0s autopkgtest [13:56:38]: starting date: 2024-03-05 0s autopkgtest [13:56:38]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [13:56:38]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.amgoz4cj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:zlib --apt-upgrade mdtraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=zlib/1:1.3.dfsg-3.1ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-8.secgroup --name adt-noble-amd64-mdtraj-20240305-135638-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 330s autopkgtest [14:02:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 330s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 331s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [24.5 kB] 331s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [1791 kB] 331s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [320 kB] 331s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 331s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [438 kB] 331s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [303 kB] 331s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 331s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [20.4 kB] 331s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6228 B] 331s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 331s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [678 kB] 331s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [2142 kB] 331s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 331s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [21.4 kB] 331s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [6356 B] 331s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 333s Fetched 5886 kB in 1s (5604 kB/s) 334s Reading package lists... 339s Reading package lists... 339s Building dependency tree... 339s Reading state information... 339s Calculating upgrade... 339s The following packages will be upgraded: 339s zlib1g 339s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 339s Need to get 62.7 kB of archives. 339s After this operation, 8192 B disk space will be freed. 339s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu1 [62.7 kB] 339s Fetched 62.7 kB in 0s (3378 kB/s) 340s (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 ... 71809 files and directories currently installed.) 340s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_amd64.deb ... 340s Unpacking zlib1g:amd64 (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ... 340s Setting up zlib1g:amd64 (1:1.3.dfsg-3.1ubuntu1) ... 340s Processing triggers for libc-bin (2.39-0ubuntu2) ... 340s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 340s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 340s Reading package lists... 340s Building dependency tree... 340s Reading state information... 341s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 341s sh: Attempting to set up Debian/Ubuntu apt sources automatically 341s sh: Distribution appears to be Ubuntu 345s Reading package lists... 345s Building dependency tree... 345s Reading state information... 346s eatmydata is already the newest version (131-1). 346s dbus is already the newest version (1.14.10-4ubuntu1). 346s dbus set to manually installed. 346s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 346s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 346s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 346s Reading package lists... 346s Building dependency tree... 346s Reading state information... 347s rng-tools-debian is already the newest version (2.4). 347s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 347s Reading package lists... 347s Building dependency tree... 347s Reading state information... 348s haveged is already the newest version (1.9.14-1ubuntu1). 348s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 348s Reading package lists... 348s Building dependency tree... 348s Reading state information... 348s The following packages will be REMOVED: 348s cloud-init* python3-configobj* python3-debconf* 349s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 349s After this operation, 3248 kB disk space will be freed. 349s (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 ... 71809 files and directories currently installed.) 349s Removing cloud-init (24.1-0ubuntu1) ... 349s Removing python3-configobj (5.0.8-3) ... 349s Removing python3-debconf (1.5.86) ... 349s Processing triggers for man-db (2.12.0-3) ... 350s (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 ... 71420 files and directories currently installed.) 350s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 351s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 351s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 351s Reading package lists... 351s Building dependency tree... 351s Reading state information... 352s linux-generic is already the newest version (6.8.0-11.11+1). 