0s autopkgtest [06:39:13]: starting date and time: 2025-02-16 06:39:13+0000 0s autopkgtest [06:39:13]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [06:39:13]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.35zzbatx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:iproute2,src:php-twig,src:postgresql-17,src:postgresql-common,src:roundcube --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu1 iproute2/6.13.0-1ubuntu1 php-twig/3.19.0-1 postgresql-17/17.3-2 postgresql-common/273 roundcube/1.6.10+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-3.secgroup --name adt-plucky-arm64-mdanalysis-20250216-063913-juju-7f2275-prod-proposed-migration-environment-15-1d162830-4ed1-4249-aec9-87eadd690d7d --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 112s autopkgtest [06:41:05]: testbed dpkg architecture: arm64 112s autopkgtest [06:41:05]: testbed apt version: 2.9.28 113s autopkgtest [06:41:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 113s autopkgtest [06:41:06]: testbed release detected to be: None 114s autopkgtest [06:41:07]: updating testbed package index (apt update) 114s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 114s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 114s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 115s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 115s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [72.6 kB] 115s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [801 kB] 115s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 115s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 115s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [165 kB] 115s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 115s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [915 kB] 115s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [10.0 kB] 115s Fetched 2098 kB in 1s (2138 kB/s) 116s Reading package lists... 117s + lsb_release --codename --short 117s + RELEASE=plucky 117s + cat 117s + [ plucky != trusty ] 117s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 119s The following packages will be upgraded: 119s dash libp11-kit0 libtasn1-6 libxdmcp6 119s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Need to get 433 kB of archives. 119s After this operation, 17.4 kB of additional disk space will be used. 119s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 dash arm64 0.5.12-12ubuntu1 [96.1 kB] 119s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libp11-kit0 arm64 0.25.5-2ubuntu2 [283 kB] 119s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libtasn1-6 arm64 4.20.0-2 [43.9 kB] 119s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libxdmcp6 arm64 1:1.1.5-1 [10.7 kB] 120s Preconfiguring packages ... 120s Fetched 433 kB in 1s (730 kB/s) 120s (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 ... 116609 files and directories currently installed.) 121s Preparing to unpack .../dash_0.5.12-12ubuntu1_arm64.deb ... 121s Unpacking dash (0.5.12-12ubuntu1) over (0.5.12-9ubuntu1) ... 121s Setting up dash (0.5.12-12ubuntu1) ... 121s (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 ... 116609 files and directories currently installed.) 121s Preparing to unpack .../libp11-kit0_0.25.5-2ubuntu2_arm64.deb ... 121s Unpacking libp11-kit0:arm64 (0.25.5-2ubuntu2) over (0.25.5-2ubuntu1) ... 121s Preparing to unpack .../libtasn1-6_4.20.0-2_arm64.deb ... 121s Unpacking libtasn1-6:arm64 (4.20.0-2) over (4.19.0-3build1) ... 121s Preparing to unpack .../libxdmcp6_1%3a1.1.5-1_arm64.deb ... 121s Unpacking libxdmcp6:arm64 (1:1.1.5-1) over (1:1.1.3-0ubuntu6) ... 121s Setting up libxdmcp6:arm64 (1:1.1.5-1) ... 121s Setting up libp11-kit0:arm64 (0.25.5-2ubuntu2) ... 121s Setting up libtasn1-6:arm64 (4.20.0-2) ... 121s Processing triggers for libc-bin (2.40-4ubuntu1) ... 121s Processing triggers for man-db (2.13.0-1) ... 122s Processing triggers for debianutils (5.21) ... 122s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 122s + /usr/lib/apt/apt-helper analyze-pattern ?true 122s + uname -r 122s + sed s/\./\\./g 122s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 122s + apt list ?obsolete 122s + tail -n+2 122s + cut -d/ -f1 122s + grep -v ^linux-.*6\.12\.0-15-generic.* 123s + true 123s + obsolete_pkgs= 123s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 124s + grep -q trusty /etc/lsb-release 124s + [ ! -d /usr/share/doc/unattended-upgrades ] 124s + [ ! -d /usr/share/doc/lxd ] 124s + [ ! -d /usr/share/doc/lxd-client ] 124s + [ ! -d /usr/share/doc/snapd ] 124s + type iptables 124s + cat 124s + chmod 755 /etc/rc.local 124s + . /etc/rc.local 124s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 124s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 124s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 124s + uname -m 124s + [ aarch64 = ppc64le ] 124s + [ -d /run/systemd/system ] 124s + systemd-detect-virt --quiet --vm 124s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 124s + cat 124s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 124s + echo COMPRESS=lz4 124s autopkgtest [06:41:17]: upgrading testbed (apt dist-upgrade and autopurge) 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 127s Entering ResolveByKeep 128s 129s The following packages will be upgraded: 129s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 129s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s Need to get 10.7 MB of archives. 129s After this operation, 358 kB of additional disk space will be used. 129s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu1 [24.0 kB] 129s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu1 [1750 kB] 130s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu1 [4246 kB] 130s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu1 [2910 kB] 130s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu1 [600 kB] 130s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 131s Preconfiguring packages ... 131s Fetched 10.7 MB in 1s (11.8 MB/s) 131s (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 ... 116609 files and directories currently installed.) 131s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_arm64.deb ... 