0s autopkgtest [01:34:16]: starting date and time: 2025-03-16 01:34:16+0000 0s autopkgtest [01:34:16]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:34:16]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eunaa0oc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scikit-learn --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-8 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-3.secgroup --name adt-plucky-amd64-mdtraj-20250316-013415-juju-7f2275-prod-proposed-migration-environment-2-32ad8818-7d37-4444-94e4-462ca337c079 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 57s autopkgtest [01:35:13]: testbed dpkg architecture: amd64 58s autopkgtest [01:35:14]: testbed apt version: 2.9.31ubuntu1 58s autopkgtest [01:35:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 58s autopkgtest [01:35:14]: testbed release detected to be: None 59s autopkgtest [01:35:15]: updating testbed package index (apt update) 59s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 60s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 60s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 60s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 60s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 60s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [84.0 kB] 60s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [66.6 kB] 60s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1844 B] 60s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 60s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [338 kB] 60s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [168 kB] 60s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [14.9 kB] 60s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [9324 B] 60s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [18.0 kB] 60s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 61s Fetched 1252 kB in 1s (1309 kB/s) 61s Reading package lists... 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Calculating upgrade... 62s Calculating upgrade... 63s The following package was automatically installed and is no longer required: 63s libnl-genl-3-200 63s Use 'sudo apt autoremove' to remove it. 63s The following NEW packages will be installed: 63s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 63s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 63s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 63s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 63s The following packages will be upgraded: 63s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 63s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 63s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 63s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 63s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 63s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 63s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 63s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 63s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 63s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 63s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 63s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 63s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 63s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 63s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 63s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 63s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 63s parted pci.ids pciutils pinentry-curses python-apt-common python3 63s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 63s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 63s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 63s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 63s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 63s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 63s xz-utils 63s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 63s Need to get 829 MB of archives. 63s After this operation, 325 MB of additional disk space will be used. 63s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 64s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 66s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 66s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 66s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 66s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 66s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 66s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 66s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 66s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 66s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 66s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 66s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 66s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 66s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 66s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 67s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 67s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 67s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 67s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 68s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 68s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 68s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 68s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 68s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 68s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 68s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 68s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 68s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 68s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 68s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 68s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 68s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 69s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 69s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 69s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 69s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 69s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 69s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 69s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 70s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 70s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 70s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 70s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 70s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 70s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 70s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 70s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 70s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 70s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 70s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 71s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 71s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 71s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 71s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 71s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 71s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 71s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 71s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 71s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 71s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 71s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 71s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 71s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 71s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 71s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 71s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 71s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 71s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 71s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 71s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 71s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 71s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 71s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 71s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 71s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 71s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 72s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 72s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 72s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 72s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 72s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 72s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 72s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 72s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 72s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 72s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 72s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 72s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 72s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 72s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 73s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 73s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 73s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 73s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 73s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 73s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 73s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 74s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 74s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 78s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 79s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 79s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 79s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 139s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 139s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 139s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 139s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 139s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 139s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 139s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 139s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 141s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 141s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 146s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 146s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 146s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 146s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 146s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 146s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 146s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 147s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 147s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 147s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 147s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 147s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 147s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 147s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 147s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 147s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 147s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 147s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 147s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 147s Preconfiguring packages ... 147s Fetched 829 MB in 1min 24s (9850 kB/s) 148s (Reading database ... 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(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 ... 109140 files and directories currently installed.) 148s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 148s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 148s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 148s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 148s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 148s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 148s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 148s Checking for services that may need to be restarted... 148s Checking init scripts... 148s Checking for services that may need to be restarted... 148s Checking init scripts... 148s Stopping some services possibly affected by the upgrade (will be restarted later): 148s cron: stopping...done. 148s 149s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 149s Setting up libc6:amd64 (2.41-1ubuntu1) ... 149s Checking for services that may need to be restarted... 149s Checking init scripts... 149s Restarting services possibly affected by the upgrade: 149s cron: restarting...done. 149s 149s Services restarted successfully. 149s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 153s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 153s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 153s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 153s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 153s Setting up python3-minimal (3.13.2-2) ... 153s (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 ... 109146 files and directories currently installed.) 153s Preparing to unpack .../0-python3_3.13.2-2_amd64.deb ... 153s Unpacking python3 (3.13.2-2) over (3.13.2-1) ... 153s Preparing to unpack .../1-libpython3.13_3.13.2-2_amd64.deb ... 153s Unpacking libpython3.13:amd64 (3.13.2-2) over (3.13.2-1) ... 153s Preparing to unpack .../2-media-types_13.0.0_all.deb ... 153s Unpacking media-types (13.0.0) over (12.0.0) ... 153s Preparing to unpack .../3-libncurses6_6.5+20250216-2_amd64.deb ... 153s Unpacking libncurses6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 154s Preparing to unpack .../4-libncursesw6_6.5+20250216-2_amd64.deb ... 154s Unpacking libncursesw6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 154s Preparing to unpack .../5-libtinfo6_6.5+20250216-2_amd64.deb ... 154s Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 154s Setting up libtinfo6:amd64 (6.5+20250216-2) ... 154s (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 ... 109146 files and directories currently installed.) 154s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 154s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 154s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 154s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 154s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 154s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 154s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 154s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 154s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 154s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 154s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 154s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 154s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 154s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 154s Selecting previously unselected package libdebuginfod-common. 154s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 154s Unpacking libdebuginfod-common (0.192-4) ... 154s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 154s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 154s Setting up libsemanage-common (3.7-2.1build1) ... 155s (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 ... 109155 files and directories currently installed.) 155s Preparing to unpack .../libsemanage2_3.7-2.1build1_amd64.deb ... 155s Unpacking libsemanage2:amd64 (3.7-2.1build1) over (3.7-2.1) ... 155s Setting up libsemanage2:amd64 (3.7-2.1build1) ... 155s (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 ... 109155 files and directories currently installed.) 155s Preparing to unpack .../libassuan9_3.0.2-2_amd64.deb ... 155s Unpacking libassuan9:amd64 (3.0.2-2) over (3.0.1-2) ... 155s Setting up libassuan9:amd64 (3.0.2-2) ... 155s (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 ... 109155 files and directories currently installed.) 155s Preparing to unpack .../00-gir1.2-girepository-2.0_1.83.4-1_amd64.deb ... 155s Unpacking gir1.2-girepository-2.0:amd64 (1.83.4-1) over (1.82.0-4) ... 155s Preparing to unpack .../01-gir1.2-glib-2.0_2.84.0-1_amd64.deb ... 155s Unpacking gir1.2-glib-2.0:amd64 (2.84.0-1) over (2.83.5-1) ... 155s Preparing to unpack .../02-libglib2.0-0t64_2.84.0-1_amd64.deb ... 155s Unpacking libglib2.0-0t64:amd64 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.../16-whiptail_0.52.24-4ubuntu2_amd64.deb ... 156s Unpacking whiptail (0.52.24-4ubuntu2) over (0.52.24-4ubuntu1) ... 156s Preparing to unpack .../17-ubuntu-minimal_1.549_amd64.deb ... 156s Unpacking ubuntu-minimal (1.549) over (1.548) ... 156s Preparing to unpack .../18-apparmor_4.1.0~beta5-0ubuntu8_amd64.deb ... 156s Unpacking apparmor (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu5) ... 157s Preparing to unpack .../19-dosfstools_4.2-1.2_amd64.deb ... 157s Unpacking dosfstools (4.2-1.2) over (4.2-1.1build1) ... 157s Preparing to unpack .../20-libnl-genl-3-200_3.7.0-1_amd64.deb ... 157s Unpacking libnl-genl-3-200:amd64 (3.7.0-1) over (3.7.0-0.3build2) ... 157s Preparing to unpack .../21-libnl-route-3-200_3.7.0-1_amd64.deb ... 157s Unpacking libnl-route-3-200:amd64 (3.7.0-1) over (3.7.0-0.3build2) ... 157s Preparing to unpack .../22-libnl-3-200_3.7.0-1_amd64.deb ... 157s Unpacking libnl-3-200:amd64 (3.7.0-1) over (3.7.0-0.3build2) ... 