352s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 352s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 352s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 352s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 352s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 352s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 356s Reading package lists... 356s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 356s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 356s Reading package lists... 357s Building dependency tree... 357s Reading state information... 357s Calculating upgrade... 357s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 357s Reading package lists... 358s Building dependency tree... 358s Reading state information... 358s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 358s autopkgtest [14:02:36]: rebooting testbed after setup commands that affected boot 372s autopkgtest [14:02:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 372s autopkgtest [14:02:50]: testbed dpkg architecture: amd64 373s autopkgtest [14:02:51]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 373s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 373s W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (main/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target CNF (main/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target CNF (main/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (universe/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target CNF (universe/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target CNF (universe/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (restricted/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target CNF (restricted/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target CNF (restricted/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (multiverse/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target CNF (multiverse/cnf/Commands-amd64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 373s W: Target CNF (multiverse/cnf/Commands-all) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 374s Get:1 http://ftpmaster.internal/ubuntu noble/universe mdtraj 1.9.9-1 (dsc) [2619 B] 374s Get:2 http://ftpmaster.internal/ubuntu noble/universe mdtraj 1.9.9-1 (tar) [21.7 MB] 374s Get:3 http://ftpmaster.internal/ubuntu noble/universe mdtraj 1.9.9-1 (diff) [299 kB] 374s gpgv: Signature made Tue Jan 16 11:10:34 2024 UTC 374s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 374s gpgv: issuer "tille@debian.org" 374s gpgv: Can't check signature: No public key 374s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.9.9-1.dsc: no acceptable signature found 375s autopkgtest [14:02:53]: testing package mdtraj version 1.9.9-1 375s autopkgtest [14:02:53]: build not needed 376s autopkgtest [14:02:54]: test command1: preparing testbed 380s Reading package lists... 380s Building dependency tree... 380s Reading state information... 381s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 381s Starting 2 pkgProblemResolver with broken count: 0 381s Done 381s Done 381s Starting pkgProblemResolver with broken count: 0 381s Starting 2 pkgProblemResolver with broken count: 0 381s Done 382s The following additional packages will be installed: 382s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 382s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-2 libdebuginfod-common 382s libdebuginfod1 libdeflate0 libdw1 libfontconfig1 libgfortran5 libgomp1 382s libgraphite2-3 libharfbuzz0b libhdf5-103-1 libimagequant0 libipt2 libjbig0 382s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 382s liblcms2-2 liblerc4 libnorm1 libopenjp2-7 libpgm-5.3-0 libpython3.12 382s libqhull-r8.0 libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 382s libsource-highlight-common libsource-highlight4v5 libsz2 libtcl8.6 libtiff6 382s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 382s libxss1 libzmq5 python-matplotlib-data python-tables-data python3-appdirs 382s python3-asttokens python3-astunparse python3-brotli python3-bytecode 382s python3-comm python3-contourpy python3-coverage python3-cpuinfo 382s python3-cycler python3-dateutil python3-debugpy python3-decorator 382s python3-entrypoints python3-executing python3-fastjsonschema 382s python3-fonttools python3-fs python3-iniconfig python3-ipykernel 382s python3-ipython python3-jedi python3-joblib python3-jupyter-client 382s python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 382s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 382s python3-nbformat python3-nest-asyncio python3-networkx python3-numexpr 382s python3-numpy python3-packaging python3-pandas python3-pandas-lib 382s python3-parso python3-pexpect python3-pil python3-pil.imagetk 382s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 382s python3-ptyprocess python3-pure-eval python3-py python3-pydevd 382s python3-pytest python3-scipy python3-sklearn python3-sklearn-lib 382s python3-stack-data python3-sympy python3-tables python3-tables-lib 