131s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 131s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_arm64.deb ... 131s Unpacking libc6-dev:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 131s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 131s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 132s Preparing to unpack .../libc6_2.41-1ubuntu1_arm64.deb ... 132s Checking for services that may need to be restarted... 132s Checking init scripts... 132s Checking for services that may need to be restarted... 132s Checking init scripts... 132s Stopping some services possibly affected by the upgrade (will be restarted later): 132s cron: stopping...done. 132s 132s Unpacking libc6:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 132s Setting up libc6:arm64 (2.41-1ubuntu1) ... 132s Checking for services that may need to be restarted... 132s Checking init scripts... 132s Restarting services possibly affected by the upgrade: 132s cron: restarting...done. 132s 132s Services restarted successfully. 133s (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 ... 116610 files and directories currently installed.) 133s Preparing to unpack .../libc-bin_2.41-1ubuntu1_arm64.deb ... 133s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 133s Setting up libc-bin (2.41-1ubuntu1) ... 133s (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 ... 116610 files and directories currently installed.) 133s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_arm64.deb ... 133s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 134s Setting up iproute2 (6.13.0-1ubuntu1) ... 134s Setting up locales (2.41-1ubuntu1) ... 134s Installing new version of config file /etc/locale.alias ... 135s Generating locales (this might take a while)... 137s en_US.UTF-8... done 137s Generation complete. 137s Setting up libc-dev-bin (2.41-1ubuntu1) ... 137s Setting up libc6-dev:arm64 (2.41-1ubuntu1) ... 137s Processing triggers for man-db (2.13.0-1) ... 139s Processing triggers for systemd (257.2-3ubuntu1) ... 140s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Starting pkgProblemResolver with broken count: 0 142s Starting 2 pkgProblemResolver with broken count: 0 142s Done 143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s autopkgtest [06:41:39]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 146s autopkgtest [06:41:39]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis 153s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.8.0-1 (dsc) [2861 B] 153s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.8.0-1 (tar) [60.8 MB] 153s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.8.0-1 (diff) [10.9 kB] 153s gpgv: Signature made Mon Feb 10 23:30:56 2025 UTC 153s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 153s gpgv: Can't check signature: No public key 153s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.8.0-1.dsc: no acceptable signature found 155s autopkgtest [06:41:48]: testing package mdanalysis version 2.8.0-1 155s autopkgtest [06:41:48]: build not needed 159s autopkgtest [06:41:52]: test test-mdanalysis: preparing testbed 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 161s Starting 2 pkgProblemResolver with broken count: 0 161s Done 161s The following NEW packages will be installed: 161s autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14 161s cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper debugedit 161s dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz 161s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 161s fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14 161s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 161s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 161s libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 161s libdebhelper-perl libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl 161s libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1 161s libgraphite2-3 libharfbuzz0b libhdf5-310 libhdf5-hl-310 libhwasan0 161s libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 libjpeg8 161s libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc libjs-underscore 161s libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0 liblzf1 161s libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0 libpython3-all-dev 161s libpython3-dev libpython3.12-dev libpython3.13-dev libqhull-r8.0 libraqm0 161s libsharpyuv0 libstdc++-14-dev libsz2 libtcl8.6 libtiff6 libtk8.6 libtool 161s libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 161s libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 m4 po-debconf 161s pybuild-plugin-pyproject python-matplotlib-data python-mdanalysis-doc 161s python3-alabaster python3-all python3-all-dev python3-biopython 161s python3-brotli python3-build python3-cairo python3-cftime python3-citeproc 161s python3-contourpy python3-cycler python3-dateutil python3-decorator 161s python3-defusedxml python3-dev python3-docutils python3-duecredit 161s python3-fasteners python3-fonttools python3-freetype python3-fs 161s python3-griddataformats python3-gsd python3-h5py python3-h5py-serial 161s python3-hypothesis python3-imagesize python3-iniconfig python3-installer 161s python3-joblib python3-kiwisolver python3-latexcodec python3-looseversion 161s python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib 161s python3-mdanalysis python3-mmtf python3-monotonic python3-mpmath 161s python3-mrcfile python3-msgpack python3-msmb-theme python3-netcdf4 161s python3-networkx python3-numpy python3-packaging python3-pandas 161s python3-pandas-lib python3-pil python3-pil.imagetk python3-platformdirs 161s python3-pluggy python3-pybtex python3-pybtex-docutils 161s python3-pyproject-hooks python3-pytest python3-pytz python3-reportlab 161s python3-rlpycairo python3-roman python3-scipy python3-seaborn python3-six 161s python3-sklearn python3-sklearn-lib python3-snowballstemmer 161s python3-sortedcontainers python3-sphinx python3-sphinx-rtd-theme 161s python3-sphinx-sitemap python3-sphinxcontrib.bibtex 161s python3-sphinxcontrib.jquery python3-sympy python3-threadpoolctl python3-tk 161s python3-toml python3-tqdm python3-tz python3-ufolib2 python3-unicodedata2 161s python3-wheel python3.12 python3.12-dev python3.12-minimal python3.12-tk 161s python3.13-dev python3.13-tk sgml-base sphinx-common sphinx-rtd-theme-common 161s tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings 161s xfonts-utils xml-core zlib1g-dev 162s 0 upgraded, 207 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 220 MB of archives. 