0s autopkgtest [15:20:51]: starting date and time: 2024-12-02 15:20:51+0000 0s autopkgtest [15:20:51]: git checkout: be626eda Fix armhf LXD image generation for plucky 0s autopkgtest [15:20:51]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m9fxwqrp/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:python-hypothesis --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-hypothesis/6.122.1-1 -- lxd -r lxd-armhf-10.145.243.197 lxd-armhf-10.145.243.197:autopkgtest/ubuntu/plucky/armhf 59s autopkgtest [15:21:50]: testbed dpkg architecture: armhf 63s autopkgtest [15:21:54]: testbed apt version: 2.9.14ubuntu1 70s autopkgtest [15:22:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 74s autopkgtest [15:22:05]: testbed release detected to be: None 90s autopkgtest [15:22:21]: updating testbed package index (apt update) 94s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 94s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [213 kB] 94s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 94s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 94s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB] 94s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [782 kB] 94s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 94s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [68.5 kB] 94s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [86.8 kB] 95s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [928 B] 95s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [634 kB] 95s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [7468 B] 95s Get:13 http://ftpmaster.internal/ubuntu plucky/universe Sources [20.7 MB] 95s Get:14 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [298 kB] 95s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1387 kB] 95s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1353 kB] 95s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [14.6 MB] 96s Get:18 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [174 kB] 99s Fetched 40.4 MB in 5s (8056 kB/s) 100s Reading package lists... 108s autopkgtest [15:22:39]: upgrading testbed (apt dist-upgrade and autopurge) 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 112s Starting 2 pkgProblemResolver with broken count: 0 112s Done 112s Entering ResolveByKeep 113s 113s The following packages will be upgraded: 113s fwupd libfwupd3 python3-software-properties software-properties-common 113s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Need to get 5190 kB of archives. 113s After this operation, 4096 B disk space will be freed. 113s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 2.0.2-2 [5020 kB] 114s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd3 armhf 2.0.2-2 [124 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf software-properties-common all 0.107 [16.5 kB] 114s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf python3-software-properties all 0.107 [30.4 kB] 114s Fetched 5190 kB in 1s (6827 kB/s) 115s (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 ... 59970 files and directories currently installed.) 115s Preparing to unpack .../fwupd_2.0.2-2_armhf.deb ... 115s Unpacking fwupd (2.0.2-2) over (2.0.2-1) ... 115s Preparing to unpack .../libfwupd3_2.0.2-2_armhf.deb ... 115s Unpacking libfwupd3:armhf (2.0.2-2) over (2.0.2-1) ... 115s Preparing to unpack .../software-properties-common_0.107_all.deb ... 115s Unpacking software-properties-common (0.107) over (0.105) ... 115s Preparing to unpack .../python3-software-properties_0.107_all.deb ... 115s Unpacking python3-software-properties (0.107) over (0.105) ... 115s Setting up libfwupd3:armhf (2.0.2-2) ... 115s Setting up python3-software-properties (0.107) ... 115s Setting up fwupd (2.0.2-2) ... 116s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 116s fwupd.service is a disabled or a static unit not running, not starting it. 116s Setting up software-properties-common (0.107) ... 116s Processing triggers for libc-bin (2.40-1ubuntu3) ... 116s Processing triggers for man-db (2.13.0-1) ... 117s Processing triggers for dbus (1.14.10-4ubuntu5) ... 119s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s Starting pkgProblemResolver with broken count: 0 120s Starting 2 pkgProblemResolver with broken count: 0 120s Done 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s autopkgtest [15:22:55]: rebooting testbed after setup commands that affected boot 199s autopkgtest [15:24:10]: testbed running kernel: Linux 6.8.0-49-generic #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 6 18:12:14 UTC 2 243s autopkgtest [15:24:54]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 274s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (dsc) [2885 B] 274s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (tar) [47.0 MB] 274s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (diff) [10.9 kB] 274s gpgv: Signature made Fri Nov 15 13:40:58 2024 UTC 274s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 274s gpgv: Can't check signature: No public key 274s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5build1.dsc: no acceptable signature found 275s autopkgtest [15:25:26]: testing package mdanalysis version 2.7.0-5build1 279s autopkgtest [15:25:30]: build not needed 286s autopkgtest [15:25:37]: test test-mdanalysis: preparing testbed 288s Reading package lists... 288s Building dependency tree... 288s Reading state information... 289s Starting pkgProblemResolver with broken count: 0 289s Starting 2 pkgProblemResolver with broken count: 0 289s Done 290s The following NEW packages will be installed: 290s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 290s cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cython3 debhelper 290s debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common 290s dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 290s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 290s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 290s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian 290s libaec0 libarchive-zip-perl libasan8 libblas3 libc-dev-bin libc6-dev 290s libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl libdeflate0 libexpat1-dev 290s libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6 290s libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 290s libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libisl23 libjbig0 290s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-mathjax 290s libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0 290s liblcms2-2 liblerc4 liblzf1 libmpc3 libnetcdf19t64 libopenjp2-7 290s libpixman-1-0 libpython3-all-dev libpython3-dev libpython3.12-dev 290s libpython3.12t64 libqhull-r8.0 libraqm0 libsharpyuv0 libstdc++-14-dev libsz2 290s libtcl8.6 libtiff6 libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2 290s libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 290s libxss1 linux-libc-dev m4 po-debconf pybuild-plugin-pyproject 290s python-matplotlib-data python-mdanalysis-doc python3-alabaster python3-all 290s python3-all-dev python3-appdirs python3-biopython python3-brotli 290s python3-build python3-cairo python3-cftime python3-citeproc 290s python3-contourpy python3-cycler python3-dateutil python3-decorator 290s python3-defusedxml python3-dev python3-docutils python3-duecredit 290s python3-fasteners python3-fonttools python3-freetype python3-fs 290s python3-griddataformats python3-gsd python3-h5py python3-h5py-serial 290s python3-hypothesis python3-imagesize python3-iniconfig python3-installer 290s python3-joblib python3-kiwisolver python3-latexcodec python3-looseversion 290s python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib 290s python3-mdanalysis python3-mmtf python3-monotonic python3-mpmath 290s python3-mrcfile python3-msgpack python3-msmb-theme python3-netcdf4 290s python3-networkx python3-numpy python3-packaging python3-pandas 290s python3-pandas-lib python3-pil python3-pil.imagetk python3-pluggy 290s python3-pybtex python3-pybtex-docutils python3-pyproject-hooks 290s python3-pytest python3-reportlab python3-rlpycairo python3-roman 290s python3-scipy python3-seaborn python3-six python3-sklearn 290s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 290s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 290s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 290s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 290s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 290s python3.12-tk python3.13-tk rpcsvc-proto sphinx-common 290s sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 290s xfonts-encodings xfonts-utils zlib1g-dev 290s 0 upgraded, 203 newly installed, 0 to remove and 0 not upgraded. 290s Need to get 198 MB of archives. 290s After this operation, 796 MB of additional disk space will be used. 290s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 291s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB] 291s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 291s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 291s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] 291s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB] 291s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.15+dfsg-2 [909 kB] 291s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 291s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 291s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 291s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 291s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 291s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 291s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 291s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 291s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 291s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 291s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 291s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 291s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 291s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.15-1 [685 kB] 291s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7build1 [525 kB] 291s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf blt armhf 2.5.3+dfsg-7build1 [4840 B] 291s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB] 291s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB] 291s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-5 [119 kB] 291s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 291s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB] 291s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 291s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 291s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [9219 kB] 291s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-8ubuntu1 [1032 B] 291s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B] 291s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB] 291s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-8ubuntu1 [43.3 kB] 291s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 291s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-8ubuntu1 [2901 kB] 292s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-8ubuntu1 [1150 kB] 292s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-8ubuntu1 [897 kB] 292s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [18.0 MB] 292s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-8ubuntu1 [498 kB] 292s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B] 292s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B] 292s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-8ubuntu1 [2569 kB] 292s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [10.5 MB] 292s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-8ubuntu1 [19.9 kB] 292s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B] 292s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B] 292s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 292s Get:50 http://ftpmaster.internal/ubuntu plucky/universe armhf cython3 armhf 3.0.11+dfsg-1ubuntu2 [3061 kB] 292s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 292s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-8 [166 kB] 292s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 292s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 292s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 292s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B] 292s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB] 292s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 292s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB] 293s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 293s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 293s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB] 293s Get:63 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20241024 [112 kB] 293s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 293s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 293s Get:66 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lyx all 2.4.2.1-1 [171 kB] 293s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 