0s autopkgtest [15:20:40]: starting date and time: 2024-12-02 15:20:40+0000
  0s autopkgtest [15:20:40]: git checkout: be626eda Fix armhf LXD image generation for plucky
  0s autopkgtest [15:20:40]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rmdnog0s/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python-hypothesis --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-hypothesis/6.122.1-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-25.secgroup --name adt-plucky-arm64-mdanalysis-20241202-152040-juju-7f2275-prod-proposed-migration-environment-15-3508065e-fb62-41a6-a4e1-b18d8311a859 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
127s autopkgtest [15:22:47]: testbed dpkg architecture: arm64
127s autopkgtest [15:22:47]: testbed apt version: 2.9.14ubuntu1
127s autopkgtest [15:22:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup
128s autopkgtest [15:22:48]: testbed release detected to be: None
128s autopkgtest [15:22:48]: updating testbed package index (apt update)
129s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
129s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
129s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
129s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
129s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [782 kB]
129s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B]
129s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB]
129s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [68.5 kB]
129s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [114 kB]
129s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [58.2 kB]
129s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [681 kB]
129s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [21.3 kB]
129s Fetched 1824 kB in 1s (2028 kB/s)
130s Reading package lists...
131s Reading package lists...
131s Building dependency tree...
131s Reading state information...
132s Calculating upgrade...
132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
132s Reading package lists...
132s Building dependency tree...
132s Reading state information...
133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
133s autopkgtest [15:22:53]: upgrading testbed (apt dist-upgrade and autopurge)
133s Reading package lists...
134s Building dependency tree...
134s Reading state information...
134s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
134s Starting 2 pkgProblemResolver with broken count: 0
134s Done
135s Entering ResolveByKeep
135s 
136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
136s Reading package lists...
136s Building dependency tree...
136s Reading state information...
136s Starting pkgProblemResolver with broken count: 0
136s Starting 2 pkgProblemResolver with broken count: 0
136s Done
137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
140s autopkgtest [15:23:00]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
140s autopkgtest [15:23:00]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis
144s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (dsc) [2885 B]
144s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (tar) [47.0 MB]
144s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5build1 (diff) [10.9 kB]
144s gpgv: Signature made Fri Nov 15 13:40:58 2024 UTC
144s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
144s gpgv: Can't check signature: No public key
144s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5build1.dsc: no acceptable signature found
146s autopkgtest [15:23:06]: testing package mdanalysis version 2.7.0-5build1
146s autopkgtest [15:23:06]: build not needed
151s autopkgtest [15:23:11]: test test-mdanalysis: preparing testbed
151s Reading package lists...
151s Building dependency tree...
151s Reading state information...
152s Starting pkgProblemResolver with broken count: 0
152s Starting 2 pkgProblemResolver with broken count: 0
152s Done
153s The following NEW packages will be installed:
153s   autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14
153s   cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper debugedit
153s   dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz
153s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome
153s   fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14
153s   g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
153s   gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian
153s   libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0
153s   libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl
153s   libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1
153s   libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0
153s   libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8
153s   libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore
153s   libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1
153s   libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 libpython3-all-dev
153s   libpython3-dev libpython3.12-dev libqhull-r8.0 libraqm0 libsharpyuv0
153s   libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libtsan2
153s   libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0
153s   libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf
153s   pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc
153s   python3-alabaster python3-all python3-all-dev python3-appdirs
153s   python3-biopython python3-brotli python3-build python3-cairo python3-cftime
153s   python3-citeproc python3-contourpy python3-cycler python3-dateutil
153s   python3-decorator python3-defusedxml python3-dev python3-docutils
153s   python3-duecredit python3-fasteners python3-fonttools python3-freetype
153s   python3-fs python3-griddataformats python3-gsd python3-h5py
153s   python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig
153s   python3-installer python3-joblib python3-kiwisolver python3-latexcodec
153s   python3-looseversion python3-lxml python3-lz4 python3-matplotlib
153s   python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic
153s   python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme
153s   python3-netcdf4 python3-networkx python3-numpy python3-packaging
153s   python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk
153s   python3-pluggy python3-pybtex python3-pybtex-docutils
153s   python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo
153s   python3-roman python3-scipy python3-seaborn python3-six python3-sklearn
153s   python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
153s   python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap
153s   python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy
153s   python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz
153s   python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev
153s   python3.12-tk python3.13-tk sphinx-common sphinx-rtd-theme-common
153s   tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings
153s   xfonts-utils zlib1g-dev
153s 0 upgraded, 200 newly installed, 0 to remove and 0 not upgraded.
153s Need to get 207 MB of archives.
153s After this operation, 944 MB of additional disk space will be used.
153s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB]
154s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB]
154s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB]
154s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB]
154s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB]
154s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB]
154s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB]
154s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
154s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
154s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB]
154s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
154s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
154s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB]
154s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB]
154s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
154s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
154s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
154s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
154s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
154s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB]
154s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB]
154s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B]
154s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB]
154s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB]
154s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB]
155s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B]
155s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B]
155s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB]
155s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB]
155s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB]
155s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB]
155s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB]
155s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB]
155s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB]
155s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB]
155s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB]
155s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB]
155s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB]
155s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB]
155s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B]
155s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B]
155s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB]
155s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB]
156s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB]
156s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B]
156s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B]
156s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B]
156s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-1ubuntu2 [2977 kB]
156s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB]
156s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-8 [166 kB]
156s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB]
156s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB]
156s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB]
156s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B]
156s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB]
156s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB]
156s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB]
156s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB]
156s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB]
156s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB]
156s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB]
156s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB]
156s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
156s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB]
156s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
156s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB]
156s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB]
156s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
156s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
156s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
156s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
156s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB]
156s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB]
156s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB]
156s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
156s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB]
156s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B]
156s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB]
156s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB]
156s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
156s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
156s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
156s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
156s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
156s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
156s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
156s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB]
156s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB]
156s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB]
156s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB]
156s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
156s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B]
156s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf19t64 arm64 1:4.9.2-6ubuntu1 [466 kB]
156s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
156s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.7-3 [5565 kB]
157s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.12.6-0ubuntu1 [10.2 kB]
157s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.12.6-0ubuntu1 [916 B]
157s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB]
157s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB]
157s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB]
157s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
157s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB]
157s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
157s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB]
157s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB]
157s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB]
157s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB]
157s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB]
157s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-toml all 0.10.2-1 [16.5 kB]
157s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wheel all 0.45.1-1 [57.7 kB]
157s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-build all 1.2.2-1 [31.0 kB]
157s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB]
157s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-pyproject all 6.20241024 [1728 B]
157s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu1 [2928 kB]
157s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
157s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-mdanalysis-doc all 2.7.0-5build1 [2323 kB]
157s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B]
157s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB]
157s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.12.6-0ubuntu1 [26.7 kB]
157s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.12.6-0ubuntu1 [908 B]
157s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB]
157s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB]
158s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB]
158s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB]
158s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.12.7-1 [9752 B]
158s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu2 [9590 B]
158s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB]
158s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu2 [473 kB]
158s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build1 [139 kB]
158s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB]
158s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B]
158s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB]
158s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB]
158s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4build1 [1694 kB]
158s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB]
158s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-1build1 [290 kB]
158s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1build1 [1591 kB]
158s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-citeproc all 0.6.0-3 [98.4 kB]
158s Get:139 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2build1 [220 kB]
158s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B]
158s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB]
158s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
158s Get:143 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-2 [42.0 kB]
158s Get:144 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 4.2-1 [10.0 kB]
158s Get:145 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB]
158s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-looseversion all 1.3.0-3 [8354 B]
158s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-duecredit all 0.10.2-2 [66.0 kB]
158s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-monotonic all 1.6-2 [5732 B]
158s Get:149 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-fasteners all 0.18-2 [12.5 kB]
158s Get:150 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB]
158s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-5 [90.7 kB]
158s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build5 [27.5 kB]
158s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5ubuntu1 [19.1 MB]
158s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB]
158s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB]
159s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB]
159s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB]
159s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB]
159s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.0-3 [1618 kB]
159s Get:160 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1014 kB]
159s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mrcfile all 1.5.3-3 [114 kB]
159s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-griddataformats all 1.0.2-2 [2107 kB]
159s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gsd arm64 3.3.0-1build1 [228 kB]
159s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB]
159s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B]
159s Get:166 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB]
159s Get:167 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-hypothesis all 6.122.1-1 [330 kB]
159s Get:168 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B]
159s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B]
159s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB]
159s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2build1 [62.0 kB]
159s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-latexcodec all 3.0.0-1 [16.6 kB]
159s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu1 [4612 kB]
159s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mda-xdrlib all 0.2.0-3 [11.4 kB]
159s Get:175 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build3 [106 kB]
159s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB]
159s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB]
159s Get:178 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-1 [92.5 kB]
159s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mdanalysis arm64 2.7.0-5build1 [2585 kB]
159s Get:180 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-common all 7.4.7-4 [775 kB]
159s Get:181 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB]
159s Get:182 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB]
159s Get:183 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sphinx all 7.4.7-4 [593 kB]
159s Get:184 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B]
159s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [23.5 kB]
159s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-msmb-theme all 1.2.0-4 [35.4 kB]
159s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1build1 [798 kB]
159s Get:188 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB]
160s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5ubuntu1 [6921 kB]
160s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB]
160s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB]
160s Get:192 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB]
160s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex all 0.24.0-4 [70.0 kB]
160s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex-docutils all 1.0.2-1 [7176 B]
160s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB]
160s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-seaborn all 0.13.2-4 [225 kB]
160s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6build1 [6350 kB]
161s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6build1 [2257 kB]
161s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-sitemap all 2.6.0-1 [6674 B]
161s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB]
162s Fetched 207 MB in 8s (25.6 MB/s)
162s Selecting previously unselected package fonts-lato.
