76s Preparing to unpack .../152-python3-lz4_4.0.2+dfsg-1build5_amd64.deb ... 76s Unpacking python3-lz4 (4.0.2+dfsg-1build5) ... 76s Selecting previously unselected package python3-scipy. 76s Preparing to unpack .../153-python3-scipy_1.13.1-5ubuntu1_amd64.deb ... 76s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 76s Selecting previously unselected package python3-mpmath. 76s Preparing to unpack .../154-python3-mpmath_1.3.0-1_all.deb ... 76s 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sphinx-rtd-theme-common. 77s Preparing to unpack .../160-sphinx-rtd-theme-common_3.0.2+dfsg-1_all.deb ... 77s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-1) ... 77s Selecting previously unselected package python3-mrcfile. 77s Preparing to unpack .../161-python3-mrcfile_1.5.3-3_all.deb ... 77s Unpacking python3-mrcfile (1.5.3-3) ... 77s Selecting previously unselected package python3-griddataformats. 77s Preparing to unpack .../162-python3-griddataformats_1.0.2-2_all.deb ... 77s Unpacking python3-griddataformats (1.0.2-2) ... 77s Selecting previously unselected package python3-gsd. 77s Preparing to unpack .../163-python3-gsd_3.3.0-1build1_amd64.deb ... 77s Unpacking python3-gsd (3.3.0-1build1) ... 77s Selecting previously unselected package python3-h5py-serial. 77s Preparing to unpack .../164-python3-h5py-serial_3.11.0-5ubuntu1_amd64.deb ... 77s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 77s Selecting previously unselected package python3-h5py. 77s Preparing to unpack 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package python3-mmtf. 78s Preparing to unpack .../176-python3-mmtf_1.1.3-1_all.deb ... 78s Unpacking python3-mmtf (1.1.3-1) ... 78s Selecting previously unselected package python3-threadpoolctl. 78s Preparing to unpack .../177-python3-threadpoolctl_3.1.0-1_all.deb ... 78s Unpacking python3-threadpoolctl (3.1.0-1) ... 78s Selecting previously unselected package python3-tqdm. 78s Preparing to unpack .../178-python3-tqdm_4.67.1-1_all.deb ... 78s Unpacking python3-tqdm (4.67.1-1) ... 78s Selecting previously unselected package python3-mdanalysis. 78s Preparing to unpack .../179-python3-mdanalysis_2.7.0-5build1_amd64.deb ... 78s Unpacking python3-mdanalysis (2.7.0-5build1) ... 78s Selecting previously unselected package sphinx-common. 78s Preparing to unpack .../180-sphinx-common_7.4.7-4_all.deb ... 78s Unpacking sphinx-common (7.4.7-4) ... 78s Selecting previously unselected package python3-alabaster. 78s Preparing to unpack .../181-python3-alabaster_0.7.16-0.1_all.deb ... 78s Unpacking 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libpython3.12-dev:amd64 (3.12.7-3) ... 121s Setting up xfonts-utils (1:7.7+7) ... 121s Setting up intltool-debian (0.35.0+20060710.6) ... 121s Setting up python3-fs (2.4.16-5) ... 122s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 122s Setting up libraqm0:amd64 (0.10.1-1build1) ... 122s Setting up python3.12-dev (3.12.7-3) ... 122s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 122s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 123s Setting up libjs-sphinxdoc (7.4.7-4) ... 123s Setting up cpp-14 (14.2.0-8ubuntu1) ... 123s Setting up dh-strip-nondeterminism (1.14.0-1) ... 123s Setting up python3-lxml:amd64 (5.3.0-1build1) ... 123s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 123s Setting up python3-contourpy (1.3.0-2build1) ... 124s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 124s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 124s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 124s Setting up liblbfgsb0:amd64 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135s Setting up g++ (4:14.1.0-2ubuntu1) ... 135s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 135s Setting up build-essential (12.10ubuntu1) ... 135s Setting up debhelper (13.20ubuntu1) ... 135s Setting up python3-fonttools (4.55.0-3) ... 136s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 136s Processing triggers for sgml-base (1.31) ... 136s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 136s Setting up python3-docutils (0.21.2+dfsg-2) ... 136s Processing triggers for install-info (7.1.1-1) ... 136s Setting up libxft2:amd64 (2.3.6-1build1) ... 136s Setting up libtk8.6:amd64 (8.6.15-1) ... 136s Processing triggers for libc-bin (2.40-1ubuntu3) ... 137s Setting up python3.12-tk (3.12.7-3) ... 137s Processing triggers for man-db (2.13.0-1) ... 138s Setting up libcairo2:amd64 (1.18.2-2) ... 138s Setting up python3.13-tk (3.13.0-2) ... 138s Setting up python3-pybtex-docutils (1.0.2-1) ... 139s Setting up python3-sphinx (7.4.7-4) ... 139s 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with SKIP_TEST_LIST= 153s ============================= test session starts ============================== 153s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 153s rootdir: /tmp/autopkgtest.0zaHFA/build.9A0/src 153s plugins: hypothesis-6.122.1, typeguard-4.4.1 153s collected 19229 items / 6 skipped 153s 157s testsuite/MDAnalysisTests/analysis/test_align.py ....................... 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[100%] 800s 800s =============================== warnings summary =============================== 800s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39 800s /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. 800s 800s Due to the on going maintenance burden of keeping command line application 800s wrappers up to date, we have decided to deprecate and eventually remove these 800s modules. 800s 800s We instead now recommend building your command line and invoking it directly 800s with the subprocess module. 800s warnings.warn( 800s 800s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings 800s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings 800s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings 800s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings 800s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings 800s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings 800s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings 800s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings 800s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings 800s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings 800s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings 800s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings 800s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings 800s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings 800s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings 800s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 800s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings 800s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings 800s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings 800s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings 800s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings 800s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings 800s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings 800s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings 800s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings 800s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings 800s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings 800s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings 800s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings 800s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings 800s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 800s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings 800s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 800s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings 800s /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. 800s warnings.warn("DCDReader currently makes independent timesteps" 800s 800s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 800s /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. 800s warnings.warn(wmsg, category=DeprecationWarning) 800s 800s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings 800s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings 800s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written 800s warnings.warn(wmsg) 800s 800s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings 800s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings 800s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings 800s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings 800s /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 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings 800s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 800s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings 800s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning 800s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings 800s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file. 800s warnings.warn('No coordinate reader found for {}. Skipping ' 800s 800s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 800s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'oh', 'h1', 'hc', 'ho', 'c3'}. These have been given an empty element record. 