162s After this operation, 992 MB of additional disk space will be used. 162s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.9-1 [2236 kB] 162s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-lato all 2.015-1 [2781 kB] 162s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 162s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.9-1 [671 kB] 162s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-5 [244 kB] 162s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 162s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 162s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.17-3 [572 kB] 162s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.23.1-1 [619 kB] 162s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 162s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 162s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 162s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 162s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 162s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 162s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 162s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 163s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 163s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 163s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 163s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 163s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 163s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 163s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 163s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 163s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 163s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 163s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [10.6 MB] 163s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu1 [1032 B] 163s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 163s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 163s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-17ubuntu1 [49.6 kB] 163s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-17ubuntu1 [145 kB] 163s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-17ubuntu1 [27.8 kB] 163s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-17ubuntu1 [2892 kB] 163s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-17ubuntu1 [1283 kB] 163s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-17ubuntu1 [2686 kB] 163s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-17ubuntu1 [1152 kB] 163s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-17ubuntu1 [1599 kB] 163s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu1 [2593 kB] 163s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [20.9 MB] 164s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu1 [526 kB] 164s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 164s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 164s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu1 [2499 kB] 164s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [12.1 MB] 164s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu1 [21.8 kB] 164s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 164s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 164s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 164s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-2ubuntu1 [2974 kB] 164s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 164s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.5.4-3build1 [168 kB] 164s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 164s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 164s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 164s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 164s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-2 [46.1 kB] 164s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 164s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.23.1-1 [998 kB] 165s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 165s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 165s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.24.1ubuntu2 [895 kB] 165s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20250108 [117 kB] 165s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 165s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 165s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 165s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 165s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 165s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 165s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 165s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 165s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 165s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 165s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 165s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 165s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libexpat1-dev arm64 2.6.4-1 [129 kB] 165s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-17ubuntu1 [437 kB] 165s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 165s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 165s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 165s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 165s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 165s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 165s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 165s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 165s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 165s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 165s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 165s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 165s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 libjson-perl all 4.10000-1 [81.9 kB] 165s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 