157s Preparing to unpack .../23-parted_3.6-5_amd64.deb ... 157s Unpacking parted (3.6-5) over (3.6-4build1) ... 157s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 157s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 157s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 157s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 157s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 157s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 157s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 157s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 157s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 157s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 157s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 157s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 157s Preparing to unpack .../29-xz-utils_5.6.4-1_amd64.deb ... 157s Unpacking xz-utils (5.6.4-1) over (5.6.3-1) ... 157s Preparing to unpack .../30-ubuntu-standard_1.549_amd64.deb ... 157s Unpacking ubuntu-standard (1.549) over (1.548) ... 157s Preparing to unpack .../31-libgprofng0_2.44-3ubuntu1_amd64.deb ... 157s Unpacking libgprofng0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 157s Preparing to unpack .../32-libctf0_2.44-3ubuntu1_amd64.deb ... 157s Unpacking libctf0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 157s Preparing to unpack .../33-libctf-nobfd0_2.44-3ubuntu1_amd64.deb ... 157s Unpacking libctf-nobfd0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 157s Preparing to unpack .../34-binutils-x86-64-linux-gnu_2.44-3ubuntu1_amd64.deb ... 157s Unpacking binutils-x86-64-linux-gnu (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 157s Preparing to unpack .../35-libbinutils_2.44-3ubuntu1_amd64.deb ... 157s Unpacking libbinutils:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 157s Preparing to unpack .../36-binutils_2.44-3ubuntu1_amd64.deb ... 157s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 157s Preparing to unpack .../37-binutils-common_2.44-3ubuntu1_amd64.deb ... 157s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 157s Preparing to unpack .../38-libsframe1_2.44-3ubuntu1_amd64.deb ... 157s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 157s Preparing to unpack .../39-hwdata_0.393-3_all.deb ... 157s Unpacking hwdata (0.393-3) over (0.392-1) ... 157s Selecting previously unselected package pnp.ids. 157s Preparing to unpack .../40-pnp.ids_0.393-3_all.deb ... 157s Unpacking pnp.ids (0.393-3) ... 157s Preparing to unpack .../41-linux-tools-common_6.14.0-10.10_all.deb ... 157s Unpacking linux-tools-common (6.14.0-10.10) over (6.12.0-16.16) ... 157s Selecting previously unselected package bpftool. 157s Preparing to unpack .../42-bpftool_7.6.0+6.14.0-10.10_amd64.deb ... 157s Unpacking bpftool (7.6.0+6.14.0-10.10) ... 157s Preparing to unpack .../43-python3-markupsafe_2.1.5-1build4_amd64.deb ... 158s Unpacking python3-markupsafe (2.1.5-1build4) over (2.1.5-1build3) ... 158s Preparing to unpack .../44-python3-jinja2_3.1.5-2ubuntu1_all.deb ... 158s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 158s Preparing to unpack .../45-cloud-init-base_25.1-0ubuntu3_all.deb ... 158s Unpacking cloud-init-base (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 158s Preparing to unpack .../46-libbrotli1_1.1.0-2build4_amd64.deb ... 158s Unpacking libbrotli1:amd64 (1.1.0-2build4) over (1.1.0-2build3) ... 158s Preparing to unpack .../47-curl_8.12.1-3ubuntu1_amd64.deb ... 158s Unpacking curl (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 158s Preparing to unpack .../48-libcurl4t64_8.12.1-3ubuntu1_amd64.deb ... 158s Unpacking libcurl4t64:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 158s Preparing to unpack .../49-exfatprogs_1.2.8-1_amd64.deb ... 158s Unpacking exfatprogs (1.2.8-1) over (1.2.7-3) ... 158s Preparing to unpack .../50-libcurl3t64-gnutls_8.12.1-3ubuntu1_amd64.deb ... 158s Unpacking libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 158s Preparing to unpack .../51-fwupd_2.0.6-4_amd64.deb ... 158s Unpacking fwupd (2.0.6-4) over (2.0.6-3) ... 159s Preparing to unpack .../52-libfwupd3_2.0.6-4_amd64.deb ... 159s Unpacking libfwupd3:amd64 (2.0.6-4) over (2.0.6-3) ... 159s Preparing to unpack .../53-libmm-glib0_1.23.4-0ubuntu3_amd64.deb ... 159s Unpacking libmm-glib0:amd64 (1.23.4-0ubuntu3) over (1.23.4-0ubuntu2) ... 159s Preparing to unpack .../54-htop_3.4.0-2_amd64.deb ... 159s Unpacking htop (3.4.0-2) over (3.3.0-5) ... 159s Preparing to unpack .../55-linux-firmware_20250310.git9e1370d3-0ubuntu1_amd64.deb ... 159s Unpacking linux-firmware (20250310.git9e1370d3-0ubuntu1) over (20250204.git0fd450ee-0ubuntu1) ... 162s Preparing to unpack .../56-initramfs-tools_0.146ubuntu1_all.deb ... 162s Unpacking initramfs-tools (0.146ubuntu1) over (0.145ubuntu3) ... 162s Preparing to unpack .../57-initramfs-tools-core_0.146ubuntu1_all.deb ... 162s Unpacking initramfs-tools-core (0.146ubuntu1) over (0.145ubuntu3) ... 162s Preparing to unpack .../58-initramfs-tools-bin_0.146ubuntu1_amd64.deb ... 162s Unpacking initramfs-tools-bin (0.146ubuntu1) over (0.145ubuntu3) ... 162s Selecting previously unselected package libdebuginfod1t64:amd64. 162s Preparing to unpack .../59-libdebuginfod1t64_0.192-4_amd64.deb ... 162s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 162s Preparing to unpack .../60-libftdi1-2_1.5-8build1_amd64.deb ... 162s Unpacking libftdi1-2:amd64 (1.5-8build1) over (1.5-8) ... 162s Preparing to unpack .../61-libgpgme11t64_1.24.2-1ubuntu2_amd64.deb ... 162s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu2) over (1.24.2-1ubuntu1) ... 162s Preparing to unpack .../62-libjemalloc2_5.3.0-3_amd64.deb ... 162s Unpacking libjemalloc2:amd64 (5.3.0-3) over (5.3.0-2build1) ... 162s Selecting previously unselected package linux-modules-6.14.0-10-generic. 162s Preparing to unpack .../63-linux-modules-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 162s Unpacking linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 162s Selecting previously unselected package linux-image-6.14.0-10-generic. 162s Preparing to unpack .../64-linux-image-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 162s Unpacking linux-image-6.14.0-10-generic (6.14.0-10.10) ... 162s Selecting previously unselected package linux-modules-extra-6.14.0-10-generic. 162s Preparing to unpack .../65-linux-modules-extra-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 162s Unpacking linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 163s Preparing to unpack .../66-linux-generic_6.14.0-10.10_amd64.deb ... 163s Unpacking linux-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 163s Preparing to unpack .../67-linux-image-generic_6.14.0-10.10_amd64.deb ... 163s Unpacking linux-image-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 163s Preparing to unpack .../68-linux-virtual_6.14.0-10.10_amd64.deb ... 163s Unpacking linux-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 163s Preparing to unpack .../69-linux-image-virtual_6.14.0-10.10_amd64.deb ... 163s Unpacking linux-image-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 163s Preparing to unpack .../70-linux-headers-virtual_6.14.0-10.10_amd64.deb ... 163s Unpacking linux-headers-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 163s Selecting previously unselected package linux-headers-6.14.0-10. 163s Preparing to unpack .../71-linux-headers-6.14.0-10_6.14.0-10.10_all.deb ... 163s Unpacking linux-headers-6.14.0-10 (6.14.0-10.10) ... 166s Selecting previously unselected package linux-headers-6.14.0-10-generic. 166s Preparing to unpack .../72-linux-headers-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 166s Unpacking linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 167s Preparing to unpack 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(1.0.6-6) over (1.0.6-5) ... 168s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 168s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 168s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 168s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 168s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 168s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 168s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 168s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 168s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 168s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 168s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 168s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 168s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 168s Setting up media-types (13.0.0) ... 168s Installing new version of config file /etc/mime.types ... 168s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 168s Setting up ubuntu-kernel-accessories (1.549) ... 168s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 168s Setting up pci.ids (0.0~2025.03.09-1) ... 168s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 168s Setting up apt-utils (2.9.33) ... 168s Setting up libdebuginfod-common (0.192-4) ... 168s Setting up exfatprogs (1.2.8-1) ... 168s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 168s Setting up bpftool (7.6.0+6.14.0-10.10) ... 168s Setting up libestr0:amd64 (0.1.11-2) ... 168s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 168s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 168s Setting up dosfstools (4.2-1.2) ... 168s Setting up rsyslog (8.2412.0-2ubuntu2) ... 168s info: The user `syslog' is already a member of `adm'. 169s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 169s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 169s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 169s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 169s Setting up systemd (257.3-1ubuntu3) ... 169s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 169s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 169s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 170s Setting up libparted2t64:amd64 (3.6-5) ... 170s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 170s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 170s Setting up linux-headers-generic (6.14.0-10.10) ... 170s Setting up libjemalloc2:amd64 (5.3.0-3) ... 170s Setting up locales (2.41-1ubuntu1) ... 170s Installing new version of config file /etc/locale.alias ... 170s Generating locales (this might take a while)... 172s en_US.UTF-8... done 172s Generation complete. 172s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 172s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 172s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 172s Installing new version of config file /etc/apparmor.d/fusermount3 ... 172s Installing new version of config file /etc/apparmor.d/lsusb ... 172s Installing new version of config file /etc/apparmor.d/openvpn ... 173s Reloading AppArmor profiles 174s Setting up libftdi1-2:amd64 (1.5-8build1) ... 174s Setting up libglib2.0-data (2.84.0-1) ... 174s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 174s Setting up libncurses6:amd64 (6.5+20250216-2) ... 174s Setting up strace (6.13+ds-1ubuntu1) ... 174s Setting up xz-utils (5.6.4-1) ... 174s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 175s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 175s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 175s Setting up udev (257.3-1ubuntu3) ... 175s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 177s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 177s Setting up libpci3:amd64 (1:3.13.0-2) ... 177s Setting up whiptail (0.52.24-4ubuntu2) ... 177s Setting up python-apt-common (2.9.9build1) ... 177s Setting up pnp.ids (0.393-3) ... 177s Setting up libnl-3-200:amd64 (3.7.0-1) ... 177s Setting up python3.13-minimal (3.13.2-2) ... 178s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 178s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 178s Setting up libc-dev-bin (2.41-1ubuntu1) ... 178s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 178s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 178s Setting up rsync (3.4.1+ds1-3) ... 179s rsync.service is a disabled or a static unit not running, not starting it. 179s Setting up python3.13-gdbm (3.13.2-2) ... 179s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 179s Setting up systemd-resolved (257.3-1ubuntu3) ... 179s Setting up initramfs-tools-bin (0.146ubuntu1) ... 179s Setting up ncurses-term (6.5+20250216-2) ... 179s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 179s Setting up libpython3.13:amd64 (3.13.2-2) ... 179s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 179s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 179s Setting up systemd-sysv (257.3-1ubuntu3) ... 179s Setting up linux-headers-virtual (6.14.0-10.10) ... 179s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 179s Setting up python3.13 (3.13.2-2) ... 180s Setting up htop (3.4.0-2) ... 180s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 182s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 182s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 182s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 182s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 182s Setting up parted (3.6-5) ... 182s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 182s Setting up python3 (3.13.2-2) ... 182s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 182s Setting up python3-markupsafe (2.1.5-1build4) ... 182s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 185s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 185s Setting up hwdata (0.393-3) ... 185s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 185s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 185s No schema files found: doing nothing. 185s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 185s Setting up linux-perf (6.14.0-10.10) ... 185s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 185s Setting up pciutils (1:3.13.0-2) ... 185s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 185s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 185s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 185s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 185s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 185s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 185s Setting up curl (8.12.1-3ubuntu1) ... 185s Setting up linux-image-virtual (6.14.0-10.10) ... 185s Setting up initramfs-tools-core (0.146ubuntu1) ... 185s Setting up linux-tools-common (6.14.0-10.10) ... 185s Setting up python3-systemd (235-1build6) ... 185s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 185s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 185s Setting up linux-image-generic (6.14.0-10.10) ... 185s Setting up python3-dbus (1.3.2-5build5) ... 185s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 185s Setting up initramfs-tools (0.146ubuntu1) ... 185s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 185s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 185s update-initramfs: deferring update (trigger activated) 185s Setting up linux-generic (6.14.0-10.10) ... 185s Setting up ubuntu-minimal (1.549) ... 185s Setting up python3-apt (2.9.9build1) ... 185s Setting up python3-bcrypt (4.2.0-2.1build1) ... 185s Setting up python3-yaml (6.0.2-1build2) ... 186s Setting up libfwupd3:amd64 (2.0.6-4) ... 186s Setting up python3-lazr.uri (1.0.6-6) ... 186s Setting up binutils (2.44-3ubuntu1) ... 186s Setting up ubuntu-standard (1.549) ... 186s Setting up cloud-init-base (25.1-0ubuntu3) ... 187s Setting up linux-virtual (6.14.0-10.10) ... 187s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 187s Setting up python3-gi (3.50.0-4build1) ... 187s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 187s Setting up fwupd (2.0.6-4) ... 187s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 188s Setting up cloud-init (25.1-0ubuntu3) ... 188s Processing triggers for man-db (2.13.0-1) ... 189s Processing triggers for dbus (1.16.2-1ubuntu1) ... 189s Processing triggers for shared-mime-info (2.4-5) ... 189s Warning: program compiled against libxml 212 using older 209 190s Processing triggers for libc-bin (2.41-1ubuntu1) ... 190s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 190s /etc/kernel/postinst.d/initramfs-tools: 190s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 190s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 199s /etc/kernel/postinst.d/zz-update-grub: 199s Sourcing file `/etc/default/grub' 199s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 199s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 199s Generating grub configuration file ... 199s Found linux image: /boot/vmlinuz-6.14.0-10-generic 199s Found initrd image: /boot/initrd.img-6.14.0-10-generic 199s Found linux image: /boot/vmlinuz-6.12.0-16-generic 199s Found initrd image: /boot/initrd.img-6.12.0-16-generic 199s Found linux image: /boot/vmlinuz-6.11.0-8-generic 199s Found initrd image: /boot/initrd.img-6.11.0-8-generic 199s Warning: os-prober will not be executed to detect other bootable partitions. 199s Systems on them will not be added to the GRUB boot configuration. 199s Check GRUB_DISABLE_OS_PROBER documentation entry. 199s Adding boot menu entry for UEFI Firmware Settings ... 199s done 199s Processing triggers for initramfs-tools (0.146ubuntu1) ... 199s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 199s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 210s Solving dependencies... 