800s warnings.warn("Unknown elements found for some " 800s 800s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 800s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning 800s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings 800s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings 800s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 800s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings 800s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings 800s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps 800s self.times[i] = ts.time 800s 800s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings 800s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning 800s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings 800s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 800s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings 800s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 800s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings 800s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings 800s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded 800s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps 800s results.append((ts.time, x.sum() / mask.sum())) 800s 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue 800s /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. 800s warnings.warn(msg) 800s 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 800s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding 800s /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 800s warnings.warn(msg) 800s 800s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 800s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 800s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings 800s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 800s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 800s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings 800s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning 800s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings 800s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings 800s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings 800s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings 800s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings 800s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 800s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings 800s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings 800s /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. 800s warnings.warn("Element information is missing, elements attribute " 800s 800s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran 800s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame 800s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections 800s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning 800s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues 800s warnings.warn("Cannot determine phi and psi angles for the first " 800s 800s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin 800s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr 800s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame 800s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot 800s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning 800s /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. 800s warnings.warn(f"All residues selected with '{select_remove}' " 800s 800s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings 800s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings 800s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings 800s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=6080) is multi-threaded, use of fork() may lead to deadlocks in the child. 800s self.pid = os.fork() 800s 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes 800s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide 800s cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms 800s 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide 800s local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) 800s 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 800s /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice 800s ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, 800s 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 800s /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide 800s ret = um.true_divide( 800s 800s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 800s /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide 800s ret = ret.dtype.type(ret / rcount) 800s 800s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 800s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning 800s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning 800s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 800s /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. 800s warnings.warn("1 A^3 CRYST1 record," 800s 800s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. 800s warnings.warn("Unit cell dimensions not found. " 800s 800s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings 800s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings 800s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings 800s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 800s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings 800s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings 800s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 800s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning 800s /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 800s warnings.warn(wmsg, DeprecationWarning) 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 800s warnings.warn("Desired number of sample points too high, using {0}" 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbond = HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbond = HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbond = HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbond = HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbond = HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbond = HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbond = HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbond = HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s HBAC( 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 800s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 800s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbond = HBAC(u, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! 800s `find_hydrogen_donors` will be removed in release 3.0.0. 800s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s D = hbonds.find_hydrogen_donors(H) 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! 800s `find_hydrogen_donors` will be removed in release 3.0.0. 800s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 800s hbonds.find_hydrogen_donors(u.atoms) 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 800s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 800s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. 800s return _methods._mean(a, axis=axis, dtype=dtype, 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 800s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 800s /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide 800s ret = ret.dtype.type(ret / rcount) 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 800s /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. 800s warnings.warn(msg.format(sel)) 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 800s /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. 800s warnings.warn(msg.format(sel)) 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 800s /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. 800s warnings.warn(msg.format(sel)) 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 800s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. 800s warnings.warn("Empty string to select atoms, empty group returned.", 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 800s /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, . 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 800s /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, . 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 800s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 800s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 800s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 800s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 800s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 800s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple 800s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content 800s /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. 800s warnings.warn(wmsg) 800s 800s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning 800s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning 800s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 800s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 800s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 800s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 800s /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.) 