165s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 165s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 165s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 165s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 165s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf19t64 arm64 1:4.9.2-6ubuntu2 [471 kB] 165s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 165s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-dev arm64 3.13.2-1 [5399 kB] 165s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-dev arm64 3.13.1-1~exp2 [10.5 kB] 165s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.12-dev arm64 3.12.9-1 [5569 kB] 165s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3-all-dev arm64 3.13.1-1~exp2 [922 B] 165s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 166s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 166s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 166s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 166s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 166s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 166s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 166s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 166s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 166s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 166s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 166s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-toml all 0.10.2-1 [16.5 kB] 166s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wheel all 0.45.1-1 [57.7 kB] 166s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-build all 1.2.2-1 [31.0 kB] 166s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 166s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-pyproject all 6.20250108 [1726 B] 166s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 166s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 166s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-mdanalysis-doc all 2.8.0-1 [3459 kB] 166s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.1-1~exp2 [894 B] 166s Get:123 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-dev arm64 3.13.2-1 [508 kB] 166s Get:124 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dev arm64 3.13.1-1~exp2 [26.7 kB] 166s Get:125 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-dev arm64 3.12.9-1 [505 kB] 166s Get:126 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all-dev arm64 3.13.1-1~exp2 [918 B] 166s Get:127 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 167s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 167s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-1 [106 kB] 167s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 167s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5 [9948 B] 167s Get:132 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB] 167s Get:133 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5 [491 kB] 167s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build1 [139 kB] 167s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 167s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 167s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.3.0-1 [1137 kB] 167s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 167s Get:139 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.85+dfsg-2 [1718 kB] 167s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build3 [342 kB] 167s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cftime arm64 1.6.4-1build2 [289 kB] 167s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1 [1600 kB] 167s Get:143 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-citeproc all 0.6.0-3 [98.4 kB] 167s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1 [216 kB] 167s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 167s Get:146 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 167s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 167s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-defusedxml all 0.7.1-3 [42.2 kB] 167s Get:149 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-roman all 5.0-1 [10.3 kB] 167s Get:150 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 167s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-looseversion all 1.3.0-3 [8354 B] 167s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-duecredit all 0.10.2-2 [66.0 kB] 167s Get:153 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-monotonic all 1.6-3 [5344 B] 167s Get:154 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-fasteners all 0.18-2 [12.5 kB] 167s Get:155 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 167s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 167s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 167s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-6 [90.7 kB] 167s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1 [27.3 kB] 167s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 168s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 168s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 168s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 168s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build2 [360 kB] 168s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 168s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2 [1615 kB] 168s Get:167 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1014 kB] 168s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mrcfile all 1.5.4-2 [116 kB] 168s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-griddataformats all 1.0.2-2 [2107 kB] 169s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gsd arm64 3.3.0-1build2 [229 kB] 169s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.12.1-1 [1453 kB] 169s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.12.1-1 [7970 B] 169s Get:173 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sortedcontainers all 2.4.0-2 [27.6 kB] 169s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hypothesis all 6.125.2-1 [333 kB] 169s Get:175 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-imagesize all 1.4.1-1 [6844 B] 169s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 169s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.4.2-2 [205 kB] 169s Get:178 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3 [62.5 kB] 169s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-latexcodec all 3.0.0-1 [16.6 kB] 169s Get:180 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3ubuntu2 [4616 kB] 169s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mda-xdrlib all 0.2.0-3 [11.4 kB] 169s Get:182 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-msgpack arm64 1.0.3-3build3 [106 kB] 169s Get:183 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mmtf all 1.1.3-1 [16.2 kB] 169s Get:184 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 169s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-2 [92.5 kB] 169s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mdanalysis arm64 2.8.0-1 [4503 kB] 169s Get:187 http://ftpmaster.internal/ubuntu plucky/main arm64 sphinx-common all 8.1.3-4 [663 kB] 169s Get:188 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-alabaster all 0.7.16-0.1 [18.5 kB] 169s Get:189 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-snowballstemmer all 2.2.0-4build1 [59.8 kB] 169s Get:190 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-sphinx all 8.1.3-4 [474 kB] 169s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.jquery all 4.1-5 [6678 B] 169s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [23.5 kB] 169s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-msmb-theme all 1.2.0-4 [35.4 kB] 169s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-netcdf4 arm64 1.7.2-1build2 [797 kB] 169s Get:195 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 170s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8 [6925 kB] 170s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 170s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 170s Get:199 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.17.0-1 [13.2 kB] 170s Get:200 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex all 0.24.0-4 [70.0 kB] 170s Get:201 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pybtex-docutils all 1.0.2-1 [7176 B] 170s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.4-1 [252 kB] 170s Get:203 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-seaborn all 0.13.2-4.1 [225 kB] 171s Get:204 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-7build1 [6372 kB] 171s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-7build1 [2258 kB] 171s Get:206 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinx-sitemap all 2.6.0-1 [6674 B] 171s Get:207 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB] 172s Fetched 220 MB in 10s (23.0 MB/s) 172s Selecting previously unselected package python3.12-minimal. 172s (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 ... 116611 files and directories currently installed.) 172s Preparing to unpack .../000-python3.12-minimal_3.12.9-1_arm64.deb ... 172s Unpacking python3.12-minimal (3.12.9-1) ... 172s Selecting previously unselected package fonts-lato. 172s Preparing to unpack .../001-fonts-lato_2.015-1_all.deb ... 172s Unpacking fonts-lato (2.015-1) ... 172s Selecting previously unselected package sgml-base. 172s Preparing to unpack .../002-sgml-base_1.31_all.deb ... 172s 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package libjs-sphinxdoc. 179s Preparing to unpack .../089-libjs-sphinxdoc_8.1.3-4_all.deb ... 179s Unpacking libjs-sphinxdoc (8.1.3-4) ... 179s Selecting previously unselected package libjson-perl. 179s Preparing to unpack .../090-libjson-perl_4.10000-1_all.deb ... 179s Unpacking libjson-perl (4.10000-1) ... 179s Selecting previously unselected package liblapack3:arm64. 179s Preparing to unpack .../091-liblapack3_3.12.1-2_arm64.deb ... 179s Unpacking liblapack3:arm64 (3.12.1-2) ... 179s Selecting previously unselected package liblbfgsb0:arm64. 179s Preparing to unpack .../092-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 179s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 179s Selecting previously unselected package liblcms2-2:arm64. 179s Preparing to unpack .../093-liblcms2-2_2.16-2_arm64.deb ... 179s Unpacking liblcms2-2:arm64 (2.16-2) ... 180s Selecting previously unselected package liblerc4:arm64. 180s Preparing to unpack .../094-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 180s 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libpython3-dev:arm64 (3.13.1-1~exp2) ... 180s Selecting previously unselected package libpython3.12-dev:arm64. 180s Preparing to unpack .../100-libpython3.12-dev_3.12.9-1_arm64.deb ... 180s Unpacking libpython3.12-dev:arm64 (3.12.9-1) ... 180s Selecting previously unselected package libpython3-all-dev:arm64. 180s Preparing to unpack .../101-libpython3-all-dev_3.13.1-1~exp2_arm64.deb ... 180s Unpacking libpython3-all-dev:arm64 (3.13.1-1~exp2) ... 180s Selecting previously unselected package libqhull-r8.0:arm64. 180s Preparing to unpack .../102-libqhull-r8.0_2020.2-6build1_arm64.deb ... 180s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 180s Selecting previously unselected package libraqm0:arm64. 180s Preparing to unpack .../103-libraqm0_0.10.2-1_arm64.deb ... 180s Unpacking libraqm0:arm64 (0.10.2-1) ... 180s Selecting previously unselected package libsharpyuv0:arm64. 180s Preparing to unpack .../104-libsharpyuv0_1.5.0-0.1_arm64.deb ... 180s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) 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python3-build (1.2.2-1) ... 181s Selecting previously unselected package python3-installer. 181s Preparing to unpack .../116-python3-installer_0.7.0+dfsg1-3_all.deb ... 181s Unpacking python3-installer (0.7.0+dfsg1-3) ... 181s Selecting previously unselected package pybuild-plugin-pyproject. 181s Preparing to unpack .../117-pybuild-plugin-pyproject_6.20250108_all.deb ... 181s Unpacking pybuild-plugin-pyproject (6.20250108) ... 181s Selecting previously unselected package python-matplotlib-data. 181s Preparing to unpack .../118-python-matplotlib-data_3.8.3-3ubuntu2_all.deb ... 181s Unpacking python-matplotlib-data (3.8.3-3ubuntu2) ... 181s Selecting previously unselected package libjs-mathjax. 