162s (Reading database ... 
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(Reading database ... 80333 files and directories currently installed.)
162s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ...
162s Unpacking fonts-lato (2.015-1) ...
162s Selecting previously unselected package m4.
162s Preparing to unpack .../001-m4_1.4.19-4build1_arm64.deb ...
162s Unpacking m4 (1.4.19-4build1) ...
163s Selecting previously unselected package autoconf.
163s Preparing to unpack .../002-autoconf_2.72-3_all.deb ...
163s Unpacking autoconf (2.72-3) ...
163s Selecting previously unselected package autotools-dev.
163s Preparing to unpack .../003-autotools-dev_20220109.1_all.deb ...
163s Unpacking autotools-dev (20220109.1) ...
163s Selecting previously unselected package automake.
163s Preparing to unpack .../004-automake_1%3a1.16.5-1.3ubuntu1_all.deb ...
163s Unpacking automake (1:1.16.5-1.3ubuntu1) ...
163s Selecting previously unselected package autopoint.
163s Preparing to unpack .../005-autopoint_0.22.5-2_all.deb ...
163s Unpacking autopoint (0.22.5-2) ...
163s Selecting previously unselected package libtcl8.6:arm64.
163s Preparing to unpack .../006-libtcl8.6_8.6.15+dfsg-2_arm64.deb ...
163s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ...
163s Selecting previously unselected package fonts-dejavu-mono.
163s Preparing to unpack .../007-fonts-dejavu-mono_2.37-8_all.deb ...
163s Unpacking fonts-dejavu-mono (2.37-8) ...
163s Selecting previously unselected package fonts-dejavu-core.
163s Preparing to unpack .../008-fonts-dejavu-core_2.37-8_all.deb ...
163s Unpacking fonts-dejavu-core (2.37-8) ...
163s Selecting previously unselected package libfontenc1:arm64.
163s Preparing to unpack .../009-libfontenc1_1%3a1.1.8-1build1_arm64.deb ...
163s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ...
163s Selecting previously unselected package x11-common.
163s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ...
163s Unpacking x11-common (1:7.7+23ubuntu3) ...
163s Selecting previously unselected package xfonts-encodings.
163s Preparing to unpack .../011-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
163s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
163s Selecting previously unselected package xfonts-utils.
163s Preparing to unpack .../012-xfonts-utils_1%3a7.7+7_arm64.deb ...
163s Unpacking xfonts-utils (1:7.7+7) ...
163s Selecting previously unselected package fonts-urw-base35.
163s Preparing to unpack .../013-fonts-urw-base35_20200910-8_all.deb ...
163s Unpacking fonts-urw-base35 (20200910-8) ...
164s Selecting previously unselected package fontconfig-config.
164s Preparing to unpack .../014-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ...
164s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
164s Selecting previously unselected package libfontconfig1:arm64.
164s Preparing to unpack .../015-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ...
164s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
164s Selecting previously unselected package libxrender1:arm64.
164s Preparing to unpack .../016-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
164s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
164s Selecting previously unselected package libxft2:arm64.
164s Preparing to unpack .../017-libxft2_2.3.6-1build1_arm64.deb ...
164s Unpacking libxft2:arm64 (2.3.6-1build1) ...
164s Selecting previously unselected package libxss1:arm64.
164s Preparing to unpack .../018-libxss1_1%3a1.2.3-1build3_arm64.deb ...
164s Unpacking libxss1:arm64 (1:1.2.3-1build3) ...
164s Selecting previously unselected package libtk8.6:arm64.
164s Preparing to unpack .../019-libtk8.6_8.6.15-1_arm64.deb ...
164s Unpacking libtk8.6:arm64 (8.6.15-1) ...
164s Selecting previously unselected package tk8.6-blt2.5.
164s Preparing to unpack .../020-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ...
164s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
164s Selecting previously unselected package blt.
164s Preparing to unpack .../021-blt_2.5.3+dfsg-7build1_arm64.deb ...
164s Unpacking blt (2.5.3+dfsg-7build1) ...
164s Selecting previously unselected package libisl23:arm64.
164s Preparing to unpack .../022-libisl23_0.27-1_arm64.deb ...
164s Unpacking libisl23:arm64 (0.27-1) ...
164s Selecting previously unselected package libmpc3:arm64.
164s Preparing to unpack .../023-libmpc3_1.3.1-1build2_arm64.deb ...
164s Unpacking libmpc3:arm64 (1.3.1-1build2) ...
164s Selecting previously unselected package cpp-14-aarch64-linux-gnu.
164s Preparing to unpack .../024-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ...
164s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package cpp-14.
165s Preparing to unpack .../025-cpp-14_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking cpp-14 (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package cpp-aarch64-linux-gnu.
165s Preparing to unpack .../026-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ...
165s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
165s Selecting previously unselected package cpp.
165s Preparing to unpack .../027-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ...
165s Unpacking cpp (4:14.1.0-2ubuntu1) ...
165s Selecting previously unselected package libcc1-0:arm64.
165s Preparing to unpack .../028-libcc1-0_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package libgomp1:arm64.
165s Preparing to unpack .../029-libgomp1_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package libitm1:arm64.
165s Preparing to unpack .../030-libitm1_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package libasan8:arm64.
165s Preparing to unpack .../031-libasan8_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package liblsan0:arm64.
165s Preparing to unpack .../032-liblsan0_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package libtsan2:arm64.
165s Preparing to unpack .../033-libtsan2_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package libubsan1:arm64.
165s Preparing to unpack .../034-libubsan1_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package libhwasan0:arm64.
165s Preparing to unpack .../035-libhwasan0_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ...
165s Selecting previously unselected package libgcc-14-dev:arm64.
165s Preparing to unpack .../036-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ...
165s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ...
166s Selecting previously unselected package gcc-14-aarch64-linux-gnu.
166s Preparing to unpack .../037-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ...
166s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ...
166s Selecting previously unselected package gcc-14.
166s Preparing to unpack .../038-gcc-14_14.2.0-8ubuntu1_arm64.deb ...
166s Unpacking gcc-14 (14.2.0-8ubuntu1) ...
166s Selecting previously unselected package gcc-aarch64-linux-gnu.
166s Preparing to unpack .../039-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ...
166s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
166s Selecting previously unselected package gcc.
166s Preparing to unpack .../040-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ...
166s Unpacking gcc (4:14.1.0-2ubuntu1) ...
166s Selecting previously unselected package libstdc++-14-dev:arm64.
166s Preparing to unpack .../041-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ...
166s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ...
166s Selecting previously unselected package g++-14-aarch64-linux-gnu.
166s Preparing to unpack .../042-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ...
166s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ...
167s Selecting previously unselected package g++-14.
167s Preparing to unpack .../043-g++-14_14.2.0-8ubuntu1_arm64.deb ...
