0s autopkgtest [16:26:48]: starting date and time: 2024-11-14 16:26:48+0000 0s autopkgtest [16:26:48]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:26:48]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m8raalw9/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:numpy --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- lxd -r lxd-armhf-10.145.243.158 lxd-armhf-10.145.243.158:autopkgtest/ubuntu/plucky/armhf 52s autopkgtest [16:27:40]: testbed dpkg architecture: armhf 54s autopkgtest [16:27:42]: testbed apt version: 2.9.8 54s autopkgtest [16:27:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 62s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 62s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 62s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [966 kB] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [112 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [688 kB] 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [5036 B] 63s Fetched 1971 kB in 1s (2064 kB/s) 63s Reading package lists... 81s tee: /proc/self/fd/2: Permission denied 103s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 103s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 104s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 106s The following packages were automatically installed and are no longer required: 106s libperl5.38t64 perl-modules-5.38 python3-netifaces 106s Use 'apt autoremove' to remove them. 106s The following NEW packages will be installed: 106s libperl5.40 perl-modules-5.40 systemd-cryptsetup 106s The following packages will be upgraded: 106s apport apport-core-dump-handler base-files base-passwd bash-completion 106s dhcpcd-base distro-info-data dpkg dpkg-dev fwupd gcc-14-base info 106s install-info iproute2 libarchive13t64 libatomic1 libattr1 106s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 106s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 106s libblockdev3 libbpf1 libbsd0 libbytesize-common libbytesize1 libdb5.3t64 106s libdpkg-perl libdrm-common libdrm2 libdw1t64 libedit2 libelf1t64 libevdev2 106s libfastjson4 libflashrom1 libftdi1-2 libfwupd2 libgcc-s1 libgnutls30t64 106s libgpgme11t64 libinih1 libjson-c5 libjson-glib-1.0-0 libjson-glib-1.0-common 106s libkeyutils1 libldap-common libldap2 liblocale-gettext-perl libmaxminddb0 106s libmnl0 libnetfilter-conntrack3 libnetplan1 libnewt0.52 libnghttp2-14 106s libnspr4 libnss-systemd libnvme1t64 libpam-systemd libpipeline1 libplymouth5 106s libpng16-16t64 libpopt0 libpython3.12-minimal libpython3.12-stdlib 106s libsgutils2-1.46-2 libssh2-1t64 libstdc++6 libsystemd-shared libsystemd0 106s libtext-charwidth-perl libtext-iconv-perl libtraceevent1 106s libtraceevent1-plugin libudev1 libudisks2-0 liburcu8t64 libutempter0 106s libuv1t64 libx11-6 libx11-data libxau6 libxmlb2 mawk motd-news-config nano 106s netplan-generator netplan.io openssh-client openssh-server 106s openssh-sftp-server pastebinit pci.ids perl perl-base plymouth 106s plymouth-theme-ubuntu-text python3-apport python3-certifi 106s python3-cffi-backend python3-configobj python3-gi python3-idna 106s python3-jaraco.functools python3-json-pointer python3-jsonpatch 106s python3-lazr.restfulclient python3-lazr.uri python3-more-itertools 106s python3-netplan python3-newt python3-oauthlib python3-problem-report 106s python3-systemd python3-typeguard python3-urllib3 python3-wadllib 106s python3-zipp python3.12 python3.12-gdbm python3.12-minimal sg3-utils 106s sg3-utils-udev ssh-import-id systemd systemd-resolved systemd-sysv 106s systemd-timesyncd tzdata udev udisks2 ufw usbutils vim-common vim-tiny 106s whiptail xxd 106s 141 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 45.4 MB of archives. 106s After this operation, 43.2 MB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu3 [5190 B] 106s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu3 [75.1 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg armhf 1.22.11ubuntu3 [1247 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-7 [3214 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-7 [4139 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-7 [263 kB] 107s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-7 [1674 kB] 107s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 107s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 107s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 107s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-9 [655 kB] 107s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf base-passwd armhf 3.6.5 [53.2 kB] 107s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12 armhf 3.12.7-3 [661 kB] 107s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-minimal armhf 3.12.7-3 [2012 kB] 107s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-stdlib armhf 3.12.7-3 [1934 kB] 107s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-minimal armhf 3.12.7-3 [822 kB] 107s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf tzdata all 2024b-1ubuntu2 [274 kB] 107s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libnss-systemd armhf 256.5-2ubuntu4 [155 kB] 107s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-timesyncd armhf 256.5-2ubuntu4 [40.7 kB] 107s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-resolved armhf 256.5-2ubuntu4 [309 kB] 107s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd-shared armhf 256.5-2ubuntu4 [2129 kB] 107s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libsystemd0 armhf 256.5-2ubuntu4 [428 kB] 107s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-sysv armhf 256.5-2ubuntu4 [11.9 kB] 107s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libpam-systemd armhf 256.5-2ubuntu4 [226 kB] 107s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf systemd armhf 256.5-2ubuntu4 [3442 kB] 107s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf udev armhf 256.5-2ubuntu4 [1949 kB] 107s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libudev1 armhf 256.5-2ubuntu4 [188 kB] 107s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf python3-problem-report all 2.30.0-0ubuntu5 [25.0 kB] 107s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf python3-apport all 2.30.0-0ubuntu5 [93.2 kB] 107s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf python3-gi armhf 3.50.0-3 [227 kB] 107s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf apport-core-dump-handler all 2.30.0-0ubuntu5 [17.9 kB] 107s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf apport all 2.30.0-0ubuntu5 [83.0 kB] 107s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libbsd0 armhf 0.12.2-2 [36.8 kB] 107s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libedit2 armhf 3.1-20240808-1 [79.0 kB] 107s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-sftp-server armhf 1:9.7p1-7ubuntu5 [35.4 kB] 108s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-server armhf 1:9.7p1-7ubuntu5 [505 kB] 108s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf openssh-client armhf 1:9.7p1-7ubuntu5 [889 kB] 108s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-8ubuntu1 [7846 B] 108s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-8ubuntu1 [51.5 kB] 108s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-8ubuntu1 [711 kB] 108s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-8ubuntu1 [40.8 kB] 108s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libattr1 armhf 1:2.5.2-2 [10.5 kB] 108s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 108s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 108s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf mawk armhf 1.3.4.20240905-1 [116 kB] 108s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf dhcpcd-base armhf 1:10.1.0-2 [188 kB] 108s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 108s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 108s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 108s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf libbpf1 armhf 1:1.5.0-1 [158 kB] 108s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libmnl0 armhf 1.0.5-3 [10.7 kB] 108s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 108s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libfastjson4 armhf 1.2304.0-2 [20.2 kB] 108s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-c5 armhf 0.18+ds-1 [33.2 kB] 108s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 108s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf netplan-generator armhf 1.1.1-1 [60.4 kB] 108s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cffi-backend armhf 1.17.1-2 [68.7 kB] 108s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf python3-netplan armhf 1.1.1-1 [24.1 kB] 108s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf netplan.io armhf 1.1.1-1 [66.4 kB] 108s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf libnetplan1 armhf 1.1.1-1 [122 kB] 108s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 108s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 108s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libpopt0 armhf 1.19+dfsg-2 [25.4 kB] 108s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 108s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 108s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 108s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 108s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf bash-completion all 1:2.14.0-2 [210 kB] 108s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 108s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf libdrm-common all 2.4.123-1 [8436 B] 108s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf libdrm2 armhf 2.4.123-1 [36.5 kB] 108s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libevdev2 armhf 1.13.3+dfsg-1 [29.7 kB] 108s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libmaxminddb0 armhf 1.11.0-1 [16.8 kB] 108s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libnetfilter-conntrack3 armhf 1.1.0-1 [38.4 kB] 108s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libnghttp2-14 armhf 1.64.0-1 [68.9 kB] 108s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libpipeline1 armhf 1.5.8-1 [26.9 kB] 108s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libpng16-16t64 armhf 1.6.44-2 [168 kB] 108s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libplymouth5 armhf 24.004.60-1ubuntu11 [140 kB] 108s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1-plugin armhf 1:1.8.3-1ubuntu1 [18.1 kB] 108s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1 armhf 1:1.8.3-1ubuntu1 [52.1 kB] 108s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf liburcu8t64 armhf 0.14.1-1 [56.6 kB] 108s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf libuv1t64 armhf 1.48.0-7 [83.3 kB] 108s Get:83 http://ftpmaster.internal/ubuntu plucky/main armhf libx11-data all 2:1.8.10-2 [116 kB] 108s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf libx11-6 armhf 2:1.8.10-2 [587 kB] 108s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libxau6 armhf 1:1.0.11-1 [6558 B] 108s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.2-1 [276 kB] 108s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf pci.ids all 0.0~2024.10.24-1 [279 kB] 108s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf plymouth-theme-ubuntu-text armhf 24.004.60-1ubuntu11 [9920 B] 108s Get:89 http://ftpmaster.internal/ubuntu plucky/main armhf plymouth armhf 24.004.60-1ubuntu11 [142 kB] 108s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-gdbm armhf 3.12.7-3 [28.7 kB] 108s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf ufw all 0.36.2-8 [170 kB] 108s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf usbutils armhf 1:018-1 [76.1 kB] 108s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf dpkg-dev all 1.22.11ubuntu3 [1088 kB] 108s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf libdpkg-perl all 1.22.11ubuntu3 [279 kB] 108s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive13t64 armhf 3.7.4-1.1 [331 kB] 108s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-7 [25.7 kB] 108s Get:97 http://ftpmaster.internal/ubuntu plucky/main armhf libflashrom1 armhf 1.4.0-3ubuntu1 [141 kB] 108s Get:98 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 108s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 108s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 108s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libxmlb2 armhf 0.3.21-1 [57.7 kB] 108s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 109s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.2.1-1 [17.4 kB] 109s Get:104 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.2.1-1 [22.4 kB] 109s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.2.1-1 [34.3 kB] 109s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.2.1-1 [6552 B] 109s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libbytesize1 armhf 2.11-1ubuntu1 [12.0 kB] 109s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libbytesize-common all 2.11-1ubuntu1 [3584 B] 109s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.2.1-1 [13.4 kB] 109s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libnvme1t64 armhf 1.11-1 [73.8 kB] 109s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.2.1-1 [17.6 kB] 109s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.2.1-1 [16.5 kB] 109s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.2.1-1 [8952 B] 109s Get:114 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.2.1-1 [44.2 kB] 109s Get:115 http://ftpmaster.internal/ubuntu plucky/main armhf libgpgme11t64 armhf 1.23.2-5ubuntu4 [123 kB] 109s Get:116 http://ftpmaster.internal/ubuntu plucky/main armhf libinih1 armhf 58-1ubuntu1 [6750 B] 109s Get:117 http://ftpmaster.internal/ubuntu plucky/main armhf libldap-common all 2.6.8+dfsg-1~exp4ubuntu3 [32.3 kB] 109s Get:118 http://ftpmaster.internal/ubuntu plucky/main armhf libldap2 armhf 2.6.8+dfsg-1~exp4ubuntu3 [173 kB] 109s Get:119 http://ftpmaster.internal/ubuntu plucky/main armhf libnspr4 armhf 2:4.35-1.1ubuntu2 [94.1 kB] 109s Get:120 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 109s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libssh2-1t64 armhf 1.11.1-1 [116 kB] 109s Get:122 http://ftpmaster.internal/ubuntu plucky/main armhf udisks2 armhf 2.10.1-11ubuntu1 [278 kB] 109s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf libudisks2-0 armhf 2.10.1-11ubuntu1 [142 kB] 109s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 109s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf pastebinit all 1.7.1-1 [14.9 kB] 109s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf python3-certifi all 2024.8.30+dfsg-1 [9742 B] 109s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf python3-configobj all 5.0.9-1 [33.9 kB] 109s Get:128 http://ftpmaster.internal/ubuntu plucky/main armhf python3-idna all 3.8-2 [47.0 kB] 109s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf python3-more-itertools all 10.5.0-1 [56.2 kB] 109s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jaraco.functools all 4.1.0-1 [11.8 kB] 109s Get:131 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-2 [8396 B] 109s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jsonpatch all 1.32-4 [12.2 kB] 109s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-4 [13.6 kB] 109s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf python3-wadllib all 2.0.0-1 [36.7 kB] 109s Get:135 http://ftpmaster.internal/ubuntu plucky/main armhf python3-oauthlib all 3.2.2-2 [89.8 kB] 109s Get:136 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.restfulclient all 0.14.6-2 [50.9 kB] 109s Get:137 http://ftpmaster.internal/ubuntu plucky/main armhf python3-systemd armhf 235-1build5 [44.0 kB] 109s Get:138 http://ftpmaster.internal/ubuntu plucky/main armhf python3-typeguard all 4.4.1-1 [29.0 kB] 109s Get:139 http://ftpmaster.internal/ubuntu plucky/main armhf python3-urllib3 all 2.0.7-2ubuntu0.1 [93.1 kB] 109s Get:140 http://ftpmaster.internal/ubuntu plucky/main armhf python3-zipp all 3.21.0-1 [10.2 kB] 110s Get:141 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 110s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 110s Get:143 http://ftpmaster.internal/ubuntu plucky/main armhf systemd-cryptsetup armhf 256.5-2ubuntu4 [122 kB] 110s Get:144 http://ftpmaster.internal/ubuntu plucky/main armhf ssh-import-id all 5.11-0ubuntu3 [10.1 kB] 110s Preconfiguring packages ... 