181s Preparing to unpack .../119-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 181s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 182s Selecting previously unselected package python-mdanalysis-doc. 182s Preparing to unpack .../120-python-mdanalysis-doc_2.8.0-1_all.deb ... 182s Unpacking python-mdanalysis-doc (2.8.0-1) ... 182s Selecting previously unselected package python3-all. 182s Preparing to unpack .../121-python3-all_3.13.1-1~exp2_arm64.deb ... 182s Unpacking python3-all (3.13.1-1~exp2) ... 182s Selecting previously unselected package python3.13-dev. 182s Preparing to unpack .../122-python3.13-dev_3.13.2-1_arm64.deb ... 182s Unpacking python3.13-dev (3.13.2-1) ... 182s Selecting previously unselected package python3-dev. 182s Preparing to unpack .../123-python3-dev_3.13.1-1~exp2_arm64.deb ... 182s Unpacking python3-dev (3.13.1-1~exp2) ... 182s Selecting previously unselected package python3.12-dev. 182s Preparing to unpack .../124-python3.12-dev_3.12.9-1_arm64.deb ... 182s Unpacking python3.12-dev (3.12.9-1) ... 182s Selecting previously unselected package python3-all-dev. 182s Preparing to unpack .../125-python3-all-dev_3.13.1-1~exp2_arm64.deb ... 182s Unpacking python3-all-dev (3.13.1-1~exp2) ... 182s Selecting previously unselected package python3-numpy. 182s Preparing to unpack .../126-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 182s Unpacking python3-numpy (1:1.26.4+ds-13) ... 183s Selecting previously unselected package python3.12-tk. 183s Preparing to unpack .../127-python3.12-tk_3.12.9-1_arm64.deb ... 183s Unpacking python3.12-tk (3.12.9-1) ... 183s Selecting previously unselected package python3.13-tk. 183s Preparing to unpack .../128-python3.13-tk_3.13.2-1_arm64.deb ... 183s Unpacking python3.13-tk (3.13.2-1) ... 183s Selecting previously unselected package python3-tk:arm64. 183s Preparing to unpack .../129-python3-tk_3.13.1-1_arm64.deb ... 183s Unpacking python3-tk:arm64 (3.13.1-1) ... 183s Selecting previously unselected package python3-pil.imagetk:arm64. 183s Preparing to unpack .../130-python3-pil.imagetk_11.1.0-5_arm64.deb ... 183s Unpacking python3-pil.imagetk:arm64 (11.1.0-5) ... 183s Selecting previously unselected package libopenjp2-7:arm64. 183s Preparing to unpack .../131-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ... 183s 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package w3c-sgml-lib. 183s Preparing to unpack .../137-w3c-sgml-lib_1.3-3_all.deb ... 183s Unpacking w3c-sgml-lib (1.3-3) ... 183s Selecting previously unselected package python3-biopython. 183s Preparing to unpack .../138-python3-biopython_1.85+dfsg-2_arm64.deb ... 183s Unpacking python3-biopython (1.85+dfsg-2) ... 184s Selecting previously unselected package python3-brotli. 184s Preparing to unpack .../139-python3-brotli_1.1.0-2build3_arm64.deb ... 184s Unpacking python3-brotli (1.1.0-2build3) ... 184s Selecting previously unselected package python3-cftime. 184s Preparing to unpack .../140-python3-cftime_1.6.4-1build2_arm64.deb ... 184s Unpacking python3-cftime (1.6.4-1build2) ... 184s Selecting previously unselected package python3-lxml:arm64. 184s Preparing to unpack .../141-python3-lxml_5.3.1-1_arm64.deb ... 184s Unpacking python3-lxml:arm64 (5.3.1-1) ... 184s Selecting previously unselected package python3-citeproc. 184s Preparing to unpack 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Selecting previously unselected package python3-roman. 184s Preparing to unpack .../148-python3-roman_5.0-1_all.deb ... 184s Unpacking python3-roman (5.0-1) ... 184s Selecting previously unselected package python3-docutils. 184s Preparing to unpack .../149-python3-docutils_0.21.2+dfsg-2_all.deb ... 184s Unpacking python3-docutils (0.21.2+dfsg-2) ... 184s Selecting previously unselected package python3-looseversion. 184s Preparing to unpack .../150-python3-looseversion_1.3.0-3_all.deb ... 184s Unpacking python3-looseversion (1.3.0-3) ... 184s Selecting previously unselected package python3-duecredit. 184s Preparing to unpack .../151-python3-duecredit_0.10.2-2_all.deb ... 184s Unpacking python3-duecredit (0.10.2-2) ... 184s Selecting previously unselected package python3-monotonic. 184s Preparing to unpack .../152-python3-monotonic_1.6-3_all.deb ... 184s Unpacking python3-monotonic (1.6-3) ... 184s Selecting previously unselected package python3-fasteners. 184s Preparing to unpack .../153-python3-fasteners_0.18-2_all.deb ... 184s Unpacking python3-fasteners (0.18-2) ... 184s Selecting previously unselected package python3-pytz. 184s Preparing to unpack .../154-python3-pytz_2025.1-3_all.deb ... 184s Unpacking python3-pytz (2025.1-3) ... 185s Selecting previously unselected package python3-tz. 185s Preparing to unpack .../155-python3-tz_2025.1-3_all.deb ... 185s Unpacking python3-tz (2025.1-3) ... 185s Selecting previously unselected package python3-platformdirs. 185s Preparing to unpack .../156-python3-platformdirs_4.3.6-1_all.deb ... 185s Unpacking python3-platformdirs (4.3.6-1) ... 185s Selecting previously unselected package python3-fs. 185s Preparing to unpack .../157-python3-fs_2.4.16-6_all.deb ... 185s Unpacking python3-fs (2.4.16-6) ... 185s Selecting previously unselected package python3-lz4. 185s Preparing to unpack .../158-python3-lz4_4.4.0+dfsg-1_arm64.deb ... 185s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 185s Selecting previously unselected package python3-scipy. 185s Preparing to unpack .../159-python3-scipy_1.14.1-4ubuntu1_arm64.deb ... 185s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 185s Selecting previously unselected package python3-mpmath. 185s Preparing to unpack .../160-python3-mpmath_1.3.0-1_all.deb ... 185s Unpacking python3-mpmath (1.3.0-1) ... 185s Selecting previously unselected package python3-sympy. 186s Preparing to unpack .../161-python3-sympy_1.13.3-1_all.deb ... 186s Unpacking python3-sympy (1.13.3-1) ... 186s Selecting previously unselected package python3-ufolib2. 186s Preparing to unpack .../162-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 186s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 186s Selecting previously unselected package python3-unicodedata2. 186s Preparing to unpack .../163-python3-unicodedata2_15.1.0+ds-1build2_arm64.deb ... 186s Unpacking python3-unicodedata2 (15.1.0+ds-1build2) ... 