167s Unpacking g++-14 (14.2.0-8ubuntu1) ...
167s Selecting previously unselected package g++-aarch64-linux-gnu.
167s Preparing to unpack .../044-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ...
167s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
167s Selecting previously unselected package g++.
167s Preparing to unpack .../045-g++_4%3a14.1.0-2ubuntu1_arm64.deb ...
167s Unpacking g++ (4:14.1.0-2ubuntu1) ...
167s Selecting previously unselected package build-essential.
167s Preparing to unpack .../046-build-essential_12.10ubuntu1_arm64.deb ...
167s Unpacking build-essential (12.10ubuntu1) ...
167s Selecting previously unselected package cython3.
167s Preparing to unpack .../047-cython3_3.0.11+dfsg-1ubuntu2_arm64.deb ...
167s Unpacking cython3 (3.0.11+dfsg-1ubuntu2) ...
167s Selecting previously unselected package libdebhelper-perl.
167s Preparing to unpack .../048-libdebhelper-perl_13.20ubuntu1_all.deb ...
167s Unpacking libdebhelper-perl (13.20ubuntu1) ...
167s Selecting previously unselected package libtool.
167s Preparing to unpack .../049-libtool_2.4.7-8_all.deb ...
167s Unpacking libtool (2.4.7-8) ...
167s Selecting previously unselected package dh-autoreconf.
167s Preparing to unpack .../050-dh-autoreconf_20_all.deb ...
167s Unpacking dh-autoreconf (20) ...
167s Selecting previously unselected package libarchive-zip-perl.
167s Preparing to unpack .../051-libarchive-zip-perl_1.68-1_all.deb ...
167s Unpacking libarchive-zip-perl (1.68-1) ...
167s Selecting previously unselected package libfile-stripnondeterminism-perl.
167s Preparing to unpack .../052-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
167s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
167s Selecting previously unselected package dh-strip-nondeterminism.
167s Preparing to unpack .../053-dh-strip-nondeterminism_1.14.0-1_all.deb ...
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168s Selecting previously unselected package fonts-font-awesome.
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168s Selecting previously unselected package libaec0:arm64.
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168s Selecting previously unselected package libpixman-1-0:arm64.
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169s Selecting previously unselected package libhdf5-hl-100t64:arm64.
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169s Selecting previously unselected package libimagequant0:arm64.
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169s Selecting previously unselected package libjpeg-turbo8:arm64.
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169s Selecting previously unselected package libjs-jquery.
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169s Selecting previously unselected package libjs-sphinxdoc.
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169s Selecting previously unselected package libjson-perl.
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169s Selecting previously unselected package liblapack3:arm64.
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169s Selecting previously unselected package liblcms2-2:arm64.
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169s Selecting previously unselected package liblerc4:arm64.
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169s Selecting previously unselected package liblzf1:arm64.
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170s Selecting previously unselected package libnetcdf19t64:arm64.
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170s Selecting previously unselected package zlib1g-dev:arm64.
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170s Selecting previously unselected package libpython3.12-dev:arm64.
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170s Unpacking libpython3.12-dev:arm64 (3.12.7-3) ...
170s Selecting previously unselected package libpython3-dev:arm64.
170s Preparing to unpack .../095-libpython3-dev_3.12.6-0ubuntu1_arm64.deb ...
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170s Selecting previously unselected package libpython3-all-dev:arm64.
170s Preparing to unpack .../096-libpython3-all-dev_3.12.6-0ubuntu1_arm64.deb ...
170s Unpacking libpython3-all-dev:arm64 (3.12.6-0ubuntu1) ...
170s Selecting previously unselected package libqhull-r8.0:arm64.
170s Preparing to unpack .../097-libqhull-r8.0_2020.2-6build1_arm64.deb ...
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170s Selecting previously unselected package libraqm0:arm64.
170s Preparing to unpack .../098-libraqm0_0.10.1-1build1_arm64.deb ...
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170s Selecting previously unselected package libsharpyuv0:arm64.
170s Preparing to unpack .../099-libsharpyuv0_1.4.0-0.1_arm64.deb ...
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170s Selecting previously unselected package libjbig0:arm64.
170s Preparing to unpack .../100-libjbig0_2.1-6.1ubuntu2_arm64.deb ...
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170s Selecting previously unselected package libwebp7:arm64.
170s Preparing to unpack .../101-libwebp7_1.4.0-0.1_arm64.deb ...
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170s Selecting previously unselected package libtiff6:arm64.
170s Preparing to unpack .../102-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ...
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170s Selecting previously unselected package libwebpdemux2:arm64.
170s Preparing to unpack .../103-libwebpdemux2_1.4.0-0.1_arm64.deb ...
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170s Selecting previously unselected package libwebpmux3:arm64.
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170s Selecting previously unselected package libxslt1.1:arm64.
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170s Selecting previously unselected package python3-packaging.
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170s Selecting previously unselected package python3-pyproject-hooks.
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170s Selecting previously unselected package python3-toml.
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170s Selecting previously unselected package python3-wheel.
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170s Selecting previously unselected package python3-build.
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171s Selecting previously unselected package python3-installer.
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171s Selecting previously unselected package pybuild-plugin-pyproject.
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171s Selecting previously unselected package python-matplotlib-data.
171s Preparing to unpack .../113-python-matplotlib-data_3.8.3-3ubuntu1_all.deb ...
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171s Selecting previously unselected package libjs-mathjax.
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171s Selecting previously unselected package python-mdanalysis-doc.
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172s Selecting previously unselected package python3-all.
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172s Selecting previously unselected package python3.12-dev.
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172s Selecting previously unselected package python3-dev.
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172s Selecting previously unselected package python3-all-dev.
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172s Selecting previously unselected package python3-appdirs.
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172s Selecting previously unselected package python3-numpy.
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172s Selecting previously unselected package python3.12-tk.
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172s Selecting previously unselected package python3-tk:arm64.
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172s Selecting previously unselected package python3-pil.imagetk:arm64.
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172s Selecting previously unselected package libopenjp2-7:arm64.
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172s Selecting previously unselected package python3-pil:arm64.
172s Preparing to unpack .../127-python3-pil_10.4.0-1ubuntu2_arm64.deb ...
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172s Selecting previously unselected package python3-cairo.
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172s Selecting previously unselected package python3-freetype.
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172s Selecting previously unselected package python3-rlpycairo.
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172s Selecting previously unselected package python3-reportlab.
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173s Selecting previously unselected package w3c-sgml-lib.
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173s Selecting previously unselected package python3-biopython.
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173s Selecting previously unselected package python3-brotli.
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173s Selecting previously unselected package python3-cftime.
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173s Selecting previously unselected package python3-lxml:arm64.
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173s Selecting previously unselected package python3-citeproc.
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173s Selecting previously unselected package python3-contourpy.
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173s Selecting previously unselected package python3-cycler.
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173s Selecting previously unselected package python3-dateutil.
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173s Selecting previously unselected package python3-decorator.
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173s Selecting previously unselected package python3-defusedxml.
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173s Selecting previously unselected package python3-roman.
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173s Selecting previously unselected package python3-docutils.
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173s Selecting previously unselected package python3-looseversion.
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173s Selecting previously unselected package python3-duecredit.
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174s Selecting previously unselected package python3-monotonic.
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174s Selecting previously unselected package python3-fasteners.
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174s Selecting previously unselected package python3-tz.
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174s Selecting previously unselected package python3-fs.
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174s Unpacking python3-fs (2.4.16-5) ...
174s Selecting previously unselected package python3-lz4.
174s Preparing to unpack .../151-python3-lz4_4.0.2+dfsg-1build5_arm64.deb ...
174s Unpacking python3-lz4 (4.0.2+dfsg-1build5) ...
174s Selecting previously unselected package python3-scipy.
174s Preparing to unpack .../152-python3-scipy_1.13.1-5ubuntu1_arm64.deb ...
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174s Selecting previously unselected package python3-mpmath.
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174s Unpacking python3-mpmath (1.3.0-1) ...
175s Selecting previously unselected package python3-sympy.
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175s Unpacking python3-sympy (1.13.3-1) ...
175s Selecting previously unselected package python3-ufolib2.
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175s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ...
175s Selecting previously unselected package python3-unicodedata2.
175s Preparing to unpack .../156-python3-unicodedata2_15.1.0+ds-1build2_arm64.deb ...