211s The following packages will be REMOVED: 211s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 211s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 211s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 211s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 211s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 211s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 211s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 211s linux-tools-6.12.0-16-generic* 211s 0 upgraded, 0 newly installed, 18 to remove and 0 not upgraded. 211s After this operation, 545 MB disk space will be freed. 211s (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 ... 148643 files and directories currently installed.) 211s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 211s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 211s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 211s Removing libpython3.12t64:amd64 (3.12.9-1) ... 211s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 211s Removing libnsl2:amd64 (1.3.0-3build3) ... 211s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 211s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 212s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 214s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 214s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 216s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 216s /etc/kernel/postrm.d/initramfs-tools: 216s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 216s /etc/kernel/postrm.d/zz-update-grub: 216s Sourcing file `/etc/default/grub' 216s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 216s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 216s Generating grub configuration file ... 216s Found linux image: /boot/vmlinuz-6.14.0-10-generic 216s Found initrd image: /boot/initrd.img-6.14.0-10-generic 216s Found linux image: /boot/vmlinuz-6.12.0-16-generic 216s Found initrd image: /boot/initrd.img-6.12.0-16-generic 216s Warning: os-prober will not be executed to detect other bootable partitions. 216s Systems on them will not be added to the GRUB boot configuration. 216s Check GRUB_DISABLE_OS_PROBER documentation entry. 216s Adding boot menu entry for UEFI Firmware Settings ... 216s done 216s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 217s W: Removing the running kernel 217s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 217s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 217s /etc/kernel/postrm.d/initramfs-tools: 217s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 217s /etc/kernel/postrm.d/zz-update-grub: 217s Sourcing file `/etc/default/grub' 217s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 217s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 217s Generating grub configuration file ... 217s Found linux image: /boot/vmlinuz-6.14.0-10-generic 217s Found initrd image: /boot/initrd.img-6.14.0-10-generic 217s Warning: os-prober will not be executed to detect other bootable partitions. 217s Systems on them will not be added to the GRUB boot configuration. 217s Check GRUB_DISABLE_OS_PROBER documentation entry. 217s Adding boot menu entry for UEFI Firmware Settings ... 217s done 217s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 217s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 218s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 219s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 219s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 219s Processing triggers for libc-bin (2.41-1ubuntu1) ... 219s (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 ... 76972 files and directories currently installed.) 219s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 219s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 219s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 219s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 219s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 219s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 219s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 219s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 219s autopkgtest [01:37:55]: upgrading testbed (apt dist-upgrade and autopurge) 219s Reading package lists... 220s Building dependency tree... 220s Reading state information... 220s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 220s Starting 2 pkgProblemResolver with broken count: 0 220s Done 220s Entering ResolveByKeep 221s 221s Calculating upgrade... 221s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 221s Reading package lists... 221s Building dependency tree... 221s Reading state information... 221s Starting pkgProblemResolver with broken count: 0 221s Starting 2 pkgProblemResolver with broken count: 0 221s Done 222s Solving dependencies... 222s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 222s autopkgtest [01:37:58]: rebooting testbed after setup commands that affected boot 246s autopkgtest [01:38:22]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 249s autopkgtest [01:38:25]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 252s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2build1 (dsc) [2701 B] 252s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2build1 (tar) [22.0 MB] 252s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdtraj 1.10.3-2build1 (diff) [297 kB] 252s gpgv: Signature made Tue Mar 4 15:08:42 2025 UTC 252s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 252s gpgv: Can't check signature: No public key 252s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.10.3-2build1.dsc: no acceptable signature found 253s autopkgtest [01:38:29]: testing package mdtraj version 1.10.3-2build1 254s autopkgtest [01:38:30]: build not needed 258s autopkgtest [01:38:34]: test command1: preparing testbed 258s Reading package lists... 258s Building dependency tree... 258s Reading state information... 258s Starting pkgProblemResolver with broken count: 0 258s Starting 2 pkgProblemResolver with broken count: 0 258s Done 259s The following NEW packages will be installed: 259s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 259s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-4 libdeflate0 259s libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 259s libhdf5-310 libhdf5-hl-310 libimagequant0 libipt2 libjbig0 libjpeg-turbo8 259s libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 259s liblerc4 libnetcdf22 libnorm1t64 libopenjp2-7 libpgm-5.3-0t64 libqhull-r8.0 259s libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 libsource-highlight-common 259s libsource-highlight4t64 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 259s libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 259s python-matplotlib-data python-tables-data python3-asttokens python3-brotli 259s python3-cftime python3-comm python3-contourpy python3-coverage 259s python3-cpuinfo python3-cycler python3-dateutil python3-debugpy 259s python3-decorator python3-executing python3-fastjsonschema python3-fonttools 259s python3-fs python3-gsd python3-iniconfig python3-ipykernel python3-ipython 259s python3-jedi python3-joblib python3-jupyter-client python3-jupyter-core 259s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 259s python3-matplotlib-inline python3-mdtraj python3-mpmath python3-nbformat 259s python3-nest-asyncio python3-netcdf4 python3-networkx python3-numexpr 259s python3-numpy python3-numpy-dev python3-packaging python3-pandas 259s python3-pandas-lib python3-parso python3-pexpect python3-pil 259s python3-pil.imagetk python3-platformdirs python3-pluggy 259s python3-prompt-toolkit python3-psutil python3-ptyprocess python3-pure-eval 259s python3-pytest python3-pytz python3-scipy python3-sklearn 259s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 259s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 259s python3-traitlets python3-typeshed python3-tz python3-ufolib2 259s python3-unicodedata2 python3-wcwidth python3-zmq python3.12-tk python3.13-tk 259s tk8.6-blt2.5 unicode-data x11-common 259s 0 upgraded, 129 newly installed, 0 to remove and 0 not upgraded. 259s Need to get 120 MB of archives. 259s After this operation, 541 MB of additional disk space will be used. 259s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 259s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 259s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 259s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 259s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 260s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 260s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 260s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 260s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 260s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 260s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 260s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 260s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 260s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 260s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 260s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 260s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 260s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 260s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libbabeltrace1 amd64 1.5.11-4build2 [186 kB] 260s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libipt2 amd64 2.1.2-1 [58.9 kB] 260s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsource-highlight-common all 3.1.9-4.3build1 [64.2 kB] 260s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libsource-highlight4t64 amd64 3.1.9-4.3build1 [258 kB] 260s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gdb amd64 16.2-2ubuntu2 [4487 kB] 260s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 260s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB] 260s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblosc1 amd64 1.21.5+ds-1build1 [36.2 kB] 260s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblosc2-4 amd64 2.16.0+ds-1 [171 kB] 260s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 260s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 260s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 260s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 260s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 260s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 260s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 260s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 260s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 260s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 260s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 260s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 260s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 260s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 260s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 260s Get:43 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf22 amd64 1:4.9.3-1 [574 kB] 260s Get:44 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1build1 [154 kB] 260s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1build1 [167 kB] 260s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 260s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 260s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 260s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libsodium23 amd64 1.0.18-1build3 [161 kB] 260s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 260s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 260s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 260s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 260s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 260s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 260s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzmq5 amd64 4.3.5-1build2 [260 kB] 260s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 260s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-tables-data all 3.10.2-2build1 [49.7 kB] 260s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-asttokens all 3.0.0-1 [20.4 kB] 260s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 260s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cftime amd64 1.6.4-2 [233 kB] 260s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 260s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-comm all 0.2.1-1 [7016 B] 260s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 260s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-coverage amd64 7.6.0+dfsg1-2build1 [153 kB] 260s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cpuinfo all 9.0.0+git20221119-3 [21.7 kB] 261s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 261s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 261s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-debugpy amd64 1.8.8+ds-2ubuntu1 [1145 kB] 261s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 261s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-executing all 2.2.0-0.1 [25.0 kB] 261s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 261s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 261s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 261s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 261s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 261s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 262s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 262s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 262s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 262s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build3 [360 kB] 262s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 262s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 262s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-gsd amd64 3.4.2-2build1 [215 kB] 262s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 262s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-parso all 0.8.4-1 [67.6 kB] 262s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-typeshed all 0.0~git20241223.ea91db2-1 [1548 kB] 262s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 262s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 262s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wcwidth all 0.2.13+dfsg1-1 [26.3 kB] 262s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-prompt-toolkit all 3.0.50-1 [257 kB] 262s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pure-eval all 0.2.3-1 [11.4 kB] 262s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 262s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-ptyprocess all 0.7.0-6 [14.8 kB] 262s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pexpect all 4.9-3 [48.1 kB] 262s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipython all 8.30.0-2 [569 kB] 263s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 263s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-psutil amd64 5.9.8-2build3 [196 kB] 263s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tornado amd64 6.4.2-1 [299 kB] 263s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-zmq amd64 26.2.1-1build1 [191 kB] 263s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-jupyter-client all 8.6.3-2 [78.5 kB] 263s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nest-asyncio all 1.5.4-1 [6256 B] 263s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 263s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ipykernel all 6.29.5-2 [82.7 kB] 263s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.4.2-3 [205 kB] 263s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 263s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 263s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 263s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 263s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-2 [107 kB] 263s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 263s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 263s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 264s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-netcdf4 amd64 1.7.2-1build4 [667 kB] 264s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 264s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 264s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 264s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8build1 [5332 kB] 265s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 265s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numexpr amd64 2.10.2-1build2 [131 kB] 265s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tables-lib amd64 3.10.2-2build1 [588 kB] 265s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tables all 3.10.2-2build1 [354 kB] 265s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mdtraj amd64 1.10.3-2build1 [1126 kB] 265s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB] 265s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 265s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.5-1 [252 kB] 265s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 265s Get:128 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [4359 kB] 265s Get:129 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 265s Fetched 120 MB in 6s (19.2 MB/s) 265s Selecting previously unselected package python3-numpy-dev:amd64. 266s (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 ... 76968 files and directories currently installed.) 266s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 266s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 266s Selecting previously unselected package libblas3:amd64. 266s Preparing to unpack .../001-libblas3_3.12.1-2_amd64.deb ... 266s Unpacking libblas3:amd64 (3.12.1-2) ... 266s Selecting previously unselected package libgfortran5:amd64. 266s Preparing to unpack .../002-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 266s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 266s Selecting previously unselected package liblapack3:amd64. 