186s Selecting previously unselected package unicode-data. 186s Preparing to unpack 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Unpacking python3-gsd (3.3.0-1build2) ... 187s Selecting previously unselected package python3-h5py-serial. 187s Preparing to unpack .../170-python3-h5py-serial_3.12.1-1_arm64.deb ... 187s Unpacking python3-h5py-serial (3.12.1-1) ... 187s Selecting previously unselected package python3-h5py. 187s Preparing to unpack .../171-python3-h5py_3.12.1-1_all.deb ... 187s Unpacking python3-h5py (3.12.1-1) ... 187s Selecting previously unselected package python3-sortedcontainers. 187s Preparing to unpack .../172-python3-sortedcontainers_2.4.0-2_all.deb ... 187s Unpacking python3-sortedcontainers (2.4.0-2) ... 187s Selecting previously unselected package python3-hypothesis. 187s Preparing to unpack .../173-python3-hypothesis_6.125.2-1_all.deb ... 187s Unpacking python3-hypothesis (6.125.2-1) ... 187s Selecting previously unselected package python3-imagesize. 187s Preparing to unpack .../174-python3-imagesize_1.4.1-1_all.deb ... 187s Unpacking python3-imagesize (1.4.1-1) ... 187s Selecting previously unselected package python3-iniconfig. 187s Preparing to unpack .../175-python3-iniconfig_1.1.1-2_all.deb ... 187s Unpacking python3-iniconfig (1.1.1-2) ... 187s Selecting previously unselected package python3-joblib. 187s Preparing to unpack .../176-python3-joblib_1.4.2-2_all.deb ... 187s Unpacking python3-joblib (1.4.2-2) ... 187s Selecting previously unselected package python3-kiwisolver. 187s Preparing to unpack .../177-python3-kiwisolver_1.4.7-3_arm64.deb ... 187s Unpacking python3-kiwisolver (1.4.7-3) ... 187s Selecting previously unselected package python3-latexcodec. 187s Preparing to unpack .../178-python3-latexcodec_3.0.0-1_all.deb ... 187s Unpacking python3-latexcodec (3.0.0-1) ... 187s Selecting previously unselected package python3-matplotlib. 187s Preparing to unpack .../179-python3-matplotlib_3.8.3-3ubuntu2_arm64.deb ... 187s Unpacking python3-matplotlib (3.8.3-3ubuntu2) ... 187s Selecting previously unselected package python3-mda-xdrlib. 187s Preparing to 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[100%] 1175s 1175s = 19099 passed, 558 skipped, 2 deselected, 7 xfailed, 3 xpassed, 104647 warnings in 874.99s (0:14:34) = 1194s 1194s DueCredit Report: 1194s - Molecular simulation analysis library / MDAnalysis (v 2.8.0) [1, 2] 1194s - Iterative Calculation of Opimal Reference / MDAnalysis.analysis.align.iterative_average (v 2.8.0) [3] 1194s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.8.0) [4] 1194s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.8.0) [5] 1194s - DSSP algorithm description / MDAnalysis.analysis.dssp (v 2.8.0) [6] 1194s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.8.0) [7] 1194s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.8.0) [8] 1194s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.8.0) [9] 1194s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.8.0) [2] 1194s - Mean Squared Displacements with tidynamics, FCA fast correlation algorithm / MDAnalysis.analysis.msd (v 2.8.0) [10, 11] 1194s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.8.0) [12] 1194s - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 2.8.0, 1.1) [13, 14] 1194s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.8.0) [15] 1194s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.8.0) [16] 1194s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.8.0) [17, 18] 1194s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.8.0) [15] 1194s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.8.0) [19] 1194s - Scientific tools library / numpy (v 1.26.4) [20] 1194s 1194s 2 packages cited 1194s 16 modules cited 1194s 0 functions cited 1194s 1194s References 1194s ---------- 1194s 1194s [1] Gowers, R. et al., 2016. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In Proceedings of the 15th Python in Science Conference. SciPy. SciPy, pp. 98–105. 1194s [2] Michaud‐Agrawal, N. et al., 2011. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10), pp.2319–2327. 1194s [3] Linke, M., Köfinger, J. & Hummer, G., 2018. Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B, 122(21), pp.5630–5639. 1194s [4] Minh, D.D.L., 2019. Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors. Journal of Computational Chemistry, 41(7), pp.715–730. 1194s [5] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 1194s [6] Kabsch, W. & Sander, C., 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features. Biopolymers, 22(12), pp.2577–2637. 1194s [7] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 1194s [8] Smith, P. et al., 2019. On the interaction of hyaluronic acid with synovial fluid lipid membranes. Physical Chemistry Chemical Physics, 21(19), pp.9845–9857. 1194s [9] Gowers, R.J. & Carbone, P., 2015. A multiscale approach to model hydrogen bonding: The case of polyamide. The Journal of Chemical Physics, 142(22). 1194s [10] de Buyl, P., 2018. tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3(28), p.877. 1194s [11] Calandrini, V. et al., 2011. nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. École thématique de la Société Française de la Neutronique, 12, pp.201–232. 1194s [12] Yang, L. et al., 2008. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure, 16(2), pp.321–330. 1194s [13] Jakupovic, E. & Beckstein, O., 2021. MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. In Proceedings of the 20th Python in Science Conference. SciPy. SciPy, pp. 40–48. 1194s [14] de Buyl, P., Colberg, P.H. & Höfling, F., 2014. H5MD: A structured, efficient, and portable file format for molecular data. Computer Physics Communications, 185(6), pp.1546–1553. 1194s [15] Bradley, A.R. et al., 2017. MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures D. Schneidman, ed.. PLOS Computational Biology, 13(6), p.1005575. 1194s [16] Lundborg, M. et al., 2013. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. Journal of Computational Chemistry, 35(3), pp.260–269. 1194s [17] Theobald, D.L., 2005. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A Foundations of Crystallography, 61(4), pp.478–480. 1194s [18] Liu, P., Agrafiotis, D.K. & Theobald, D.L., Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7), pp.1561–1563. 