175s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ...
175s Selecting previously unselected package unicode-data.
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175s Unpacking unicode-data (15.1.0-1) ...
175s Selecting previously unselected package python3-fonttools.
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175s Selecting previously unselected package sphinx-rtd-theme-common.
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175s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-1) ...
175s Selecting previously unselected package python3-mrcfile.
175s Preparing to unpack .../160-python3-mrcfile_1.5.3-3_all.deb ...
175s Unpacking python3-mrcfile (1.5.3-3) ...
175s Selecting previously unselected package python3-griddataformats.
175s Preparing to unpack .../161-python3-griddataformats_1.0.2-2_all.deb ...
175s Unpacking python3-griddataformats (1.0.2-2) ...
176s Selecting previously unselected package python3-gsd.
176s Preparing to unpack .../162-python3-gsd_3.3.0-1build1_arm64.deb ...
176s Unpacking python3-gsd (3.3.0-1build1) ...
176s Selecting previously unselected package python3-h5py-serial.
176s Preparing to unpack .../163-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ...
176s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ...
176s Selecting previously unselected package python3-h5py.
176s Preparing to unpack .../164-python3-h5py_3.11.0-5ubuntu1_all.deb ...
176s Unpacking python3-h5py (3.11.0-5ubuntu1) ...
176s Selecting previously unselected package python3-sortedcontainers.
176s Preparing to unpack .../165-python3-sortedcontainers_2.4.0-2_all.deb ...
176s Unpacking python3-sortedcontainers (2.4.0-2) ...
176s Selecting previously unselected package python3-hypothesis.
176s Preparing to unpack .../166-python3-hypothesis_6.122.1-1_all.deb ...
176s Unpacking python3-hypothesis (6.122.1-1) ...
176s Selecting previously unselected package python3-imagesize.
176s Preparing to unpack .../167-python3-imagesize_1.4.1-1_all.deb ...
176s Unpacking python3-imagesize (1.4.1-1) ...
176s Selecting previously unselected package python3-iniconfig.
176s Preparing to unpack .../168-python3-iniconfig_1.1.1-2_all.deb ...
176s Unpacking python3-iniconfig (1.1.1-2) ...
176s Selecting previously unselected package python3-joblib.
176s Preparing to unpack .../169-python3-joblib_1.3.2-5_all.deb ...
176s Unpacking python3-joblib (1.3.2-5) ...
176s Selecting previously unselected package python3-kiwisolver.
176s Preparing to unpack .../170-python3-kiwisolver_1.4.7-2build1_arm64.deb ...
176s Unpacking python3-kiwisolver (1.4.7-2build1) ...
176s Selecting previously unselected package python3-latexcodec.
176s Preparing to unpack .../171-python3-latexcodec_3.0.0-1_all.deb ...
176s Unpacking python3-latexcodec (3.0.0-1) ...
176s Selecting previously unselected package python3-matplotlib.
176s Preparing to unpack .../172-python3-matplotlib_3.8.3-3ubuntu1_arm64.deb ...
176s Unpacking python3-matplotlib (3.8.3-3ubuntu1) ...
176s Selecting previously unselected package python3-mda-xdrlib.
176s Preparing to unpack .../173-python3-mda-xdrlib_0.2.0-3_all.deb ...
176s Unpacking python3-mda-xdrlib (0.2.0-3) ...
176s Selecting previously unselected package python3-msgpack.
176s Preparing to unpack .../174-python3-msgpack_1.0.3-3build3_arm64.deb ...
176s Unpacking python3-msgpack (1.0.3-3build3) ...
176s Selecting previously unselected package python3-mmtf.
176s Preparing to unpack .../175-python3-mmtf_1.1.3-1_all.deb ...
176s Unpacking python3-mmtf (1.1.3-1) ...
176s Selecting previously unselected package python3-threadpoolctl.
176s Preparing to unpack .../176-python3-threadpoolctl_3.1.0-1_all.deb ...
176s Unpacking python3-threadpoolctl (3.1.0-1) ...
176s Selecting previously unselected package python3-tqdm.
176s Preparing to unpack .../177-python3-tqdm_4.67.1-1_all.deb ...
176s Unpacking python3-tqdm (4.67.1-1) ...
176s Selecting previously unselected package python3-mdanalysis.
177s Preparing to unpack .../178-python3-mdanalysis_2.7.0-5build1_arm64.deb ...
177s Unpacking python3-mdanalysis (2.7.0-5build1) ...
177s Selecting previously unselected package sphinx-common.
177s Preparing to unpack .../179-sphinx-common_7.4.7-4_all.deb ...
177s Unpacking sphinx-common (7.4.7-4) ...
177s Selecting previously unselected package python3-alabaster.
177s Preparing to unpack .../180-python3-alabaster_0.7.16-0.1_all.deb ...
177s Unpacking python3-alabaster (0.7.16-0.1) ...
177s Selecting previously unselected package python3-snowballstemmer.
177s Preparing to unpack .../181-python3-snowballstemmer_2.2.0-4build1_all.deb ...
177s Unpacking python3-snowballstemmer (2.2.0-4build1) ...
177s Selecting previously unselected package python3-sphinx.
177s Preparing to unpack .../182-python3-sphinx_7.4.7-4_all.deb ...
177s Unpacking python3-sphinx (7.4.7-4) ...
177s Selecting previously unselected package python3-sphinxcontrib.jquery.
177s Preparing to unpack .../183-python3-sphinxcontrib.jquery_4.1-5_all.deb ...
177s Unpacking python3-sphinxcontrib.jquery (4.1-5) ...
177s Selecting previously unselected package python3-sphinx-rtd-theme.
177s Preparing to unpack .../184-python3-sphinx-rtd-theme_3.0.2+dfsg-1_all.deb ...
177s Unpacking python3-sphinx-rtd-theme (3.0.2+dfsg-1) ...
177s Selecting previously unselected package python3-msmb-theme.
177s Preparing to unpack .../185-python3-msmb-theme_1.2.0-4_all.deb ...
177s Unpacking python3-msmb-theme (1.2.0-4) ...
177s Selecting previously unselected package python3-netcdf4.
177s Preparing to unpack .../186-python3-netcdf4_1.7.2-1build1_arm64.deb ...
177s Unpacking python3-netcdf4 (1.7.2-1build1) ...
177s Selecting previously unselected package python3-networkx.
177s Preparing to unpack .../187-python3-networkx_3.2.1-4ubuntu1_all.deb ...
177s Unpacking python3-networkx (3.2.1-4ubuntu1) ...
178s Selecting previously unselected package python3-pandas-lib:arm64.
178s Preparing to unpack .../188-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_arm64.deb ...
178s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ...
178s Selecting previously unselected package python3-pandas.
178s Preparing to unpack .../189-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ...
178s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ...
179s Selecting previously unselected package python3-pluggy.
179s Preparing to unpack .../190-python3-pluggy_1.5.0-1_all.deb ...
179s Unpacking python3-pluggy (1.5.0-1) ...
179s Selecting previously unselected package python3-six.
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179s Unpacking python3-six (1.16.0-7) ...
179s Selecting previously unselected package python3-pybtex.
179s Preparing to unpack .../192-python3-pybtex_0.24.0-4_all.deb ...
179s Unpacking python3-pybtex (0.24.0-4) ...
179s Selecting previously unselected package python3-pybtex-docutils.
179s Preparing to unpack .../193-python3-pybtex-docutils_1.0.2-1_all.deb ...
179s Unpacking python3-pybtex-docutils (1.0.2-1) ...
179s Selecting previously unselected package python3-pytest.
179s Preparing to unpack .../194-python3-pytest_8.3.3-1_all.deb ...
179s Unpacking python3-pytest (8.3.3-1) ...
179s Selecting previously unselected package python3-seaborn.
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179s Unpacking python3-seaborn (0.13.2-4) ...
179s Selecting previously unselected package python3-sklearn-lib:arm64.
179s Preparing to unpack .../196-python3-sklearn-lib_1.4.2+dfsg-6build1_arm64.deb ...
179s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-6build1) ...
179s Selecting previously unselected package python3-sklearn.
179s Preparing to unpack .../197-python3-sklearn_1.4.2+dfsg-6build1_all.deb ...
179s Unpacking python3-sklearn (1.4.2+dfsg-6build1) ...
179s Selecting previously unselected package python3-sphinx-sitemap.