382s python3-threadpoolctl python3-tk python3-tornado python3-traitlets 382s python3-ufolib2 python3-unicodedata2 python3-wcwidth python3-zmq 382s tk8.6-blt2.5 unicode-data x11-common 382s Suggested packages: 382s blt-demo gdb-doc gdbserver libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 382s python-bytecode-doc python-coverage-doc python-cycler-doc 382s python-fastjsonschema-doc python-ipython-doc python3-pip python-lxml-doc 382s cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 382s inkscape ipython3 librsvg2-common python3-cairocffi python3-gi-cairo 382s python3-gobject python3-pyqt5 python3-sip texlive-extra-utils 382s texlive-latex-extra python-mdtraj-doc python-mpmath-doc python3-gmpy2 382s python-networkx-doc python3-gdal python3-pydot python3-pygraphviz gcc 382s gfortran python3-dev python-pandas-doc python3-statsmodels 382s python-pexpect-doc python-pil-doc subversion pydevd python-scipy-doc 382s python3-dap python-sklearn-doc texlive-fonts-extra python-sympy-doc 382s python3-netcdf4 python-tables-doc vitables tix python3-tk-dbg python3-pycurl 382s python-tornado-doc python3-twisted 382s Recommended packages: 382s libc-dbg javascript-common python3-simplejson python3-bs4 python3-cssselect 382s python3-html5lib python3-bottleneck python3-odf python3-openpyxl 382s python3-numba python3-olefile g++ | c++-compiler isympy-common 382s The following NEW packages will be installed: 382s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 382s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-2 libdebuginfod-common 382s libdebuginfod1 libdeflate0 libdw1 libfontconfig1 libgfortran5 libgomp1 382s libgraphite2-3 libharfbuzz0b libhdf5-103-1 libimagequant0 libipt2 libjbig0 382s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 382s liblcms2-2 liblerc4 libnorm1 libopenjp2-7 libpgm-5.3-0 libpython3.12 382s libqhull-r8.0 libraqm0 libsharpyuv0 libsnappy1v5 libsodium23 382s libsource-highlight-common libsource-highlight4v5 libsz2 libtcl8.6 libtiff6 382s libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 382s libxss1 libzmq5 python-matplotlib-data python-tables-data python3-appdirs 382s python3-asttokens python3-astunparse python3-brotli python3-bytecode 382s python3-comm python3-contourpy python3-coverage python3-cpuinfo 382s python3-cycler python3-dateutil python3-debugpy python3-decorator 382s python3-entrypoints python3-executing python3-fastjsonschema 382s python3-fonttools python3-fs python3-iniconfig python3-ipykernel 382s python3-ipython python3-jedi python3-joblib python3-jupyter-client 382s python3-jupyter-core python3-kiwisolver python3-lxml python3-lz4 382s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 382s python3-nbformat python3-nest-asyncio python3-networkx python3-numexpr 382s python3-numpy python3-packaging python3-pandas python3-pandas-lib 382s python3-parso python3-pexpect python3-pil python3-pil.imagetk 382s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 382s python3-ptyprocess python3-pure-eval python3-py python3-pydevd 382s python3-pytest python3-scipy python3-sklearn python3-sklearn-lib 382s python3-stack-data python3-sympy python3-tables python3-tables-lib 382s python3-threadpoolctl python3-tk python3-tornado python3-traitlets 382s python3-ufolib2 python3-unicodedata2 python3-wcwidth python3-zmq 382s tk8.6-blt2.5 unicode-data x11-common 382s 0 upgraded, 128 newly installed, 0 to remove and 0 not upgraded. 382s 1 not fully installed or removed. 382s Need to get 107 MB of archives. 382s After this operation, 518 MB of additional disk space will be used. 382s Get:1 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-astunparse all 1.6.3-2 [13.5 kB] 382s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 382s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240221-2.1ubuntu1 [928 kB] 382s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 382s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 python3-numpy amd64 1:1.24.2-2 [7141 kB] 382s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 382s Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [30.4 kB] 382s Get:8 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-scipy amd64 1.11.4-6 [19.4 MB] 382s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240221-2.1ubuntu1 [147 kB] 382s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 382s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 python3-dateutil all 2.8.2-3 [79.2 kB] 382s Get:12 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pandas-lib amd64 2.1.4+dfsg-4ubuntu2 [8348 kB] 382s Get:13 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 382s Get:14 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-cpuinfo all 9.0.0-1 [21.2 kB] 382s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 python3-packaging all 23.2-1 [40.6 kB] 382s Get:16 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-numexpr amd64 2.9.0-1 [92.8 kB] 382s Get:17 http://ftpmaster.internal/ubuntu noble/universe