293s Get:68 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 293s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-4 [126 kB] 293s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 293s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 293s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 293s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 293s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 293s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.4-1 [121 kB] 293s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 293s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 293s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 293s Get:79 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 293s Get:80 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 293s Get:81 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 293s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 293s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 293s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 293s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 293s Get:86 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 293s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 293s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 293s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-perl all 4.10000-1 [81.9 kB] 293s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-4 [2086 kB] 293s Get:91 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 293s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 293s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 293s Get:94 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 293s Get:95 http://ftpmaster.internal/ubuntu plucky/universe armhf libnetcdf19t64 armhf 1:4.9.2-6ubuntu1 [419 kB] 293s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.7-3 [2075 kB] 293s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 293s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.7-3 [4344 kB] 293s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-dev armhf 3.12.6-0ubuntu1 [10.2 kB] 293s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-all-dev armhf 3.12.6-0ubuntu1 [914 B] 293s Get:101 http://ftpmaster.internal/ubuntu plucky/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 293s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 293s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 293s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 294s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 294s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 294s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 294s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 294s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu1 [150 kB] 294s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.2-1 [51.5 kB] 294s Get:111 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 294s Get:112 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-toml all 0.10.2-1 [16.5 kB] 294s Get:113 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-wheel all 0.45.1-1 [57.7 kB] 294s Get:114 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-build all 1.2.2-1 [31.0 kB] 294s Get:115 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 294s Get:116 http://ftpmaster.internal/ubuntu plucky/universe armhf pybuild-plugin-pyproject all 6.20241024 [1728 B] 294s Get:117 http://ftpmaster.internal/ubuntu plucky/universe armhf python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB] 294s Get:118 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 294s Get:119 http://ftpmaster.internal/ubuntu plucky/universe armhf python-mdanalysis-doc all 2.7.0-5build1 [2323 kB] 294s Get:120 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 294s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.7-3 [505 kB] 294s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dev armhf 3.12.6-0ubuntu1 [26.7 kB] 294s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all-dev armhf 3.12.6-0ubuntu1 [908 B] 294s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf python3-appdirs all 1.4.4-4 [10.9 kB] 294s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 294s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-tk armhf 3.12.7-3 [112 kB] 294s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-tk armhf 3.13.0-2 [103 kB] 294s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tk armhf 3.12.7-1 [9752 B] 294s Get:129 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pil.imagetk armhf 10.4.0-1ubuntu2 [8970 B] 294s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 294s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu2 [446 kB] 294s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2build1 [129 kB] 294s Get:133 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 294s Get:134 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 294s Get:135 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 295s Get:136 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 295s Get:137 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4build1 [1672 kB] 295s Get:138 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-brotli armhf 1.1.0-2build3 [324 kB] 295s Get:139 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cftime armhf 1.6.4-1build1 [304 kB] 295s Get:140 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lxml armhf 5.3.0-1build1 [1630 kB] 295s Get:141 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-citeproc all 0.6.0-3 [98.4 kB] 295s Get:142 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-contourpy armhf 1.3.0-2build1 [238 kB] 295s Get:143 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cycler all 0.12.1-1 [9716 B] 295s Get:144 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 295s Get:145 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 295s Get:146 http://ftpmaster.internal/ubuntu plucky/main armhf python3-defusedxml all 0.7.1-2 [42.0 kB] 295s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf python3-roman all 4.2-1 [10.0 kB] 295s Get:148 http://ftpmaster.internal/ubuntu plucky/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 295s Get:149 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-looseversion all 1.3.0-3 [8354 B] 295s Get:150 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-duecredit all 0.10.2-2 [66.0 kB] 295s Get:151 http://ftpmaster.internal/ubuntu plucky/main armhf python3-monotonic all 1.6-2 [5732 B] 295s Get:152 http://ftpmaster.internal/ubuntu plucky/main armhf python3-fasteners all 0.18-2 [12.5 kB] 295s Get:153 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 295s Get:154 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fs all 2.4.16-5 [90.7 kB] 295s Get:155 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-lz4 armhf 4.0.2+dfsg-1build5 [25.5 kB] 295s Get:156 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5ubuntu1 [19.1 MB] 296s Get:157 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 296s Get:158 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sympy all 1.13.3-1 [4228 kB] 296s Get:159 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 296s Get:160 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-unicodedata2 armhf 15.1.0+ds-1build2 [357 kB] 296s Get:161 http://ftpmaster.internal/ubuntu plucky/universe armhf unicode-data all 15.1.0-1 [8878 kB] 297s Get:162 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fonttools armhf 4.55.0-3 [1626 kB] 297s Get:163 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1014 kB] 297s Get:164 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mrcfile all 1.5.3-3 [114 kB] 297s Get:165 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-griddataformats all 1.0.2-2 [2107 kB] 297s Get:166 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-gsd armhf 3.3.0-1build1 [224 kB] 297s Get:167 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-5ubuntu1 [1061 kB] 297s Get:168 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-5ubuntu1 [7974 B] 297s Get:169 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sortedcontainers all 2.4.0-2 [27.6 kB] 297s Get:170 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-hypothesis all 6.122.1-1 [330 kB] 297s Get:171 http://ftpmaster.internal/ubuntu plucky/main armhf python3-imagesize all 1.4.1-1 [6844 B] 297s Get:172 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 297s Get:173 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.3.2-5 [206 kB] 297s Get:174 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-kiwisolver armhf 1.4.7-2build1 [71.1 kB] 297s Get:175 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-latexcodec all 3.0.0-1 [16.6 kB] 297s Get:176 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-matplotlib armhf 3.8.3-3ubuntu1 [4597 kB] 297s Get:177 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 297s Get:178 http://ftpmaster.internal/ubuntu plucky/main armhf python3-msgpack armhf 1.0.3-3build3 [106 kB] 297s Get:179 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB] 297s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-threadpoolctl all 3.1.0-1 [21.3 kB] 297s Get:181 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.1-1 [92.5 kB] 297s Get:182 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mdanalysis armhf 2.7.0-5build1 [2381 kB] 297s Get:183 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-common all 7.4.7-4 [775 kB] 297s Get:184 http://ftpmaster.internal/ubuntu plucky/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB] 297s Get:185 http://ftpmaster.internal/ubuntu plucky/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 297s Get:186 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sphinx all 7.4.7-4 [593 kB] 298s Get:187 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 298s Get:188 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [23.5 kB] 298s Get:189 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-msmb-theme all 1.2.0-4 [35.4 kB] 298s Get:190 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-netcdf4 armhf 1.7.2-1build1 [849 kB] 298s Get:191 http://ftpmaster.internal/ubuntu plucky/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 298s Get:192 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5ubuntu1 [7608 kB] 298s Get:193 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 299s Get:194 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 299s Get:195 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 299s Get:196 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex all 0.24.0-4 [70.0 kB] 299s Get:197 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex-docutils all 1.0.2-1 [7176 B] 299s Get:198 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.3-1 [251 kB] 299s Get:199 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-seaborn all 0.13.2-4 [225 kB] 299s Get:200 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn-lib armhf 1.4.2+dfsg-6build1 [6321 kB] 299s Get:201 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn all 1.4.2+dfsg-6build1 [2257 kB] 299s Get:202 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-sitemap all 2.6.0-1 [6674 B] 299s Get:203 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 300s Fetched 198 MB in 10s (20.8 MB/s) 300s Selecting previously unselected package fonts-lato. 300s (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 ... 59970 files and directories currently installed.) 300s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 300s Unpacking fonts-lato (2.015-1) ... 301s Selecting previously unselected package m4. 301s Preparing to unpack .../001-m4_1.4.19-4build1_armhf.deb ... 301s Unpacking m4 (1.4.19-4build1) ... 301s Selecting previously unselected package autoconf. 301s Preparing to unpack .../002-autoconf_2.72-3_all.deb ... 301s Unpacking autoconf (2.72-3) ... 301s Selecting previously unselected package autotools-dev. 301s Preparing to unpack .../003-autotools-dev_20220109.1_all.deb ... 301s Unpacking autotools-dev (20220109.1) ... 301s Selecting previously unselected package automake. 301s Preparing to unpack .../004-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 301s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 301s Selecting previously unselected package autopoint. 301s Preparing to unpack .../005-autopoint_0.22.5-2_all.deb ... 301s Unpacking autopoint (0.22.5-2) ... 301s Selecting previously unselected package libtcl8.6:armhf. 301s Preparing to unpack .../006-libtcl8.6_8.6.15+dfsg-2_armhf.deb ... 301s Unpacking libtcl8.6:armhf (8.6.15+dfsg-2) ... 301s Selecting previously unselected package libfreetype6:armhf. 301s Preparing to unpack .../007-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 301s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 301s Selecting previously unselected package fonts-dejavu-mono. 301s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8_all.deb ... 301s Unpacking fonts-dejavu-mono (2.37-8) ... 301s Selecting previously unselected package fonts-dejavu-core. 301s Preparing to unpack .../009-fonts-dejavu-core_2.37-8_all.deb ... 301s Unpacking fonts-dejavu-core (2.37-8) ... 