179s Preparing to unpack .../198-python3-sphinx-sitemap_2.6.0-1_all.deb ...
179s Unpacking python3-sphinx-sitemap (2.6.0-1) ...
179s Selecting previously unselected package python3-sphinxcontrib.bibtex.
179s Preparing to unpack .../199-python3-sphinxcontrib.bibtex_2.6.2-1_all.deb ...
179s Unpacking python3-sphinxcontrib.bibtex (2.6.2-1) ...
179s Setting up dh-python (6.20241024) ...
180s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
180s Setting up liblcms2-2:arm64 (2.16-2) ...
180s Setting up python3-iniconfig (1.1.1-2) ...
180s Setting up libpixman-1-0:arm64 (0.44.0-3) ...
180s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ...
180s Setting up w3c-sgml-lib (1.3-3) ...
208s Setting up fonts-lato (2.015-1) ...
208s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
208s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
208s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
208s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
208s Setting up python3-joblib (1.3.2-5) ...
209s Setting up python3-lz4 (4.0.2+dfsg-1build5) ...
209s Setting up libxcb-render0:arm64 (1.17.0-2) ...
209s Setting up python3-defusedxml (0.7.1-2) ...
209s Setting up libarchive-zip-perl (1.68-1) ...
209s Setting up python3-alabaster (0.7.16-0.1) ...
209s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ...
209s Setting up fonts-lyx (2.4.2.1-1) ...
209s Setting up libdebhelper-perl (13.20ubuntu1) ...
209s Setting up python3-tqdm (4.67.1-1) ...
209s Setting up python3-threadpoolctl (3.1.0-1) ...
209s Setting up x11-common (1:7.7+23ubuntu3) ...
210s Setting up libdeflate0:arm64 (1.22-1) ...
210s Setting up m4 (1.4.19-4build1) ...
210s Setting up python3-latexcodec (3.0.0-1) ...
210s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ...
210s Setting up python3-all (3.12.6-0ubuntu1) ...
210s Setting up libxcb-shm0:arm64 (1.17.0-2) ...
210s Setting up python3-sortedcontainers (2.4.0-2) ...
210s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ...
210s Setting up python3-freetype (2.5.1-1) ...
210s Setting up python3-networkx (3.2.1-4ubuntu1) ...
212s Setting up python3-wheel (0.45.1-1) ...
212s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
212s Setting up python3-mda-xdrlib (0.2.0-3) ...
212s Setting up libaec0:arm64 (1.1.3-1) ...
212s Setting up python3-tz (2024.1-2) ...
212s Setting up python3-monotonic (1.6-2) ...
212s Setting up unicode-data (15.1.0-1) ...
212s Setting up python3-six (1.16.0-7) ...
212s Setting up python3-roman (4.2-1) ...
212s Setting up python3-decorator (5.1.1-5) ...
213s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ...
213s Setting up autotools-dev (20220109.1) ...
213s Setting up libblas3:arm64 (3.12.0-4) ...
213s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
213s Setting up python3-packaging (24.2-1) ...
213s Setting up libexpat1-dev:arm64 (2.6.4-1) ...
213s Setting up python3-pyproject-hooks (1.2.0-1) ...
213s Setting up python3-snowballstemmer (2.2.0-4build1) ...
213s Setting up python3-brotli (1.1.0-2build3) ...
213s Setting up liblzf1:arm64 (3.6-4) ...
213s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
213s Setting up python3-cycler (0.12.1-1) ...
213s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
213s Setting up fonts-dejavu-mono (2.37-8) ...
213s Setting up python3-kiwisolver (1.4.7-2build1) ...
213s Setting up libmpc3:arm64 (1.3.1-1build2) ...
213s Setting up cython3 (3.0.11+dfsg-1ubuntu2) ...
214s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ...
214s Setting up autopoint (0.22.5-2) ...
214s Setting up fonts-dejavu-core (2.37-8) ...
214s Setting up python3-fasteners (0.18-2) ...
214s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
214s Setting up python3-toml (0.10.2-1) ...
215s Setting up python3-installer (0.7.0+dfsg1-3) ...
215s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ...
215s Setting up autoconf (2.72-3) ...
215s Setting up python3-pluggy (1.5.0-1) ...
215s Setting up libwebp7:arm64 (1.4.0-0.1) ...
215s Setting up python3-pybtex (0.24.0-4) ...
215s Setting up libubsan1:arm64 (14.2.0-8ubuntu1) ...
215s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
215s Setting up dwz (0.15-1build6) ...
215s Setting up python3-looseversion (1.3.0-3) ...
215s Setting up libhwasan0:arm64 (14.2.0-8ubuntu1) ...
215s Setting up libasan8:arm64 (14.2.0-8ubuntu1) ...
215s Setting up docutils-common (0.21.2+dfsg-2) ...
215s Setting up libjson-perl (4.10000-1) ...
215s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ...
215s Setting up debugedit (1:5.1-1) ...
215s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ...
215s Setting up libharfbuzz0b:arm64 (10.0.1-1) ...
215s Setting up python3-dateutil (2.9.0-3) ...
215s Setting up python3-msgpack (1.0.3-3build3) ...
216s Setting up libxss1:arm64 (1:1.2.3-1build3) ...
216s Setting up libtsan2:arm64 (14.2.0-8ubuntu1) ...
216s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
216s Setting up python3-mpmath (1.3.0-1) ...
216s Setting up libisl23:arm64 (0.27-1) ...
216s Setting up python3-build (1.2.2-1) ...
216s Setting up python-matplotlib-data (3.8.3-3ubuntu1) ...
216s Setting up libwebpmux3:arm64 (1.4.0-0.1) ...
216s Setting up python3-appdirs (1.4.4-4) ...
216s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
216s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-1) ...
216s Setting up libcc1-0:arm64 (14.2.0-8ubuntu1) ...
216s Setting up liblsan0:arm64 (14.2.0-8ubuntu1) ...
216s Setting up libsz2:arm64 (1.1.3-1) ...
216s Setting up libitm1:arm64 (14.2.0-8ubuntu1) ...
216s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
216s Setting up python3-imagesize (1.4.1-1) ...
216s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
216s Setting up automake (1:1.16.5-1.3ubuntu1) ...
216s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
216s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
216s Setting up python3-sympy (1.13.3-1) ...
223s Setting up liblapack3:arm64 (3.12.0-4) ...
223s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
223s Setting up gettext (0.22.5-2) ...
223s Setting up pybuild-plugin-pyproject (6.20241024) ...
223s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
223s Setting up python3-pytest (8.3.3-1) ...
224s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ...
224s Setting up python3-hypothesis (6.122.1-1) ...
224s Setting up libpython3.12-dev:arm64 (3.12.7-3) ...
224s Setting up xfonts-utils (1:7.7+7) ...
224s Setting up intltool-debian (0.35.0+20060710.6) ...
224s Setting up python3-fs (2.4.16-5) ...
224s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
224s Setting up libraqm0:arm64 (0.10.1-1build1) ...
224s Setting up python3.12-dev (3.12.7-3) ...
224s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ...
226s Setting up libjs-sphinxdoc (7.4.7-4) ...
226s Setting up dh-strip-nondeterminism (1.14.0-1) ...
226s Setting up cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ...
226s Setting up python3-lxml:arm64 (5.3.0-1build1) ...
226s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
226s Setting up python3-contourpy (1.3.0-2build1) ...
226s Setting up libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ...
226s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ...
226s Setting up libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ...
226s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
226s Setting up python3-mrcfile (1.5.3-3) ...
226s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ...
226s Setting up libnetcdf19t64:arm64 (1:4.9.2-6ubuntu1) ...
226s Setting up python3-scipy (1.13.1-5ubuntu1) ...
230s Setting up libpython3-dev:arm64 (3.12.6-0ubuntu1) ...
230s Setting up python3-citeproc (0.6.0-3) ...
230s Setting up po-debconf (1.0.21+nmu1) ...
230s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ...
230s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-6build1) ...
230s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
230s Setting up python3-gsd (3.3.0-1build1) ...
230s Setting up python3-mmtf (1.1.3-1) ...
231s Setting up fonts-urw-base35 (20200910-8) ...
231s Setting up python-mdanalysis-doc (2.7.0-5build1) ...
231s Setting up python3-pil:arm64 (10.4.0-1ubuntu2) ...