110s Fetched 45.4 MB in 4s (12.9 MB/s) 110s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59386 files and directories currently installed.) 110s Preparing to unpack .../motd-news-config_13.5ubuntu3_all.deb ... 110s Unpacking motd-news-config (13.5ubuntu3) over (13.3ubuntu6) ... 110s Preparing to unpack .../base-files_13.5ubuntu3_armhf.deb ... 110s Unpacking base-files (13.5ubuntu3) over (13.3ubuntu6) ... 111s Setting up base-files (13.5ubuntu3) ... 111s Installing new version of config file /etc/issue ... 111s Installing new version of config file /etc/issue.net ... 111s Installing new version of config file /etc/lsb-release ... 111s motd-news.service is a disabled or a static unit not running, not starting it. 111s (Reading database ... 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libblockdev-loop3:armhf (3.2.1-1) ... 129s Setting up systemd (256.5-2ubuntu4) ... 129s /usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring. 129s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 129s /usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring. 129s Setting up vim-tiny (2:9.1.0777-1ubuntu1) ... 129s Setting up libblockdev3:armhf (3.2.1-1) ... 129s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 129s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 129s Setting up libblockdev-part3:armhf (3.2.1-1) ... 129s Setting up sg3-utils-udev (1.46-3ubuntu5) ... 129s update-initramfs: deferring update (trigger activated) 129s Setting up libperl5.40:armhf (5.40.0-7) ... 129s Setting up perl (5.40.0-7) ... 129s Setting up systemd-cryptsetup (256.5-2ubuntu4) ... 129s Setting up libnvme1t64 (1.11-1) ... 129s Setting up systemd-timesyncd (256.5-2ubuntu4) ... 130s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 130s Setting up udev (256.5-2ubuntu4) ... 131s Setting up libdpkg-perl (1.22.11ubuntu3) ... 131s Setting up libblockdev-nvme3:armhf (3.2.1-1) ... 131s Setting up libdrm2:armhf (2.4.123-1) ... 131s Setting up whiptail (0.52.24-2ubuntu4) ... 131s Setting up libtraceevent1-plugin:armhf (1:1.8.3-1ubuntu1) ... 131s Setting up libplymouth5:armhf (24.004.60-1ubuntu11) ... 131s Setting up python3-netplan (1.1.1-1) ... 131s Setting up netplan-generator (1.1.1-1) ... 131s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 131s Setting up systemd-resolved (256.5-2ubuntu4) ... 131s Setting up openssh-sftp-server (1:9.7p1-7ubuntu5) ... 131s Setting up udisks2 (2.10.1-11ubuntu1) ... 131s vda: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/uevent': Permission denied 131s vda1: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda1/uevent': Permission denied 131s vda15: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda15/uevent': Permission denied 131s vda2: Failed to write 'change' to '/sys/devices/pci0000:00/0000:00:01.3/0000:04:00.0/virtio2/block/vda/vda2/uevent': Permission denied 131s loop0: Failed to write 'change' to '/sys/devices/virtual/block/loop0/uevent': Permission denied 131s loop1: Failed to write 'change' to '/sys/devices/virtual/block/loop1/uevent': Permission denied 131s loop2: Failed to write 'change' to '/sys/devices/virtual/block/loop2/uevent': Permission denied 131s loop3: Failed to write 'change' to '/sys/devices/virtual/block/loop3/uevent': Permission denied 131s loop4: Failed to write 'change' to '/sys/devices/virtual/block/loop4/uevent': Permission denied 131s loop5: Failed to write 'change' to '/sys/devices/virtual/block/loop5/uevent': Permission denied 131s loop6: Failed to write 'change' to '/sys/devices/virtual/block/loop6/uevent': Permission denied 131s loop7: Failed to write 'change' to '/sys/devices/virtual/block/loop7/uevent': Permission denied 131s loop8: Failed to write 'change' to '/sys/devices/virtual/block/loop8/uevent': Permission denied 132s Setting up systemd-sysv (256.5-2ubuntu4) ... 132s Setting up openssh-server (1:9.7p1-7ubuntu5) ... 133s Setting up plymouth (24.004.60-1ubuntu11) ... 133s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 133s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 133s Setting up libfwupd2:armhf (1.9.26-2) ... 133s Setting up libnss-systemd:armhf (256.5-2ubuntu4) ... 133s Setting up dpkg-dev (1.22.11ubuntu3) ... 133s Setting up netplan.io (1.1.1-1) ... 133s Setting up plymouth-theme-ubuntu-text (24.004.60-1ubuntu11) ... 133s update-initramfs: deferring update (trigger activated) 133s Setting up libpam-systemd:armhf (256.5-2ubuntu4) ... 134s Setting up fwupd (1.9.26-2) ... 134s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 134s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 134s fwupd.service is a disabled or a static unit not running, not starting it. 134s Setting up apport-core-dump-handler (2.30.0-0ubuntu5) ... 135s Setting up apport (2.30.0-0ubuntu5) ... 135s Installing new version of config file /etc/apport/crashdb.conf ... 135s apport-autoreport.service is a disabled or a static unit not running, not starting it. 135s Processing triggers for dbus (1.14.10-4ubuntu5) ... 135s Processing triggers for shared-mime-info (2.4-5) ... 136s Processing triggers for install-info (7.1.1-1) ... 136s Processing triggers for initramfs-tools (0.142ubuntu34) ... 136s Processing triggers for libc-bin (2.40-1ubuntu3) ... 136s Processing triggers for rsyslog (8.2406.0-1ubuntu2) ... 136s Processing triggers for man-db (2.12.1-3) ... 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s The following packages will be REMOVED: 139s libperl5.38t64* perl-modules-5.38* python3-netifaces* 139s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 139s After this operation, 41.7 MB disk space will be freed. 139s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61505 files and directories currently installed.) 139s Removing libperl5.38t64:armhf (5.38.2-5) ... 139s Removing perl-modules-5.38 (5.38.2-5) ... 139s Removing python3-netifaces:armhf (0.11.0-2build3) ... 139s Processing triggers for man-db (2.12.1-3) ... 140s Processing triggers for libc-bin (2.40-1ubuntu3) ... 142s autopkgtest [16:29:10]: rebooting testbed after setup commands that affected boot 209s autopkgtest [16:30:17]: testbed running kernel: Linux 6.8.0-47-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Oct 2 16:39:14 UTC 2 235s autopkgtest [16:30:43]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 251s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B] 251s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB] 251s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB] 251s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC 251s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 251s gpgv: issuer "dparsons@debian.org" 251s gpgv: Can't check signature: No public key 251s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found 253s autopkgtest [16:31:01]: testing package mdanalysis version 2.7.0-5 255s autopkgtest [16:31:03]: build not needed 260s autopkgtest [16:31:08]: test test-mdanalysis: preparing testbed 270s Reading package lists... 271s Building dependency tree... 271s Reading state information... 272s Starting pkgProblemResolver with broken count: 0 272s Starting 2 pkgProblemResolver with broken count: 0 272s Done 272s The following additional packages will be installed: 272s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 272s cpp-14-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cython3 debhelper 272s debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common 272s dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 272s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 272s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 272s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gettext intltool-debian 272s libaec0 libarchive-zip-perl libasan8 libblas3 libc-dev-bin libc6-dev 272s libcairo2 libcc1-0 libcrypt-dev libdebhelper-perl libdeflate0 libexpat1-dev 272s libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6 272s libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 272s libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libisl23 libjbig0 272s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-mathjax 272s libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0 272s liblcms2-2 liblerc4 liblzf1 libmpc3 libnetcdf19t64 libopenjp2-7 272s libpixman-1-0 libpython3-all-dev libpython3-dev libpython3.12-dev 272s libpython3.12t64 libqhull-r8.0 libraqm0 libsharpyuv0 libstdc++-14-dev libsz2 272s libtcl8.6 libtiff6 libtk8.6 libtool libubsan1 libwebp7 libwebpdemux2 272s libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 272s libxss1 linux-libc-dev m4 po-debconf pybuild-plugin-pyproject 272s python-matplotlib-data python-mdanalysis-doc python3-alabaster python3-all 272s python3-all-dev python3-appdirs python3-biopython python3-brotli 272s python3-build python3-cairo python3-cftime python3-citeproc 272s python3-contourpy python3-cycler python3-dateutil python3-decorator 272s python3-defusedxml python3-dev python3-docutils python3-duecredit 272s python3-fasteners python3-fonttools python3-freetype python3-fs 272s python3-griddataformats python3-gsd python3-h5py python3-h5py-serial 272s python3-hypothesis python3-imagesize python3-iniconfig python3-installer 272s python3-joblib python3-kiwisolver python3-latexcodec python3-looseversion 272s python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib 272s python3-mdanalysis python3-mmtf python3-monotonic python3-mpmath 272s python3-mrcfile python3-msgpack python3-msmb-theme python3-netcdf4 272s python3-networkx python3-numpy python3-packaging python3-pandas 272s python3-pandas-lib python3-pil python3-pil.imagetk python3-pluggy 272s python3-pybtex python3-pybtex-docutils python3-pyproject-hooks 272s python3-pytest python3-reportlab python3-rlpycairo python3-roman 272s python3-scipy python3-seaborn python3-six python3-sklearn 272s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 272s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 272s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 272s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 272s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 272s python3.12-tk rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common 272s tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 272s xfonts-utils xml-core zlib1g-dev 272s Suggested packages: 272s autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales 272s cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf 272s fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 272s gdb-arm-linux-gnueabihf gettext-doc libasprintf-dev libgettextpo-dev 272s libc-devtools glibc-doc libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix 272s libjs-mathjax-doc liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc 272s gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl bwa clustalo 272s clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank 272s probcons python3-mysqldb python3-rdflib python3-psycopg2 raxml samtools 272s t-coffee wise python3-pip python3-venv python-build-doc python-cycler-doc 272s docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french 272s texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc 272s python-hypothesis-doc python-installer-doc python-joblib-doc 272s python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg 272s fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common 272s python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject 272s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 272s texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal 272s python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc 272s python3-statsmodels python-pil-doc python-pybtex-doc 272s python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools 272s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 272s python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm 272s fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre 272s texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic 272s python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg 272s python3.13-tk sgml-base-doc 272s Recommended packages: 272s manpages manpages-dev libarchive-cpio-perl javascript-common libjson-xs-perl 272s libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+ 272s libpaper-utils python3-click python3-simplejson python3-psutil python3-bs4 272s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 272s python3-odf python3-openpyxl python3-tables python3-olefile 272s fonts-dejavu-extra isympy-common 273s The following NEW packages will be installed: 273s autoconf automake autopkgtest-satdep autopoint autotools-dev blt 273s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 273s cpp-arm-linux-gnueabihf cython3 debhelper debugedit dh-autoreconf dh-python 273s dh-strip-nondeterminism docutils-common dwz fontconfig-config 273s fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx 273s fonts-mathjax fonts-urw-base35 g++ g++-14 g++-14-arm-linux-gnueabihf 273s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 273s gcc-arm-linux-gnueabihf gettext intltool-debian libaec0 libarchive-zip-perl 273s libasan8 libblas3 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev 273s libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl 273s libfontconfig1 libfontenc1 libfreetype6 libgcc-14-dev libgfortran5 libgomp1 273s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 273s libimagequant0 libisl23 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 273s libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore libjson-perl 273s liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblzf1 libmpc3 libnetcdf19t64 273s libopenjp2-7 libpixman-1-0 libpython3-all-dev libpython3-dev 273s libpython3.12-dev libpython3.12t64 libqhull-r8.0 libraqm0 libsharpyuv0 273s libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool libubsan1 273s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 273s libxrender1 libxslt1.1 libxss1 linux-libc-dev m4 po-debconf 273s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 273s python3-alabaster python3-all python3-all-dev python3-appdirs 273s python3-biopython python3-brotli python3-build python3-cairo python3-cftime 273s python3-citeproc python3-contourpy python3-cycler python3-dateutil 273s python3-decorator python3-defusedxml python3-dev python3-docutils 273s python3-duecredit python3-fasteners python3-fonttools python3-freetype 273s python3-fs python3-griddataformats python3-gsd python3-h5py 273s python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig 273s python3-installer python3-joblib python3-kiwisolver python3-latexcodec 273s python3-looseversion python3-lxml python3-lz4 python3-matplotlib 273s python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic 273s python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme 273s python3-netcdf4 python3-networkx python3-numpy python3-packaging 273s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 273s python3-pluggy python3-pybtex python3-pybtex-docutils 273s python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo 273s python3-roman python3-scipy python3-seaborn python3-six python3-sklearn 273s python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers 273s python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap 273s python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy 273s python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz 273s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev 273s python3.12-tk rpcsvc-proto sgml-base sphinx-common sphinx-rtd-theme-common 273s tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 273s xfonts-utils xml-core zlib1g-dev 273s 0 upgraded, 205 newly installed, 0 to remove and 0 not upgraded. 