266s Preparing to unpack .../003-liblapack3_3.12.1-2_amd64.deb ... 266s Unpacking liblapack3:amd64 (3.12.1-2) ... 266s Selecting previously unselected package python3-numpy. 266s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 266s Unpacking python3-numpy (1:2.2.3+ds-5) ... 266s Selecting previously unselected package libtcl8.6:amd64. 266s Preparing to unpack .../005-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 266s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 266s Selecting previously unselected package fonts-dejavu-mono. 266s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 266s Unpacking fonts-dejavu-mono (2.37-8) ... 266s Selecting previously unselected package fonts-dejavu-core. 266s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 266s Unpacking fonts-dejavu-core (2.37-8) ... 266s Selecting previously unselected package fontconfig-config. 266s Preparing to unpack .../008-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 266s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 266s Selecting previously unselected package libfontconfig1:amd64. 266s Preparing to unpack .../009-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 266s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 266s Selecting previously unselected package libxrender1:amd64. 266s Preparing to unpack .../010-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 266s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 266s Selecting previously unselected package libxft2:amd64. 266s Preparing to unpack .../011-libxft2_2.3.6-1build1_amd64.deb ... 266s Unpacking libxft2:amd64 (2.3.6-1build1) ... 266s Selecting previously unselected package x11-common. 266s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu3_all.deb ... 266s Unpacking x11-common (1:7.7+23ubuntu3) ... 266s Selecting previously unselected package libxss1:amd64. 266s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_amd64.deb ... 266s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 266s Selecting previously unselected package libtk8.6:amd64. 266s Preparing to unpack .../014-libtk8.6_8.6.16-1_amd64.deb ... 266s Unpacking libtk8.6:amd64 (8.6.16-1) ... 267s Selecting previously unselected package tk8.6-blt2.5. 267s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 267s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 267s Selecting previously unselected package blt. 267s Preparing to unpack .../016-blt_2.5.3+dfsg-8_amd64.deb ... 267s Unpacking blt (2.5.3+dfsg-8) ... 267s Selecting previously unselected package fonts-lyx. 267s Preparing to unpack .../017-fonts-lyx_2.4.3-1_all.deb ... 267s Unpacking fonts-lyx (2.4.3-1) ... 267s Selecting previously unselected package libbabeltrace1:amd64. 267s Preparing to unpack .../018-libbabeltrace1_1.5.11-4build2_amd64.deb ... 267s Unpacking libbabeltrace1:amd64 (1.5.11-4build2) ... 267s Selecting previously unselected package libipt2. 267s Preparing to unpack .../019-libipt2_2.1.2-1_amd64.deb ... 267s Unpacking libipt2 (2.1.2-1) ... 267s Selecting previously unselected package libsource-highlight-common. 267s Preparing to unpack .../020-libsource-highlight-common_3.1.9-4.3build1_all.deb ... 267s Unpacking libsource-highlight-common (3.1.9-4.3build1) ... 267s Selecting previously unselected package libsource-highlight4t64:amd64. 267s Preparing to unpack .../021-libsource-highlight4t64_3.1.9-4.3build1_amd64.deb ... 267s Unpacking libsource-highlight4t64:amd64 (3.1.9-4.3build1) ... 267s Selecting previously unselected package gdb. 267s Preparing to unpack .../022-gdb_16.2-2ubuntu2_amd64.deb ... 267s Unpacking gdb (16.2-2ubuntu2) ... 267s Selecting previously unselected package libaec0:amd64. 267s Preparing to unpack .../023-libaec0_1.1.3-1_amd64.deb ... 267s Unpacking libaec0:amd64 (1.1.3-1) ... 267s Selecting previously unselected package libsnappy1v5:amd64. 267s Preparing to unpack .../024-libsnappy1v5_1.2.1-1_amd64.deb ... 267s Unpacking libsnappy1v5:amd64 (1.2.1-1) ... 267s Selecting previously unselected package libblosc1:amd64. 267s Preparing to unpack .../025-libblosc1_1.21.5+ds-1build1_amd64.deb ... 267s Unpacking libblosc1:amd64 (1.21.5+ds-1build1) ... 267s Selecting previously unselected package libblosc2-4:amd64. 267s Preparing to unpack .../026-libblosc2-4_2.16.0+ds-1_amd64.deb ... 267s Unpacking libblosc2-4:amd64 (2.16.0+ds-1) ... 267s Selecting previously unselected package libdeflate0:amd64. 267s Preparing to unpack .../027-libdeflate0_1.23-1_amd64.deb ... 267s Unpacking libdeflate0:amd64 (1.23-1) ... 267s Selecting previously unselected package libgomp1:amd64. 267s Preparing to unpack .../028-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 267s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 267s Selecting previously unselected package libgraphite2-3:amd64. 267s Preparing to unpack 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267s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 267s Selecting previously unselected package libjpeg-turbo8:amd64. 267s Preparing to unpack .../035-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 267s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 267s Selecting previously unselected package libjpeg8:amd64. 267s Preparing to unpack .../036-libjpeg8_8c-2ubuntu11_amd64.deb ... 267s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 267s Selecting previously unselected package libjs-jquery. 267s Preparing to unpack .../037-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 267s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 267s Selecting previously unselected package libjs-jquery-ui. 267s Preparing to unpack .../038-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 267s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 267s Selecting previously unselected package liblbfgsb0:amd64. 267s Preparing to unpack .../039-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 267s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 267s Selecting previously unselected package liblcms2-2:amd64. 267s Preparing to unpack .../040-liblcms2-2_2.16-2_amd64.deb ... 267s Unpacking liblcms2-2:amd64 (2.16-2) ... 267s Selecting previously unselected package liblerc4:amd64. 267s Preparing to unpack .../041-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 267s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 267s Selecting previously unselected package libnetcdf22:amd64. 267s Preparing to unpack .../042-libnetcdf22_1%3a4.9.3-1_amd64.deb ... 267s Unpacking libnetcdf22:amd64 (1:4.9.3-1) ... 267s Selecting previously unselected package libnorm1t64:amd64. 267s Preparing to unpack .../043-libnorm1t64_1.5.9+dfsg-3.1build1_amd64.deb ... 267s Unpacking libnorm1t64:amd64 (1.5.9+dfsg-3.1build1) ... 267s Selecting previously unselected package libpgm-5.3-0t64:amd64. 267s Preparing to unpack .../044-libpgm-5.3-0t64_5.3.128~dfsg-2.1build1_amd64.deb ... 267s Unpacking libpgm-5.3-0t64:amd64 (5.3.128~dfsg-2.1build1) ... 267s Selecting previously unselected package libqhull-r8.0:amd64. 267s Preparing to unpack .../045-libqhull-r8.0_2020.2-6build1_amd64.deb ... 267s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 267s Selecting previously unselected package libraqm0:amd64. 267s Preparing to unpack .../046-libraqm0_0.10.2-1_amd64.deb ... 267s Unpacking libraqm0:amd64 (0.10.2-1) ... 267s Selecting previously unselected package libsharpyuv0:amd64. 267s Preparing to unpack .../047-libsharpyuv0_1.5.0-0.1_amd64.deb ... 267s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 267s Selecting previously unselected package libsodium23:amd64. 267s Preparing to unpack .../048-libsodium23_1.0.18-1build3_amd64.deb ... 267s Unpacking libsodium23:amd64 (1.0.18-1build3) ... 267s Selecting previously unselected package libjbig0:amd64. 267s Preparing to unpack .../049-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 267s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 267s Selecting previously unselected package libwebp7:amd64. 267s Preparing to unpack .../050-libwebp7_1.5.0-0.1_amd64.deb ... 267s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 268s Selecting previously unselected package libtiff6:amd64. 268s Preparing to unpack .../051-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 268s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 268s Selecting previously unselected package libwebpdemux2:amd64. 268s Preparing to unpack .../052-libwebpdemux2_1.5.0-0.1_amd64.deb ... 268s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 268s Selecting previously unselected package libwebpmux3:amd64. 268s Preparing to unpack .../053-libwebpmux3_1.5.0-0.1_amd64.deb ... 268s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 268s Selecting previously unselected package libxslt1.1:amd64. 268s Preparing to unpack .../054-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 268s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 268s Selecting previously unselected package libzmq5:amd64. 268s Preparing to unpack .../055-libzmq5_4.3.5-1build2_amd64.deb ... 268s Unpacking libzmq5:amd64 (4.3.5-1build2) ... 268s Selecting previously unselected package python-matplotlib-data. 268s Preparing to unpack .../056-python-matplotlib-data_3.8.3-7build1_all.deb ... 268s Unpacking python-matplotlib-data (3.8.3-7build1) ... 268s Selecting previously unselected package python-tables-data. 268s Preparing to unpack .../057-python-tables-data_3.10.2-2build1_all.deb ... 268s Unpacking python-tables-data (3.10.2-2build1) ... 268s Selecting previously unselected package python3-asttokens. 268s Preparing to unpack .../058-python3-asttokens_3.0.0-1_all.deb ... 268s Unpacking python3-asttokens (3.0.0-1) ... 268s Selecting previously unselected package python3-brotli. 268s Preparing to unpack .../059-python3-brotli_1.1.0-2build4_amd64.deb ... 268s Unpacking python3-brotli (1.1.0-2build4) ... 268s Selecting previously unselected package python3-cftime. 268s Preparing to unpack .../060-python3-cftime_1.6.4-2_amd64.deb ... 268s Unpacking python3-cftime (1.6.4-2) ... 268s Selecting previously unselected package python3-traitlets. 268s Preparing to unpack .../061-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 268s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 268s Selecting previously unselected package python3-comm. 268s Preparing to unpack .../062-python3-comm_0.2.1-1_all.deb ... 268s Unpacking python3-comm (0.2.1-1) ... 268s Selecting previously unselected package python3-contourpy. 268s Preparing to unpack .../063-python3-contourpy_1.3.1-1build1_amd64.deb ... 268s Unpacking python3-contourpy (1.3.1-1build1) ... 268s Selecting previously unselected package python3-coverage. 268s Preparing to unpack .../064-python3-coverage_7.6.0+dfsg1-2build1_amd64.deb ... 268s Unpacking python3-coverage (7.6.0+dfsg1-2build1) ... 268s Selecting previously unselected package python3-cpuinfo. 268s Preparing to unpack .../065-python3-cpuinfo_9.0.0+git20221119-3_all.deb ... 268s Unpacking python3-cpuinfo (9.0.0+git20221119-3) ... 268s Selecting previously unselected package python3-cycler. 268s Preparing to unpack .../066-python3-cycler_0.12.1-1_all.deb ... 268s Unpacking python3-cycler (0.12.1-1) ... 268s Selecting previously unselected package python3-dateutil. 268s Preparing to unpack .../067-python3-dateutil_2.9.0-3_all.deb ... 268s Unpacking python3-dateutil (2.9.0-3) ... 268s Selecting previously unselected package python3-debugpy. 268s Preparing to unpack .../068-python3-debugpy_1.8.8+ds-2ubuntu1_amd64.deb ... 268s Unpacking python3-debugpy (1.8.8+ds-2ubuntu1) ... 268s Selecting previously unselected package python3-decorator. 268s Preparing to unpack .../069-python3-decorator_5.1.1-5_all.deb ... 268s Unpacking python3-decorator (5.1.1-5) ... 268s Selecting previously unselected package python3-executing. 268s Preparing to unpack .../070-python3-executing_2.2.0-0.1_all.deb ... 268s Unpacking python3-executing (2.2.0-0.1) ... 268s Selecting previously unselected package python3-fastjsonschema. 268s Preparing to unpack .../071-python3-fastjsonschema_2.21.1-1_all.deb ... 268s Unpacking python3-fastjsonschema (2.21.1-1) ... 268s Selecting previously unselected package python3-platformdirs. 268s Preparing to unpack .../072-python3-platformdirs_4.3.6-1_all.deb ... 268s Unpacking python3-platformdirs (4.3.6-1) ... 268s Selecting previously unselected package python3-fs. 268s Preparing to unpack .../073-python3-fs_2.4.16-7_all.deb ... 268s Unpacking python3-fs (2.4.16-7) ... 268s Selecting previously unselected package python3-lxml:amd64. 268s Preparing to unpack .../074-python3-lxml_5.3.1-1build1_amd64.deb ... 268s Unpacking python3-lxml:amd64 (5.3.1-1build1) ... 268s Selecting previously unselected package python3-lz4. 268s Preparing to unpack .../075-python3-lz4_4.4.0+dfsg-1build1_amd64.deb ... 268s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 268s Selecting previously unselected package python3-scipy. 268s Preparing to unpack .../076-python3-scipy_1.14.1-4ubuntu2_amd64.deb ... 268s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 269s Selecting previously unselected package python3-mpmath. 269s Preparing to unpack .../077-python3-mpmath_1.3.0-1_all.deb ... 269s Unpacking python3-mpmath (1.3.0-1) ... 269s Selecting previously unselected package python3-sympy. 269s Preparing to unpack .../078-python3-sympy_1.13.3-5_all.deb ... 269s Unpacking python3-sympy (1.13.3-5) ... 269s Selecting previously unselected package python3-ufolib2. 269s Preparing to unpack .../079-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 269s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 269s Selecting previously unselected package python3-unicodedata2. 269s Preparing to unpack .../080-python3-unicodedata2_15.1.0+ds-1build3_amd64.deb ... 269s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 269s Selecting previously unselected package unicode-data. 269s Preparing to unpack .../081-unicode-data_15.1.0-1_all.deb ... 269s Unpacking unicode-data (15.1.0-1) ... 269s Selecting previously unselected package python3-fonttools. 269s Preparing to unpack .../082-python3-fonttools_4.55.3-2build1_amd64.deb ... 269s Unpacking python3-fonttools (4.55.3-2build1) ... 269s Selecting previously unselected package python3-gsd. 269s Preparing to unpack .../083-python3-gsd_3.4.2-2build1_amd64.deb ... 269s Unpacking python3-gsd (3.4.2-2build1) ... 269s Selecting previously unselected package python3-iniconfig. 269s Preparing to unpack .../084-python3-iniconfig_1.1.1-2_all.deb ... 269s Unpacking python3-iniconfig (1.1.1-2) ... 269s Selecting previously unselected package python3-parso. 269s Preparing to unpack .../085-python3-parso_0.8.4-1_all.deb ... 269s Unpacking python3-parso (0.8.4-1) ... 269s Selecting previously unselected package python3-typeshed. 269s Preparing to unpack .../086-python3-typeshed_0.0~git20241223.ea91db2-1_all.deb ... 269s Unpacking python3-typeshed (0.0~git20241223.ea91db2-1) ... 270s Selecting previously unselected package python3-jedi. 270s Preparing to unpack .../087-python3-jedi_0.19.1+ds1-1_all.deb ... 270s Unpacking python3-jedi (0.19.1+ds1-1) ... 270s Selecting previously unselected package python3-matplotlib-inline. 270s Preparing to unpack .../088-python3-matplotlib-inline_0.1.6-2_all.deb ... 270s Unpacking python3-matplotlib-inline (0.1.6-2) ... 270s Selecting previously unselected package python3-wcwidth. 270s Preparing to unpack .../089-python3-wcwidth_0.2.13+dfsg1-1_all.deb ... 270s Unpacking python3-wcwidth (0.2.13+dfsg1-1) ... 270s Selecting previously unselected package python3-prompt-toolkit. 270s Preparing to unpack .../090-python3-prompt-toolkit_3.0.50-1_all.deb ... 270s Unpacking python3-prompt-toolkit (3.0.50-1) ... 270s Selecting previously unselected package python3-pure-eval. 270s Preparing to unpack .../091-python3-pure-eval_0.2.3-1_all.deb ... 270s Unpacking python3-pure-eval (0.2.3-1) ... 270s Selecting previously unselected package python3-stack-data. 270s Preparing to unpack .../092-python3-stack-data_0.6.3-1_all.deb ... 270s Unpacking python3-stack-data (0.6.3-1) ... 270s Selecting previously unselected package python3-ptyprocess. 270s Preparing to unpack .../093-python3-ptyprocess_0.7.0-6_all.deb ... 270s Unpacking python3-ptyprocess (0.7.0-6) ... 270s Selecting previously unselected package python3-pexpect. 270s Preparing to unpack .../094-python3-pexpect_4.9-3_all.deb ... 270s Unpacking python3-pexpect (4.9-3) ... 270s Selecting previously unselected package python3-ipython. 270s Preparing to unpack .../095-python3-ipython_8.30.0-2_all.deb ... 270s Unpacking python3-ipython (8.30.0-2) ... 271s Selecting previously unselected package python3-jupyter-core. 271s Preparing to unpack .../096-python3-jupyter-core_5.7.2-5_all.deb ... 271s Unpacking python3-jupyter-core (5.7.2-5) ... 271s Selecting previously unselected package python3-psutil. 271s Preparing to unpack .../097-python3-psutil_5.9.8-2build3_amd64.deb ... 271s Unpacking python3-psutil (5.9.8-2build3) ... 271s Selecting previously unselected package python3-tornado. 271s Preparing to unpack .../098-python3-tornado_6.4.2-1_amd64.deb ... 271s Unpacking python3-tornado (6.4.2-1) ... 271s Selecting previously unselected package python3-zmq. 271s Preparing to unpack .../099-python3-zmq_26.2.1-1build1_amd64.deb ... 271s Unpacking python3-zmq (26.2.1-1build1) ... 271s Selecting previously unselected package python3-jupyter-client. 271s Preparing to unpack .../100-python3-jupyter-client_8.6.3-2_all.deb ... 271s Unpacking python3-jupyter-client (8.6.3-2) ... 271s Selecting previously unselected package python3-nest-asyncio. 