301s Selecting previously unselected package libfontenc1:armhf. 301s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 301s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 301s Selecting previously unselected package x11-common. 301s Preparing to unpack .../011-x11-common_1%3a7.7+23ubuntu3_all.deb ... 301s Unpacking x11-common (1:7.7+23ubuntu3) ... 301s Selecting previously unselected package xfonts-encodings. 301s Preparing to unpack .../012-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 301s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 301s Selecting previously unselected package xfonts-utils. 301s Preparing to unpack .../013-xfonts-utils_1%3a7.7+7_armhf.deb ... 301s Unpacking xfonts-utils (1:7.7+7) ... 301s Selecting previously unselected package fonts-urw-base35. 301s Preparing to unpack .../014-fonts-urw-base35_20200910-8_all.deb ... 301s Unpacking fonts-urw-base35 (20200910-8) ... 301s Selecting previously unselected package fontconfig-config. 301s Preparing to unpack .../015-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 301s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 301s Selecting previously unselected package libfontconfig1:armhf. 302s Preparing to unpack .../016-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 302s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 302s Selecting previously unselected package libxrender1:armhf. 302s Preparing to unpack .../017-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 302s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 302s Selecting previously unselected package libxft2:armhf. 302s Preparing to unpack .../018-libxft2_2.3.6-1build1_armhf.deb ... 302s Unpacking libxft2:armhf (2.3.6-1build1) ... 302s Selecting previously unselected package libxss1:armhf. 302s Preparing to unpack .../019-libxss1_1%3a1.2.3-1build3_armhf.deb ... 302s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 302s Selecting previously unselected package libtk8.6:armhf. 302s Preparing to unpack .../020-libtk8.6_8.6.15-1_armhf.deb ... 302s Unpacking libtk8.6:armhf (8.6.15-1) ... 302s Selecting previously unselected package tk8.6-blt2.5. 302s Preparing to unpack .../021-tk8.6-blt2.5_2.5.3+dfsg-7build1_armhf.deb ... 302s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 302s Selecting previously unselected package blt. 302s Preparing to unpack .../022-blt_2.5.3+dfsg-7build1_armhf.deb ... 302s Unpacking blt (2.5.3+dfsg-7build1) ... 302s Selecting previously unselected package libc-dev-bin. 302s Preparing to unpack .../023-libc-dev-bin_2.40-1ubuntu3_armhf.deb ... 302s Unpacking libc-dev-bin (2.40-1ubuntu3) ... 302s Selecting previously unselected package linux-libc-dev:armhf. 302s Preparing to unpack .../024-linux-libc-dev_6.11.0-8.8_armhf.deb ... 302s Unpacking linux-libc-dev:armhf (6.11.0-8.8) ... 302s Selecting previously unselected package libcrypt-dev:armhf. 302s Preparing to unpack .../025-libcrypt-dev_1%3a4.4.36-5_armhf.deb ... 302s Unpacking libcrypt-dev:armhf (1:4.4.36-5) ... 302s Selecting previously unselected package rpcsvc-proto. 302s Preparing to unpack .../026-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 302s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 302s Selecting previously unselected package libc6-dev:armhf. 302s Preparing to unpack .../027-libc6-dev_2.40-1ubuntu3_armhf.deb ... 302s Unpacking libc6-dev:armhf (2.40-1ubuntu3) ... 302s Selecting previously unselected package libisl23:armhf. 302s Preparing to unpack .../028-libisl23_0.27-1_armhf.deb ... 302s Unpacking libisl23:armhf (0.27-1) ... 302s Selecting previously unselected package libmpc3:armhf. 302s Preparing to unpack .../029-libmpc3_1.3.1-1build2_armhf.deb ... 302s Unpacking libmpc3:armhf (1.3.1-1build2) ... 302s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 302s Preparing to unpack .../030-cpp-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 302s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 303s Selecting previously unselected package cpp-14. 303s Preparing to unpack .../031-cpp-14_14.2.0-8ubuntu1_armhf.deb ... 303s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 303s Selecting previously unselected package cpp-arm-linux-gnueabihf. 303s Preparing to unpack .../032-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 303s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 303s Selecting previously unselected package cpp. 303s Preparing to unpack .../033-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ... 303s Unpacking cpp (4:14.1.0-2ubuntu1) ... 303s Selecting previously unselected package libcc1-0:armhf. 303s Preparing to unpack .../034-libcc1-0_14.2.0-8ubuntu1_armhf.deb ... 303s Unpacking libcc1-0:armhf (14.2.0-8ubuntu1) ... 303s Selecting previously unselected package libgomp1:armhf. 303s Preparing to unpack .../035-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 303s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 303s Selecting previously unselected package libasan8:armhf. 303s Preparing to unpack .../036-libasan8_14.2.0-8ubuntu1_armhf.deb ... 303s Unpacking libasan8:armhf (14.2.0-8ubuntu1) ... 303s Selecting previously unselected package libubsan1:armhf. 303s Preparing to unpack .../037-libubsan1_14.2.0-8ubuntu1_armhf.deb ... 303s Unpacking libubsan1:armhf (14.2.0-8ubuntu1) ... 303s Selecting previously unselected package libgcc-14-dev:armhf. 303s Preparing to unpack .../038-libgcc-14-dev_14.2.0-8ubuntu1_armhf.deb ... 303s Unpacking libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 303s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 303s Preparing to unpack .../039-gcc-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 303s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 303s Selecting previously unselected package gcc-14. 303s Preparing to unpack .../040-gcc-14_14.2.0-8ubuntu1_armhf.deb ... 303s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 303s Selecting previously unselected package gcc-arm-linux-gnueabihf. 303s Preparing to unpack .../041-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 303s Unpacking gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 303s Selecting previously unselected package gcc. 304s Preparing to unpack .../042-gcc_4%3a14.1.0-2ubuntu1_armhf.deb ... 304s Unpacking gcc (4:14.1.0-2ubuntu1) ... 304s Selecting previously unselected package libstdc++-14-dev:armhf. 304s Preparing to unpack .../043-libstdc++-14-dev_14.2.0-8ubuntu1_armhf.deb ... 304s Unpacking libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 304s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 304s Preparing to unpack .../044-g++-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 304s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 304s Selecting previously unselected package g++-14. 304s Preparing to unpack .../045-g++-14_14.2.0-8ubuntu1_armhf.deb ... 304s Unpacking g++-14 (14.2.0-8ubuntu1) ... 304s Selecting previously unselected package g++-arm-linux-gnueabihf. 304s Preparing to unpack .../046-g++-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 304s Unpacking g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 304s Selecting previously unselected package g++. 304s Preparing to unpack .../047-g++_4%3a14.1.0-2ubuntu1_armhf.deb ... 304s Unpacking g++ (4:14.1.0-2ubuntu1) ... 304s Selecting previously unselected package build-essential. 304s Preparing to unpack .../048-build-essential_12.10ubuntu1_armhf.deb ... 304s Unpacking build-essential (12.10ubuntu1) ... 304s Selecting previously unselected package cython3. 304s Preparing to unpack .../049-cython3_3.0.11+dfsg-1ubuntu2_armhf.deb ... 304s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ... 304s Selecting previously unselected package libdebhelper-perl. 304s Preparing to unpack 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dh-strip-nondeterminism (1.14.0-1) ... 305s Selecting previously unselected package debugedit. 305s Preparing to unpack .../056-debugedit_1%3a5.1-1_armhf.deb ... 305s Unpacking debugedit (1:5.1-1) ... 305s Selecting previously unselected package dwz. 305s Preparing to unpack .../057-dwz_0.15-1build6_armhf.deb ... 305s Unpacking dwz (0.15-1build6) ... 305s Selecting previously unselected package gettext. 305s Preparing to unpack .../058-gettext_0.22.5-2_armhf.deb ... 305s Unpacking gettext (0.22.5-2) ... 305s Selecting previously unselected package intltool-debian. 305s Preparing to unpack .../059-intltool-debian_0.35.0+20060710.6_all.deb ... 305s Unpacking intltool-debian (0.35.0+20060710.6) ... 305s Selecting previously unselected package po-debconf. 305s Preparing to unpack .../060-po-debconf_1.0.21+nmu1_all.deb ... 305s Unpacking po-debconf (1.0.21+nmu1) ... 305s Selecting previously unselected package debhelper. 305s Preparing to unpack .../061-debhelper_13.20ubuntu1_all.deb ... 305s Unpacking debhelper (13.20ubuntu1) ... 305s Selecting previously unselected package dh-python. 305s Preparing to unpack .../062-dh-python_6.20241024_all.deb ... 305s Unpacking dh-python (6.20241024) ... 305s Selecting previously unselected package docutils-common. 305s Preparing to unpack .../063-docutils-common_0.21.2+dfsg-2_all.deb ... 305s Unpacking docutils-common (0.21.2+dfsg-2) ... 305s Selecting previously unselected package fonts-font-awesome. 305s Preparing to unpack .../064-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 305s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 305s Selecting previously unselected package fonts-lyx. 305s Preparing to unpack .../065-fonts-lyx_2.4.2.1-1_all.deb ... 305s Unpacking fonts-lyx (2.4.2.1-1) ... 305s Selecting previously unselected package fonts-mathjax. 305s Preparing to unpack .../066-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 305s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 305s Selecting previously unselected package libaec0:armhf. 305s Preparing to unpack .../067-libaec0_1.1.3-1_armhf.deb ... 305s Unpacking libaec0:armhf (1.1.3-1) ... 305s Selecting previously unselected package libblas3:armhf. 305s Preparing to unpack .../068-libblas3_3.12.0-4_armhf.deb ... 305s Unpacking libblas3:armhf (3.12.0-4) ... 305s Selecting previously unselected package libpixman-1-0:armhf. 305s Preparing to unpack .../069-libpixman-1-0_0.44.0-3_armhf.deb ... 305s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 305s Selecting previously unselected package libxcb-render0:armhf. 305s Preparing to unpack .../070-libxcb-render0_1.17.0-2_armhf.deb ... 305s Unpacking libxcb-render0:armhf (1.17.0-2) ... 305s Selecting previously unselected package libxcb-shm0:armhf. 305s Preparing to unpack .../071-libxcb-shm0_1.17.0-2_armhf.deb ... 305s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 305s Selecting previously unselected package libcairo2:armhf. 305s Preparing to unpack .../072-libcairo2_1.18.2-2_armhf.deb ... 305s Unpacking libcairo2:armhf (1.18.2-2) ... 305s Selecting previously unselected package libdeflate0:armhf. 305s Preparing to unpack .../073-libdeflate0_1.22-1_armhf.deb ... 305s Unpacking libdeflate0:armhf (1.22-1) ... 305s Selecting previously unselected package libexpat1-dev:armhf. 305s Preparing to unpack .../074-libexpat1-dev_2.6.4-1_armhf.deb ... 305s Unpacking libexpat1-dev:armhf (2.6.4-1) ... 305s Selecting previously unselected package libgfortran5:armhf. 306s Preparing to unpack .../075-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 306s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 306s Selecting previously unselected package libgraphite2-3:armhf. 306s Preparing to unpack .../076-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 306s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 306s Selecting previously unselected package libharfbuzz0b:armhf. 306s Preparing to unpack .../077-libharfbuzz0b_10.0.1-1_armhf.deb ... 306s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 306s Selecting previously unselected package libsz2:armhf. 306s Preparing to unpack .../078-libsz2_1.1.3-1_armhf.deb ... 306s Unpacking libsz2:armhf (1.1.3-1) ... 306s Selecting previously unselected package libhdf5-103-1t64:armhf. 306s Preparing to unpack .../079-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 306s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 306s Selecting previously unselected package libhdf5-hl-100t64:armhf. 306s Preparing to unpack .../080-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 306s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 306s Selecting previously unselected package libimagequant0:armhf. 306s Preparing to unpack .../081-libimagequant0_2.18.0-1build1_armhf.deb ... 306s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 306s Selecting previously unselected package libjpeg-turbo8:armhf. 306s Preparing to unpack .../082-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 306s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 306s Selecting previously unselected package libjpeg8:armhf. 306s Preparing to unpack .../083-libjpeg8_8c-2ubuntu11_armhf.deb ... 306s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 306s Selecting previously unselected package libjs-jquery. 