231s Setting up cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
231s Setting up python3-griddataformats (1.0.2-2) ...
231s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ...
237s Setting up libpython3-all-dev:arm64 (3.12.6-0ubuntu1) ...
237s Setting up sphinx-common (7.4.7-4) ...
237s Setting up python3-dev (3.12.6-0ubuntu1) ...
237s Setting up python3-h5py (3.11.0-5ubuntu1) ...
237s Setting up python3-sklearn (1.4.2+dfsg-6build1) ...
239s Setting up python3-cftime (1.6.4-1build1) ...
239s Setting up cpp-14 (14.2.0-8ubuntu1) ...
239s Setting up cpp (4:14.1.0-2ubuntu1) ...
239s Setting up gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ...
239s Setting up python3-netcdf4 (1.7.2-1build1) ...
239s Setting up python3-all-dev (3.12.6-0ubuntu1) ...
239s Setting up gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
239s Setting up g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ...
239s Setting up python3-duecredit (0.10.2-2) ...
239s Setting up gcc-14 (14.2.0-8ubuntu1) ...
239s Setting up g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ...
239s Setting up g++-14 (14.2.0-8ubuntu1) ...
239s Setting up libtool (2.4.7-8) ...
239s Setting up gcc (4:14.1.0-2ubuntu1) ...
239s Setting up dh-autoreconf (20) ...
239s Setting up g++ (4:14.1.0-2ubuntu1) ...
239s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
239s Setting up build-essential (12.10ubuntu1) ...
239s Setting up debhelper (13.20ubuntu1) ...
239s Setting up python3-fonttools (4.55.0-3) ...
240s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ...
240s Processing triggers for sgml-base (1.31) ...
240s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
240s Setting up python3-docutils (0.21.2+dfsg-2) ...
241s Processing triggers for install-info (7.1.1-1) ...
241s Setting up libxft2:arm64 (2.3.6-1build1) ...
241s Setting up libtk8.6:arm64 (8.6.15-1) ...
241s Processing triggers for libc-bin (2.40-1ubuntu3) ...
241s Setting up python3.12-tk (3.12.7-3) ...
241s Processing triggers for man-db (2.13.0-1) ...
243s Setting up libcairo2:arm64 (1.18.2-2) ...
243s Setting up python3.13-tk (3.13.0-2) ...
243s Setting up python3-pybtex-docutils (1.0.2-1) ...
243s Setting up python3-sphinx (7.4.7-4) ...
243s Setting up python3-sphinxcontrib.bibtex (2.6.2-1) ...
244s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
244s Setting up python3-cairo (1.26.1-2build1) ...
244s Setting up python3-sphinx-sitemap (2.6.0-1) ...
244s Setting up blt (2.5.3+dfsg-7build1) ...
244s Setting up python3-tk:arm64 (3.12.7-1) ...
244s Setting up python3-sphinxcontrib.jquery (4.1-5) ...
244s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu2) ...
244s Setting up python3-rlpycairo (0.3.0-3) ...
244s Setting up python3-reportlab (4.2.5-1) ...
245s Setting up python3-biopython (1.84+dfsg-4build1) ...
246s Setting up python3-matplotlib (3.8.3-3ubuntu1) ...
248s Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-1) ...
248s Setting up python3-mdanalysis (2.7.0-5build1) ...
248s Setting up python3-seaborn (0.13.2-4) ...
248s Setting up python3-msmb-theme (1.2.0-4) ...
249s Processing triggers for libc-bin (2.40-1ubuntu3) ...
250s autopkgtest [15:24:50]: test test-mdanalysis: [-----------------------
250s skipping tests with SKIP_TEST_LIST=
260s ============================= test session starts ==============================
260s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
260s rootdir: /tmp/autopkgtest.fAxSVr/build.PVm/src
260s plugins: typeguard-4.4.1, hypothesis-6.122.1
260s collected 19229 items / 6 skipped
260s 
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594s testsuite/MDAnalysisTests/coordinates/test_pqr.py ...................... [ 15%]
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602s testsuite/MDAnalysisTests/coordinates/test_trz.py ...................... [ 18%]
602s ..                                                                       [ 18%]
602s testsuite/MDAnalysisTests/coordinates/test_txyz.py ......                [ 18%]
602s testsuite/MDAnalysisTests/coordinates/test_windows.py .................. [ 18%]
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603s testsuite/MDAnalysisTests/coordinates/test_writer_api.py .ss............ [ 19%]
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603s testsuite/MDAnalysisTests/coordinates/test_writer_registration.py ....   [ 19%]
605s testsuite/MDAnalysisTests/coordinates/test_xdr.py ...................... [ 19%]
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731s testsuite/MDAnalysisTests/core/test_group_traj_access.py ............... [ 27%]
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765s testsuite/MDAnalysisTests/core/test_topology.py ........................ [ 31%]
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765s testsuite/MDAnalysisTests/core/test_topologyattrs.py ................... [ 31%]
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864s testsuite/MDAnalysisTests/topology/test_dlpoly.py ...................... [ 86%]
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973s ...................                                                      [ 98%]
973s testsuite/MDAnalysisTests/utils/test_log.py .                            [ 98%]
973s testsuite/MDAnalysisTests/utils/test_meta.py ....                        [ 98%]
974s testsuite/MDAnalysisTests/utils/test_modelling.py .............          [ 98%]
975s testsuite/MDAnalysisTests/utils/test_persistence.py .......              [ 98%]
986s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%]
986s ..............ss..                                                       [ 98%]
986s testsuite/MDAnalysisTests/utils/test_qcprot.py ......                    [ 98%]
988s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%]
988s                                                                          [ 98%]
989s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 98%]
989s ...............                                                          [ 99%]
989s testsuite/MDAnalysisTests/utils/test_transformations.py ................ [ 99%]
989s ........................................................................ [ 99%]
989s ........................................................                 [ 99%]
989s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%]
989s .......                                                                  [ 99%]
990s testsuite/MDAnalysisTests/visualization/test_streamlines.py ...          [100%]
990s 
990s =============================== warnings summary ===============================
990s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39
990s   /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
990s   
990s   Due to the on going maintenance burden of keeping command line application
990s   wrappers up to date, we have decided to deprecate and eventually remove these
990s   modules.
990s   
990s   We instead now recommend building your command line and invoking it directly
990s   with the subprocess module.
990s     warnings.warn(
990s 
990s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings
990s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings
990s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings
990s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings
990s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings
990s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings
990s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings
990s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings
990s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings
990s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings
990s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings
990s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings
990s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings
990s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings
990s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings
990s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
990s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings
990s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings
990s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings
990s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings
990s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings
990s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings
990s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings
990s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings
990s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings
990s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings
990s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings
990s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings
990s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings
990s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
990s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings
990s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
990s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings
990s   /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.
990s     warnings.warn("DCDReader currently makes independent timesteps"
990s 
990s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52
990s   /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.
990s     warnings.warn(wmsg, category=DeprecationWarning)
990s 
990s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter]
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles'
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings
990s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings
990s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written
990s     warnings.warn(wmsg)
990s 
990s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings
990s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings
990s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings
990s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings
990s   /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
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings
990s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
990s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings
990s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning
990s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
990s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'c3', 'h1', 'ho', 'oh', 'hc'}. These have been given an empty element record.
990s     warnings.warn("Unknown elements found for some "
990s 
990s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
990s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning
990s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings
990s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings
990s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
990s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings
990s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings
990s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps
990s     self.times[i] = ts.time
990s 
990s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings
990s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning
990s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings
990s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
990s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings
990s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings
990s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings
990s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded
990s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps
990s     results.append((ts.time, x.sum() / mask.sum()))
990s 
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue
990s   /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.
990s     warnings.warn(msg)
990s 
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
990s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding
990s   /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
990s     warnings.warn(msg)
990s 
990s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
990s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
990s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings
990s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
990s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
990s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings
990s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning
990s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings
990s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings
990s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings
990s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
990s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings
990s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings
990s   /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.
990s     warnings.warn("Element information is missing, elements attribute "
990s 
990s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran
990s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame
990s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections
990s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues
990s     warnings.warn("Cannot determine phi and psi angles for the first "
990s 
990s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin
990s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr
990s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame
990s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot
990s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning
990s   /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.