273s Need to get 187 MB/187 MB of archives. 273s After this operation, 726 MB of additional disk space will be used. 273s Get:1 /tmp/autopkgtest.9K7Ne2/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [1016 B] 273s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-lato all 2.015-1 [2781 kB] 273s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 273s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf m4 armhf 1.4.19-4build1 [235 kB] 273s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf autoconf all 2.72-3 [382 kB] 273s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf autotools-dev all 20220109.1 [44.9 kB] 273s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] 273s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf autopoint all 0.22.5-2 [616 kB] 273s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.15+dfsg-2 [909 kB] 273s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 273s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 273s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 273s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 273s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 273s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 273s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 273s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 274s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 274s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 274s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 274s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 274s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 274s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.15-1 [685 kB] 274s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7build1 [525 kB] 274s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf blt armhf 2.5.3+dfsg-7build1 [4840 B] 274s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libc-dev-bin armhf 2.40-1ubuntu3 [19.2 kB] 274s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.11.0-8.8 [1628 kB] 274s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.36-4build1 [120 kB] 274s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 274s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libc6-dev armhf 2.40-1ubuntu3 [1370 kB] 274s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 274s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 274s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [9219 kB] 274s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-8ubuntu1 [1032 B] 274s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [5464 B] 274s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.1.0-2ubuntu1 [22.4 kB] 274s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 14.2.0-8ubuntu1 [43.3 kB] 274s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 274s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 14.2.0-8ubuntu1 [2901 kB] 274s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 14.2.0-8ubuntu1 [1150 kB] 274s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-8ubuntu1 [897 kB] 274s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [18.0 MB] 275s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-8ubuntu1 [498 kB] 275s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [1222 B] 275s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.1.0-2ubuntu1 [5002 B] 275s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-8ubuntu1 [2569 kB] 275s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-8ubuntu1 [10.5 MB] 275s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-8ubuntu1 [19.9 kB] 275s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.1.0-2ubuntu1 [968 B] 275s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.1.0-2ubuntu1 [1084 B] 275s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 275s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf cython3 armhf 3.0.11+dfsg-1ubuntu1 [2391 kB] 275s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 275s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libtool all 2.4.7-7build1 [166 kB] 275s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf dh-autoreconf all 20 [16.1 kB] 275s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] 275s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 275s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf dh-strip-nondeterminism all 1.14.0-1 [5058 B] 275s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf debugedit armhf 1:5.1-1 [46.5 kB] 275s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf dwz armhf 0.15-1build6 [116 kB] 275s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf gettext armhf 0.22.5-2 [995 kB] 275s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] 275s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf po-debconf all 1.0.21+nmu1 [233 kB] 275s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf debhelper all 13.20ubuntu1 [893 kB] 275s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf dh-python all 6.20241024 [112 kB] 275s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 275s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 275s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 275s Get:69 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lyx all 2.4.2.1-1 [171 kB] 275s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 275s Get:71 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 275s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 275s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 275s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 275s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 275s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 275s Get:77 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 275s Get:78 http://ftpmaster.internal/ubuntu plucky/main armhf libexpat1-dev armhf 2.6.2-2 [121 kB] 275s Get:79 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 276s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 276s Get:81 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 276s Get:82 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 276s Get:83 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 276s Get:84 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 276s Get:85 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 276s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu2 [125 kB] 276s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 276s Get:88 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 276s Get:89 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 276s Get:90 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 276s Get:91 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 276s Get:92 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-perl all 4.10000-1 [81.9 kB] 276s Get:93 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 276s Get:94 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 276s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 276s Get:96 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu2 [151 kB] 276s Get:97 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 276s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf libnetcdf19t64 armhf 1:4.9.2-6ubuntu1 [419 kB] 276s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.7-3 [2075 kB] 276s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 276s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12-dev armhf 3.12.7-3 [4344 kB] 276s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-dev armhf 3.12.6-0ubuntu1 [10.2 kB] 276s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3-all-dev armhf 3.12.6-0ubuntu1 [914 B] 276s Get:104 http://ftpmaster.internal/ubuntu plucky/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 276s Get:105 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.1-1build1 [12.4 kB] 276s Get:106 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 276s Get:107 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 276s Get:108 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 276s Get:109 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 276s Get:110 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.4.0-0.1 [11.8 kB] 276s Get:111 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.4.0-0.1 [22.5 kB] 276s Get:112 http://ftpmaster.internal/ubuntu plucky/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu1 [150 kB] 276s Get:113 http://ftpmaster.internal/ubuntu plucky/main armhf python3-packaging all 24.1-1 [41.4 kB] 276s Get:114 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 276s Get:115 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-toml all 0.10.2-1 [16.5 kB] 276s Get:116 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-wheel all 0.44.0-1 [54.2 kB] 277s Get:117 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-build all 1.2.2-1 [31.0 kB] 277s Get:118 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 277s Get:119 http://ftpmaster.internal/ubuntu plucky/universe armhf pybuild-plugin-pyproject all 6.20241024 [1728 B] 277s Get:120 http://ftpmaster.internal/ubuntu plucky/universe armhf python-matplotlib-data all 3.8.3-3 [2928 kB] 277s Get:121 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 277s Get:122 http://ftpmaster.internal/ubuntu plucky/universe armhf python-mdanalysis-doc all 2.7.0-5 [2323 kB] 277s Get:123 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 277s Get:124 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-dev armhf 3.12.7-3 [505 kB] 277s Get:125 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dev armhf 3.12.6-0ubuntu1 [26.7 kB] 277s Get:126 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all-dev armhf 3.12.6-0ubuntu1 [908 B] 277s Get:127 http://ftpmaster.internal/ubuntu plucky/main armhf python3-appdirs all 1.4.4-4 [10.9 kB] 277s Get:128 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 277s Get:129 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-tk armhf 3.12.7-3 [112 kB] 277s Get:130 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tk armhf 3.12.6-1ubuntu1 [9806 B] 277s Get:131 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pil.imagetk armhf 10.4.0-1ubuntu1 [8848 B] 277s Get:132 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.0-2ubuntu1 [170 kB] 277s Get:133 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 10.4.0-1ubuntu1 [428 kB] 277s Get:134 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2 [114 kB] 277s Get:135 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 277s Get:136 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 277s Get:137 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.2.5-1 [1107 kB] 277s Get:138 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 277s Get:139 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.84+dfsg-4 [1666 kB] 277s Get:140 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-brotli armhf 1.1.0-2build2 [321 kB] 277s Get:141 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cftime armhf 1.6.4-1 [202 kB] 277s Get:142 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lxml armhf 5.3.0-1 [1234 kB] 277s Get:143 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-citeproc all 0.6.0-3 [98.4 kB] 277s Get:144 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-contourpy armhf 1.3.0-2 [192 kB] 277s Get:145 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cycler all 0.12.1-1 [9716 B] 277s Get:146 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 277s Get:147 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-2 [80.3 kB] 277s Get:148 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 277s Get:149 http://ftpmaster.internal/ubuntu plucky/main armhf python3-defusedxml all 0.7.1-2 [42.0 kB] 277s Get:150 http://ftpmaster.internal/ubuntu plucky/main armhf python3-roman all 4.2-1 [10.0 kB] 277s Get:151 http://ftpmaster.internal/ubuntu plucky/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 277s Get:152 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-looseversion all 1.3.0-3 [8354 B] 277s Get:153 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-duecredit all 0.10.2-2 [66.0 kB] 277s Get:154 http://ftpmaster.internal/ubuntu plucky/main armhf python3-monotonic all 1.6-2 [5732 B] 277s Get:155 http://ftpmaster.internal/ubuntu plucky/main armhf python3-fasteners all 0.18-2 [12.5 kB] 277s Get:156 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB] 278s Get:157 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 278s Get:158 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 278s Get:159 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sympy all 1.13.3-1 [4228 kB] 278s Get:160 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 278s Get:161 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fs all 2.4.16-4 [91.3 kB] 278s Get:162 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-lz4 armhf 4.0.2+dfsg-1build4 [24.8 kB] 278s Get:163 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-unicodedata2 armhf 15.1.0+ds-1build1 [361 kB] 278s Get:164 http://ftpmaster.internal/ubuntu plucky/universe armhf unicode-data all 15.1.0-1 [8878 kB] 278s Get:165 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fonttools armhf 4.46.0-1build2 [1402 kB] 279s Get:166 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB] 279s Get:167 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mrcfile all 1.5.3-3 [114 kB] 279s Get:168 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-griddataformats all 1.0.2-2 [2107 kB] 279s Get:169 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-gsd armhf 3.3.0-1 [197 kB] 279s Get:170 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-5ubuntu1 [1061 kB] 279s Get:171 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-5ubuntu1 [7974 B] 279s Get:172 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sortedcontainers all 2.4.0-2 [27.6 kB] 279s Get:173 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-hypothesis all 6.116.0-1 [326 kB] 279s Get:174 http://ftpmaster.internal/ubuntu plucky/main armhf python3-imagesize all 1.4.1-1 [6844 B] 279s Get:175 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 279s Get:176 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.3.2-5 [206 kB] 279s Get:177 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-kiwisolver armhf 1.4.7-2build1 [71.1 kB] 279s Get:178 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-latexcodec all 3.0.0-1 [16.6 kB] 279s Get:179 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-matplotlib armhf 3.8.3-3 [4500 kB] 279s Get:180 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 279s Get:181 http://ftpmaster.internal/ubuntu plucky/main armhf python3-msgpack armhf 1.0.3-3build2 [76.1 kB] 279s Get:182 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mmtf all 1.1.3-1 [16.2 kB] 279s Get:183 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-threadpoolctl all 3.1.0-1 [21.3 kB] 279s Get:184 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-tqdm all 4.67.0-1 [91.6 kB] 279s Get:185 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mdanalysis armhf 2.7.0-5 [1882 kB] 279s Get:186 http://ftpmaster.internal/ubuntu plucky/main armhf sphinx-common all 7.4.7-4 [775 kB] 279s Get:187 http://ftpmaster.internal/ubuntu plucky/main armhf python3-alabaster all 0.7.16-0.1 [18.5 kB] 279s Get:188 http://ftpmaster.internal/ubuntu plucky/main armhf python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 279s Get:189 http://ftpmaster.internal/ubuntu plucky/main armhf python3-sphinx all 7.4.7-4 [593 kB] 279s Get:190 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 279s Get:191 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB] 279s Get:192 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-msmb-theme all 1.2.0-4 [35.4 kB] 279s Get:193 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-netcdf4 armhf 1.7.2-1 [589 kB] 279s Get:194 http://ftpmaster.internal/ubuntu plucky/main armhf python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 279s Get:195 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5 [4728 kB] 280s Get:196 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5 [3112 kB] 280s Get:197 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 280s Get:198 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex all 0.24.0-4 [70.0 kB] 280s Get:199 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pybtex-docutils all 1.0.2-1 [7176 B] 280s Get:200 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.3-1 [251 kB] 280s Get:201 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-seaborn all 0.13.2-4 [225 kB] 280s Get:202 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn-lib armhf 1.4.2+dfsg-6 [3751 kB] 280s Get:203 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 280s Get:204 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinx-sitemap all 2.6.0-1 [6674 B] 280s Get:205 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 281s Fetched 187 MB in 8s (24.7 MB/s) 281s Selecting previously unselected package fonts-lato. 281s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59565 files and directories currently installed.) 