800s phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi 800s 800s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j 800s /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 800s warnings.warn("Column index entered (j = {:d} is smaller than row " 800s 800s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps 800s dt=self.trajectory.ts.dt * step, 800s 800s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] 800s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] 800s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] 800s /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 800s warnings.warn(wmsg, DeprecationWarning) 800s 800s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 800s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings 800s /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. 800s warnings.warn("The `u` attribute is superflous and will be removed " 800s 800s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] 800s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm 800s /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. 800s warnings.warn("The `density` attribute was deprecated in " 800s 800s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata 800s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. 800s warnings.warn(msg, category=MissingDataWarning) 800s 800s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps 800s self.timesteps.append(self._ts.time) 800s 800s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning 800s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default 800s warnings.warn("{} does not support time selection. Reverting to " 800s 800s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default 800s warnings.warn("{} does not support data selection. Reverting to " 800s 800s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings 800s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings 800s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 800s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning 800s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings 800s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps 800s return self.ts.dt 800s 800s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings 800s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 800s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 800s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps 800s ts.data['time'] = step_num * ts.dt 800s 800s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats 800s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_unsupported_filetypes 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 800s self.close() 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close 800s self._apply('close') 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply 800s return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] 800s ^^^^^^^^^^^^ 800s AttributeError: 'ChainReader' object has no attribute 'readers' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing 800s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain 800s warnings.warn("Missing frame in continuous chain", UserWarning) 800s 800s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps 800s time_frame_0 = ts.time - ts.frame*ts.dt # assumes ts.dt is constant 800s 800s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps 800s frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps 800s step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps 800s self._add_step_to_frame_data(ts.time) 800s 800s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings 800s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 800s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps 800s if not np.allclose(A.time, B.time): 800s 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] 800s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array 800s /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 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 800s self.close() 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close 800s self._file.close() 800s ^^^^^^^^^^ 800s AttributeError: 'DCDReader' object has no attribute '_file' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms 800s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit 800s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__ 800s self.close() 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close 800s self._file.close() 800s ^^^^^^^^^^ 800s AttributeError: 'DCDWriter' object has no attribute '_file' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings 800s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings 800s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings 800s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 800s /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. 800s warnings.warn(msg) 800s 800s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps 800s return self.ts.time 800s 800s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps 800s assert_equal(reader.ts.dt, reader.dt) 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps 800s time_frame = time_frame_0 + frame_index*ts.dt 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps 800s reader_p = pickle.loads(pickle.dumps(reader)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings 800s /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 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] 800s warnings.warn(wmsg) 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 800s /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`. 800s warnings.warn(wmsg) 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. 800s warnings.warn("Not all velocities were present. " 800s 800s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps 800s reader_p = pickle.loads(pickle.dumps(reader)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader 800s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps 800s reader_p = pickle.loads(pickle.dumps(reader)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 800s self.close() 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close 800s self._file.close() 800s ^^^^^^^^^^ 800s AttributeError: 'H5MDReader' object has no attribute '_file' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 800s for aux in self.aux_list: 800s ^^^^^^^^^^^^^ 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 800s return self._auxs.keys() 800s ^^^^^^^^^^ 800s AttributeError: 'H5MDReader' object has no attribute '_auxs' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings 800s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 800s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 800s warnings.warn('Guessed all Masses to 1.0') 800s 800s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit 800s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 800s for aux in self.aux_list: 800s ^^^^^^^^^^^^^ 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 800s return self._auxs.keys() 800s ^^^^^^^^^^ 800s AttributeError: 'DCDReader' object has no attribute '_auxs' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view 800s /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 800s warnings.warn("MemoryReader.timeseries inclusive `stop` " 800s 800s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader 800s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps 800s reader_p = pickle.loads(pickle.dumps(reader)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 800s /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 800s warnings.warn(wmsg) 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps 800s ts.time) # in-place ! (hope this works...) 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps 800s time_list = [ts.time for ts in u.trajectory] 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps 800s assert u.trajectory.ts.dt == pytest.approx(ref) 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 800s /tmp/autopkgtest.0zaHFA/build.9A0/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.) 800s return self._test_write_trajectory(universe, outfile) 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] 800s /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. 800s warnings.warn(wmsg) 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 800s /tmp/autopkgtest.0zaHFA/build.9A0/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.) 800s return self._test_write_trajectory(universe, outfile) 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings 800s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 800s warnings.warn("Found missing chainIDs." 