306s Preparing to unpack .../084-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 306s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 306s Selecting previously unselected package libjs-jquery-ui. 306s Preparing to unpack .../085-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 306s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 306s Selecting previously unselected package libjs-underscore. 306s Preparing to unpack .../086-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 306s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 306s Selecting previously unselected package libjs-sphinxdoc. 306s Preparing to unpack .../087-libjs-sphinxdoc_7.4.7-4_all.deb ... 306s Unpacking libjs-sphinxdoc (7.4.7-4) ... 306s Selecting previously unselected package libjson-perl. 306s Preparing to unpack .../088-libjson-perl_4.10000-1_all.deb ... 306s Unpacking libjson-perl (4.10000-1) ... 306s Selecting previously unselected package liblapack3:armhf. 306s Preparing to unpack .../089-liblapack3_3.12.0-4_armhf.deb ... 306s Unpacking liblapack3:armhf (3.12.0-4) ... 306s Selecting previously unselected package liblbfgsb0:armhf. 306s Preparing to unpack .../090-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 306s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 306s Selecting previously unselected package liblcms2-2:armhf. 306s Preparing to unpack .../091-liblcms2-2_2.16-2_armhf.deb ... 306s Unpacking liblcms2-2:armhf (2.16-2) ... 306s Selecting previously unselected package liblerc4:armhf. 306s Preparing to unpack .../092-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 306s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 306s Selecting previously unselected package liblzf1:armhf. 306s Preparing to unpack .../093-liblzf1_3.6-4_armhf.deb ... 306s Unpacking liblzf1:armhf (3.6-4) ... 306s Selecting previously unselected package libnetcdf19t64:armhf. 306s Preparing to unpack .../094-libnetcdf19t64_1%3a4.9.2-6ubuntu1_armhf.deb ... 306s Unpacking libnetcdf19t64:armhf (1:4.9.2-6ubuntu1) ... 306s Selecting previously unselected package libpython3.12t64:armhf. 306s Preparing to unpack .../095-libpython3.12t64_3.12.7-3_armhf.deb ... 306s Unpacking libpython3.12t64:armhf (3.12.7-3) ... 306s Selecting previously unselected package zlib1g-dev:armhf. 306s Preparing to unpack .../096-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 306s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 307s Selecting previously unselected package libpython3.12-dev:armhf. 307s Preparing to unpack .../097-libpython3.12-dev_3.12.7-3_armhf.deb ... 307s Unpacking libpython3.12-dev:armhf (3.12.7-3) ... 307s Selecting previously unselected package libpython3-dev:armhf. 307s Preparing to unpack .../098-libpython3-dev_3.12.6-0ubuntu1_armhf.deb ... 307s Unpacking libpython3-dev:armhf (3.12.6-0ubuntu1) ... 307s Selecting previously unselected package libpython3-all-dev:armhf. 307s Preparing to unpack .../099-libpython3-all-dev_3.12.6-0ubuntu1_armhf.deb ... 307s Unpacking libpython3-all-dev:armhf (3.12.6-0ubuntu1) ... 307s Selecting previously unselected package libqhull-r8.0:armhf. 307s Preparing to unpack .../100-libqhull-r8.0_2020.2-6build1_armhf.deb ... 307s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 307s Selecting previously unselected package libraqm0:armhf. 307s Preparing to unpack .../101-libraqm0_0.10.1-1build1_armhf.deb ... 307s Unpacking libraqm0:armhf (0.10.1-1build1) ... 307s Selecting previously unselected package libsharpyuv0:armhf. 307s Preparing to unpack .../102-libsharpyuv0_1.4.0-0.1_armhf.deb ... 307s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 307s Selecting previously unselected package libjbig0:armhf. 307s Preparing to unpack .../103-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 307s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 307s Selecting previously unselected package libwebp7:armhf. 307s Preparing to unpack .../104-libwebp7_1.4.0-0.1_armhf.deb ... 307s Unpacking libwebp7:armhf (1.4.0-0.1) ... 307s Selecting previously unselected package libtiff6:armhf. 307s Preparing to unpack .../105-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 307s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 307s Selecting previously unselected package libwebpdemux2:armhf. 307s Preparing to unpack .../106-libwebpdemux2_1.4.0-0.1_armhf.deb ... 307s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 307s Selecting previously unselected package libwebpmux3:armhf. 307s Preparing to unpack .../107-libwebpmux3_1.4.0-0.1_armhf.deb ... 307s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 307s Selecting previously unselected package libxslt1.1:armhf. 307s Preparing to unpack .../108-libxslt1.1_1.1.39-0exp1ubuntu1_armhf.deb ... 307s Unpacking libxslt1.1:armhf (1.1.39-0exp1ubuntu1) ... 307s Selecting previously unselected package python3-packaging. 307s Preparing to unpack .../109-python3-packaging_24.2-1_all.deb ... 307s Unpacking python3-packaging (24.2-1) ... 307s Selecting previously unselected package python3-pyproject-hooks. 307s Preparing to unpack .../110-python3-pyproject-hooks_1.2.0-1_all.deb ... 307s Unpacking python3-pyproject-hooks (1.2.0-1) ... 307s Selecting previously unselected package python3-toml. 307s Preparing to unpack .../111-python3-toml_0.10.2-1_all.deb ... 307s Unpacking python3-toml (0.10.2-1) ... 307s Selecting previously unselected package python3-wheel. 307s Preparing to unpack .../112-python3-wheel_0.45.1-1_all.deb ... 307s Unpacking python3-wheel (0.45.1-1) ... 307s Selecting previously unselected package python3-build. 307s Preparing to unpack .../113-python3-build_1.2.2-1_all.deb ... 307s Unpacking python3-build (1.2.2-1) ... 307s Selecting previously unselected package python3-installer. 307s Preparing to unpack .../114-python3-installer_0.7.0+dfsg1-3_all.deb ... 307s Unpacking python3-installer (0.7.0+dfsg1-3) ... 307s Selecting previously unselected package pybuild-plugin-pyproject. 307s Preparing to unpack .../115-pybuild-plugin-pyproject_6.20241024_all.deb ... 307s Unpacking pybuild-plugin-pyproject (6.20241024) ... 307s Selecting previously unselected package python-matplotlib-data. 307s Preparing to unpack .../116-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ... 307s Unpacking python-matplotlib-data (3.8.3-3ubuntu1) ... 308s Selecting previously unselected package libjs-mathjax. 308s Preparing to unpack .../117-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 308s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 308s Selecting previously unselected package python-mdanalysis-doc. 308s Preparing to unpack .../118-python-mdanalysis-doc_2.7.0-5build1_all.deb ... 308s Unpacking python-mdanalysis-doc (2.7.0-5build1) ... 308s Selecting previously unselected package python3-all. 308s Preparing to unpack .../119-python3-all_3.12.6-0ubuntu1_armhf.deb ... 308s Unpacking python3-all (3.12.6-0ubuntu1) ... 308s Selecting previously unselected package python3.12-dev. 308s Preparing to unpack .../120-python3.12-dev_3.12.7-3_armhf.deb ... 308s Unpacking python3.12-dev (3.12.7-3) ... 308s Selecting previously unselected package python3-dev. 308s Preparing to unpack .../121-python3-dev_3.12.6-0ubuntu1_armhf.deb ... 308s Unpacking python3-dev (3.12.6-0ubuntu1) ... 308s Selecting previously unselected package python3-all-dev. 308s Preparing to unpack .../122-python3-all-dev_3.12.6-0ubuntu1_armhf.deb ... 308s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 308s Selecting previously unselected package python3-appdirs. 309s Preparing to unpack .../123-python3-appdirs_1.4.4-4_all.deb ... 309s Unpacking python3-appdirs (1.4.4-4) ... 309s Selecting previously unselected package python3-numpy. 309s Preparing to unpack .../124-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 309s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 309s Selecting previously unselected package python3.12-tk. 309s Preparing to unpack .../125-python3.12-tk_3.12.7-3_armhf.deb ... 309s Unpacking python3.12-tk (3.12.7-3) ... 309s Selecting previously unselected package python3.13-tk. 309s Preparing to unpack .../126-python3.13-tk_3.13.0-2_armhf.deb ... 309s Unpacking python3.13-tk (3.13.0-2) ... 309s Selecting previously unselected package python3-tk:armhf. 309s Preparing to unpack .../127-python3-tk_3.12.7-1_armhf.deb ... 309s Unpacking python3-tk:armhf (3.12.7-1) ... 309s Selecting previously unselected package python3-pil.imagetk:armhf. 309s Preparing to unpack .../128-python3-pil.imagetk_10.4.0-1ubuntu2_armhf.deb ... 309s Unpacking python3-pil.imagetk:armhf (10.4.0-1ubuntu2) ... 309s Selecting previously unselected package libopenjp2-7:armhf. 309s Preparing to unpack .../129-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 309s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 309s Selecting previously unselected package python3-pil:armhf. 309s Preparing to unpack .../130-python3-pil_10.4.0-1ubuntu2_armhf.deb ... 309s Unpacking python3-pil:armhf (10.4.0-1ubuntu2) ... 309s Selecting previously unselected package python3-cairo. 309s Preparing to unpack .../131-python3-cairo_1.26.1-2build1_armhf.deb ... 309s Unpacking python3-cairo (1.26.1-2build1) ... 309s Selecting previously unselected package python3-freetype. 309s Preparing to unpack .../132-python3-freetype_2.5.1-1_all.deb ... 309s Unpacking python3-freetype (2.5.1-1) ... 309s Selecting previously unselected package python3-rlpycairo. 309s Preparing to unpack .../133-python3-rlpycairo_0.3.0-3_all.deb ... 309s Unpacking python3-rlpycairo (0.3.0-3) ... 309s Selecting previously unselected package python3-reportlab. 309s Preparing to unpack .../134-python3-reportlab_4.2.5-1_all.deb ... 309s Unpacking python3-reportlab (4.2.5-1) ... 309s Selecting previously unselected package w3c-sgml-lib. 309s Preparing to unpack .../135-w3c-sgml-lib_1.3-3_all.deb ... 309s Unpacking w3c-sgml-lib (1.3-3) ... 310s Selecting previously unselected package python3-biopython. 310s Preparing to unpack .../136-python3-biopython_1.84+dfsg-4build1_armhf.deb ... 310s Unpacking python3-biopython (1.84+dfsg-4build1) ... 310s Selecting previously unselected package python3-brotli. 310s Preparing to unpack .../137-python3-brotli_1.1.0-2build3_armhf.deb ... 310s Unpacking python3-brotli (1.1.0-2build3) ... 310s Selecting previously unselected package python3-cftime. 310s Preparing to unpack .../138-python3-cftime_1.6.4-1build1_armhf.deb ... 310s Unpacking python3-cftime (1.6.4-1build1) ... 310s Selecting previously unselected package python3-lxml:armhf. 310s Preparing to unpack .../139-python3-lxml_5.3.0-1build1_armhf.deb ... 310s Unpacking python3-lxml:armhf (5.3.0-1build1) ... 310s Selecting previously unselected package python3-citeproc. 310s Preparing to unpack .../140-python3-citeproc_0.6.0-3_all.deb ... 310s Unpacking python3-citeproc (0.6.0-3) ... 310s Selecting previously unselected package python3-contourpy. 310s Preparing to unpack .../141-python3-contourpy_1.3.0-2build1_armhf.deb ... 310s Unpacking python3-contourpy (1.3.0-2build1) ... 310s Selecting previously unselected package python3-cycler. 310s Preparing to unpack .../142-python3-cycler_0.12.1-1_all.deb ... 310s Unpacking python3-cycler (0.12.1-1) ... 310s Selecting previously unselected package python3-dateutil. 310s Preparing to unpack .../143-python3-dateutil_2.9.0-3_all.deb ... 310s Unpacking python3-dateutil (2.9.0-3) ... 310s Selecting previously unselected package python3-decorator. 310s Preparing to unpack .../144-python3-decorator_5.1.1-5_all.deb ... 310s Unpacking python3-decorator (5.1.1-5) ... 310s Selecting previously unselected package python3-defusedxml. 310s Preparing to unpack .../145-python3-defusedxml_0.7.1-2_all.deb ... 310s Unpacking python3-defusedxml (0.7.1-2) ... 310s Selecting previously unselected package python3-roman. 310s Preparing to unpack .../146-python3-roman_4.2-1_all.deb ... 310s Unpacking python3-roman (4.2-1) ... 310s Selecting previously unselected package python3-docutils. 310s Preparing to unpack .../147-python3-docutils_0.21.2+dfsg-2_all.deb ... 310s Unpacking python3-docutils (0.21.2+dfsg-2) ... 310s Selecting previously unselected package python3-looseversion. 310s Preparing to unpack .../148-python3-looseversion_1.3.0-3_all.deb ... 310s Unpacking python3-looseversion (1.3.0-3) ... 310s Selecting previously unselected package python3-duecredit. 310s Preparing to unpack .../149-python3-duecredit_0.10.2-2_all.deb ... 310s Unpacking python3-duecredit (0.10.2-2) ... 310s Selecting previously unselected package python3-monotonic. 310s Preparing to unpack .../150-python3-monotonic_1.6-2_all.deb ... 310s Unpacking python3-monotonic (1.6-2) ... 310s Selecting previously unselected package python3-fasteners. 310s Preparing to unpack .../151-python3-fasteners_0.18-2_all.deb ... 310s Unpacking python3-fasteners (0.18-2) ... 310s Selecting previously unselected package python3-tz. 310s Preparing to unpack .../152-python3-tz_2024.1-2_all.deb ... 310s Unpacking python3-tz (2024.1-2) ... 311s Selecting previously unselected package python3-fs. 311s Preparing to unpack .../153-python3-fs_2.4.16-5_all.deb ... 