281s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ... 281s Unpacking fonts-lato (2.015-1) ... 281s Selecting previously unselected package sgml-base. 281s Preparing to unpack .../001-sgml-base_1.31_all.deb ... 281s Unpacking sgml-base (1.31) ... 281s Selecting previously unselected package m4. 281s Preparing to unpack .../002-m4_1.4.19-4build1_armhf.deb ... 281s Unpacking m4 (1.4.19-4build1) ... 281s Selecting previously unselected package autoconf. 281s Preparing to unpack .../003-autoconf_2.72-3_all.deb ... 281s Unpacking autoconf (2.72-3) ... 281s Selecting previously unselected package autotools-dev. 281s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ... 281s Unpacking autotools-dev (20220109.1) ... 282s Selecting previously unselected package automake. 282s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 282s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 282s Selecting previously unselected package autopoint. 282s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ... 282s Unpacking autopoint (0.22.5-2) ... 282s Selecting previously unselected package libtcl8.6:armhf. 282s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_armhf.deb ... 282s Unpacking libtcl8.6:armhf (8.6.15+dfsg-2) ... 282s Selecting previously unselected package libfreetype6:armhf. 282s Preparing to unpack .../008-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 282s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 282s Selecting previously unselected package fonts-dejavu-mono. 282s Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ... 282s Unpacking fonts-dejavu-mono (2.37-8) ... 282s Selecting previously unselected package fonts-dejavu-core. 282s Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ... 282s Unpacking fonts-dejavu-core (2.37-8) ... 282s Selecting previously unselected package libfontenc1:armhf. 282s Preparing to unpack .../011-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 282s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 282s Selecting previously unselected package x11-common. 282s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ... 282s Unpacking x11-common (1:7.7+23ubuntu3) ... 282s Selecting previously unselected package xfonts-encodings. 282s Preparing to unpack .../013-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 282s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 282s Selecting previously unselected package xfonts-utils. 282s Preparing to unpack .../014-xfonts-utils_1%3a7.7+7_armhf.deb ... 282s Unpacking xfonts-utils (1:7.7+7) ... 282s Selecting previously unselected package fonts-urw-base35. 282s Preparing to unpack .../015-fonts-urw-base35_20200910-8_all.deb ... 282s Unpacking fonts-urw-base35 (20200910-8) ... 282s Selecting previously unselected package fontconfig-config. 282s Preparing to unpack .../016-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 282s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 282s Selecting previously unselected package libfontconfig1:armhf. 282s Preparing to unpack .../017-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 282s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 282s Selecting previously unselected package libxrender1:armhf. 282s Preparing to unpack .../018-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 282s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 282s Selecting previously unselected package libxft2:armhf. 282s Preparing to unpack .../019-libxft2_2.3.6-1build1_armhf.deb ... 282s Unpacking libxft2:armhf (2.3.6-1build1) ... 282s Selecting previously unselected package libxss1:armhf. 282s Preparing to unpack .../020-libxss1_1%3a1.2.3-1build3_armhf.deb ... 282s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 282s Selecting previously unselected package libtk8.6:armhf. 282s Preparing to unpack .../021-libtk8.6_8.6.15-1_armhf.deb ... 282s Unpacking libtk8.6:armhf (8.6.15-1) ... 283s Selecting previously unselected package tk8.6-blt2.5. 283s Preparing to unpack .../022-tk8.6-blt2.5_2.5.3+dfsg-7build1_armhf.deb ... 283s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 283s Selecting previously unselected package blt. 283s Preparing to unpack .../023-blt_2.5.3+dfsg-7build1_armhf.deb ... 283s Unpacking blt (2.5.3+dfsg-7build1) ... 283s Selecting previously unselected package libc-dev-bin. 283s Preparing to unpack .../024-libc-dev-bin_2.40-1ubuntu3_armhf.deb ... 283s Unpacking libc-dev-bin (2.40-1ubuntu3) ... 283s Selecting previously unselected package linux-libc-dev:armhf. 283s Preparing to unpack .../025-linux-libc-dev_6.11.0-8.8_armhf.deb ... 283s Unpacking linux-libc-dev:armhf (6.11.0-8.8) ... 283s Selecting previously unselected package libcrypt-dev:armhf. 283s Preparing to unpack .../026-libcrypt-dev_1%3a4.4.36-4build1_armhf.deb ... 283s Unpacking libcrypt-dev:armhf (1:4.4.36-4build1) ... 283s Selecting previously unselected package rpcsvc-proto. 283s Preparing to unpack .../027-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 283s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 283s Selecting previously unselected package libc6-dev:armhf. 283s Preparing to unpack .../028-libc6-dev_2.40-1ubuntu3_armhf.deb ... 283s Unpacking libc6-dev:armhf (2.40-1ubuntu3) ... 283s Selecting previously unselected package libisl23:armhf. 283s Preparing to unpack .../029-libisl23_0.27-1_armhf.deb ... 283s Unpacking libisl23:armhf (0.27-1) ... 283s Selecting previously unselected package libmpc3:armhf. 283s Preparing to unpack .../030-libmpc3_1.3.1-1build2_armhf.deb ... 283s Unpacking libmpc3:armhf (1.3.1-1build2) ... 283s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 283s Preparing to unpack .../031-cpp-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 283s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 283s Selecting previously unselected package cpp-14. 283s Preparing to unpack .../032-cpp-14_14.2.0-8ubuntu1_armhf.deb ... 283s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 283s Selecting previously unselected package cpp-arm-linux-gnueabihf. 283s Preparing to unpack .../033-cpp-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 283s Unpacking cpp-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 283s Selecting previously unselected package cpp. 283s Preparing to unpack .../034-cpp_4%3a14.1.0-2ubuntu1_armhf.deb ... 283s Unpacking cpp (4:14.1.0-2ubuntu1) ... 283s Selecting previously unselected package libcc1-0:armhf. 283s Preparing to unpack .../035-libcc1-0_14.2.0-8ubuntu1_armhf.deb ... 283s Unpacking libcc1-0:armhf (14.2.0-8ubuntu1) ... 283s Selecting previously unselected package libgomp1:armhf. 283s Preparing to unpack .../036-libgomp1_14.2.0-8ubuntu1_armhf.deb ... 283s Unpacking libgomp1:armhf (14.2.0-8ubuntu1) ... 283s Selecting previously unselected package libasan8:armhf. 283s Preparing to unpack .../037-libasan8_14.2.0-8ubuntu1_armhf.deb ... 283s Unpacking libasan8:armhf (14.2.0-8ubuntu1) ... 284s Selecting previously unselected package libubsan1:armhf. 284s Preparing to unpack .../038-libubsan1_14.2.0-8ubuntu1_armhf.deb ... 284s Unpacking libubsan1:armhf (14.2.0-8ubuntu1) ... 284s Selecting previously unselected package libgcc-14-dev:armhf. 284s Preparing to unpack .../039-libgcc-14-dev_14.2.0-8ubuntu1_armhf.deb ... 284s Unpacking libgcc-14-dev:armhf (14.2.0-8ubuntu1) ... 284s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 284s Preparing to unpack .../040-gcc-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 284s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 284s Selecting previously unselected package gcc-14. 284s Preparing to unpack .../041-gcc-14_14.2.0-8ubuntu1_armhf.deb ... 284s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 284s Selecting previously unselected package gcc-arm-linux-gnueabihf. 284s Preparing to unpack .../042-gcc-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 284s Unpacking gcc-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 284s Selecting previously unselected package gcc. 284s Preparing to unpack .../043-gcc_4%3a14.1.0-2ubuntu1_armhf.deb ... 284s Unpacking gcc (4:14.1.0-2ubuntu1) ... 284s Selecting previously unselected package libstdc++-14-dev:armhf. 284s Preparing to unpack .../044-libstdc++-14-dev_14.2.0-8ubuntu1_armhf.deb ... 284s Unpacking libstdc++-14-dev:armhf (14.2.0-8ubuntu1) ... 284s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 284s Preparing to unpack .../045-g++-14-arm-linux-gnueabihf_14.2.0-8ubuntu1_armhf.deb ... 284s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-8ubuntu1) ... 285s Selecting previously unselected package g++-14. 285s Preparing to unpack .../046-g++-14_14.2.0-8ubuntu1_armhf.deb ... 285s Unpacking g++-14 (14.2.0-8ubuntu1) ... 285s Selecting previously unselected package g++-arm-linux-gnueabihf. 285s Preparing to unpack .../047-g++-arm-linux-gnueabihf_4%3a14.1.0-2ubuntu1_armhf.deb ... 285s Unpacking g++-arm-linux-gnueabihf (4:14.1.0-2ubuntu1) ... 285s Selecting previously unselected package g++. 285s Preparing to unpack .../048-g++_4%3a14.1.0-2ubuntu1_armhf.deb ... 285s Unpacking g++ (4:14.1.0-2ubuntu1) ... 285s Selecting previously unselected package build-essential. 285s Preparing to unpack .../049-build-essential_12.10ubuntu1_armhf.deb ... 285s Unpacking build-essential (12.10ubuntu1) ... 285s Selecting previously unselected package cython3. 285s Preparing to unpack .../050-cython3_3.0.11+dfsg-1ubuntu1_armhf.deb ... 285s Unpacking cython3 (3.0.11+dfsg-1ubuntu1) ... 285s Selecting previously unselected package libdebhelper-perl. 285s Preparing to unpack .../051-libdebhelper-perl_13.20ubuntu1_all.deb ... 285s Unpacking libdebhelper-perl (13.20ubuntu1) ... 285s Selecting previously unselected package libtool. 285s Preparing to unpack .../052-libtool_2.4.7-7build1_all.deb ... 285s Unpacking libtool (2.4.7-7build1) ... 285s Selecting previously unselected package dh-autoreconf. 285s Preparing to unpack .../053-dh-autoreconf_20_all.deb ... 285s Unpacking dh-autoreconf (20) ... 285s Selecting previously unselected package libarchive-zip-perl. 285s Preparing to unpack .../054-libarchive-zip-perl_1.68-1_all.deb ... 285s Unpacking libarchive-zip-perl (1.68-1) ... 285s Selecting previously unselected package libfile-stripnondeterminism-perl. 285s Preparing to unpack .../055-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 285s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 285s Selecting previously unselected package dh-strip-nondeterminism. 285s Preparing to unpack .../056-dh-strip-nondeterminism_1.14.0-1_all.deb ... 285s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 285s Selecting previously unselected package debugedit. 285s Preparing to unpack .../057-debugedit_1%3a5.1-1_armhf.deb ... 285s Unpacking debugedit (1:5.1-1) ... 285s Selecting previously unselected package dwz. 285s Preparing to unpack .../058-dwz_0.15-1build6_armhf.deb ... 285s Unpacking dwz (0.15-1build6) ... 285s Selecting previously unselected package gettext. 285s Preparing to unpack .../059-gettext_0.22.5-2_armhf.deb ... 285s Unpacking gettext (0.22.5-2) ... 285s Selecting previously unselected package intltool-debian. 285s Preparing to unpack .../060-intltool-debian_0.35.0+20060710.6_all.deb ... 285s Unpacking intltool-debian (0.35.0+20060710.6) ... 285s Selecting previously unselected package po-debconf. 285s Preparing to unpack .../061-po-debconf_1.0.21+nmu1_all.deb ... 285s Unpacking po-debconf (1.0.21+nmu1) ... 285s Selecting previously unselected package debhelper. 285s Preparing to unpack .../062-debhelper_13.20ubuntu1_all.deb ... 285s Unpacking debhelper (13.20ubuntu1) ... 285s Selecting previously unselected package dh-python. 285s Preparing to unpack .../063-dh-python_6.20241024_all.deb ... 285s Unpacking dh-python (6.20241024) ... 285s Selecting previously unselected package xml-core. 285s Preparing to unpack .../064-xml-core_0.19_all.deb ... 285s Unpacking xml-core (0.19) ... 285s Selecting previously unselected package docutils-common. 285s Preparing to unpack .../065-docutils-common_0.21.2+dfsg-2_all.deb ... 285s Unpacking docutils-common (0.21.2+dfsg-2) ... 285s Selecting previously unselected package fonts-font-awesome. 285s Preparing to unpack .../066-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 285s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 285s Selecting previously unselected package fonts-lyx. 286s Preparing to unpack .../067-fonts-lyx_2.4.2.1-1_all.deb ... 286s Unpacking fonts-lyx (2.4.2.1-1) ... 286s Selecting previously unselected package fonts-mathjax. 286s Preparing to unpack .../068-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 286s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 286s Selecting previously unselected package libaec0:armhf. 286s Preparing to unpack .../069-libaec0_1.1.3-1_armhf.deb ... 286s Unpacking libaec0:armhf (1.1.3-1) ... 286s Selecting previously unselected package libblas3:armhf. 286s Preparing to unpack .../070-libblas3_3.12.0-3build2_armhf.deb ... 286s Unpacking libblas3:armhf (3.12.0-3build2) ... 286s Selecting previously unselected package libpixman-1-0:armhf. 286s Preparing to unpack .../071-libpixman-1-0_0.44.0-3_armhf.deb ... 286s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 286s Selecting previously unselected package libxcb-render0:armhf. 286s Preparing to unpack .../072-libxcb-render0_1.17.0-2_armhf.deb ... 286s Unpacking libxcb-render0:armhf (1.17.0-2) ... 286s Selecting previously unselected package libxcb-shm0:armhf. 286s Preparing to unpack .../073-libxcb-shm0_1.17.0-2_armhf.deb ... 286s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 286s Selecting previously unselected package libcairo2:armhf. 286s Preparing to unpack .../074-libcairo2_1.18.2-2_armhf.deb ... 286s Unpacking libcairo2:armhf (1.18.2-2) ... 286s Selecting previously unselected package libdeflate0:armhf. 286s Preparing to unpack .../075-libdeflate0_1.22-1_armhf.deb ... 286s Unpacking libdeflate0:armhf (1.22-1) ... 286s Selecting previously unselected package libexpat1-dev:armhf. 286s Preparing to unpack .../076-libexpat1-dev_2.6.2-2_armhf.deb ... 286s Unpacking libexpat1-dev:armhf (2.6.2-2) ... 286s Selecting previously unselected package libgfortran5:armhf. 286s Preparing to unpack .../077-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 286s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 286s Selecting previously unselected package libgraphite2-3:armhf. 286s Preparing to unpack .../078-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 286s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 286s Selecting previously unselected package libharfbuzz0b:armhf. 