271s Preparing to unpack .../101-python3-nest-asyncio_1.5.4-1_all.deb ... 271s Unpacking python3-nest-asyncio (1.5.4-1) ... 271s Selecting previously unselected package python3-packaging. 271s Preparing to unpack .../102-python3-packaging_24.2-1_all.deb ... 271s Unpacking python3-packaging (24.2-1) ... 271s Selecting previously unselected package python3-ipykernel. 271s Preparing to unpack .../103-python3-ipykernel_6.29.5-2_all.deb ... 271s Unpacking python3-ipykernel (6.29.5-2) ... 271s Selecting previously unselected package python3-joblib. 271s Preparing to unpack .../104-python3-joblib_1.4.2-3_all.deb ... 271s Unpacking python3-joblib (1.4.2-3) ... 271s Selecting previously unselected package python3-kiwisolver. 271s Preparing to unpack .../105-python3-kiwisolver_1.4.7-3build1_amd64.deb ... 271s Unpacking python3-kiwisolver (1.4.7-3build1) ... 271s Selecting previously unselected package libopenjp2-7:amd64. 271s Preparing to unpack .../106-libopenjp2-7_2.5.3-2_amd64.deb ... 271s Unpacking libopenjp2-7:amd64 (2.5.3-2) ... 271s Selecting previously unselected package python3-pil:amd64. 271s Preparing to unpack .../107-python3-pil_11.1.0-5build1_amd64.deb ... 271s Unpacking python3-pil:amd64 (11.1.0-5build1) ... 271s Selecting previously unselected package python3.12-tk. 271s Preparing to unpack .../108-python3.12-tk_3.12.9-1_amd64.deb ... 271s Unpacking python3.12-tk (3.12.9-1) ... 271s Selecting previously unselected package python3.13-tk. 271s Preparing to unpack .../109-python3.13-tk_3.13.2-2_amd64.deb ... 271s Unpacking python3.13-tk (3.13.2-2) ... 271s Selecting previously unselected package python3-tk:amd64. 271s Preparing to unpack .../110-python3-tk_3.13.1-1_amd64.deb ... 271s Unpacking python3-tk:amd64 (3.13.1-1) ... 271s Selecting previously unselected package python3-pil.imagetk:amd64. 271s Preparing to unpack .../111-python3-pil.imagetk_11.1.0-5build1_amd64.deb ... 271s Unpacking python3-pil.imagetk:amd64 (11.1.0-5build1) ... 271s Selecting previously unselected package python3-matplotlib. 271s Preparing to unpack .../112-python3-matplotlib_3.8.3-7build1_amd64.deb ... 271s Unpacking python3-matplotlib (3.8.3-7build1) ... 271s Selecting previously unselected package python3-netcdf4. 271s Preparing to unpack .../113-python3-netcdf4_1.7.2-1build4_amd64.deb ... 271s Unpacking python3-netcdf4 (1.7.2-1build4) ... 271s Selecting previously unselected package python3-networkx. 272s Preparing to unpack .../114-python3-networkx_3.2.1-4ubuntu1_all.deb ... 272s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 272s Selecting previously unselected package python3-pytz. 272s Preparing to unpack .../115-python3-pytz_2025.1-3_all.deb ... 272s Unpacking python3-pytz (2025.1-3) ... 272s Selecting previously unselected package python3-tz. 272s Preparing to unpack .../116-python3-tz_2025.1-3_all.deb ... 272s Unpacking python3-tz (2025.1-3) ... 272s Selecting previously unselected package python3-pandas-lib:amd64. 272s Preparing to unpack .../117-python3-pandas-lib_2.2.3+dfsg-8build1_amd64.deb ... 272s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8build1) ... 272s Selecting previously unselected package python3-pandas. 272s Preparing to unpack .../118-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 272s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 273s Selecting previously unselected package python3-numexpr. 273s Preparing to unpack .../119-python3-numexpr_2.10.2-1build2_amd64.deb ... 273s Unpacking python3-numexpr (2.10.2-1build2) ... 273s Selecting previously unselected package python3-tables-lib. 273s Preparing to unpack .../120-python3-tables-lib_3.10.2-2build1_amd64.deb ... 273s Unpacking python3-tables-lib (3.10.2-2build1) ... 273s Selecting previously unselected package python3-tables. 273s Preparing to unpack .../121-python3-tables_3.10.2-2build1_all.deb ... 273s Unpacking python3-tables (3.10.2-2build1) ... 273s Selecting previously unselected package python3-mdtraj. 273s Preparing to unpack .../122-python3-mdtraj_1.10.3-2build1_amd64.deb ... 273s Unpacking python3-mdtraj (1.10.3-2build1) ... 273s Selecting previously unselected package python3-nbformat. 273s Preparing to unpack .../123-python3-nbformat_5.9.1-1_all.deb ... 273s Unpacking python3-nbformat (5.9.1-1) ... 273s Selecting previously unselected package python3-pluggy. 273s Preparing to unpack .../124-python3-pluggy_1.5.0-1_all.deb ... 273s Unpacking python3-pluggy (1.5.0-1) ... 273s Selecting previously unselected package python3-pytest. 273s Preparing to unpack .../125-python3-pytest_8.3.5-1_all.deb ... 273s Unpacking python3-pytest (8.3.5-1) ... 273s Selecting previously unselected package python3-threadpoolctl. 273s Preparing to unpack .../126-python3-threadpoolctl_3.1.0-1_all.deb ... 273s Unpacking python3-threadpoolctl (3.1.0-1) ... 273s Selecting previously unselected package python3-sklearn-lib:amd64. 273s Preparing to unpack .../127-python3-sklearn-lib_1.4.2+dfsg-8_amd64.deb ... 273s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 273s Selecting previously unselected package python3-sklearn. 273s Preparing to unpack .../128-python3-sklearn_1.4.2+dfsg-8_all.deb ... 273s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 273s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 273s Setting up liblcms2-2:amd64 (2.16-2) ... 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297s Processing triggers for man-db (2.13.0-1) ... 298s autopkgtest [01:39:14]: test command1: pytest-3 -k 'not (nmr.ipynb or test_image_molecules) and not (test_3 or test_pdb_from_url or test_1vii_url_and_gz)' 298s autopkgtest [01:39:14]: test command1: [----------------------- 299s ============================= test session starts ============================== 299s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3 299s cachedir: .pytest_cache 299s rootdir: /tmp/autopkgtest.WsEzHt/build.l8U/src 299s configfile: pyproject.toml 299s testpaths: tests, examples 299s plugins: typeguard-4.4.2 300s collecting ... collected 1145 items / 12 deselected / 1133 selected 300s 300s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 300s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 300s tests/test_alignment.py::test_transform PASSED [ 0%] 300s tests/test_alignment.py::test_transform2 PASSED [ 0%] 301s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 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tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.standard_dimensions] PASSED [ 12%] 307s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit] SKIPPED [ 12%] 307s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_definitions] SKIPPED [ 12%] 307s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_math] SKIPPED [ 12%] 307s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_operators] SKIPPED [ 12%] 307s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unitcell] PASSED [ 12%] 307s tests/test_docstrings.py::test_docstrings[mdtraj.utils.validation] PASSED [ 12%] 307s tests/test_docstrings.py::test_docstrings[mdtraj.utils.zipped] PASSED [ 12%] 307s tests/test_drid.py::test_drid_1 PASSED [ 13%] 307s tests/test_drid.py::test_drid_2 PASSED [ 13%] 307s tests/test_dssp.py::test_1[1bpi.pdb] PASSED [ 13%] 307s tests/test_dssp.py::test_1[1vii.pdb] PASSED [ 13%] 307s tests/test_dssp.py::test_1[4ZUO.pdb] PASSED [ 13%] 307s tests/test_dssp.py::test_1[1am7_protein.pdb] PASSED [ 13%] 307s tests/test_dssp.py::test_2[2EQQ.pdb] PASSED [ 13%] 307s tests/test_dssp.py::test_4 PASSED [ 13%] 307s tests/test_dssp.py::test_5 PASSED [ 13%] 307s tests/test_dssp.py::test_7 PASSED [ 13%] 307s tests/test_dtr.py::test_read PASSED [ 13%] 307s tests/test_dtr.py::test_read_1 PASSED [ 14%] 307s tests/test_dtr.py::test_read_2 PASSED [ 14%] 307s tests/test_dtr.py::test_read_3 PASSED [ 14%] 307s tests/test_dtr.py::test_read_stride PASSED [ 14%] 307s tests/test_dtr.py::test_read_4 PASSED [ 14%] 307s tests/test_dtr.py::test_read_5 PASSED [ 14%] 307s tests/test_dtr.py::test_read_6 PASSED [ 14%] 307s tests/test_dtr.py::test_read_7 PASSED [ 14%] 307s tests/test_dtr.py::test_read_8 PASSED [ 14%] 308s tests/test_dtr.py::test_write_1 PASSED [ 14%] 310s tests/test_dtr.py::test_write_2 PASSED [ 14%] 310s tests/test_dtr.py::test_write_3 PASSED [ 15%] 310s tests/test_dtr.py::test_write_4 PASSED [ 15%] 310s tests/test_dtr.py::test_seek PASSED 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tests/test_geometry.py::test_angle_triclinic_0 PASSED [ 16%] 310s tests/test_geometry.py::test_angle_1 PASSED [ 16%] 310s tests/test_geometry.py::test_dihedral_performance SKIPPED (Not doing...) [ 16%] 310s tests/test_geometry.py::test_angle_performance SKIPPED (Not doing pe...) 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[ 20%] 316s tests/test_hdf5.py::test_topology PASSED [ 20%] 316s tests/test_hdf5.py::test_constraints PASSED [ 20%] 316s tests/test_hdf5.py::test_constraints2 PASSED [ 20%] 316s tests/test_hdf5.py::test_read_0 PASSED [ 20%] 316s tests/test_hdf5.py::test_read_1 SKIPPED (requires openmm.units) [ 20%] 316s tests/test_hdf5.py::test_read_slice_0 PASSED [ 20%] 316s tests/test_hdf5.py::test_read_slice_1 PASSED [ 20%] 316s tests/test_hdf5.py::test_read_slice_2 PASSED [ 20%] 316s tests/test_hdf5.py::test_read_slice_3 PASSED [ 20%] 316s tests/test_hdf5.py::test_do_overwrite PASSED [ 21%] 316s tests/test_hdf5.py::test_vsite_elements PASSED [ 21%] 316s tests/test_hdf5.py::test_dont_overwrite PASSED [ 21%] 316s tests/test_hdf5.py::test_attributes PASSED [ 21%] 316s tests/test_hdf5.py::test_append PASSED [ 21%] 318s tests/test_hoomdxml.py::test_load PASSED [ 21%] 318s tests/test_hoomdxml.py::test_load_no_chains PASSED [ 21%] 318s tests/test_hoomdxml.py::test_load_no_ions PASSED [ 21%] 318s tests/test_hoomdxml.py::test_correct_ordering PASSED [ 21%] 318s tests/test_io.py::test_overwrite_1 PASSED [ 21%] 318s tests/test_io.py::test_overwrite_2 PASSED [ 21%] 318s tests/test_io.py::test_io::test_load_1 PASSED [ 21%] 318s tests/test_io.py::test_io::test_load_2 PASSED [ 22%] 318s tests/test_io.py::test_io::test_load_3 PASSED [ 22%] 318s tests/test_io.py::test_io::test_save PASSED [ 22%] 318s tests/test_io.py::test_io_int::test_load_1 PASSED [ 22%] 318s tests/test_io.py::test_io_int::test_load_2 PASSED [ 22%] 318s tests/test_io.py::test_io_int::test_load_3 PASSED [ 22%] 318s tests/test_io.py::test_io_int::test_save PASSED [ 22%] 318s tests/test_io.py::test_groups PASSED [ 22%] 318s tests/test_lammpstrj.py::test_read_0 PASSED [ 22%] 318s tests/test_lammpstrj.py::test_read_1 PASSED [ 22%] 318s tests/test_lammpstrj.py::test_read_write_0 PASSED [ 22%] 318s tests/test_lammpstrj.py::test_mdwrite PASSED [ 23%] 318s tests/test_lammpstrj.py::test_multiread PASSED [ 23%] 318s tests/test_lammpstrj.py::test_seek PASSED [ 23%] 318s tests/test_lammpstrj.py::test_custom PASSED [ 23%] 318s tests/test_lh5.py::test_write_coordinates PASSED [ 23%] 318s tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 23%] 318s tests/test_lh5.py::test_write_multiple PASSED [ 23%] 318s tests/test_lh5.py::test_topology PASSED [ 23%] 318s tests/test_lh5.py::test_read_slice_0 PASSED [ 23%] 318s tests/test_lh5.py::test_vsite_elements PASSED [ 23%] 318s tests/test_lh5.py::test_do_overwrite_0 PASSED [ 23%] 318s tests/test_lh5.py::test_do_overwrite_1 PASSED [ 24%] 319s tests/test_load.py::test_load_single PASSED [ 24%] 319s tests/test_load.py::test_load_single_top_none PASSED [ 24%] 319s tests/test_load.py::test_load_single_list PASSED [ 24%] 319s tests/test_load.py::test_load_many_list PASSED [ 24%] 319s tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 24%] 319s tests/test_lprmsd.py::test_munkres_0 PASSED [ 24%] 319s tests/test_lprmsd.py::test_lprmsd_null PASSED [ 24%] 319s tests/test_lprmsd.py::test_lprmsd_0 PASSED [ 24%] 319s tests/test_lprmsd.py::test_lprmsd_1 PASSED [ 24%] 319s tests/test_lprmsd.py::test_lprmsd_2 PASSED [ 24%] 319s tests/test_lprmsd.py::test_lprmsd_3 PASSED [ 24%] 319s tests/test_lprmsd.py::test_lprmsd_4 PASSED [ 25%] 319s tests/test_lprmsd.py::test_lprmsd_5 PASSED [ 25%] 320s tests/test_mdconvert.py::test_index PASSED [ 25%] 320s tests/test_mdconvert.py::test_slice PASSED [ 25%] 329s tests/test_mdconvert.py::test_pairwise[from-xtc] PASSED [ 25%] 338s tests/test_mdconvert.py::test_pairwise[from-dcd] PASSED [ 25%] 347s tests/test_mdconvert.py::test_pairwise[from-trr] PASSED [ 25%] 366s tests/test_mdconvert.py::test_pairwise[from-nc] PASSED [ 25%] 375s tests/test_mdconvert.py::test_pairwise[from-pdb] PASSED [ 25%] 385s tests/test_mdconvert.py::test_pairwise[from-h5] PASSED [ 25%] 395s tests/test_mdconvert.py::test_pairwise[from-lh5] PASSED [ 25%] 404s tests/test_mdconvert.py::test_pairwise[from-netcdf] PASSED [ 26%] 404s tests/test_mdcrd.py::test_read_0 PASSED [ 26%] 404s tests/test_mdcrd.py::test_read_1 PASSED [ 26%] 404s tests/test_mdcrd.py::test_read_write_0 PASSED [ 26%] 404s tests/test_mdcrd.py::test_read_write_1 PASSED [ 26%] 404s tests/test_mdcrd.py::test_read_write_2 PASSED [ 26%] 404s tests/test_mdcrd.py::test_multiread PASSED [ 26%] 404s tests/test_mdcrd.py::test_seek PASSED [ 26%] 404s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 26%] 404s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 404s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 404s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 27%] 404s tests/test_mol2.py::test_mol2_dataframe PASSED [ 27%] 404s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 27%] 404s tests/test_mol2.py::test_mol2_warnings PASSED [ 27%] 404s tests/test_mol2.py::test_mol2_status_bits PASSED [ 27%] 404s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 27%] 404s tests/test_mol2.py::test_mol2_element_name PASSED [ 27%] 404s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 27%] 404s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 27%] 404s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 27%] 404s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 27%] 404s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 404s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 28%] 404s tests/test_mol2.py::test_mol2_n_residues PASSED [ 28%] 404s tests/test_neighborlist.py::test_nonperiodic PASSED [ 28%] 404s tests/test_neighborlist.py::test_periodic PASSED [ 28%] 405s tests/test_neighborlist.py::test_triclinic PASSED [ 28%] 405s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 28%] 405s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 28%] 406s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 28%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_after_close PASSED [ 28%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_shape PASSED [ 28%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_1 PASSED [ 28%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_2 PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_chunk_3 PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_1 PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_2 PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_1 PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_ragged_2 PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_read_write_25 PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_write_3 PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_n_atoms PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_overwrite PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_do_not_overwrite PASSED [ 29%] 406s tests/test_netcdf.py::TestNetCDFNetCDF4::test_trajectory_save_load PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_read_after_close PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_shape PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_1 PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_2 PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_read_chunk_3 PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_1 PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_2 PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_1 PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_ragged_2 PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_read_write_25 PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_write_3 PASSED [ 30%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_n_atoms PASSED [ 31%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_do_overwrite PASSED [ 31%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_do_not_overwrite PASSED [ 31%] 406s tests/test_netcdf.py::TestNetCDFScipy::test_trajectory_save_load PASSED [ 31%] 406s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 31%] 406s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 31%] 406s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 31%] 406s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 31%] 406s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 31%] 406s tests/test_order.py::test_nematic_order PASSED [ 31%] 406s tests/test_order.py::test_director PASSED [ 31%] 406s tests/test_order.py::test_inertia PASSED [ 32%] 406s tests/test_order.py::test_nematic_order_args PASSED [ 32%] 406s tests/test_order.py::test_order_from_traj PASSED [ 32%] 406s tests/test_order.py::test_directors_angle_from_traj PASSED [ 32%] 406s tests/test_pdb.py::test_pdbread PASSED [ 32%] 406s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 32%] 406s tests/test_pdb.py::test_pdbwrite PASSED [ 32%] 406s tests/test_pdb.py::test_load_multiframe PASSED [ 32%] 407s tests/test_pdb.py::test_4ZUO PASSED [ 32%] 407s tests/test_pdb.py::test_2EQQ_0 PASSED [ 32%] 408s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 32%] 408s tests/test_pdb.py::test_write_large PASSED [ 33%] 408s tests/test_pdb.py::test_write_large_2 PASSED [ 33%] 408s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 33%] 