311s Unpacking python3-fs (2.4.16-5) ... 311s Selecting previously unselected package python3-lz4. 311s Preparing to unpack .../154-python3-lz4_4.0.2+dfsg-1build5_armhf.deb ... 311s Unpacking python3-lz4 (4.0.2+dfsg-1build5) ... 311s Selecting previously unselected package python3-scipy. 311s Preparing to unpack .../155-python3-scipy_1.13.1-5ubuntu1_armhf.deb ... 311s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 311s Selecting previously unselected package python3-mpmath. 311s Preparing to unpack .../156-python3-mpmath_1.3.0-1_all.deb ... 311s Unpacking python3-mpmath (1.3.0-1) ... 311s Selecting previously unselected package python3-sympy. 311s Preparing to unpack .../157-python3-sympy_1.13.3-1_all.deb ... 311s Unpacking python3-sympy (1.13.3-1) ... 312s Selecting previously unselected package python3-ufolib2. 312s Preparing to unpack .../158-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 312s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 312s Selecting previously unselected package python3-unicodedata2. 312s Preparing to unpack .../159-python3-unicodedata2_15.1.0+ds-1build2_armhf.deb ... 312s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 312s Selecting previously unselected package unicode-data. 312s Preparing to unpack .../160-unicode-data_15.1.0-1_all.deb ... 312s Unpacking unicode-data (15.1.0-1) ... 312s Selecting previously unselected package python3-fonttools. 312s Preparing to unpack .../161-python3-fonttools_4.55.0-3_armhf.deb ... 312s Unpacking python3-fonttools (4.55.0-3) ... 312s Selecting previously unselected package sphinx-rtd-theme-common. 312s Preparing to unpack .../162-sphinx-rtd-theme-common_3.0.2+dfsg-1_all.deb 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... 313s Selecting previously unselected package python3-sortedcontainers. 313s Preparing to unpack .../168-python3-sortedcontainers_2.4.0-2_all.deb ... 313s Unpacking python3-sortedcontainers (2.4.0-2) ... 313s Selecting previously unselected package python3-hypothesis. 313s Preparing to unpack .../169-python3-hypothesis_6.122.1-1_all.deb ... 313s Unpacking python3-hypothesis (6.122.1-1) ... 313s Selecting previously unselected package python3-imagesize. 313s Preparing to unpack .../170-python3-imagesize_1.4.1-1_all.deb ... 313s Unpacking python3-imagesize (1.4.1-1) ... 313s Selecting previously unselected package python3-iniconfig. 313s Preparing to unpack .../171-python3-iniconfig_1.1.1-2_all.deb ... 313s Unpacking python3-iniconfig (1.1.1-2) ... 313s Selecting previously unselected package python3-joblib. 313s Preparing to unpack .../172-python3-joblib_1.3.2-5_all.deb ... 313s Unpacking python3-joblib (1.3.2-5) ... 313s Selecting previously unselected package python3-kiwisolver. 313s Preparing to unpack .../173-python3-kiwisolver_1.4.7-2build1_armhf.deb ... 313s Unpacking python3-kiwisolver (1.4.7-2build1) ... 313s Selecting previously unselected package python3-latexcodec. 313s Preparing to unpack .../174-python3-latexcodec_3.0.0-1_all.deb ... 313s Unpacking python3-latexcodec (3.0.0-1) ... 313s Selecting previously unselected package python3-matplotlib. 313s Preparing to unpack .../175-python3-matplotlib_3.8.3-3ubuntu1_armhf.deb ... 313s Unpacking python3-matplotlib (3.8.3-3ubuntu1) ... 313s Selecting previously unselected package python3-mda-xdrlib. 313s Preparing to unpack .../176-python3-mda-xdrlib_0.2.0-3_all.deb ... 313s Unpacking python3-mda-xdrlib (0.2.0-3) ... 313s Selecting previously unselected package python3-msgpack. 313s Preparing to unpack .../177-python3-msgpack_1.0.3-3build3_armhf.deb ... 313s Unpacking python3-msgpack (1.0.3-3build3) ... 313s Selecting previously unselected package python3-mmtf. 313s Preparing to unpack .../178-python3-mmtf_1.1.3-1_all.deb ... 313s Unpacking python3-mmtf (1.1.3-1) ... 313s Selecting previously unselected package python3-threadpoolctl. 313s Preparing to unpack .../179-python3-threadpoolctl_3.1.0-1_all.deb ... 313s Unpacking python3-threadpoolctl (3.1.0-1) ... 313s Selecting previously unselected package python3-tqdm. 313s Preparing to unpack .../180-python3-tqdm_4.67.1-1_all.deb ... 313s Unpacking python3-tqdm (4.67.1-1) ... 313s Selecting previously unselected package python3-mdanalysis. 313s Preparing to unpack .../181-python3-mdanalysis_2.7.0-5build1_armhf.deb ... 313s Unpacking python3-mdanalysis (2.7.0-5build1) ... 313s Selecting previously unselected package sphinx-common. 313s Preparing to unpack .../182-sphinx-common_7.4.7-4_all.deb ... 313s Unpacking sphinx-common (7.4.7-4) ... 313s Selecting previously unselected package python3-alabaster. 313s Preparing to unpack .../183-python3-alabaster_0.7.16-0.1_all.deb ... 313s Unpacking python3-alabaster (0.7.16-0.1) ... 313s Selecting previously unselected package python3-snowballstemmer. 313s Preparing to unpack .../184-python3-snowballstemmer_2.2.0-4build1_all.deb ... 313s Unpacking python3-snowballstemmer (2.2.0-4build1) ... 313s Selecting previously unselected package python3-sphinx. 314s Preparing to unpack .../185-python3-sphinx_7.4.7-4_all.deb ... 314s Unpacking python3-sphinx (7.4.7-4) ... 314s Selecting previously unselected package python3-sphinxcontrib.jquery. 314s Preparing to unpack .../186-python3-sphinxcontrib.jquery_4.1-5_all.deb ... 314s Unpacking python3-sphinxcontrib.jquery (4.1-5) ... 314s Selecting previously unselected package python3-sphinx-rtd-theme. 314s Preparing to unpack .../187-python3-sphinx-rtd-theme_3.0.2+dfsg-1_all.deb ... 314s Unpacking python3-sphinx-rtd-theme (3.0.2+dfsg-1) ... 314s Selecting previously unselected package python3-msmb-theme. 314s Preparing to unpack .../188-python3-msmb-theme_1.2.0-4_all.deb ... 314s Unpacking python3-msmb-theme (1.2.0-4) ... 314s Selecting previously unselected package python3-netcdf4. 314s Preparing to unpack .../189-python3-netcdf4_1.7.2-1build1_armhf.deb ... 314s Unpacking python3-netcdf4 (1.7.2-1build1) ... 314s Selecting previously unselected package python3-networkx. 314s Preparing to unpack .../190-python3-networkx_3.2.1-4ubuntu1_all.deb ... 314s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 314s Selecting previously unselected package python3-pandas-lib:armhf. 314s Preparing to unpack .../191-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_armhf.deb ... 314s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 315s Selecting previously unselected package python3-pandas. 315s Preparing to unpack .../192-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 315s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 315s Selecting previously unselected package python3-pluggy. 315s Preparing to unpack .../193-python3-pluggy_1.5.0-1_all.deb ... 315s Unpacking python3-pluggy (1.5.0-1) ... 315s Selecting previously unselected package python3-six. 315s Preparing to unpack .../194-python3-six_1.16.0-7_all.deb ... 315s Unpacking python3-six (1.16.0-7) ... 315s Selecting previously unselected package python3-pybtex. 315s Preparing to unpack .../195-python3-pybtex_0.24.0-4_all.deb ... 315s Unpacking python3-pybtex (0.24.0-4) ... 315s Selecting previously unselected package python3-pybtex-docutils. 315s Preparing to unpack .../196-python3-pybtex-docutils_1.0.2-1_all.deb ... 315s Unpacking python3-pybtex-docutils (1.0.2-1) ... 315s Selecting previously unselected package python3-pytest. 315s Preparing to unpack .../197-python3-pytest_8.3.3-1_all.deb ... 315s Unpacking python3-pytest (8.3.3-1) ... 315s Selecting previously unselected package python3-seaborn. 315s Preparing to unpack .../198-python3-seaborn_0.13.2-4_all.deb ... 315s Unpacking python3-seaborn (0.13.2-4) ... 315s Selecting previously unselected package python3-sklearn-lib:armhf. 315s Preparing to unpack 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libsharpyuv0:armhf (1.4.0-0.1) ... 316s Setting up w3c-sgml-lib (1.3-3) ... 344s Setting up fonts-lato (2.015-1) ... 344s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 344s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 344s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 344s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 344s Setting up python3-joblib (1.3.2-5) ... 344s Setting up python3-lz4 (4.0.2+dfsg-1build5) ... 344s Setting up libxcb-render0:armhf (1.17.0-2) ... 344s Setting up python3-defusedxml (0.7.1-2) ... 344s Setting up libarchive-zip-perl (1.68-1) ... 344s Setting up python3-alabaster (0.7.16-0.1) ... 344s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 344s Setting up fonts-lyx (2.4.2.1-1) ... 344s Setting up libdebhelper-perl (13.20ubuntu1) ... 344s Setting up python3-tqdm (4.67.1-1) ... 345s Setting up python3-threadpoolctl (3.1.0-1) ... 345s Setting up x11-common (1:7.7+23ubuntu3) ... 345s Setting up libdeflate0:armhf (1.22-1) ... 345s Setting up linux-libc-dev:armhf (6.11.0-8.8) ... 345s Setting up m4 (1.4.19-4build1) ... 345s Setting up python3-latexcodec (3.0.0-1) ... 345s Setting up libqhull-r8.0:armhf (2020.2-6build1) ... 345s Setting up python3-all (3.12.6-0ubuntu1) ... 345s Setting up libxcb-shm0:armhf (1.17.0-2) ... 345s Setting up python3-sortedcontainers (2.4.0-2) ... 345s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 345s Setting up python3-networkx (3.2.1-4ubuntu1) ... 347s Setting up python3-wheel (0.45.1-1) ... 347s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 347s Setting up python3-mda-xdrlib (0.2.0-3) ... 347s Setting up libaec0:armhf (1.1.3-1) ... 347s Setting up python3-tz (2024.1-2) ... 347s Setting up python3-monotonic (1.6-2) ... 347s Setting up unicode-data (15.1.0-1) ... 347s Setting up python3-six (1.16.0-7) ... 347s Setting up libpython3.12t64:armhf (3.12.7-3) ... 347s Setting up python3-roman (4.2-1) ... 347s Setting up python3-decorator (5.1.1-5) ... 347s Setting up libfontenc1:armhf (1:1.1.8-1build1) ... 347s Setting up autotools-dev (20220109.1) ... 347s Setting up libblas3:armhf (3.12.0-4) ... 347s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 347s Setting up python3-packaging (24.2-1) ... 348s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 348s Setting up python3-pyproject-hooks (1.2.0-1) ... 348s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 348s Setting up python3-snowballstemmer (2.2.0-4build1) ... 348s Setting up python3-brotli (1.1.0-2build3) ... 348s Setting up liblzf1:armhf (3.6-4) ... 348s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 348s Setting up python3-cycler (0.12.1-1) ... 348s Setting up libimagequant0:armhf (2.18.0-1build1) ... 348s Setting up fonts-dejavu-mono (2.37-8) ... 348s Setting up python3-kiwisolver (1.4.7-2build1) ... 348s Setting up libmpc3:armhf (1.3.1-1build2) ... 348s Setting up cython3 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(1.1.39-0exp1ubuntu1) ... 350s Setting up debugedit (1:5.1-1) ... 350s Setting up libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 350s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 350s Setting up python3-dateutil (2.9.0-3) ... 350s Setting up python3-msgpack (1.0.3-3build3) ... 350s Setting up libxss1:armhf (1:1.2.3-1build3) ... 350s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 350s Setting up libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 350s Setting up python3-mpmath (1.3.0-1) ... 351s Setting up libisl23:armhf (0.27-1) ... 351s Setting up python3-build (1.2.2-1) ... 351s Setting up libc-dev-bin (2.40-1ubuntu3) ... 351s Setting up python-matplotlib-data (3.8.3-3ubuntu1) ... 351s Setting up libwebpmux3:armhf (1.4.0-0.1) ... 351s Setting up python3-appdirs (1.4.4-4) ... 351s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 351s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-1) ... 351s Setting up libcc1-0:armhf (14.2.0-8ubuntu1) ... 351s Setting up libsz2:armhf (1.1.3-1) ... 351s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 351s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 351s Setting up python3-imagesize (1.4.1-1) ... 351s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 351s Setting up automake (1:1.16.5-1.3ubuntu1) ... 351s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 351s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 351s Setting up python3-sympy (1.13.3-1) ... 358s Setting up liblapack3:armhf (3.12.0-4) ... 358s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 358s Setting up gettext (0.22.5-2) ... 358s Setting up pybuild-plugin-pyproject (6.20241024) ... 358s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 358s Setting up python3-pytest (8.3.3-1) ... 359s Setting up libwebpdemux2:armhf (1.4.0-0.1) ... 359s Setting up python3-hypothesis (6.122.1-1) ... 359s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 359s Setting up python3-freetype (2.5.1-1) ... 359s Setting up xfonts-utils (1:7.7+7) ... 359s Setting up intltool-debian (0.35.0+20060710.6) ... 359s Setting up python3-fs (2.4.16-5) ... 360s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 360s Setting up libraqm0:armhf (0.10.1-1build1) ... 360s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 362s Setting up libjs-sphinxdoc (7.4.7-4) ... 362s Setting up cpp-14 (14.2.0-8ubuntu1) ... 