286s Preparing to unpack .../079-libharfbuzz0b_10.0.1-1_armhf.deb ... 286s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 286s Selecting previously unselected package libsz2:armhf. 286s Preparing to unpack .../080-libsz2_1.1.3-1_armhf.deb ... 286s Unpacking libsz2:armhf (1.1.3-1) ... 286s Selecting previously unselected package libhdf5-103-1t64:armhf. 286s Preparing to unpack .../081-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 286s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 286s Selecting previously unselected package libhdf5-hl-100t64:armhf. 286s Preparing to unpack .../082-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 286s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 286s Selecting previously unselected package libimagequant0:armhf. 286s Preparing to unpack .../083-libimagequant0_2.18.0-1build1_armhf.deb ... 286s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 286s Selecting previously unselected package libjpeg-turbo8:armhf. 286s Preparing to unpack .../084-libjpeg-turbo8_2.1.5-2ubuntu2_armhf.deb ... 286s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu2) ... 286s Selecting previously unselected package libjpeg8:armhf. 286s Preparing to unpack .../085-libjpeg8_8c-2ubuntu11_armhf.deb ... 286s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 286s Selecting previously unselected package libjs-jquery. 286s Preparing to unpack .../086-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 286s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 286s Selecting previously unselected package libjs-jquery-ui. 286s Preparing to unpack .../087-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 286s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 287s Selecting previously unselected package libjs-underscore. 287s Preparing to unpack .../088-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 287s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 287s Selecting previously unselected package libjs-sphinxdoc. 287s Preparing to unpack .../089-libjs-sphinxdoc_7.4.7-4_all.deb ... 287s Unpacking libjs-sphinxdoc (7.4.7-4) ... 287s Selecting previously unselected package libjson-perl. 287s Preparing to unpack .../090-libjson-perl_4.10000-1_all.deb ... 287s Unpacking libjson-perl (4.10000-1) ... 287s Selecting previously unselected package liblapack3:armhf. 287s Preparing to unpack .../091-liblapack3_3.12.0-3build2_armhf.deb ... 287s Unpacking liblapack3:armhf (3.12.0-3build2) ... 287s Selecting previously unselected package liblbfgsb0:armhf. 287s Preparing to unpack .../092-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 287s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 287s Selecting previously unselected package liblcms2-2:armhf. 287s Preparing to unpack .../093-liblcms2-2_2.16-2_armhf.deb ... 287s Unpacking liblcms2-2:armhf (2.16-2) ... 287s Selecting previously unselected package liblerc4:armhf. 287s Preparing to unpack .../094-liblerc4_4.0.0+ds-4ubuntu2_armhf.deb ... 287s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu2) ... 287s Selecting previously unselected package liblzf1:armhf. 287s Preparing to unpack .../095-liblzf1_3.6-4_armhf.deb ... 287s Unpacking liblzf1:armhf (3.6-4) ... 287s Selecting previously unselected package libnetcdf19t64:armhf. 287s Preparing to unpack .../096-libnetcdf19t64_1%3a4.9.2-6ubuntu1_armhf.deb ... 287s Unpacking libnetcdf19t64:armhf (1:4.9.2-6ubuntu1) ... 287s Selecting previously unselected package libpython3.12t64:armhf. 287s Preparing to unpack .../097-libpython3.12t64_3.12.7-3_armhf.deb ... 287s Unpacking libpython3.12t64:armhf (3.12.7-3) ... 287s Selecting previously unselected package zlib1g-dev:armhf. 287s Preparing to unpack .../098-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 287s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 287s Selecting previously unselected package libpython3.12-dev:armhf. 287s Preparing to unpack .../099-libpython3.12-dev_3.12.7-3_armhf.deb ... 287s Unpacking libpython3.12-dev:armhf (3.12.7-3) ... 287s Selecting previously unselected package libpython3-dev:armhf. 287s Preparing to unpack .../100-libpython3-dev_3.12.6-0ubuntu1_armhf.deb ... 287s Unpacking libpython3-dev:armhf (3.12.6-0ubuntu1) ... 287s Selecting previously unselected package libpython3-all-dev:armhf. 287s Preparing to unpack .../101-libpython3-all-dev_3.12.6-0ubuntu1_armhf.deb ... 287s Unpacking libpython3-all-dev:armhf (3.12.6-0ubuntu1) ... 287s Selecting previously unselected package libqhull-r8.0:armhf. 287s Preparing to unpack .../102-libqhull-r8.0_2020.2-6build1_armhf.deb ... 287s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 287s Selecting previously unselected package libraqm0:armhf. 287s Preparing to unpack .../103-libraqm0_0.10.1-1build1_armhf.deb ... 287s Unpacking libraqm0:armhf (0.10.1-1build1) ... 287s Selecting previously unselected package libsharpyuv0:armhf. 287s Preparing to unpack .../104-libsharpyuv0_1.4.0-0.1_armhf.deb ... 287s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 287s Selecting previously unselected package libjbig0:armhf. 287s Preparing to unpack .../105-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 287s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 287s Selecting previously unselected package libwebp7:armhf. 287s Preparing to unpack .../106-libwebp7_1.4.0-0.1_armhf.deb ... 287s Unpacking libwebp7:armhf (1.4.0-0.1) ... 287s Selecting previously unselected package libtiff6:armhf. 287s Preparing to unpack .../107-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 287s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 287s Selecting previously unselected package libwebpdemux2:armhf. 287s Preparing to unpack .../108-libwebpdemux2_1.4.0-0.1_armhf.deb ... 287s Unpacking libwebpdemux2:armhf (1.4.0-0.1) ... 287s Selecting previously unselected package libwebpmux3:armhf. 287s Preparing to unpack .../109-libwebpmux3_1.4.0-0.1_armhf.deb ... 287s Unpacking libwebpmux3:armhf (1.4.0-0.1) ... 287s Selecting previously unselected package libxslt1.1:armhf. 287s Preparing to unpack .../110-libxslt1.1_1.1.39-0exp1ubuntu1_armhf.deb ... 287s Unpacking libxslt1.1:armhf (1.1.39-0exp1ubuntu1) ... 288s Selecting previously unselected package python3-packaging. 288s Preparing to unpack .../111-python3-packaging_24.1-1_all.deb ... 288s Unpacking python3-packaging (24.1-1) ... 288s Selecting previously unselected package python3-pyproject-hooks. 288s Preparing to unpack .../112-python3-pyproject-hooks_1.2.0-1_all.deb ... 288s Unpacking python3-pyproject-hooks (1.2.0-1) ... 288s Selecting previously unselected package python3-toml. 288s Preparing to unpack .../113-python3-toml_0.10.2-1_all.deb ... 288s Unpacking python3-toml (0.10.2-1) ... 288s Selecting previously unselected package python3-wheel. 288s Preparing to unpack .../114-python3-wheel_0.44.0-1_all.deb ... 288s Unpacking python3-wheel (0.44.0-1) ... 288s Selecting previously unselected package python3-build. 288s Preparing to unpack .../115-python3-build_1.2.2-1_all.deb ... 288s Unpacking python3-build (1.2.2-1) ... 288s Selecting previously unselected package python3-installer. 288s Preparing to unpack .../116-python3-installer_0.7.0+dfsg1-3_all.deb ... 288s Unpacking python3-installer (0.7.0+dfsg1-3) ... 288s Selecting previously unselected package pybuild-plugin-pyproject. 288s Preparing to unpack .../117-pybuild-plugin-pyproject_6.20241024_all.deb ... 288s Unpacking pybuild-plugin-pyproject (6.20241024) ... 288s Selecting previously unselected package python-matplotlib-data. 288s Preparing to unpack .../118-python-matplotlib-data_3.8.3-3_all.deb ... 288s Unpacking python-matplotlib-data (3.8.3-3) ... 288s Selecting previously unselected package libjs-mathjax. 288s Preparing to unpack .../119-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 288s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 289s Selecting previously unselected package python-mdanalysis-doc. 289s Preparing to unpack .../120-python-mdanalysis-doc_2.7.0-5_all.deb ... 289s Unpacking python-mdanalysis-doc (2.7.0-5) ... 289s Selecting previously unselected package python3-all. 289s Preparing to unpack .../121-python3-all_3.12.6-0ubuntu1_armhf.deb ... 289s Unpacking python3-all (3.12.6-0ubuntu1) ... 289s Selecting previously unselected package python3.12-dev. 289s Preparing to unpack .../122-python3.12-dev_3.12.7-3_armhf.deb ... 289s Unpacking python3.12-dev (3.12.7-3) ... 289s Selecting previously unselected package python3-dev. 289s Preparing to unpack .../123-python3-dev_3.12.6-0ubuntu1_armhf.deb ... 289s Unpacking python3-dev (3.12.6-0ubuntu1) ... 289s Selecting previously unselected package python3-all-dev. 289s Preparing to unpack .../124-python3-all-dev_3.12.6-0ubuntu1_armhf.deb ... 289s Unpacking python3-all-dev (3.12.6-0ubuntu1) ... 289s Selecting previously unselected package python3-appdirs. 289s Preparing to unpack .../125-python3-appdirs_1.4.4-4_all.deb ... 289s Unpacking python3-appdirs (1.4.4-4) ... 289s Selecting previously unselected package python3-numpy. 289s Preparing to unpack .../126-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 289s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 289s Selecting previously unselected package python3.12-tk. 289s Preparing to unpack .../127-python3.12-tk_3.12.7-3_armhf.deb ... 289s Unpacking python3.12-tk (3.12.7-3) ... 289s Selecting previously unselected package python3-tk:armhf. 289s Preparing to unpack .../128-python3-tk_3.12.6-1ubuntu1_armhf.deb ... 289s Unpacking python3-tk:armhf (3.12.6-1ubuntu1) ... 289s Selecting previously unselected package python3-pil.imagetk:armhf. 289s Preparing to unpack .../129-python3-pil.imagetk_10.4.0-1ubuntu1_armhf.deb ... 289s Unpacking python3-pil.imagetk:armhf (10.4.0-1ubuntu1) ... 289s Selecting previously unselected package libopenjp2-7:armhf. 289s Preparing to unpack .../130-libopenjp2-7_2.5.0-2ubuntu1_armhf.deb ... 289s Unpacking libopenjp2-7:armhf (2.5.0-2ubuntu1) ... 289s Selecting previously unselected package python3-pil:armhf. 289s Preparing to unpack .../131-python3-pil_10.4.0-1ubuntu1_armhf.deb ... 289s Unpacking python3-pil:armhf (10.4.0-1ubuntu1) ... 289s Selecting previously unselected package python3-cairo. 289s Preparing to unpack .../132-python3-cairo_1.26.1-2_armhf.deb ... 289s Unpacking python3-cairo (1.26.1-2) ... 289s Selecting previously unselected package python3-freetype. 289s Preparing to unpack .../133-python3-freetype_2.5.1-1_all.deb ... 289s Unpacking python3-freetype (2.5.1-1) ... 289s Selecting previously unselected package python3-rlpycairo. 289s Preparing to unpack .../134-python3-rlpycairo_0.3.0-3_all.deb ... 289s Unpacking python3-rlpycairo (0.3.0-3) ... 289s Selecting previously unselected package python3-reportlab. 289s Preparing to unpack .../135-python3-reportlab_4.2.5-1_all.deb ... 289s Unpacking python3-reportlab (4.2.5-1) ... 290s Selecting previously unselected package w3c-sgml-lib. 290s Preparing to unpack .../136-w3c-sgml-lib_1.3-3_all.deb ... 290s Unpacking w3c-sgml-lib (1.3-3) ... 290s Selecting previously unselected package python3-biopython. 290s Preparing to unpack .../137-python3-biopython_1.84+dfsg-4_armhf.deb ... 290s Unpacking python3-biopython (1.84+dfsg-4) ... 290s Selecting previously unselected package python3-brotli. 290s Preparing to unpack .../138-python3-brotli_1.1.0-2build2_armhf.deb ... 290s Unpacking python3-brotli (1.1.0-2build2) ... 290s Selecting previously unselected package python3-cftime. 290s Preparing to unpack .../139-python3-cftime_1.6.4-1_armhf.deb ... 290s Unpacking python3-cftime (1.6.4-1) ... 290s Selecting previously unselected package python3-lxml:armhf. 290s Preparing to unpack .../140-python3-lxml_5.3.0-1_armhf.deb ... 290s Unpacking python3-lxml:armhf (5.3.0-1) ... 290s Selecting previously unselected package python3-citeproc. 290s Preparing to unpack .../141-python3-citeproc_0.6.0-3_all.deb ... 290s Unpacking python3-citeproc (0.6.0-3) ... 290s Selecting previously unselected package python3-contourpy. 290s Preparing to unpack .../142-python3-contourpy_1.3.0-2_armhf.deb ... 290s Unpacking python3-contourpy (1.3.0-2) ... 290s Selecting previously unselected package python3-cycler. 290s Preparing to unpack .../143-python3-cycler_0.12.1-1_all.deb ... 290s Unpacking python3-cycler (0.12.1-1) ... 290s Selecting previously unselected package python3-six. 290s Preparing to unpack .../144-python3-six_1.16.0-7_all.deb ... 290s Unpacking python3-six (1.16.0-7) ... 290s Selecting previously unselected package python3-dateutil. 290s Preparing to unpack .../145-python3-dateutil_2.9.0-2_all.deb ... 290s Unpacking python3-dateutil (2.9.0-2) ... 290s Selecting previously unselected package python3-decorator. 290s Preparing to unpack .../146-python3-decorator_5.1.1-5_all.deb ... 290s Unpacking python3-decorator (5.1.1-5) ... 290s Selecting previously unselected package python3-defusedxml. 290s Preparing to unpack .../147-python3-defusedxml_0.7.1-2_all.deb ... 290s Unpacking python3-defusedxml (0.7.1-2) ... 290s Selecting previously unselected package python3-roman. 290s Preparing to unpack .../148-python3-roman_4.2-1_all.deb ... 290s Unpacking python3-roman (4.2-1) ... 291s Selecting previously unselected package python3-docutils. 291s Preparing to unpack .../149-python3-docutils_0.21.2+dfsg-2_all.deb ... 291s Unpacking python3-docutils (0.21.2+dfsg-2) ... 291s Selecting previously unselected package python3-looseversion. 291s Preparing to unpack .../150-python3-looseversion_1.3.0-3_all.deb ... 291s Unpacking python3-looseversion (1.3.0-3) ... 291s Selecting previously unselected package python3-duecredit. 291s Preparing to unpack .../151-python3-duecredit_0.10.2-2_all.deb ... 291s Unpacking python3-duecredit (0.10.2-2) ... 291s Selecting previously unselected package python3-monotonic. 291s Preparing to unpack .../152-python3-monotonic_1.6-2_all.deb ... 291s Unpacking python3-monotonic (1.6-2) ... 291s Selecting previously unselected package python3-fasteners. 291s Preparing to unpack .../153-python3-fasteners_0.18-2_all.deb ... 291s Unpacking python3-fasteners (0.18-2) ... 291s Selecting previously unselected package python3-scipy. 291s Preparing to unpack .../154-python3-scipy_1.13.1-5_armhf.deb ... 291s Unpacking python3-scipy (1.13.1-5) ... 291s Selecting previously unselected package python3-ufolib2. 291s Preparing to unpack .../155-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 291s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 291s Selecting previously unselected package python3-mpmath. 291s Preparing to unpack .../156-python3-mpmath_1.3.0-1_all.deb ... 291s Unpacking python3-mpmath (1.3.0-1) ... 291s Selecting previously unselected package python3-sympy. 291s Preparing to unpack .../157-python3-sympy_1.13.3-1_all.deb ... 291s Unpacking python3-sympy (1.13.3-1) ... 292s Selecting previously unselected package python3-tz. 292s Preparing to unpack .../158-python3-tz_2024.1-2_all.deb ... 292s Unpacking python3-tz (2024.1-2) ... 292s Selecting previously unselected package python3-fs. 292s Preparing to unpack .../159-python3-fs_2.4.16-4_all.deb ... 292s Unpacking python3-fs (2.4.16-4) ... 292s Selecting previously unselected package python3-lz4. 292s Preparing to unpack .../160-python3-lz4_4.0.2+dfsg-1build4_armhf.deb ... 292s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 292s Selecting previously unselected package python3-unicodedata2. 292s Preparing to unpack .../161-python3-unicodedata2_15.1.0+ds-1build1_armhf.deb ... 292s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 292s Selecting previously unselected package unicode-data. 292s Preparing to unpack .../162-unicode-data_15.1.0-1_all.deb ... 292s Unpacking unicode-data (15.1.0-1) ... 292s Selecting previously unselected package python3-fonttools. 292s Preparing to unpack .../163-python3-fonttools_4.46.0-1build2_armhf.deb ... 292s Unpacking python3-fonttools (4.46.0-1build2) ... 