408s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 33%] 408s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 33%] 408s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 33%] 408s tests/test_pdb.py::test_1ncw PASSED [ 33%] 408s tests/test_pdb.py::test_segment_id PASSED [ 33%] 408s tests/test_pdb.py::test_bfactors PASSED [ 33%] 409s tests/test_pdb.py::test_hex PASSED [ 33%] 410s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 33%] 410s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 33%] 410s tests/test_pdb.py::test_multichain_load_cycle_noter PASSED [ 34%] 410s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 34%] 410s tests/test_pdb.py::test_chimera_indexing PASSED [ 34%] 410s tests/test_pdb.py::test_chimera_indexing_skip PASSED [ 34%] 410s tests/test_pdb.py::test_vmd_indexing PASSED [ 34%] 410s tests/test_pdb.py::test_overflow_indexing PASSED [ 34%] 410s tests/test_pdb.py::test_blank_indexing PASSED [ 34%] 410s tests/test_pdb.py::test_pdb_charge_read PASSED [ 34%] 410s tests/test_pdb.py::test_pdb_charge_write PASSED [ 34%] 410s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 34%] 410s tests/test_prmtop.py::test_load_prmtop PASSED [ 34%] 410s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 35%] 410s tests/test_psf.py::test_load_psf PASSED [ 35%] 413s tests/test_psf.py::test_multichain_psf PASSED [ 35%] 413s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 35%] 413s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 35%] 413s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 35%] 413s tests/test_quaternion.py::test_quaternion_0 PASSED [ 35%] 413s tests/test_quaternion.py::test_quaternion_1 PASSED [ 35%] 413s tests/test_quaternion.py::test_quaternion_2 PASSED [ 35%] 415s tests/test_rdf.py::test_rdf_norm PASSED [ 35%] 415s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 35%] 415s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 36%] 419s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 36%] 419s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 36%] 419s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 36%] 419s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 36%] 420s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 36%] 420s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 36%] 420s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 36%] 421s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 36%] 421s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 36%] 421s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 36%] 421s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 36%] 421s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 37%] 421s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 37%] 422s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 37%] 422s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 37%] 422s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 37%] 422s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 37%] 422s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 37%] 422s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 37%] 422s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 37%] 422s tests/test_restart.py::test_read_after_close PASSED [ 37%] 422s tests/test_restart.py::test_shape PASSED [ 37%] 422s tests/test_restart.py::test_shape_2 PASSED [ 38%] 422s tests/test_restart.py::test_read_write_1 PASSED [ 38%] 422s tests/test_restart.py::test_read_write_2 PASSED [ 38%] 422s tests/test_restart.py::test_read_write_3 PASSED [ 38%] 422s tests/test_restart.py::test_read_write_4 PASSED [ 38%] 422s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 38%] 422s tests/test_rmsd.py::test_precentered_1 PASSED [ 38%] 422s tests/test_rmsd.py::test_precentered_2 PASSED [ 38%] 422s tests/test_rmsd.py::test_superpose_0 PASSED [ 38%] 422s tests/test_rmsd.py::test_superpose_1 PASSED [ 38%] 422s tests/test_rmsd.py::test_superpose_2 PASSED [ 38%] 422s tests/test_rmsd.py::test_superpose_refinds PASSED [ 39%] 423s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 39%] 423s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 39%] 423s tests/test_rmsd.py::test_average_structure PASSED [ 39%] 423s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 39%] 423s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 39%] 423s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 39%] 423s tests/test_rmsd_memmap.py::test_1 PASSED [ 39%] 423s tests/test_rmsd_memmap.py::test_2 PASSED [ 39%] 423s tests/test_sasa.py::test_sasa_0 PASSED [ 39%] 423s tests/test_sasa.py::test_sasa_1 PASSED [ 39%] 423s tests/test_sasa.py::test_sasa_2 PASSED [ 39%] 423s tests/test_sasa.py::test_sasa_3 PASSED [ 40%] 424s tests/test_sasa.py::test_sasa_4 PASSED [ 40%] 424s tests/test_sasa.py::test_sasa_5 PASSED [ 40%] 424s tests/test_sasa.py::test_sasa_6 PASSED [ 40%] 425s tests/test_sasa.py::test_sasa_7 PASSED [ 40%] 425s tests/test_selection.py::test_range PASSED [ 40%] 425s tests/test_selection.py::test_unary_2 PASSED [ 40%] 425s tests/test_selection.py::test_unary_3 PASSED [ 40%] 425s tests/test_selection.py::test_binary_1 PASSED [ 40%] 425s tests/test_selection.py::test_binary_2 PASSED [ 40%] 425s tests/test_selection.py::test_simple PASSED [ 40%] 425s tests/test_selection.py::test_alias PASSED [ 41%] 425s tests/test_selection.py::test_unary_1 PASSED [ 41%] 425s tests/test_selection.py::test_binary_selection_operator PASSED [ 41%] 425s tests/test_selection.py::test_raises PASSED [ 41%] 425s tests/test_selection.py::test_raises2 PASSED [ 41%] 425s tests/test_selection.py::test_bool PASSED [ 41%] 425s tests/test_selection.py::test_nested_bool PASSED [ 41%] 425s tests/test_selection.py::test_values PASSED [ 41%] 425s tests/test_selection.py::test_element PASSED [ 41%] 425s tests/test_selection.py::test_not PASSED [ 41%] 425s tests/test_selection.py::test_re PASSED [ 41%] 425s tests/test_selection.py::test_within SKIPPED (failed to parse selection) [ 42%] 425s tests/test_selection.py::test_quotes PASSED [ 42%] 425s tests/test_selection.py::test_top PASSED [ 42%] 425s tests/test_selection.py::test_top_2 PASSED [ 42%] 425s tests/test_selection.py::test_backbone PASSED [ 42%] 425s tests/test_selection.py::test_sidechain PASSED [ 42%] 425s tests/test_selection.py::test_literal PASSED [ 42%] 425s tests/test_selection.py::test_in PASSED [ 42%] 425s tests/test_shape.py::test_gyration PASSED [ 42%] 426s tests/test_shape.py::test_principal_moments PASSED [ 42%] 426s tests/test_shape.py::test_asphericity PASSED [ 42%] 426s tests/test_shape.py::test_shape_metrics PASSED [ 42%] 426s tests/test_thermodynamic_properties.py::test_volume PASSED [ 43%] 426s tests/test_thermodynamic_properties.py::test_density PASSED [ 43%] 426s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 43%] 426s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 43%] 426s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 43%] 426s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 43%] 426s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 43%] 426s tests/test_topology.py::test_topology_openmm_preserve_chain_id_when_specified SKIPPED [ 43%] 426s tests/test_topology.py::test_topology_openmm_roundtrip_chain_id SKIPPED [ 43%] 426s tests/test_topology.py::test_topology_openmm_preserve_chain_id_even_when_empty SKIPPED [ 43%] 426s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 43%] 426s tests/test_topology.py::test_topology_openmm_formal_charges SKIPPED [ 44%] 426s tests/test_topology.py::test_topology_pandas PASSED [ 44%] 426s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 44%] 426s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 44%] 426s tests/test_topology.py::test_topology_numbers PASSED [ 44%] 426s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 44%] 426s tests/test_topology.py::test_chain PASSED [ 44%] 426s tests/test_topology.py::test_residue PASSED [ 44%] 426s tests/test_topology.py::test_segment_id PASSED [ 44%] 426s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 44%] 426s tests/test_topology.py::test_pickle PASSED [ 44%] 426s tests/test_topology.py::test_atoms_by_name PASSED [ 45%] 426s tests/test_topology.py::test_select_atom_indices PASSED [ 45%] 426s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 45%] 426s tests/test_topology.py::test_n_bonds PASSED [ 45%] 426s tests/test_topology.py::test_load_unknown_topology PASSED [ 45%] 426s tests/test_topology.py::test_unique_pairs PASSED [ 45%] 427s tests/test_topology.py::test_select_pairs PASSED [ 45%] 427s tests/test_topology.py::test_to_fasta PASSED [ 45%] 427s tests/test_topology.py::test_subset PASSED [ 45%] 427s tests/test_topology.py::test_subset_re_index_residues PASSED [ 45%] 427s tests/test_topology.py::test_molecules PASSED [ 45%] 427s tests/test_topology.py::test_copy_and_hash PASSED [ 45%] 427s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 46%] 427s tests/test_topology.py::test_topology_join PASSED [ 46%] 428s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 46%] 428s tests/test_trajectory.py::test_mismatch PASSED [ 46%] 428s tests/test_trajectory.py::test_box PASSED [ 46%] 428s tests/test_trajectory.py::test_load_pdb_box PASSED [ 46%] 428s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 46%] 428s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 46%] 428s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 46%] 428s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 46%] 428s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 46%] 428s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 47%] 428s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 47%] 428s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 47%] 428s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 47%] 428s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 47%] 428s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 47%] 428s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 47%] 428s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 47%] 428s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 47%] 428s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 47%] 428s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 47%] 428s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 48%] 428s tests/test_trajectory.py::test_slice PASSED [ 48%] 428s tests/test_trajectory.py::test_slice2 PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[nc] PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[h5] PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[trr] PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 48%] 428s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 49%] 428s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 49%] 428s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 49%] 428s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 49%] 428s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 49%] 428s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 49%] 428s tests/test_trajectory.py::test_read_path[gro] PASSED [ 49%] 428s tests/test_trajectory.py::test_write_path[nc] PASSED [ 49%] 428s tests/test_trajectory.py::test_write_path[h5] PASSED [ 49%] 428s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 49%] 428s tests/test_trajectory.py::test_write_path[trr] PASSED [ 49%] 428s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 50%] 428s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 50%] 428s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 50%] 429s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 50%] 429s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 50%] 429s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 50%] 429s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 50%] 429s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 50%] 429s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 50%] 429s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 50%] 429s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 50%] 429s tests/test_trajectory.py::test_write_path[gro] PASSED [ 51%] 429s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 51%] 429s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 51%] 429s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 51%] 429s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 51%] 429s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 51%] 429s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 51%] 431s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 51%] 431s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 51%] 431s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 51%] 431s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 51%] 431s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 51%] 432s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 52%] 432s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 52%] 432s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 52%] 432s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 52%] 432s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 52%] 432s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 52%] 432s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 52%] 432s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 52%] 432s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 52%] 432s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 52%] 432s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 52%] 433s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 53%] 434s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 53%] 434s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 53%] 434s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 53%] 434s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 53%] 434s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 53%] 434s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 53%] 434s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 53%] 434s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 53%] 434s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 53%] 434s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 53%] 435s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 54%] 435s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 54%] 435s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 54%] 435s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 54%] 435s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 54%] 436s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 54%] 436s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 54%] 436s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 54%] 436s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 54%] 436s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 54%] 436s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 54%] 436s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 54%] 436s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 55%] 436s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 55%] 437s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 55%] 437s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 55%] 437s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 55%] 437s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 55%] 437s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 55%] 437s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 55%] 437s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 55%] 438s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 55%] 438s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 55%] 438s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 56%] 438s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 56%] 438s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 56%] 438s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 56%] 438s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 56%] 438s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 56%] 438s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 56%] 438s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 56%] 438s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 56%] 438s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 56%] 438s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 56%] 438s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 57%] 438s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 57%] 438s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 57%] 439s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 57%] 439s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 57%] 440s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 57%] 440s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 57%] 440s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 57%] 440s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 57%] 440s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 57%] 440s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 57%] 440s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 57%] 440s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 58%] 440s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 58%] 441s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 59%] 441s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 59%] 442s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 59%] 442s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 59%] 442s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 59%] 442s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 59%] 442s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 59%] 442s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 59%] 442s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 