362s Setting up dh-strip-nondeterminism (1.14.0-1) ... 362s Setting up python3-lxml:armhf (5.3.0-1build1) ... 362s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 362s Setting up libc6-dev:armhf (2.40-1ubuntu3) ... 362s Setting up python3-contourpy (1.3.0-2build1) ... 362s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 362s Setting up libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 362s Setting up cpp-arm-linux-gnueabihf 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update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 375s Setting up build-essential (12.10ubuntu1) ... 375s Setting up libpython3-dev:armhf (3.12.6-0ubuntu1) ... 375s Setting up debhelper (13.20ubuntu1) ... 375s Setting up libpython3-all-dev:armhf (3.12.6-0ubuntu1) ... 375s Setting up python3-dev (3.12.6-0ubuntu1) ... 375s Setting up python3-all-dev (3.12.6-0ubuntu1) ... 375s Setting up python3-fonttools (4.55.0-3) ... 376s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 376s Processing triggers for sgml-base (1.31) ... 376s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 376s Setting up python3-docutils (0.21.2+dfsg-2) ... 377s Processing triggers for install-info (7.1.1-1) ... 377s Setting up libxft2:armhf (2.3.6-1build1) ... 377s Setting up libtk8.6:armhf (8.6.15-1) ... 377s Processing triggers for libc-bin (2.40-1ubuntu3) ... 377s Setting up python3.12-tk (3.12.7-3) ... 377s Processing triggers for man-db (2.13.0-1) ... 379s Setting up 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python3-msmb-theme (1.2.0-4) ... 385s Processing triggers for libc-bin (2.40-1ubuntu3) ... 395s autopkgtest [15:27:26]: test test-mdanalysis: [----------------------- 397s skipping tests with SKIP_TEST_LIST= 407s ============================= test session starts ============================== 407s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 407s rootdir: /tmp/autopkgtest.AzmosB/build.E5H/src 407s plugins: typeguard-4.4.1, hypothesis-6.122.1 407s collected 19229 items / 6 skipped 407s 412s testsuite/MDAnalysisTests/analysis/test_align.py ....................... 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[100%] 1184s 1184s =============================== warnings summary =============================== 1184s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39 1184s /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. 1184s 1184s Due to the on going maintenance burden of keeping command line application 1184s wrappers up to date, we have decided to deprecate and eventually remove these 1184s modules. 1184s 1184s We instead now recommend building your command line and invoking it directly 1184s with the subprocess module. 1184s warnings.warn( 1184s 1184s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings 1184s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings 1184s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings 1184s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings 1184s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings 1184s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings 1184s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings 1184s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings 1184s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings 1184s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings 1184s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings 1184s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings 1184s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1184s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings 1184s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings 1184s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings 1184s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings 1184s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings 1184s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings 1184s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings 1184s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings 1184s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings 1184s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings 1184s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings 1184s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings 1184s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings 1184s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1184s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings 1184s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1184s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings 1184s /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. 1184s warnings.warn("DCDReader currently makes independent timesteps" 1184s 1184s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 1184s /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. 1184s warnings.warn(wmsg, category=DeprecationWarning) 1184s 1184s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings 1184s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written 1184s warnings.warn(wmsg) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings 1184s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings 1184s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings 1184s /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 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings 1184s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1184s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings 1184s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning 1184s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'ho', 'hc', 'h1', 'c3', 'oh'}. These have been given an empty element record. 1184s warnings.warn("Unknown elements found for some " 1184s 1184s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning 1184s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings 1184s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings 1184s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1184s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings 1184s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings 1184s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps 1184s self.times[i] = ts.time 1184s 1184s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning 1184s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings 1184s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1184s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings 1184s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings 1184s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings 1184s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded 1184s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps 1184s results.append((ts.time, x.sum() / mask.sum())) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue 1184s /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. 1184s warnings.warn(msg) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1184s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding 1184s /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 1184s warnings.warn(msg) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1184s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1184s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1184s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings 1184s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning 1184s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings 1184s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings 1184s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings 1184s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1184s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings 1184s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings 1184s /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. 1184s warnings.warn("Element information is missing, elements attribute " 1184s 1184s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran 1184s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame 1184s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections 1184s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues 1184s warnings.warn("Cannot determine phi and psi angles for the first " 1184s 1184s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin 1184s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr 1184s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame 1184s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot 1184s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning 1184s /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. 1184s warnings.warn(f"All residues selected with '{select_remove}' " 1184s 1184s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings 1184s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings 1184s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=5099) is multi-threaded, use of fork() may lead to deadlocks in the child. 1184s self.pid = os.fork() 1184s 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes 1184s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide 1184s cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms 1184s 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide 1184s local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1184s /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice 1184s ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1184s /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide 1184s ret = um.true_divide( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1184s /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide 1184s ret = ret.dtype.type(ret / rcount) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1184s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning 1184s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning 1184s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1184s /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. 1184s warnings.warn("1 A^3 CRYST1 record," 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. 1184s warnings.warn("Unit cell dimensions not found. " 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings 1184s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings 1184s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings 1184s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1184s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings 1184s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1184s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning 1184s /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 1184s warnings.warn(wmsg, DeprecationWarning) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 1184s warnings.warn("Desired number of sample points too high, using {0}" 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbond = HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbond = HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbond = HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbond = HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbond = HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbond = HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbond = HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbond = HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s HBAC( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1184s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1184s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbond = HBAC(u, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1184s `find_hydrogen_donors` will be removed in release 3.0.0. 1184s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s D = hbonds.find_hydrogen_donors(H) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1184s `find_hydrogen_donors` will be removed in release 3.0.0. 1184s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1184s hbonds.find_hydrogen_donors(u.atoms) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1184s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1184s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. 1184s return _methods._mean(a, axis=axis, dtype=dtype, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1184s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1184s /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide 1184s ret = ret.dtype.type(ret / rcount) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1184s /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. 1184s warnings.warn(msg.format(sel)) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1184s /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. 1184s warnings.warn(msg.format(sel)) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1184s /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. 1184s warnings.warn(msg.format(sel)) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. 1184s warnings.warn("Empty string to select atoms, empty group returned.", 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1184s /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, . 