292s Selecting previously unselected package sphinx-rtd-theme-common. 292s Preparing to unpack .../164-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ... 292s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ... 292s Selecting previously unselected package python3-mrcfile. 292s Preparing to unpack .../165-python3-mrcfile_1.5.3-3_all.deb ... 292s Unpacking python3-mrcfile (1.5.3-3) ... 292s Selecting previously unselected package python3-griddataformats. 293s Preparing to unpack .../166-python3-griddataformats_1.0.2-2_all.deb ... 293s Unpacking python3-griddataformats (1.0.2-2) ... 293s Selecting previously unselected package python3-gsd. 293s Preparing to unpack .../167-python3-gsd_3.3.0-1_armhf.deb ... 293s Unpacking python3-gsd (3.3.0-1) ... 293s Selecting previously unselected package python3-h5py-serial. 293s Preparing to unpack .../168-python3-h5py-serial_3.11.0-5ubuntu1_armhf.deb ... 293s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 293s Selecting previously unselected package python3-h5py. 293s Preparing to unpack .../169-python3-h5py_3.11.0-5ubuntu1_all.deb ... 293s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 293s Selecting previously unselected package python3-sortedcontainers. 293s Preparing to unpack .../170-python3-sortedcontainers_2.4.0-2_all.deb ... 293s Unpacking python3-sortedcontainers (2.4.0-2) ... 293s Selecting previously unselected package python3-hypothesis. 293s Preparing to unpack .../171-python3-hypothesis_6.116.0-1_all.deb ... 293s Unpacking python3-hypothesis (6.116.0-1) ... 293s Selecting previously unselected package python3-imagesize. 293s Preparing to unpack .../172-python3-imagesize_1.4.1-1_all.deb ... 293s Unpacking python3-imagesize (1.4.1-1) ... 293s Selecting previously unselected package python3-iniconfig. 293s Preparing to unpack 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python3-mda-xdrlib (0.2.0-3) ... 293s Selecting previously unselected package python3-msgpack. 293s Preparing to unpack .../179-python3-msgpack_1.0.3-3build2_armhf.deb ... 293s Unpacking python3-msgpack (1.0.3-3build2) ... 293s Selecting previously unselected package python3-mmtf. 293s Preparing to unpack .../180-python3-mmtf_1.1.3-1_all.deb ... 293s Unpacking python3-mmtf (1.1.3-1) ... 293s Selecting previously unselected package python3-threadpoolctl. 293s Preparing to unpack .../181-python3-threadpoolctl_3.1.0-1_all.deb ... 293s Unpacking python3-threadpoolctl (3.1.0-1) ... 293s Selecting previously unselected package python3-tqdm. 293s Preparing to unpack .../182-python3-tqdm_4.67.0-1_all.deb ... 293s Unpacking python3-tqdm (4.67.0-1) ... 293s Selecting previously unselected package python3-mdanalysis. 293s Preparing to unpack .../183-python3-mdanalysis_2.7.0-5_armhf.deb ... 293s Unpacking python3-mdanalysis (2.7.0-5) ... 294s Selecting previously unselected package sphinx-common. 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[100%] 1217s 1217s =============================== warnings summary =============================== 1217s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39 1217s /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. 1217s 1217s Due to the on going maintenance burden of keeping command line application 1217s wrappers up to date, we have decided to deprecate and eventually remove these 1217s modules. 1217s 1217s We instead now recommend building your command line and invoking it directly 1217s with the subprocess module. 1217s warnings.warn( 1217s 1217s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings 1217s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings 1217s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings 1217s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings 1217s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings 1217s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings 1217s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings 1217s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings 1217s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings 1217s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings 1217s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings 1217s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings 1217s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1217s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings 1217s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings 1217s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings 1217s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings 1217s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings 1217s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings 1217s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings 1217s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings 1217s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings 1217s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings 1217s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings 1217s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings 1217s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings 1217s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings 1217s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings 1217s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings 1217s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings 1217s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings 1217s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1217s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings 1217s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning 1217s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings 1217s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1217s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings 1217s /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. 1217s warnings.warn("DCDReader currently makes independent timesteps" 1217s 1217s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52 1217s /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. 1217s warnings.warn(wmsg, category=DeprecationWarning) 1217s 1217s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122 1217s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter] 1217s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter] 1217s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter] 1217s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles' 1217s warnings.warn( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings 1217s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1217s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings 1217s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written 1217s warnings.warn(wmsg) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings 1217s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings 1217s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings 1217s /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 1217s warnings.warn( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings 1217s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1217s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings 1217s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning 1217s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings 1217s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1217s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1217s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1217s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file. 1217s warnings.warn('No coordinate reader found for {}. Skipping ' 1217s 1217s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1217s /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'c3', 'h1', 'oh', 'ho', 'hc'}. These have been given an empty element record. 1217s warnings.warn("Unknown elements found for some " 1217s 1217s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning 1217s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings 1217s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1217s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 1217s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings 1217s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1217s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings 1217s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings 1217s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1217s /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps 1217s self.times[i] = ts.time 1217s 1217s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning 1217s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings 1217s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings 1217s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1217s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings 1217s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1217s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings 1217s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings 1217s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1217s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A 1217s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded 1217s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps 1217s results.append((ts.time, x.sum() / mask.sum())) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue 1217s /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. 1217s warnings.warn(msg) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape 1217s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding 1217s /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 1217s warnings.warn(msg) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning 1217s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1217s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings 1217s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1217s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings 1217s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning 1217s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings 1217s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings 1217s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings 1217s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings 1217s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings 1217s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1217s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings 1217s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1217s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1217s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings 1217s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings 1217s /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. 1217s warnings.warn("Element information is missing, elements attribute " 1217s 1217s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran 1217s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame 1217s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections 1217s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning 1217s /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues 1217s warnings.warn("Cannot determine phi and psi angles for the first " 1217s 1217s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin 1217s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr 1217s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame 1217s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot 1217s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning 1217s /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. 1217s warnings.warn(f"All residues selected with '{select_remove}' " 1217s 1217s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings 1217s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings 1217s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings 1217s /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=5333) is multi-threaded, use of fork() may lead to deadlocks in the child. 1217s self.pid = os.fork() 1217s 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes 1217s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide 1217s cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms 1217s 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings 1217s /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide 1217s local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T # (n_res-3, 3) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1217s /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice 1217s ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1217s /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide 1217s ret = um.true_divide( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings 1217s /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide 1217s ret = ret.dtype.type(ret / rcount) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings 1217s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings 1217s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning 1217s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning 1217s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning 1217s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1217s /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. 1217s warnings.warn("1 A^3 CRYST1 record," 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1217s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1217s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning 1217s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values. 1217s warnings.warn("Unit cell dimensions not found. " 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1217s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1217s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1217s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1217s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' ' 1217s warnings.warn("Found no information for attr: '{}'" 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1217s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1217s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning 1217s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1217s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings 1217s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0' 1217s warnings.warn("Found no information for attr: '{}'" 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings 1217s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning 1217s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings 1217s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings 1217s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings 1217s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings 1217s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning 1217s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings 1217s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings 1217s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1217s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning 1217s /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 1217s warnings.warn(wmsg, DeprecationWarning) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings 1217s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6 1217s warnings.warn("Desired number of sample points too high, using {0}" 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbond = HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbond = HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbond = HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbond = HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbond = HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbond = HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbond = HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbond = HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s HBAC( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated! 1217s `HydrogenBondAutoCorrel` will be removed in release 3.0.0. 