amd64 python-tables-data all 3.9.2-1 [56.7 kB] 382s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libsnappy1v5 amd64 1.1.10-1 [28.4 kB] 382s Get:19 http://ftpmaster.internal/ubuntu noble/universe amd64 libblosc1 amd64 1.21.5+ds-1 [36.5 kB] 382s Get:20 http://ftpmaster.internal/ubuntu noble/universe amd64 libblosc2-2 amd64 2.13.1+ds-1ubuntu1 [164 kB] 382s Get:21 http://ftpmaster.internal/ubuntu noble/universe amd64 libaec0 amd64 1.1.2-1 [22.6 kB] 382s Get:22 http://ftpmaster.internal/ubuntu noble/universe amd64 libsz2 amd64 1.1.2-1 [5416 B] 382s Get:23 http://ftpmaster.internal/ubuntu noble/universe amd64 libhdf5-103-1 amd64 1.10.10+repack-3ubuntu1 [1327 kB] 382s Get:24 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-tables-lib amd64 3.9.2-1 [1136 kB] 382s Get:25 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-tables all 3.9.2-1 [467 kB] 382s Get:26 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-mdtraj amd64 1.9.9-1 [1798 kB] 382s Get:27 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-traitlets all 5.5.0-2 [85.0 kB] 382s Get:28 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-comm all 0.2.1-1 [7016 B] 382s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libdw1 amd64 0.190-1 [260 kB] 382s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libbabeltrace1 amd64 1.5.11-3build1 [163 kB] 382s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libdebuginfod-common all 0.190-1 [14.0 kB] 382s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libdebuginfod1 amd64 0.190-1 [16.9 kB] 382s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libipt2 amd64 2.0.6-1 [45.2 kB] 382s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libpython3.12 amd64 3.12.2-1 [2359 kB] 382s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libsource-highlight-common all 3.1.9-4.3 [64.1 kB] 382s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libsource-highlight4v5 amd64 3.1.9-4.2build2 [257 kB] 382s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 gdb amd64 15.0.50.20240219-0ubuntu1 [4069 kB] 382s Get:38 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-bytecode all 0.15.1-3 [44.7 kB] 382s Get:39 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-coverage amd64 7.3.2-0ubuntu1 [146 kB] 382s Get:40 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pydevd amd64 2.10.0+ds-10ubuntu1 [637 kB] 382s Get:41 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-debugpy all 1.8.0+ds-4ubuntu1 [652 kB] 382s Get:42 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 382s Get:43 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-jedi all 0.18.2-1ubuntu1 [692 kB] 382s Get:44 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 382s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 382s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 python3-pexpect all 4.9-2 [48.1 kB] 382s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 382s Get:48 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-prompt-toolkit all 3.0.43-1 [256 kB] 382s Get:49 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-asttokens all 2.4.1-1 [20.9 kB] 382s Get:50 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-executing all 2.0.1-0.1 [23.3 kB] 382s Get:51 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pure-eval all 0.2.2-1 [11.3 kB] 382s Get:52 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 382s Get:53 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-ipython all 8.20.0-1 [561 kB] 382s Get:54 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-platformdirs all 4.2.0-1 [16.1 kB] 382s Get:55 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-jupyter-core all 5.3.2-1 [25.4 kB] 382s Get:56 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-entrypoints all 0.4-2 [7146 B] 382s Get:57 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-nest-asyncio all 1.5.4-1 [6256 B] 382s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 python3-tornado amd64 6.4.0-1 [297 kB] 382s Get:59 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-py all 1.11.0-2 [72.7 kB] 382s Get:60 http://ftpmaster.internal/ubuntu noble/universe amd64 libnorm1 amd64 1.5.9+dfsg-3 [179 kB] 382s Get:61 http://ftpmaster.internal/ubuntu noble/universe amd64 libpgm-5.3-0 amd64 5.3.128~dfsg-2 [161 kB] 382s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libsodium23 amd64 1.0.18-1build2 [164 kB] 382s Get:63 http://ftpmaster.internal/ubuntu noble/universe amd64 libzmq5 amd64 4.3.5-1 [261 kB] 382s Get:64 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-zmq amd64 24.0.1-5 [378 kB] 382s Get:65 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-jupyter-client all 7.4.9-2ubuntu1 [90.5 kB] 382s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 python3-psutil amd64 5.9.8-1 [195 kB] 382s Get:67 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-ipykernel all 6.24.0-3 [105 kB] 382s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 382s Get:69 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 