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1184s /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, . 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1184s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1184s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1184s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1184s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1184s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1184s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple 1184s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content 1184s /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. 1184s warnings.warn(wmsg) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning 1184s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning 1184s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1184s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1184s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1184s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1184s /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.) 1184s phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi 1184s 1184s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j 1184s /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 1184s warnings.warn("Column index entered (j = {:d} is smaller than row " 1184s 1184s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps 1184s dt=self.trajectory.ts.dt * step, 1184s 1184s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] 1184s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] 1184s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] 1184s /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 1184s warnings.warn(wmsg, DeprecationWarning) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1184s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings 1184s /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. 1184s warnings.warn("The `u` attribute is superflous and will be removed " 1184s 1184s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] 1184s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm 1184s /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. 1184s warnings.warn("The `density` attribute was deprecated in " 1184s 1184s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata 1184s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. 1184s warnings.warn(msg, category=MissingDataWarning) 1184s 1184s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps 1184s self.timesteps.append(self._ts.time) 1184s 1184s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning 1184s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default 1184s warnings.warn("{} does not support time selection. Reverting to " 1184s 1184s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default 1184s warnings.warn("{} does not support data selection. Reverting to " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1184s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings 1184s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps 1184s return self.ts.dt 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1184s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps 1184s ts.data['time'] = step_num * ts.dt 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_unitcell_triclinic[RefNAMDtriclinicDCD] 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDWriterWithRealTrajectory::test_write_trajectory[True-True-False] 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1184s self.close() 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close 1184s self._apply('close') 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply 1184s return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] 1184s ^^^^^^^^^^^^ 1184s AttributeError: 'ChainReader' object has no attribute 'readers' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing 1184s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain 1184s warnings.warn("Missing frame in continuous chain", UserWarning) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps 1184s time_frame_0 = ts.time - ts.frame*ts.dt # assumes ts.dt is constant 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps 1184s frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps 1184s step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps 1184s self._add_step_to_frame_data(ts.time) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps 1184s if not np.allclose(A.time, B.time): 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] 1184s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array 1184s /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 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1184s self.close() 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close 1184s self._file.close() 1184s ^^^^^^^^^^ 1184s AttributeError: 'DCDReader' object has no attribute '_file' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms 1184s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit 1184s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__ 1184s self.close() 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close 1184s self._file.close() 1184s ^^^^^^^^^^ 1184s AttributeError: 'DCDWriter' object has no attribute '_file' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings 1184s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings 1184s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1184s /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. 1184s warnings.warn(msg) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps 1184s return self.ts.time 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps 1184s assert_equal(reader.ts.dt, reader.dt) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps 1184s time_frame = time_frame_0 + frame_index*ts.dt 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps 1184s reader_p = pickle.loads(pickle.dumps(reader)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings 1184s /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 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] 1184s warnings.warn(wmsg) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1184s /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`. 1184s warnings.warn(wmsg) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. 1184s warnings.warn("Not all velocities were present. " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps 1184s reader_p = pickle.loads(pickle.dumps(reader)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader 1184s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps 1184s reader_p = pickle.loads(pickle.dumps(reader)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1184s self.close() 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close 1184s self._file.close() 1184s ^^^^^^^^^^ 1184s AttributeError: 'H5MDReader' object has no attribute '_file' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1184s for aux in self.aux_list: 1184s ^^^^^^^^^^^^^ 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1184s return self._auxs.keys() 1184s ^^^^^^^^^^ 1184s AttributeError: 'H5MDReader' object has no attribute '_auxs' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1184s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 1184s warnings.warn('Guessed all Masses to 1.0') 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit 1184s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1184s for aux in self.aux_list: 1184s ^^^^^^^^^^^^^ 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1184s return self._auxs.keys() 1184s ^^^^^^^^^^ 1184s AttributeError: 'DCDReader' object has no attribute '_auxs' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view 1184s /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 1184s warnings.warn("MemoryReader.timeseries inclusive `stop` " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader 1184s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps 1184s reader_p = pickle.loads(pickle.dumps(reader)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1184s /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 1184s warnings.warn(wmsg) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps 1184s ts.time) # in-place ! (hope this works...) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps 1184s time_list = [ts.time for ts in u.trajectory] 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps 1184s assert u.trajectory.ts.dt == pytest.approx(ref) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 1184s /tmp/autopkgtest.AzmosB/build.E5H/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.) 1184s return self._test_write_trajectory(universe, outfile) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] 1184s /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. 1184s warnings.warn(wmsg) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1184s /tmp/autopkgtest.AzmosB/build.E5H/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.) 1184s return self._test_write_trajectory(universe, outfile) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 1184s warnings.warn("Found missing chainIDs." 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom] 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond] 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom] 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree] 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond] 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom] 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps 1184s time = ts.time 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1184s self.close() 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close 1184s if self.trjfile is not None: 1184s ^^^^^^^^^^^^ 1184s AttributeError: 'NCDFWriter' object has no attribute 'trjfile' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' 1184s warnings.warn("Found no information for attr: '{}'" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' 1184s warnings.warn("Found chainIDs using unnaccepted character." 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' 1184s warnings.warn("Found chainIDs with invalid length." 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed 1184s warnings.warn("Serial numbers went over 100,000. " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed 1184s warnings.warn("Invalid atom serials were present, bonds will not" 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed 1184s warnings.warn("Invalid atom serials were present, " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment 1184s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1184s /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. 1184s warnings.warn(wmsg) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1184s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1184s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1184s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1184s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges 1184s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps 1184s assert_equal(ts.dt, 1.0) # default value 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps 1184s assert_equal(ts.time, 0.0) # default to 1.0 (dt) * 0 (frame) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps 1184s assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1184s for aux in self.aux_list: 1184s ^^^^^^^^^^^^^ 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1184s return self._auxs.keys() 1184s ^^^^^^^^^^ 1184s AttributeError: 'TNGReader' object has no attribute '_auxs' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms 1184s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe 1184s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe 1184s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1184s self.close() 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close 1184s if self.trjfile is None: 1184s ^^^^^^^^^^^^ 1184s AttributeError: 'TRJReader' object has no attribute 'trjfile' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps 1184s data['time'] = ts.time 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1184s /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 1184s warnings.warn("Timestep didn't have the following attributes: '{0}', " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1184s /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. 1184s warnings.warn("Timestep didn't have velocity information, " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1184s /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 1184s warnings.warn("Timestep didn't have dimensions information, " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1184s self.close() 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close 1184s if self.trzfile is None: 1184s ^^^^^^^^^^^^ 1184s AttributeError: 'TRZWriter' object has no attribute 'trzfile' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1184s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1184s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1184s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1184s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1184s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1184s /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. 