990s     warnings.warn(f"All residues selected with '{select_remove}' "
990s 
990s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings
990s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings
990s   /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=6021) is multi-threaded, use of fork() may lead to deadlocks in the child.
990s     self.pid = os.fork()
990s 
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes
990s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide
990s     cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms
990s 
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide
990s     local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T  # (n_res-3, 3)
990s 
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
990s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice
990s     ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
990s 
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
990s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide
990s     ret = um.true_divide(
990s 
990s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
990s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide
990s     ret = ret.dtype.type(ret / rcount)
990s 
990s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
990s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning
990s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning
990s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
990s   /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.
990s     warnings.warn("1 A^3 CRYST1 record,"
990s 
990s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values.
990s     warnings.warn("Unit cell dimensions not found. "
990s 
990s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' '
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings
990s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings
990s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings
990s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
990s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings
990s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
990s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning
990s   /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
990s     warnings.warn(wmsg, DeprecationWarning)
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6
990s     warnings.warn("Desired number of sample points too high, using {0}"
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbond = HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbond = HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbond = HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbond = HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbond = HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbond = HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbond = HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbond = HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     HBAC(
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
990s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
990s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbond = HBAC(u,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated!
990s   `find_hydrogen_donors` will be removed in release 3.0.0.
990s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     D = hbonds.find_hydrogen_donors(H)
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated!
990s   `find_hydrogen_donors` will be removed in release 3.0.0.
990s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
990s     hbonds.find_hydrogen_donors(u.atoms)
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
990s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
990s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
990s     return _methods._mean(a, axis=axis, dtype=dtype,
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
990s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
990s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
990s     ret = ret.dtype.type(ret / rcount)
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
990s   /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.
990s     warnings.warn(msg.format(sel))
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
990s   /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.
990s     warnings.warn(msg.format(sel))
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
990s   /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.
990s     warnings.warn(msg.format(sel))
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned.
990s     warnings.warn("Empty string to select atoms, empty group returned.",
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
990s   /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, .
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
990s   /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, .
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
990s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
990s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
990s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
990s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
990s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
990s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple
990s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content
990s   /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.
990s     warnings.warn(wmsg)
990s 
990s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning
990s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning
990s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
990s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
990s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
990s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
990s   /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.)
990s     phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi
990s 
990s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j
990s   /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
990s     warnings.warn("Column index entered (j = {:d} is smaller than row "
990s 
990s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps
990s     dt=self.trajectory.ts.dt * step,
990s 
990s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8]
990s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0]
990s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8]
990s   /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
990s     warnings.warn(wmsg, DeprecationWarning)
990s 
990s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
990s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings
990s   /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.
990s     warnings.warn("The `u` attribute is superflous and will be removed "
990s 
990s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267]
990s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm
990s   /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.
990s     warnings.warn("The `density` attribute was deprecated in "
990s 
990s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata
990s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first.
990s     warnings.warn(msg, category=MissingDataWarning)
990s 
990s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps
990s     self.timesteps.append(self._ts.time)
990s 
990s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning
990s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default
990s     warnings.warn("{} does not support time selection. Reverting to "
990s 
990s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default
990s     warnings.warn("{} does not support data selection. Reverting to "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings
990s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings
990s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
990s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings
990s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps
990s     return self.ts.dt
990s 
990s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings
990s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
990s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps
990s     ts.data['time'] = step_num * ts.dt
990s 
990s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats
990s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_unsupported_filetypes
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf6e8de2db7e0>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
990s       self.close()
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close
990s       self._apply('close')
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply
990s       return [reader.__getattribute__(method)(**kwargs) for reader in self.readers]
990s                                                                       ^^^^^^^^^^^^
990s   AttributeError: 'ChainReader' object has no attribute 'readers'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing
990s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain
990s     warnings.warn("Missing frame in continuous chain", UserWarning)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps
990s     time_frame_0 = ts.time - ts.frame*ts.dt  # assumes ts.dt is constant
990s 
990s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps
990s     frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps
990s     step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps
990s     self._add_step_to_frame_data(ts.time)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames]
990s   /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. 
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids]
990s   /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. 
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names]
990s   /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. 
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors]
990s   /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. 
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings
990s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
990s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps
990s     if not np.allclose(A.time, B.time):
990s 
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1]
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2]
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3]
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0]
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1]
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2]
990s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array
990s   /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
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf6e8de2db7e0>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
990s       self.close()
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close
990s       self._file.close()
990s       ^^^^^^^^^^
990s   AttributeError: 'DCDReader' object has no attribute '_file'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms
990s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit
990s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function DCDWriter.__del__ at 0xf6e8de3062a0>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__
990s       self.close()
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close
990s       self._file.close()
990s       ^^^^^^^^^^
990s   AttributeError: 'DCDWriter' object has no attribute '_file'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings
990s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings
990s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
990s   /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.
990s     warnings.warn(msg)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps
990s     return self.ts.time
990s 
990s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter]
990s   /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. 
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps
990s     assert_equal(reader.ts.dt, reader.dt)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps
990s     time_frame = time_frame_0 + frame_index*ts.dt
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps
990s     reader_p = pickle.loads(pickle.dumps(reader))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings
990s   /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
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.]
990s     warnings.warn(wmsg)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
990s   /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`.
990s     warnings.warn(wmsg)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present.  Unset velocities set to zero.
990s     warnings.warn("Not all velocities were present.  "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps
990s     reader_p = pickle.loads(pickle.dumps(reader))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader
990s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps
990s     reader_p = pickle.loads(pickle.dumps(reader))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf6e8de2db7e0>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
990s       self.close()
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close
990s       self._file.close()
990s       ^^^^^^^^^^
990s   AttributeError: 'H5MDReader' object has no attribute '_file'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM'
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf6e8de2db7e0>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
990s       for aux in self.aux_list:
990s                  ^^^^^^^^^^^^^
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
990s       return self._auxs.keys()
990s              ^^^^^^^^^^
990s   AttributeError: 'H5MDReader' object has no attribute '_auxs'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings
990s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
990s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0
990s     warnings.warn('Guessed all Masses to 1.0')
990s 
990s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit
990s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf6e8de2db7e0>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
990s       for aux in self.aux_list:
990s                  ^^^^^^^^^^^^^
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
990s       return self._auxs.keys()
990s              ^^^^^^^^^^
990s   AttributeError: 'DCDReader' object has no attribute '_auxs'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view
990s   /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
990s     warnings.warn("MemoryReader.timeseries inclusive `stop` "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader
990s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps
990s     reader_p = pickle.loads(pickle.dumps(reader))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
990s   /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
990s     warnings.warn(wmsg)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps
990s     ts.time)  # in-place ! (hope this works...)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps
990s     time_list = [ts.time for ts in u.trajectory]
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps
990s     assert u.trajectory.ts.dt == pytest.approx(ref)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4
990s   /tmp/autopkgtest.fAxSVr/build.PVm/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.)
990s     return self._test_write_trajectory(universe, outfile)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0]
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0]
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0]
990s   /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.
990s     warnings.warn(wmsg)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
990s   /tmp/autopkgtest.fAxSVr/build.PVm/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.)
990s     return self._test_write_trajectory(universe, outfile)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of ''
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings
990s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'
990s     warnings.warn("Found missing chainIDs."
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom]
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond]
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom]
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree]
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond]
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom]
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps
990s     time = ts.time
990s 
990s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0xf6e8de2dbb00>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
990s       self.close()
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close
990s       if self.trjfile is not None:
990s          ^^^^^^^^^^^^
990s   AttributeError: 'NCDFWriter' object has no attribute 'trjfile'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
990s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK'
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' '
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
990s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1'
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
990s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X'
990s     warnings.warn("Found no information for attr: '{}'"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@]
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X'
990s     warnings.warn("Found chainIDs using unnaccepted character."
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA]
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X'
990s     warnings.warn("Found chainIDs with invalid length."
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000.  Higher serials have been guessed
990s     warnings.warn("Serial numbers went over 100,000.  "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed
990s     warnings.warn("Invalid atom serials were present, bonds will not"
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed
990s     warnings.warn("Invalid atom serials were present, "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment
990s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
990s   /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.