59%] 442s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 59%] 442s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 59%] 442s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 60%] 443s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 60%] 443s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 60%] 443s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 60%] 444s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 60%] 444s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 60%] 444s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 60%] 444s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 60%] 444s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 60%] 444s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 60%] 444s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 60%] 444s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 60%] 444s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 61%] 444s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 61%] 444s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 61%] 444s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 61%] 444s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 61%] 444s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 61%] 444s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 61%] 445s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 61%] 445s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 61%] 445s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 61%] 445s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 61%] 445s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 62%] 445s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 63%] 445s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 63%] 446s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 63%] 446s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 63%] 446s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 63%] 446s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 63%] 446s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 63%] 446s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 63%] 446s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 63%] 446s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 63%] 446s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 63%] 446s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 63%] 446s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 64%] 447s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 64%] 447s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 64%] 447s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 64%] 448s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 64%] 448s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 64%] 448s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 64%] 448s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 64%] 448s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 64%] 448s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 64%] 448s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 64%] 448s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 65%] 448s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 65%] 448s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 65%] 448s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 448s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 449s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 449s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 449s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 449s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 449s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 449s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 449s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 66%] 449s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 66%] 449s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 449s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 449s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 449s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 449s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 449s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 450s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 450s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 450s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 450s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 450s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 67%] 451s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 451s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 452s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 452s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 452s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 452s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 453s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 453s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 453s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 453s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 453s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 68%] 453s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 453s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 453s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 453s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 453s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 454s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 455s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 455s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 455s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 455s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 456s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 69%] 456s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 456s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 456s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 456s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 456s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 456s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 456s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 456s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 456s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 456s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 456s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 456s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 456s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 456s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 457s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 457s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 457s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 457s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 457s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 457s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 457s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 457s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 457s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 71%] 457s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 457s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 457s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 457s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 457s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 457s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 457s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 457s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 457s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 458s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 458s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 72%] 458s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 72%] 458s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 458s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 459s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 459s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 459s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 459s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 459s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 459s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 459s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 459s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 459s tests/test_trajectory.py::test_load[trr] PASSED [ 73%] 459s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 459s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 459s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 459s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 460s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 460s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 460s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 461s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 461s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 461s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 74%] 461s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 74%] 462s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 462s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 462s tests/test_trajectory.py::test_center PASSED [ 75%] 462s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 75%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 75%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 462s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 462s tests/test_trajectory.py::test_restrict_atoms PASSED [ 76%] 462s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 76%] 462s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 76%] 462s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 77%] 462s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 462s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 463s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 463s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 463s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 463s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 463s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 463s tests/test_trajectory.py::test_join PASSED [ 78%] 463s tests/test_trajectory.py::test_md_join PASSED [ 78%] 463s tests/test_trajectory.py::test_stack_1 PASSED [ 78%] 463s tests/test_trajectory.py::test_stack_2 PASSED [ 78%] 463s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 78%] 463s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 79%] 463s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 463s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 463s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 463s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 463s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 80%] 463s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 80%] 463s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 463s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 463s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 463s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 464s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 464s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 464s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 464s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 81%] 464s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 81%] 464s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 81%] 464s tests/test_trajectory.py::test_iterload[nc] PASSED [ 81%] 464s tests/test_trajectory.py::test_iterload[h5] PASSED [ 81%] 464s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 464s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 82%] 464s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 464s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 464s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 467s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 469s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 470s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 471s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 83%] 471s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 83%] 473s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 83%] 473s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 83%] 474s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 83%] 474s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 475s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 477s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 477s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 477s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 477s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 477s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 84%] 477s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 84%] 477s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 84%] 477s tests/test_trajectory.py::test_save_load[nc] PASSED [ 84%] 477s tests/test_trajectory.py::test_save_load[h5] PASSED [ 84%] 477s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 84%] 477s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 85%] 477s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 477s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 86%] 477s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 87%] 477s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 88%] 477s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 88%] 477s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 477s tests/test_trajectory.py::test_length PASSED [ 89%] 477s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 477s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 477s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 89%] 477s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 89%] 477s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 89%] 477s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 89%] 477s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 89%] 477s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 89%] 477s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 89%] 477s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 477s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 477s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 477s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 90%] 477s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 90%] 477s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 90%] 477s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 90%] 477s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 90%] 478s tests/test_trajectory.py::test_hashing PASSED [ 90%] 478s tests/test_trajectory.py::test_smooth PASSED [ 90%] 478s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 90%] 478s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 90%] 478s tests/test_trajectory.py::test_atom_slicing PASSED [ 91%] 478s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 478s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 478s tests/test_trr.py::test_1 PASSED [ 91%] 478s tests/test_trr.py::test_read_stride PASSED [ 91%] 478s tests/test_trr.py::test_read_stride_n_frames PASSED [ 91%] 478s tests/test_trr.py::test_read_stride_offsets PASSED [ 91%] 478s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 91%] 478s tests/test_trr.py::test_read_stride_switching PASSED [ 91%] 478s tests/test_trr.py::test_write_read PASSED [ 91%] 478s tests/test_trr.py::test_read_atomindices_1 PASSED [ 91%] 478s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 478s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 478s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 478s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 478s tests/test_trr.py::test_malformed PASSED [ 92%] 478s tests/test_trr.py::test_tell PASSED [ 92%] 478s tests/test_trr.py::test_seek PASSED [ 92%] 478s tests/test_trr.py::test_get_velocities PASSED [ 92%] 478s tests/test_trr.py::test_get_forces PASSED [ 92%] 478s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 92%] 478s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 92%] 478s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 478s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 478s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 478s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 478s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 478s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 478s tests/test_utils.py::test_ensure_type_2 PASSED [ 93%] 478s tests/test_utils.py::test_ensure_type_25 PASSED [ 93%] 478s tests/test_utils.py::test_ensure_type_3 PASSED [ 93%] 478s tests/test_utils.py::test_ensure_type_4 PASSED [ 93%] 478s tests/test_utils.py::test_ensure_type_5 PASSED [ 93%] 478s tests/test_utils.py::test_ensure_type_6 PASSED [ 93%] 478s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 478s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 478s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 478s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 478s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 478s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 478s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 478s tests/test_utils.py::test_ensure_type_14 PASSED [ 94%] 478s tests/test_utils.py::test_ensure_type_15 PASSED [ 94%] 478s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 94%] 478s tests/test_utils.py::test_delay_import PASSED [ 94%] 478s tests/test_utils.py::test_unit_0 PASSED [ 95%] 478s tests/test_utils.py::test_unit_1 PASSED [ 95%] 478s tests/test_utils.py::test_unit_2 PASSED [ 95%] 478s