1184s warnings.warn("Element information is missing, elements attribute " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1184s /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 1184s warnings.warn(wmsg, DeprecationWarning) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] 1184s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] 1184s /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' 1184s warnings.warn(wmsg) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD 1184s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps 1184s time = ts.time 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD 1184s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps 1184s time = ts.time 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1184s self.close() 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1184s self._xdr.close() 1184s ^^^^^^^^^ 1184s AttributeError: 'XTCWriter' object has no attribute '_xdr' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container 1184s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1184s 1184s Traceback (most recent call last): 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1184s self.close() 1184s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1184s self._xdr.close() 1184s ^^^^^^^^^ 1184s AttributeError: 'TRRWriter' object has no attribute '_xdr' 1184s 1184s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1184s /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. 1184s Consider setting 'refresh_offsets=True' when loading your Universe. 1184s warnings.warn(f"Reading offsets from {fname} failed, " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly 1184s /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. 1184s warnings.warn(f"Cannot write lock/offset file in same location as " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1184s /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. 1184s Consider setting 'refresh_offsets=True' when loading your Universe. 1184s warnings.warn(f"Reading offsets from {fname} failed, " 1184s 1184s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly 1184s /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. 1184s warnings.warn(f"Cannot write lock/offset file in same location as " 1184s 1184s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] 1184s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] 1184s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] 1184s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce 1184s return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1184s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1184s /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. 1184s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings 1184s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings 1184s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings 1184s /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. 1184s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1184s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1184s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide 1184s return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() 1184s 1184s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings 1184s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide 1184s _centers /= _weights.sum(axis=1)[:, None] 1184s 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1184s /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`. 1184s warnings.warn(msg, category=SelectionWarning) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1184s /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`. 1184s warnings.warn(msg, category=SelectionWarning) 1184s 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] 1184s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] 1184s /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`. 1184s warnings.warn(msg, category=SelectionWarning) 1184s 1184s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] 1184s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] 1184s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] 1184s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] 1184s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] 1184s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc 1184s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc 1184s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options 1184s /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 1184s warnings.warn("The 'pbc' kwarg has been deprecated and will be " 1184s 1184s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel 1184s /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`. 1184s warnings.warn(msg, category=SelectionWarning) 1184s 1184s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] 1184s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] 1184s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] 1184s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] 1184s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] 1184s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide 1184s x = np.dot(a, b) / (norm(a) * norm(b)) 1184s 1184s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt 1184s ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) 1184s 1184s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt 1184s box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - 1184s 1184s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide 1184s a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) 1184s 1184s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide 1184s b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) 1184s 1184s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide 1184s c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) 1184s 1184s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide 1184s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1184s 1184s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide 1184s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1184s 1184s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 1184s /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps 1184s cls(buf, protocol).dump(obj) 1184s 1184s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps 1184s ps = pickle.dumps(ref_reader) 1184s 1184s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] 1184s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd 1184s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd 1184s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset 1184s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific 1184s /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. 1184s warnings.warn('Cannot average position for non sequential' 1184s 1184s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name] 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname] 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type] 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid] 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' 1184s warnings.warn("PDB file is missing resid information. " 1184s 1184s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX 1184s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1184s 1184s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2] 1184s /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. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2] 1184s /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. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2] 1184s /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. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2] 1184s /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. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1184s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings 1184s /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. 1184s warnings.warn(msg) 1184s 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts 1184s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr] 1184s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file. 1184s warnings.warn('No coordinate reader found for {}. Skipping ' 1184s 1184s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses 1184s /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. 1184s warnings.warn(msg, category=SelectionWarning) 1184s 1184s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 1184s /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. 1184s warnings.warn( 1184s 1184s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps 1184s return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1184s 1184s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps 1184s pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1184s 1184s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps 1184s return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL) 1184s 1184s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps 1184s return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL) 1184s 1184s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps 1184s return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL) 1184s 1184s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps 1184s pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL) 1184s 1184s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag 1184s /tmp/autopkgtest.AzmosB/build.E5H/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps 1184s pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL) 1184s 1184s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings 1184s /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream 1184s warnings.warn("Constructed NamedStream from a NamedStream", 1184s 1184s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] 1184s /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. 1184s warnings.warn(wmsg, DeprecationWarning) 1184s 1184s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1184s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8131 warnings in 786.31s (0:13:06) = 1206s 1206s DueCredit Report: 1206s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] 1206s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] 1206s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] 1206s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] 1206s - HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] 1206s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] 1206s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] 1206s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] 1206s - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] 1206s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] 1206s - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] 1206s - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 2.7.0, 1.1) [15, 16] 1206s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] 1206s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] 1206s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] 1206s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] 1206s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] 1206s - Scientific tools library / numpy (v 1.26.4) [22] 1206s 1206s 2 packages cited 1206s 16 modules cited 1206s 0 functions cited 1206s 1206s References 1206s ---------- 1206s 1206s [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. 1206s [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. 1206s [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. 1206s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 1206s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 1206s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460. 1206s [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. 1206s [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. 1206s [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. 1206s [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). 1206s [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. 1206s [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. 1206s [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. 1206s [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. 1206s [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. 1206s [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. 1206s [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. 1206s [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. 1206s [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. 1206s [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. 1206s [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. 1206s [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. 1209s autopkgtest [15:41:00]: test test-mdanalysis: -----------------------] 1213s autopkgtest [15:41:04]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 1213s test-mdanalysis PASS 1217s autopkgtest [15:41:08]: @@@@@@@@@@@@@@@@@@@@ summary 1217s test-mdanalysis PASS