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom] 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond] 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom] 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree] 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond] 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom] 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps 800s time = ts.time 800s 800s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 800s self.close() 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close 800s if self.trjfile is not None: 800s ^^^^^^^^^^^^ 800s AttributeError: 'NCDFWriter' object has no attribute 'trjfile' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 800s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 800s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 800s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' 800s warnings.warn("Found no information for attr: '{}'" 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' 800s warnings.warn("Found chainIDs using unnaccepted character." 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' 800s warnings.warn("Found chainIDs with invalid length." 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed 800s warnings.warn("Serial numbers went over 100,000. " 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed 800s warnings.warn("Invalid atom serials were present, bonds will not" 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed 800s warnings.warn("Invalid atom serials were present, " 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment 800s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 800s /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. 800s warnings.warn(wmsg) 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 800s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 800s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 800s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 800s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 800s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 800s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges 800s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps 800s assert_equal(ts.dt, 1.0) # default value 800s 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps 800s assert_equal(ts.time, 0.0) # default to 1.0 (dt) * 0 (frame) 800s 800s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 800s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps 800s assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt) 800s 800s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 800s for aux in self.aux_list: 800s ^^^^^^^^^^^^^ 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 800s return self._auxs.keys() 800s ^^^^^^^^^^ 800s AttributeError: 'TNGReader' object has no attribute '_auxs' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms 800s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe 800s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe 800s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 800s self.close() 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close 800s if self.trjfile is None: 800s ^^^^^^^^^^^^ 800s AttributeError: 'TRJReader' object has no attribute 'trjfile' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps 800s data['time'] = ts.time 800s 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 800s /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 800s warnings.warn("Timestep didn't have the following attributes: '{0}', " 800s 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 800s /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. 800s warnings.warn("Timestep didn't have velocity information, " 800s 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 800s /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 800s warnings.warn("Timestep didn't have dimensions information, " 800s 800s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 800s self.close() 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close 800s if self.trzfile is None: 800s ^^^^^^^^^^^^ 800s AttributeError: 'TRZWriter' object has no attribute 'trzfile' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 800s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 800s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 800s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 800s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 800s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 800s /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. 800s warnings.warn("Element information is missing, elements attribute " 800s 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 800s /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 800s warnings.warn(wmsg, DeprecationWarning) 800s 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] 800s /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. 800s warnings.warn( 800s 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] 800s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] 800s /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' 800s warnings.warn(wmsg) 800s 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD 800s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps 800s time = ts.time 800s 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD 800s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps 800s time = ts.time 800s 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 800s self.close() 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 800s self._xdr.close() 800s ^^^^^^^^^ 800s AttributeError: 'XTCWriter' object has no attribute '_xdr' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container 800s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 800s 800s Traceback (most recent call last): 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 800s self.close() 800s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 800s self._xdr.close() 800s ^^^^^^^^^ 800s AttributeError: 'TRRWriter' object has no attribute '_xdr' 800s 800s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 800s 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 800s /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. 800s Consider setting 'refresh_offsets=True' when loading your Universe. 800s warnings.warn(f"Reading offsets from {fname} failed, " 800s 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly 800s /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. 800s warnings.warn(f"Cannot write lock/offset file in same location as " 800s 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 800s /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. 800s Consider setting 'refresh_offsets=True' when loading your Universe. 800s warnings.warn(f"Reading offsets from {fname} failed, " 800s 800s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly 800s /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. 800s warnings.warn(f"Cannot write lock/offset file in same location as " 800s 800s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] 800s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] 800s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] 800s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce 800s return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 800s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 800s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21 800s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 800s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 801s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 801s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 801s /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. 801s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings 801s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings 801s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings 801s /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. 801s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 801s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings 801s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 801s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 801s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide 801s return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() 801s 801s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings 801s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide 801s _centers /= _weights.sum(axis=1)[:, None] 801s 801s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 801s /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`. 801s warnings.warn(msg, category=SelectionWarning) 801s 801s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 801s /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`. 801s warnings.warn(msg, category=SelectionWarning) 801s 801s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] 801s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] 801s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] 801s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] 801s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] 801s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] 801s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] 801s /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`. 