990s     warnings.warn(wmsg)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
990s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
990s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
990s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
990s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges
990s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
990s   /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. 
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps
990s     assert_equal(ts.dt, 1.0)  # default value
990s 
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps
990s     assert_equal(ts.time, 0.0)  # default to 1.0 (dt) * 0 (frame)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps
990s     assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf6e8de2db7e0>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
990s       for aux in self.aux_list:
990s                  ^^^^^^^^^^^^^
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
990s       return self._auxs.keys()
990s              ^^^^^^^^^^
990s   AttributeError: 'TNGReader' object has no attribute '_auxs'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms
990s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe
990s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe
990s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks!
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0xf6e8de2db7e0>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
990s       self.close()
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close
990s       if self.trjfile is None:
990s          ^^^^^^^^^^^^
990s   AttributeError: 'TRJReader' object has no attribute 'trjfile'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps
990s     data['time'] = ts.time
990s 
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
990s   /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
990s     warnings.warn("Timestep didn't have the following attributes: '{0}', "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
990s   /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. 
990s     warnings.warn("Timestep didn't have velocity information, "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
990s   /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
990s     warnings.warn("Timestep didn't have dimensions information, "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0xf6e8de2dbb00>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
990s       self.close()
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close
990s       if self.trzfile is None:
990s          ^^^^^^^^^^^^
990s   AttributeError: 'TRZWriter' object has no attribute 'trzfile'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
990s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
990s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
990s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
990s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
990s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
990s   /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.
990s     warnings.warn("Element information is missing, elements attribute "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
990s   /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
990s     warnings.warn(wmsg, DeprecationWarning)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter]
990s   /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. 
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter]
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter]
990s   /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. 
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter]
990s   /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. 
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter]
990s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter]
990s   /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'
990s     warnings.warn(wmsg)
990s 
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD
990s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps
990s     time = ts.time
990s 
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD
990s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps
990s     time = ts.time
990s 
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0xf6e8da344680>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
990s       self.close()
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
990s       self._xdr.close()
990s       ^^^^^^^^^
990s   AttributeError: 'XTCWriter' object has no attribute '_xdr'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container
990s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0xf6e8da344680>
990s   
990s   Traceback (most recent call last):
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
990s       self.close()
990s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
990s       self._xdr.close()
990s       ^^^^^^^^^
990s   AttributeError: 'TRRWriter' object has no attribute '_xdr'
990s   
990s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
990s 
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
990s   /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.
990s   Consider setting 'refresh_offsets=True' when loading your Universe.
990s     warnings.warn(f"Reading offsets from {fname} failed, "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly
990s   /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.
990s     warnings.warn(f"Cannot write lock/offset file in same location as "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
990s   /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.
990s   Consider setting 'refresh_offsets=True' when loading your Universe.
990s     warnings.warn(f"Reading offsets from {fname} failed, "
990s 
990s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly
990s   /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.
990s     warnings.warn(f"Cannot write lock/offset file in same location as "
990s 
990s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms]
990s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues]
990s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments]
990s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce
990s     return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
990s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
990s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
990s   /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.
990s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings
990s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings
990s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings
990s   /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.
990s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
990s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
990s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
990s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide
990s     return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum()
990s 
990s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings
990s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide
990s     _centers /= _weights.sum(axis=1)[:, None]
990s 
990s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
990s   /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`.
990s     warnings.warn(msg, category=SelectionWarning)
990s 
990s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
990s   /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`.
990s     warnings.warn(msg, category=SelectionWarning)
990s 
990s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12]
990s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13]
990s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15]
990s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16]
990s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17]
990s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18]
990s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19]
990s   /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`.
990s     warnings.warn(msg, category=SelectionWarning)
990s 
990s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments]
990s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules]
990s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues]
990s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group]
990s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments]
990s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc
990s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc
990s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options
990s   /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
990s     warnings.warn("The 'pbc' kwarg has been deprecated and will be "
990s 
990s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel
990s   /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`.
990s     warnings.warn(msg, category=SelectionWarning)
990s 
990s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial]
990s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp]
990s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial]
990s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp]
990s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan]
990s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide
990s     x = np.dot(a, b) / (norm(a) * norm(b))
990s 
990s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt
990s     ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2)
990s 
990s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt
990s     box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 -
990s 
990s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide
990s     a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z)))
990s 
990s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide
990s     b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z)))
990s 
990s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide
990s     c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y)))
990s 
990s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide
990s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
990s 
990s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide
990s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
990s 
990s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2]
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3]
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4]
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5]
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6]
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7]
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10]
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11]
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14]
990s   /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps
990s     cls(buf, protocol).dump(obj)
990s 
990s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps
990s     ps = pickle.dumps(ref_reader)
990s 
990s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0]
990s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd
990s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd
990s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset
990s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific
990s   /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset.
990s     warnings.warn('Cannot average position for non sequential'
990s 
990s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name]
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname]
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type]
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid]
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information.  Defaulted to '1'
990s     warnings.warn("PDB file is missing resid information.  "
990s 
990s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX
990s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
990s 
990s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2]
990s   /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.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2]
990s   /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.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2]
990s   /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.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2]
990s   /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.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
990s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings
990s   /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.
990s     warnings.warn(msg)
990s 
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts
990s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr]
990s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file.
990s     warnings.warn('No coordinate reader found for {}. Skipping '
990s 
990s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses
990s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses.
990s     warnings.warn(msg, category=SelectionWarning)
990s 
990s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2
990s   /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.
990s     warnings.warn(
990s 
990s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps
990s     return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
990s 
990s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps
990s     pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
990s 
990s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps
990s     return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL)
990s 
990s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps
990s     return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL)
990s 
990s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps
990s     return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL)
990s 
990s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps
990s     pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL)
990s 
990s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag
990s   /tmp/autopkgtest.fAxSVr/build.PVm/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps
990s     pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL)
990s 
990s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings
990s   /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream
990s     warnings.warn("Constructed NamedStream from a NamedStream",
990s 
990s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159]
990s   /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.
990s     warnings.warn(wmsg, DeprecationWarning)
990s 
990s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
990s = 18631 passed, 594 skipped, 7 xfailed, 3 xpassed, 8130 warnings in 739.51s (0:12:19) =
1014s 
1014s DueCredit Report:
1014s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2]
1014s   - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3]
1014s   - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4]
1014s   - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5]
1014s   - HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8]
1014s   - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9]
1014s   - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10]
1014s   - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2]
1014s   - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.7.0) [11, 12]
1014s   - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13]
1014s   - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14]
1014s   - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 2.7.0, 1.1) [15, 16]
1014s   - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17]
1014s   - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18]
1014s   - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20]
1014s   - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17]
1014s   - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21]
1014s - Scientific tools library / numpy (v 1.26.4) [22]
1014s 
1014s 2 packages cited
1014s 16 modules cited
1014s 0 functions cited
1014s 
1014s References
1014s ----------
1014s 
1014s [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.
1014s [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.
1014s [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.
1014s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858.
1014s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415.
1014s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460.
1014s [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.
1014s [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.
1014s [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.
1014s [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).
1014s [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.
1014s [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.
1014s [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.
1014s [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.
1014s [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.
1014s [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.
1014s [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.
1014s [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.
1014s [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.
1014s [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.
1014s [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.
1014s [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.
1017s autopkgtest [15:37:37]: test test-mdanalysis: -----------------------]
1018s test-mdanalysis      PASS
1018s autopkgtest [15:37:38]: test test-mdanalysis:  - - - - - - - - - - results - - - - - - - - - -
1018s autopkgtest [15:37:38]: @@@@@@@@@@@@@@@@@@@@ summary
1018s test-mdanalysis      PASS
1029s nova [W] Using flock in prodstack6-arm64
1029s flock: timeout while waiting to get lock
1029s Creating nova instance adt-plucky-arm64-mdanalysis-20241202-152040-juju-7f2275-prod-proposed-migration-environment-15-3508065e-fb62-41a6-a4e1-b18d8311a859 from image adt/ubuntu-plucky-arm64-server-20241202.img (UUID 3fe1076a-d108-48d5-9332-a0e516b6b932)...