1217s The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbond = HBAC(u, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1217s `find_hydrogen_donors` will be removed in release 3.0.0. 1217s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s D = hbonds.find_hydrogen_donors(H) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds 1217s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated! 1217s `find_hydrogen_donors` will be removed in release 3.0.0. 1217s The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel. 1217s hbonds.find_hydrogen_donors(u.atoms) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1217s /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. 1217s warnings.warn( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type 1217s /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. 1217s warnings.warn( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1217s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1217s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice. 1217s return _methods._mean(a, axis=axis, dtype=dtype, 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1 1217s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules 1217s /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide 1217s ret = ret.dtype.type(ret / rcount) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds 1217s /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. 1217s warnings.warn( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type 1217s /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. 1217s warnings.warn( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1217s /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. 1217s warnings.warn( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens 1217s /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. 1217s warnings.warn( 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1217s /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. 1217s warnings.warn(msg.format(sel)) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1217s /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. 1217s warnings.warn(msg.format(sel)) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1217s /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. 1217s warnings.warn(msg.format(sel)) 1217s 1217s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned. 1218s warnings.warn("Empty string to select atoms, empty group returned.", 1218s 1218s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1218s /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, . 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis 1218s /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, . 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1218s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1218s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1218s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings 1218s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1218s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning 1218s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple 1218s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content 1218s /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. 1218s warnings.warn(wmsg) 1218s 1218s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning 1218s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning 1218s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1218s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497] 1218s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1218s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721] 1218s /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.) 1218s phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi 1218s 1218s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j 1218s /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 1218s warnings.warn("Column index entered (j = {:d} is smaller than row " 1218s 1218s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps 1218s dt=self.trajectory.ts.dt * step, 1218s 1218s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8] 1218s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0] 1218s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8] 1218s /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 1218s warnings.warn(wmsg, DeprecationWarning) 1218s 1218s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1218s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings 1218s /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. 1218s warnings.warn("The `u` attribute is superflous and will be removed " 1218s 1218s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267] 1218s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm 1218s /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. 1218s warnings.warn("The `density` attribute was deprecated in " 1218s 1218s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata 1218s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first. 1218s warnings.warn(msg, category=MissingDataWarning) 1218s 1218s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps 1218s self.timesteps.append(self._ts.time) 1218s 1218s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning 1218s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default 1218s warnings.warn("{} does not support time selection. Reverting to " 1218s 1218s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default 1218s warnings.warn("{} does not support data selection. Reverting to " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1218s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings 1218s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps 1218s return self.ts.dt 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning 1218s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps 1218s ts.data['time'] = step_num * ts.dt 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_unitcell_triclinic[RefNAMDtriclinicDCD] 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDWriterWithRealTrajectory::test_write_trajectory[True-True-False] 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1218s self.close() 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close 1218s self._apply('close') 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply 1218s return [reader.__getattribute__(method)(**kwargs) for reader in self.readers] 1218s ^^^^^^^^^^^^ 1218s AttributeError: 'ChainReader' object has no attribute 'readers' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing 1218s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain 1218s warnings.warn("Missing frame in continuous chain", UserWarning) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps 1218s time_frame_0 = ts.time - ts.frame*ts.dt # assumes ts.dt is constant 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps 1218s frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps 1218s step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps 1218s self._add_step_to_frame_data(ts.time) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames] 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids] 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names] 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors] 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps 1218s if not np.allclose(A.time, B.time): 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1] 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2] 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3] 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0] 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1] 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2] 1218s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array 1218s /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 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1218s self.close() 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close 1218s self._file.close() 1218s ^^^^^^^^^^ 1218s AttributeError: 'DCDReader' object has no attribute '_file' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms 1218s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit 1218s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__ 1218s self.close() 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close 1218s self._file.close() 1218s ^^^^^^^^^^ 1218s AttributeError: 'DCDWriter' object has no attribute '_file' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings 1218s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings 1218s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings 1218s /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. 1218s warnings.warn(msg) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps 1218s return self.ts.time 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter] 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps 1218s assert_equal(reader.ts.dt, reader.dt) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps 1218s time_frame = time_frame_0 + frame_index*ts.dt 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps 1218s reader_p = pickle.loads(pickle.dumps(reader)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings 1218s /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 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.] 1218s warnings.warn(wmsg) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings 1218s /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`. 1218s warnings.warn(wmsg) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present. Unset velocities set to zero. 1218s warnings.warn("Not all velocities were present. " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps 1218s reader_p = pickle.loads(pickle.dumps(reader)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader 1218s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps 1218s reader_p = pickle.loads(pickle.dumps(reader)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1218s self.close() 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close 1218s self._file.close() 1218s ^^^^^^^^^^ 1218s AttributeError: 'H5MDReader' object has no attribute '_file' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' ' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' ' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1218s for aux in self.aux_list: 1218s ^^^^^^^^^^^^^ 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1218s return self._auxs.keys() 1218s ^^^^^^^^^^ 1218s AttributeError: 'H5MDReader' object has no attribute '_auxs' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings 1218s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0 1218s warnings.warn('Guessed all Masses to 1.0') 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit 1218s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1218s for aux in self.aux_list: 1218s ^^^^^^^^^^^^^ 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1218s return self._auxs.keys() 1218s ^^^^^^^^^^ 1218s AttributeError: 'DCDReader' object has no attribute '_auxs' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view 1218s /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 1218s warnings.warn("MemoryReader.timeseries inclusive `stop` " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader 1218s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps 1218s reader_p = pickle.loads(pickle.dumps(reader)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1218s /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 1218s warnings.warn(wmsg) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps 1218s ts.time) # in-place ! (hope this works...) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps 1218s time_list = [ts.time for ts in u.trajectory] 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps 1218s assert u.trajectory.ts.dt == pytest.approx(ref) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4 1218s /tmp/autopkgtest.9K7Ne2/build.8is/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.) 1218s return self._test_write_trajectory(universe, outfile) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0] 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0] 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0] 1218s /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. 1218s warnings.warn(wmsg) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf 1218s /tmp/autopkgtest.9K7Ne2/build.8is/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.) 1218s return self._test_write_trajectory(universe, outfile) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of '' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X' 1218s warnings.warn("Found missing chainIDs." 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom] 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond] 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom] 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree] 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond] 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom] 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps 1218s time = ts.time 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1218s self.close() 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close 1218s if self.trjfile is not None: 1218s ^^^^^^^^^^^^ 1218s AttributeError: 'NCDFWriter' object has no attribute 'trjfile' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' ' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter] 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X' 1218s warnings.warn("Found no information for attr: '{}'" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@] 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X' 1218s warnings.warn("Found chainIDs using unnaccepted character." 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA] 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X' 1218s warnings.warn("Found chainIDs with invalid length." 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000. Higher serials have been guessed 1218s warnings.warn("Serial numbers went over 100,000. " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed 1218s warnings.warn("Invalid atom serials were present, bonds will not" 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed 1218s warnings.warn("Invalid atom serials were present, " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment 1218s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1218s /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. 1218s warnings.warn(wmsg) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1218s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1218s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings 1218s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings 1218s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1218s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges 1218s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps 1218s assert_equal(ts.dt, 1.0) # default value 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps 1218s assert_equal(ts.time, 0.0) # default to 1.0 (dt) * 0 (frame) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps 1218s assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__ 1218s for aux in self.aux_list: 1218s ^^^^^^^^^^^^^ 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list 1218s return self._auxs.keys() 1218s ^^^^^^^^^^ 1218s AttributeError: 'TNGReader' object has no attribute '_auxs' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms 1218s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe 1218s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe 1218s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks! 