801s warnings.warn(msg, category=SelectionWarning) 801s 801s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] 801s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] 801s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] 801s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] 801s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] 801s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc 801s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc 801s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options 801s /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 801s warnings.warn("The 'pbc' kwarg has been deprecated and will be " 801s 801s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel 801s /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`. 801s warnings.warn(msg, category=SelectionWarning) 801s 801s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] 801s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] 801s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] 801s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] 801s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] 801s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide 801s x = np.dot(a, b) / (norm(a) * norm(b)) 801s 801s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt 801s ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) 801s 801s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt 801s box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - 801s 801s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide 801s a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) 801s 801s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide 801s b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) 801s 801s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide 801s c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) 801s 801s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide 801s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 801s 801s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide 801s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 801s 801s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 801s /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps 801s cls(buf, protocol).dump(obj) 801s 801s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps 801s ps = pickle.dumps(ref_reader) 801s 801s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] 801s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd 801s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd 801s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset 801s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific 801s /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. 801s warnings.warn('Cannot average position for non sequential' 801s 801s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name] 801s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname] 801s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type] 801s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid] 801s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' 801s warnings.warn("PDB file is missing resid information. " 801s 801s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX 801s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 801s 801s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2] 801s /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. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2] 801s /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. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2] 801s /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. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2] 801s /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. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 801s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 801s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 801s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings 801s /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. 801s warnings.warn(msg) 801s 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts 801s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr] 801s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file. 801s warnings.warn('No coordinate reader found for {}. Skipping ' 801s 801s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses 801s /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. 801s warnings.warn(msg, category=SelectionWarning) 801s 801s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 801s /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. 801s warnings.warn( 801s 801s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps 801s return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 801s 801s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps 801s pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 801s 801s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps 801s return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL) 801s 801s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps 801s return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL) 801s 801s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps 801s return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL) 801s 801s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps 801s pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL) 801s 801s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag 801s /tmp/autopkgtest.0zaHFA/build.9A0/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps 801s pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL) 801s 801s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings 801s /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream 801s warnings.warn("Constructed NamedStream from a NamedStream", 801s 801s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] 801s /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. 801s warnings.warn(wmsg, DeprecationWarning) 801s 801s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 801s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8130 warnings in 655.73s (0:10:55) = 812s 812s DueCredit Report: 812s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] 812s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] 812s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] 812s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] 812s - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] 812s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] 812s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] 812s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] 812s - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] 812s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] 812s - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] 812s - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 1.1, 2.7.0) [15, 16] 812s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] 812s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] 812s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] 812s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] 812s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] 812s - Scientific tools library / numpy (v 1.26.4) [22] 812s 812s 2 packages cited 812s 16 modules cited 812s 0 functions cited 812s 812s References 812s ---------- 812s 812s [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. 812s [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. 812s [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. 812s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 812s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 812s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460. 812s [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. 812s [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. 812s [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. 812s [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). 812s [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. 812s [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. 812s [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. 812s [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. 812s [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. 812s [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. 812s [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. 812s [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. 812s [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. 812s [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. 812s [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. 812s [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. 815s autopkgtest [15:34:09]: test test-mdanalysis: -----------------------] 815s autopkgtest [15:34:09]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 815s test-mdanalysis PASS 815s autopkgtest [15:34:09]: @@@@@@@@@@@@@@@@@@@@ summary 815s test-mdanalysis PASS 826s nova [W] Skipping flock for amd64 826s Creating nova instance adt-plucky-amd64-mdanalysis-20241202-152034-juju-7f2275-prod-proposed-migration-environment-20-71342017-8f27-4c90-bc28-0987fa7b0db3 from image adt/ubuntu-plucky-amd64-server-20241130.img (UUID 46fc820e-f57d-4f95-9552-34230b3cb565)...