382s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 383s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 383s Get:72 http://ftpmaster.internal/ubuntu noble/universe amd64 fonts-lyx all 2.4.0~RC3-1 [170 kB] 383s Get:73 http://ftpmaster.internal/ubuntu noble/universe amd64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 383s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libimagequant0 amd64 2.18.0-1 [36.3 kB] 383s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] 383s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 383s Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 liblcms2-2 amd64 2.14-2 [161 kB] 383s Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libopenjp2-7 amd64 2.5.0-2 [174 kB] 383s Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 383s Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB] 383s Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libraqm0 amd64 0.10.1-1 [14.6 kB] 383s Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 383s Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] 383s Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] 383s Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB] 383s Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB] 383s Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB] 383s Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libwebpdemux2 amd64 1.3.2-0.4 [12.4 kB] 383s Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 libwebpmux3 amd64 1.3.2-0.4 [25.6 kB] 383s Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 python3-pil amd64 10.2.0-1 [487 kB] 383s Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB] 383s Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB] 383s Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB] 383s Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 383s Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] 383s Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 383s Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] 383s Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB] 383s Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [630 kB] 383s Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 blt amd64 2.5.3+dfsg-7 [4826 B] 383s Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 python3-tk amd64 3.11.5-1 [112 kB] 383s Get:102 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pil.imagetk amd64 10.2.0-1 [9584 B] 383s Get:103 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-contourpy amd64 1.0.7-1build2 [283 kB] 383s Get:104 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-cycler all 0.11.0-2 [8202 B] 383s Get:105 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-brotli amd64 1.1.0-2 [340 kB] 383s Get:106 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 383s Get:107 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-mpmath all 1.2.1-3 [421 kB] 383s Get:108 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-sympy all 1.12-7 [3966 kB] 383s Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 383s Get:110 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-fs all 2.4.16-3 [91.1 kB] 383s Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libxslt1.1 amd64 1.1.35-1 [164 kB] 383s Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 python3-lxml amd64 5.1.0-1 [2179 kB] 383s Get:113 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build2 [27.0 kB] 383s Get:114 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1 [367 kB] 383s Get:115 http://ftpmaster.internal/ubuntu noble/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 383s Get:116 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-fonttools amd64 4.46.0-1 [1693 kB] 383s Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-kiwisolver amd64 1.4.4-1build2 [69.4 kB] 383s Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 libqhull-r8.0 amd64 2020.2-6 [194 kB] 383s Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-matplotlib amd64 3.6.3-1ubuntu3 [7486 kB] 383s Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-fastjsonschema all 2.19.0-1 [19.6 kB] 383s Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB] 383s Get:122 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 383s Get:123 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pluggy all 1.4.0-1 [20.4 kB] 383s Get:124 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-pytest all 7.4.4-1 [305 kB] 383s Get:125 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-joblib all 1.3.2-1 [207 kB] 383s Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 383s Get:127 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-sklearn-lib amd64 1.4.1.post1+dfsg-1 [7003 kB] 383s Get:128 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-sklearn all 1.4.1.post1+dfsg-1 [2261 kB] 384s Preconfiguring packages ... 384s Fetched 107 MB in 1s (94.6 MB/s) 384s Selecting previously unselected package python3-astunparse. 384s (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 ... 