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__ 1218s self.close() 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close 1218s if self.trjfile is None: 1218s ^^^^^^^^^^^^ 1218s AttributeError: 'TRJReader' object has no attribute 'trjfile' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps 1218s data['time'] = ts.time 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1218s /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 1218s warnings.warn("Timestep didn't have the following attributes: '{0}', " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1218s /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. 1218s warnings.warn("Timestep didn't have velocity information, " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1218s /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 1218s warnings.warn("Timestep didn't have dimensions information, " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__ 1218s self.close() 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close 1218s if self.trzfile is None: 1218s ^^^^^^^^^^^^ 1218s AttributeError: 'TRZWriter' object has no attribute 'trzfile' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1218s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1218s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1218s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1218s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length 1218s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize 1218s /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. 1218s warnings.warn("Element information is missing, elements attribute " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter] 1218s /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 1218s warnings.warn(wmsg, DeprecationWarning) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter] 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter] 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter] 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter] 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter] 1218s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter] 1218s /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' 1218s warnings.warn(wmsg) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD 1218s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps 1218s time = ts.time 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD 1218s /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps 1218s time = ts.time 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1218s self.close() 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1218s self._xdr.close() 1218s ^^^^^^^^^ 1218s AttributeError: 'XTCWriter' object has no attribute '_xdr' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container 1218s /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: 1218s 1218s Traceback (most recent call last): 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__ 1218s self.close() 1218s File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close 1218s self._xdr.close() 1218s ^^^^^^^^^ 1218s AttributeError: 'TRRWriter' object has no attribute '_xdr' 1218s 1218s warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1218s /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. 1218s Consider setting 'refresh_offsets=True' when loading your Universe. 1218s warnings.warn(f"Reading offsets from {fname} failed, " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly 1218s /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. 1218s warnings.warn(f"Cannot write lock/offset file in same location as " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails 1218s /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. 1218s Consider setting 'refresh_offsets=True' when loading your Universe. 1218s warnings.warn(f"Reading offsets from {fname} failed, " 1218s 1218s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly 1218s /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. 1218s warnings.warn(f"Cannot write lock/offset file in same location as " 1218s 1218s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms] 1218s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues] 1218s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments] 1218s /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce 1218s return ufunc.reduce(obj, axis, dtype, out, **passkwargs) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz] 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz] 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings 1218s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings 1218s /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. 1218s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings 1218s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings 1218s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings 1218s /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. 1218s warnings.warn(BFACTOR_WARNING, DeprecationWarning) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1218s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings 1218s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide 1218s return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum() 1218s 1218s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings 1218s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide 1218s _centers /= _weights.sum(axis=1)[:, None] 1218s 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1218s /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`. 1218s warnings.warn(msg, category=SelectionWarning) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11] 1218s /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`. 1218s warnings.warn(msg, category=SelectionWarning) 1218s 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12] 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13] 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15] 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16] 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17] 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18] 1218s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19] 1218s /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`. 1218s warnings.warn(msg, category=SelectionWarning) 1218s 1218s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments] 1218s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules] 1218s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues] 1218s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group] 1218s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments] 1218s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc 1218s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc 1218s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options 1218s /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 1218s warnings.warn("The 'pbc' kwarg has been deprecated and will be " 1218s 1218s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel 1218s /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`. 1218s warnings.warn(msg, category=SelectionWarning) 1218s 1218s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial] 1218s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp] 1218s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial] 1218s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp] 1218s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan] 1218s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide 1218s x = np.dot(a, b) / (norm(a) * norm(b)) 1218s 1218s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt 1218s ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2) 1218s 1218s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt 1218s box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 - 1218s 1218s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide 1218s a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z))) 1218s 1218s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide 1218s b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z))) 1218s 1218s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide 1218s c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y))) 1218s 1218s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide 1218s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1218s 1218s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide 1218s ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c 1218s 1218s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2] 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3] 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4] 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5] 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6] 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7] 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10] 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11] 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14] 1218s /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps 1218s cls(buf, protocol).dump(obj) 1218s 1218s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps 1218s ps = pickle.dumps(ref_reader) 1218s 1218s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0] 1218s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd 1218s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd 1218s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset 1218s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific 1218s /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset. 1218s warnings.warn('Cannot average position for non sequential' 1218s 1218s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name] 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname] 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type] 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid] 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information. Defaulted to '1' 1218s warnings.warn("PDB file is missing resid information. " 1218s 1218s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX 1218s warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type)) 1218s 1218s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2] 1218s /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. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2] 1218s /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. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2] 1218s /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. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2] 1218s /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. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings 1218s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings 1218s /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. 1218s warnings.warn(msg) 1218s 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts 1218s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr] 1218s /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file. 1218s warnings.warn('No coordinate reader found for {}. Skipping ' 1218s 1218s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses 1218s /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses. 1218s warnings.warn(msg, category=SelectionWarning) 1218s 1218s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2 1218s /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. 1218s warnings.warn( 1218s 1218s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps 1218s return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1218s 1218s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps 1218s pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL) 1218s 1218s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps 1218s return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL) 1218s 1218s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps 1218s return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL) 1218s 1218s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps 1218s return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL) 1218s 1218s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps 1218s pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL) 1218s 1218s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag 1218s /tmp/autopkgtest.9K7Ne2/build.8is/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps 1218s pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL) 1218s 1218s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings 1218s /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream 1218s warnings.warn("Constructed NamedStream from a NamedStream", 1218s 1218s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159] 1218s /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. 1218s warnings.warn(wmsg, DeprecationWarning) 1218s 1218s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1218s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8131 warnings in 811.09s (0:13:31) = 1241s 1241s DueCredit Report: 1241s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2] 1241s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3] 1241s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4] 1241s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5] 1241s - HOLE trajectory analysis with orderparameters, HOLE program / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8] 1241s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9] 1241s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10] 1241s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2] 1241s - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.7.0) [11, 12] 1241s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13] 1241s - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14] 1241s - MDAnalysis trajectory reader/writer of the H5MDformat, Specifications of the H5MD standard / MDAnalysis.coordinates.H5MD (v 2.7.0, 1.1) [15, 16] 1241s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17] 1241s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18] 1241s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20] 1241s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17] 1241s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21] 1241s - Scientific tools library / numpy (v 1.26.4) [22] 1241s 1241s 2 packages cited 1241s 16 modules cited 1241s 0 functions cited 1241s 1241s References 1241s ---------- 1241s 1241s [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. 1241s [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. 1241s [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. 1241s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 1241s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 1241s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460. 1241s [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. 1241s [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. 1241s [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. 1241s [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). 1241s [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. 1241s [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. 1241s [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. 1241s [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. 1241s [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. 1241s [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. 1241s [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. 1241s [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. 1241s [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. 1241s [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. 1241s [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. 1241s [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. 1244s autopkgtest [16:47:32]: test test-mdanalysis: -----------------------] 1247s autopkgtest [16:47:35]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 1247s test-mdanalysis PASS 1251s autopkgtest [16:47:39]: @@@@@@@@@@@@@@@@@@@@ summary 1251s test-mdanalysis PASS