1194s [19] Kulke, M. & Vermaas, J.V., 2022. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 18(10), pp.6161–6171. 1194s [20] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30. 1208s ============================= test session starts ============================== 1208s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 1208s rootdir: /tmp/autopkgtest.Pkhs0U/build.8Lr/src 1208s plugins: hypothesis-6.125.2, typeguard-4.4.1 1208s collected 19667 items / 2 deselected / 6 skipped / 19665 selected 1208s 1212s testsuite/MDAnalysisTests/analysis/test_align.py ....................... [ 0%] 1225s .....................s.ss.s........ [ 0%] 1225s testsuite/MDAnalysisTests/analysis/test_atomicdistances.py ... [ 0%] 1225s testsuite/MDAnalysisTests/analysis/test_backends.py .......... [ 0%] 1233s testsuite/MDAnalysisTests/analysis/test_base.py ........................ [ 0%] 1255s ....................................................................... [ 0%] 1258s testsuite/MDAnalysisTests/analysis/test_bat.py ................... [ 0%] 1260s testsuite/MDAnalysisTests/analysis/test_contacts.py .................... 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[100%] 2009s 2009s = 19103 passed, 558 skipped, 2 deselected, 7 xfailed, 3 xpassed, 104648 warnings in 809.50s (0:13:29) = 2010s 2010s DueCredit Report: 2010s - Molecular simulation analysis library / MDAnalysis (v 2.8.0) [1, 2] 2010s - Iterative Calculation of Opimal Reference / MDAnalysis.analysis.align.iterative_average (v 2.8.0) [3] 2010s - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.8.0) [4] 2010s - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.8.0) [5] 2010s - DSSP algorithm description / MDAnalysis.analysis.dssp (v 2.8.0) [6] 2010s - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.8.0) [7] 2010s - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.8.0) [8] 2010s - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.8.0) [9] 2010s - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.8.0) [2] 2010s - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.8.0) [10, 11] 2010s - Cumulative overlap / MDAnalysis.analysis.pca (v 2.8.0) [12] 2010s - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 1.1, 2.8.0) [13, 14] 2010s - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.8.0) [15] 2010s - The TNG paper / MDAnalysis.coordinates.TNG (v 2.8.0) [16] 2010s - QCProt implementation / MDAnalysis.lib.qcprot (v 2.8.0) [17, 18] 2010s - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.8.0) [15] 2010s - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.8.0) [19] 2010s - Scientific tools library / numpy (v 1.26.4) [20] 2010s 2010s 2 packages cited 2010s 16 modules cited 2010s 0 functions cited 2010s 2010s References 2010s ---------- 2010s 2010s [1] Gowers, R. et al., 2016. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In Proceedings of the 15th Python in Science Conference. SciPy. SciPy, pp. 98–105. 2010s [2] Michaud‐Agrawal, N. et al., 2011. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10), pp.2319–2327. 2010s [3] Linke, M., Köfinger, J. & Hummer, G., 2018. Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations. The Journal of Physical Chemistry B, 122(21), pp.5630–5639. 2010s [4] Minh, D.D.L., 2019. Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors. Journal of Computational Chemistry, 41(7), pp.715–730. 2010s [5] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858. 2010s [6] Kabsch, W. & Sander, C., 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features. Biopolymers, 22(12), pp.2577–2637. 2010s [7] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415. 2010s [8] Smith, P. et al., 2019. On the interaction of hyaluronic acid with synovial fluid lipid membranes. Physical Chemistry Chemical Physics, 21(19), pp.9845–9857. 2010s [9] Gowers, R.J. & Carbone, P., 2015. A multiscale approach to model hydrogen bonding: The case of polyamide. The Journal of Chemical Physics, 142(22). 2010s [10] de Buyl, P., 2018. tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3(28), p.877. 2010s [11] Calandrini, V. et al., 2011. nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. École thématique de la Société Française de la Neutronique, 12, pp.201–232. 2010s [12] Yang, L. et al., 2008. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure, 16(2), pp.321–330. 2010s [13] Jakupovic, E. & Beckstein, O., 2021. MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. In Proceedings of the 20th Python in Science Conference. SciPy. SciPy, pp. 40–48. 2010s [14] de Buyl, P., Colberg, P.H. & Höfling, F., 2014. H5MD: A structured, efficient, and portable file format for molecular data. Computer Physics Communications, 185(6), pp.1546–1553. 2010s [15] Bradley, A.R. et al., 2017. MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures D. Schneidman, ed.. PLOS Computational Biology, 13(6), p.1005575. 2010s [16] Lundborg, M. et al., 2013. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. Journal of Computational Chemistry, 35(3), pp.260–269. 2010s [17] Theobald, D.L., 2005. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A Foundations of Crystallography, 61(4), pp.478–480. 2010s [18] Liu, P., Agrafiotis, D.K. & Theobald, D.L., Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7), pp.1561–1563. 2010s [19] Kulke, M. & Vermaas, J.V., 2022. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 18(10), pp.6161–6171. 2010s [20] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30. 2014s autopkgtest [07:12:47]: test test-mdanalysis: -----------------------] 2015s test-mdanalysis PASS 2015s autopkgtest [07:12:48]: test test-mdanalysis: - - - - - - - - - - results - - - - - - - - - - 2015s autopkgtest [07:12:48]: @@@@@@@@@@@@@@@@@@@@ summary 2015s test-mdanalysis PASS 2070s nova [W] Using flock in prodstack6-arm64 2070s Creating nova instance adt-plucky-arm64-mdanalysis-20250216-063913-juju-7f2275-prod-proposed-migration-environment-15-1d162830-4ed1-4249-aec9-87eadd690d7d from image adt/ubuntu-plucky-arm64-server-20250215.img (UUID 8f82fa69-4462-4e93-a46b-73be9ea2c381)... 2070s nova [W] Timed out waiting for 0e64475e-ac70-4ba7-904e-dc9f1142cb58 to get deleted.