tests/test_utils.py::test_unit_3 PASSED [ 95%] 478s tests/test_xml.py::test_xml PASSED [ 95%] 478s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 478s tests/test_xtc.py::test_read_stride PASSED [ 95%] 478s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 478s tests/test_xtc.py::test_read_stride_offsets PASSED [ 95%] 478s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 95%] 478s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 95%] 478s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 478s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 478s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 478s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 478s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 478s tests/test_xtc.py::test_write_0 PASSED [ 96%] 478s tests/test_xtc.py::test_write_1 PASSED [ 96%] 478s tests/test_xtc.py::test_write_2 PASSED [ 96%] 478s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 478s tests/test_xtc.py::test_write_error_0 PASSED [ 96%] 478s tests/test_xtc.py::test_read_error_1 PASSED [ 96%] 478s tests/test_xtc.py::test_read_error_2 PASSED [ 96%] 478s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 478s tests/test_xtc.py::test_tell PASSED [ 97%] 478s tests/test_xtc.py::test_seek PASSED [ 97%] 478s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 478s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 478s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 478s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 478s tests/test_xtc.py::test_short_traj PASSED [ 97%] 478s tests/test_xtc.py::test_flush PASSED [ 97%] 478s tests/test_xyz.py::test_read_0 PASSED [ 97%] 478s tests/test_xyz.py::test_read_1 PASSED [ 97%] 478s tests/test_xyz.py::test_read_gz PASSED [ 98%] 478s tests/test_xyz.py::test_read_write PASSED [ 98%] 478s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 478s tests/test_xyz.py::test_multiread PASSED [ 98%] 478s tests/test_xyz.py::test_seek PASSED [ 98%] 478s tests/test_xyz.py::test_len PASSED [ 98%] 478s tests/test_zipped.py::test_read_gz PASSED [ 98%] 478s tests/test_zipped.py::test_write_gz PASSED [ 98%] 478s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 478s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 480s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 98%] 482s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 482s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 483s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 483s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 485s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 487s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 487s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 487s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 488s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 490s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 491s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 492s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [100%] 492s 492s =============================== warnings summary =============================== 492s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 492s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:56: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 492s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 492s 492s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 492s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:57: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 492s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 492s 492s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 492s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 492s given by the platformdirs library. To remove this warning and 492s see the appropriate new directories, set the environment variable 492s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 492s The use of platformdirs will be the default in `jupyter_core` v6 492s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 492s 492s examples/test_examples.py:26 492s /tmp/autopkgtest.WsEzHt/build.l8U/src/examples/test_examples.py:26: PytestUnknownMarkWarning: Unknown pytest.mark.flaky - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 492s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 492s 492s tests/test_contact.py::test_contact_0 492s tests/test_contact.py::test_contact_4 492s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:220: UserWarning: selected topology includes at least one glycine residue, which has no heavy atoms in its sidechain. The distances involving glycine residues will be computed using the sidechain hydrogen instead. 492s warnings.warn( 492s 492s tests/test_contact.py::test_contact_3 492s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:271: RuntimeWarning: overflow encountered in exp 492s np.exp( 492s 492s tests/test_contact.py::test_contact_3 492s /tmp/autopkgtest.WsEzHt/build.l8U/src/tests/test_contact.py:115: RuntimeWarning: divide by zero encountered in scalar divide 492s beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), 492s 492s tests/test_dcd.py::test_do_overwrite 492s tests/test_dcd.py::test_ragged_1 492s tests/test_dcd.py::test_ragged_2 492s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 492s warnings.warn( 492s 492s tests/test_distance.py::test_6 492s :488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject 492s 492s tests/test_drid.py::test_drid_2 492s /tmp/autopkgtest.WsEzHt/build.l8U/src/tests/test_drid.py:62: RuntimeWarning: divide by zero encountered in divide 492s recip = 1 / squareform(pdist(t.xyz[i])) 492s 492s tests/test_dssp.py::test_1[1vii.pdb] 492s tests/test_gro.py::test_read_write 492s tests/test_gro.py::test_read_write_precision 492s tests/test_gro.py::test_load 492s tests/test_shape.py::test_principal_moments 492s tests/test_shape.py::test_asphericity 492s tests/test_shape.py::test_shape_metrics 492s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:208: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 492s warnings.warn( 492s 492s tests/test_geometry.py::test_dihedral_indices 492s tests/test_geometry.py::test_dihedral_indices 492s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:237: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 492s warnings.warn( 492s 492s tests/test_gro.py::test_load 492s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 492s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:364: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 492s warnings.warn( 492s 492s tests/test_pdb.py::test_blank_indexing 492s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:204: UserWarning: Need to guess atom number starting from atom 100000. 492s warnings.warn(f'Need to guess atom number {num_str} starting from atom {pdbstructure._next_atom_number}.') 492s 492s tests/test_pdb.py::test_blank_indexing 492s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbstructure.py:271: UserWarning: Need to guess residue number string starting from residue10000, atom 100000. 492s warnings.warn(f'Need to guess residue number string {num_str} starting from residue{pdbstructure._next_residue_number}, atom {pdbstructure._next_atom_number}.') 492s 492s tests/test_rdf.py::test_rdf_norm 492s tests/test_rdf.py::test_rdf_t_norm[0] 492s tests/test_rdf.py::test_rdf_t_norm[2] 492s tests/test_rdf.py::test_rdf_t_norm[4] 492s tests/test_selection.py::test_re 492s tests/test_selection.py::test_re 492s tests/test_topology.py::test_select_pairs 492s tests/test_topology.py::test_select_pairs 492s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:199: DeprecationWarning: Call.__init__ got an unexpected keyword argument 'starargs'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 492s left=ast.Call( 492s 492s tests/test_rdf.py::test_rdf_norm 492s tests/test_rdf.py::test_rdf_t_norm[0] 492s tests/test_rdf.py::test_rdf_t_norm[2] 492s tests/test_rdf.py::test_rdf_t_norm[4] 492s tests/test_selection.py::test_re 492s tests/test_selection.py::test_re 492s tests/test_topology.py::test_select_pairs 492s tests/test_topology.py::test_select_pairs 492s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:199: DeprecationWarning: Call.__init__ got an unexpected keyword argument 'kwargs'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 492s left=ast.Call( 492s 492s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 492s tests/test_trajectory.py::test_atom_slicing 492s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:84: UserWarning: atom_indices are not monotonically increasing 492s warnings.warn("atom_indices are not monotonically increasing") 492s 492s tests/test_utils.py::test_ensure_type_8 492s tests/test_utils.py::test_ensure_type_9 492s tests/test_utils.py::test_ensure_type_13 492s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=float64 to 492s warnings.warn( 492s 492s tests/test_utils.py::test_ensure_type_11 492s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting dtype=int64 to 492s warnings.warn( 492s 492s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 492s =========================== short test summary info ============================ 492s SKIPPED [1] tests/test_dihedral.py:56: pymol executable not found 492s SKIPPED [1] tests/test_dihedral.py:181: pymol executable not found 492s SKIPPED [16] tests/test_docstrings.py:38: Skip checking certain modules' docstrings 492s SKIPPED [1] tests/test_geometry.py:300: Not doing performance testing 492s SKIPPED [1] tests/test_geometry.py:322: Not doing performance testing 492s SKIPPED [1] tests/test_hdf5.py:104: requires openmm.units 492s SKIPPED [1] tests/test_hdf5.py:156: requires openmm.units 492s SKIPPED [1] tests/test_hdf5.py:223: requires openmm.units 492s SKIPPED [1] tests/test_mol2.py:59: Requires obabel 492s SKIPPED [1] tests/test_netcdf.py:271: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 492s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 492s SKIPPED [1] tests/test_nmr.py:26: PPM binary not found 492s SKIPPED [1] tests/test_nmr.py:42: SHIFTX2 binary not found or running on travis. 492s SKIPPED [1] tests/test_pdbx.py:43: test_pdbx.py needs OpenMM. 492s SKIPPED [2] tests/test_psf.py:93: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 492s SKIPPED [1] tests/test_rdf.py:64: Binning does not match up with gromacs currently. 492s SKIPPED [1] tests/test_rdf.py:200: Binning does not match up with gromacs currently. 492s SKIPPED [1] tests/test_reporter.py:58: test_reporter.py needs OpenMM. 492s SKIPPED [1] tests/test_reporter.py:145: test_reporter.py needs OpenMM. 492s SKIPPED [1] tests/test_reporter.py:245: test_reporter.py needs OpenMM. 492s SKIPPED [1] tests/test_selection.py:267: failed to parse selection 492s SKIPPED [1] tests/test_thermodynamic_properties.py:161: Thermal expansion test doesn't work. 492s SKIPPED [1] tests/test_topology.py:45: needs OpenMM 492s SKIPPED [1] tests/test_topology.py:62: needs OpenMM 492s SKIPPED [1] tests/test_topology.py:72: needs OpenMM 492s SKIPPED [1] tests/test_topology.py:81: needs OpenMM 492s SKIPPED [1] tests/test_topology.py:91: needs OpenMM 492s SKIPPED [1] tests/test_topology.py:97: needs OpenMM 492s SKIPPED [1] tests/test_topology.py:247: needs OpenMM 492s SKIPPED [1] tests/test_trajectory.py:129: xyz does not store box information 492s SKIPPED [1] tests/test_trajectory.py:129: xyz.gz does not store box information 492s SKIPPED [1] tests/test_trajectory.py:129: lh5 does not store box information 492s SKIPPED [1] tests/test_trajectory.py:129: pdb does not store box information 492s SKIPPED [1] tests/test_trajectory.py:129: pdb.gz does not store box information 492s SKIPPED [1] tests/test_trajectory.py:226: mdcrd can only store rectilinear boxes 492s SKIPPED [1] tests/test_trajectory.py:224: ncrst can only store 1 frame per file 492s SKIPPED [1] tests/test_trajectory.py:224: rst7 can only store 1 frame per file 492s SKIPPED [14] tests/test_trajectory.py:248: mdcrd can only store rectilinear boxes 492s SKIPPED [14] tests/test_trajectory.py:246: ncrst can only store 1 frame per file 492s SKIPPED [14] tests/test_trajectory.py:246: rst7 can only store 1 frame per file 492s SKIPPED [4] tests/test_trajectory.py:256: dtr needs to write unitcells 492s SKIPPED [4] tests/test_trajectory.py:256: lammpstrj needs to write unitcells 492s SKIPPED [2] tests/test_trajectory.py:640: Only 1 frame per file format 492s SKIPPED [2] examples/test_examples.py:77: Network access required 492s SKIPPED [1] examples/test_examples.py:77: Openmm required for example notebook `simulation-with-openmm.ipynb` 492s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 492s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 492s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 492s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 492s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 492s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 492s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 492s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 492s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 492s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 492s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 492s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 492s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 492s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 492s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 492s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 492s = 964 passed, 108 skipped, 12 deselected, 61 xfailed, 48 warnings in 192.65s (0:03:12) = 493s autopkgtest [01:42:29]: test command1: -----------------------] 493s command1 PASS 493s autopkgtest [01:42:29]: test command1: - - - - - - - - - - results - - - - - - - - - - 494s autopkgtest [01:42:30]: test command2: preparing testbed 494s Reading package lists... 494s Building dependency tree... 494s Reading state information... 494s Starting pkgProblemResolver with broken count: 0 494s Starting 2 pkgProblemResolver with broken count: 0 494s Done 494s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 495s autopkgtest [01:42:31]: test command2: pytest-3 -k 'test_3 or test_pdb_from_url or test_1vii_url_and_gz' 495s autopkgtest [01:42:31]: test command2: [----------------------- 496s ============================= test session starts ============================== 496s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 -- /usr/bin/python3 496s cachedir: .pytest_cache 496s rootdir: /tmp/autopkgtest.WsEzHt/build.l8U/src 496s configfile: pyproject.toml 496s testpaths: tests, examples 496s plugins: typeguard-4.4.2 497s collecting ... collected 1145 items / 1135 deselected / 10 selected 497s 497s tests/test_distance.py::test_3 PASSED [ 10%] 497s tests/test_distance.py::test_3p PASSED [ 20%] 499s tests/test_dssp.py::test_3[1GAI] PASSED [ 30%] 502s tests/test_dssp.py::test_3[6gsv] PASSED [ 40%] 504s tests/test_dssp.py::test_3[2AAC] PASSED [ 50%] 504s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 60%] 508s tests/test_pdb.py::test_pdb_from_url PASSED [ 70%] 508s tests/test_pdb.py::test_3nch_conect PASSED [ 80%] 510s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 90%] 513s tests/test_pdb.py::test_1vii_url_and_gz PASSED [100%] 513s 513s =============================== warnings summary =============================== 513s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:56 513s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:56: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 513s THIS_ATOM = ast.Name(id="atom", ctx=ast.Load(), SINGLETON=True) 513s 513s ../../../../usr/lib/python3/dist-packages/mdtraj/core/selection.py:57 513s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:57: DeprecationWarning: Name.__init__ got an unexpected keyword argument 'SINGLETON'. Support for arbitrary keyword arguments is deprecated and will be removed in Python 3.15. 513s RE_MODULE = ast.Name(id="re", ctx=ast.Load(), SINGLETON=True) 513s 513s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:22 513s /usr/lib/python3/dist-packages/jupyter_client/connect.py:22: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 513s given by the platformdirs library. To remove this warning and 513s see the appropriate new directories, set the environment variable 513s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 513s The use of platformdirs will be the default in `jupyter_core` v6 513s from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write 513s 513s examples/test_examples.py:26 513s /tmp/autopkgtest.WsEzHt/build.l8U/src/examples/test_examples.py:26: PytestUnknownMarkWarning: Unknown pytest.mark.flaky - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 513s pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 513s 513s tests/test_pdb.py::test_1vii_url_and_gz 513s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:208: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 513s warnings.warn( 513s 513s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 513s =============== 10 passed, 1135 deselected, 5 warnings in 17.50s =============== 514s autopkgtest [01:42:50]: test command2: -----------------------] 515s command2 PASS 515s autopkgtest [01:42:51]: test command2: - - - - - - - - - - results - - - - - - - - - - 515s autopkgtest [01:42:51]: @@@@@@@@@@@@@@@@@@@@ summary 515s command1 PASS 515s command2 PASS 520s nova [W] Skipping flock for amd64 520s Creating nova instance adt-plucky-amd64-mdtraj-20250316-013415-juju-7f2275-prod-proposed-migration-environment-2-32ad8818-7d37-4444-94e4-462ca337c079 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 520s nova [W] Timed out waiting for 9b2c6765-219a-4d7c-a7dd-4b67de15e6b9 to get deleted.