71365 files and directories currently installed.) 384s Preparing to unpack .../000-python3-astunparse_1.6.3-2_all.deb ... 384s Unpacking python3-astunparse (1.6.3-2) ... 384s Selecting previously unselected package libblas3:amd64. 384s Preparing to unpack .../001-libblas3_3.12.0-3_amd64.deb ... 384s Unpacking libblas3:amd64 (3.12.0-3) ... 384s Selecting previously unselected package libgfortran5:amd64. 384s Preparing to unpack .../002-libgfortran5_14-20240221-2.1ubuntu1_amd64.deb ... 384s Unpacking libgfortran5:amd64 (14-20240221-2.1ubuntu1) ... 384s Selecting previously unselected package liblapack3:amd64. 384s Preparing to unpack .../003-liblapack3_3.12.0-3_amd64.deb ... 384s Unpacking liblapack3:amd64 (3.12.0-3) ... 384s Selecting previously unselected package python3-numpy. 384s Preparing to unpack .../004-python3-numpy_1%3a1.24.2-2_amd64.deb ... 384s Unpacking python3-numpy (1:1.24.2-2) ... 384s Selecting previously unselected package python3-decorator. 384s Preparing to unpack .../005-python3-decorator_5.1.1-5_all.deb ... 384s Unpacking python3-decorator (5.1.1-5) ... 384s Selecting previously unselected package liblbfgsb0:amd64. 384s Preparing to unpack .../006-liblbfgsb0_3.0+dfsg.4-1_amd64.deb ... 384s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1) ... 384s Selecting previously unselected package python3-scipy. 384s Preparing to unpack .../007-python3-scipy_1.11.4-6_amd64.deb ... 384s Unpacking python3-scipy (1.11.4-6) ... 385s Selecting previously unselected package libgomp1:amd64. 385s Preparing to unpack .../008-libgomp1_14-20240221-2.1ubuntu1_amd64.deb ... 385s Unpacking libgomp1:amd64 (14-20240221-2.1ubuntu1) ... 385s Selecting previously unselected package python3-networkx. 385s Preparing to unpack .../009-python3-networkx_2.8.8-1ubuntu1_all.deb ... 385s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 385s Selecting previously unselected package python3-dateutil. 385s Preparing to unpack .../010-python3-dateutil_2.8.2-3_all.deb ... 385s Unpacking python3-dateutil (2.8.2-3) ... 385s Selecting previously unselected package python3-pandas-lib:amd64. 385s Preparing to unpack .../011-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_amd64.deb ... 385s Unpacking python3-pandas-lib:amd64 (2.1.4+dfsg-4ubuntu2) ... 385s Selecting previously unselected package python3-pandas. 385s Preparing to unpack .../012-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 385s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 386s Selecting previously unselected package python3-cpuinfo. 386s Preparing to unpack .../013-python3-cpuinfo_9.0.0-1_all.deb ... 386s Unpacking python3-cpuinfo (9.0.0-1) ... 386s Selecting previously unselected package python3-packaging. 386s Preparing to unpack .../014-python3-packaging_23.2-1_all.deb ... 386s Unpacking python3-packaging (23.2-1) ... 386s Selecting previously unselected package python3-numexpr. 386s Preparing to unpack .../015-python3-numexpr_2.9.0-1_amd64.deb ... 386s Unpacking python3-numexpr (2.9.0-1) ... 386s Selecting previously unselected package python-tables-data. 386s Preparing to unpack .../016-python-tables-data_3.9.2-1_all.deb ... 386s Unpacking python-tables-data (3.9.2-1) ... 386s Selecting previously unselected package libsnappy1v5:amd64. 386s Preparing to unpack .../017-libsnappy1v5_1.1.10-1_amd64.deb ... 386s Unpacking libsnappy1v5:amd64 (1.1.10-1) ... 386s Selecting previously unselected package libblosc1:amd64. 386s Preparing to unpack .../018-libblosc1_1.21.5+ds-1_amd64.deb ... 386s Unpacking libblosc1:amd64 (1.21.5+ds-1) ... 386s Selecting previously unselected package libblosc2-2:amd64. 386s Preparing to unpack .../019-libblosc2-2_2.13.1+ds-1ubuntu1_amd64.deb ... 386s Unpacking libblosc2-2:amd64 (2.13.1+ds-1ubuntu1) ... 386s Selecting previously unselected package libaec0:amd64. 386s Preparing to unpack .../020-libaec0_1.1.2-1_amd64.deb ... 386s Unpacking libaec0:amd64 (1.1.2-1) ... 386s Selecting previously unselected package libsz2:amd64. 386s Preparing to unpack .../021-libsz2_1.1.2-1_amd64.deb ... 386s Unpacking libsz2:amd64 (1.1.2-1) ... 386s Selecting previously unselected package libhdf5-103-1:amd64. 386s Preparing to unpack .../022-libhdf5-103-1_1.10.10+repack-3ubuntu1_amd64.deb ... 386s Unpacking libhdf5-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 386s Selecting previously unselected package python3-tables-lib. 386s Preparing to unpack .../023-python3-tables-lib_3.9.2-1_amd64.deb ... 386s Unpacking python3-tables-lib (3.9.2-1) ... 386s Selecting previously unselected package python3-tables. 386s Preparing to unpack .../024-python3-tables_3.9.2-1_all.deb ... 386s Unpacking python3-tables (3.9.2-1) ... 386s Selecting previously unselected package python3-mdtraj. 386s Preparing to unpack .../025-python3-mdtraj_1.9.9-1_amd64.deb ... 386s Unpacking python3-mdtraj (1.9.9-1) ... 386s Selecting previously unselected package python3-traitlets. 386s Preparing to unpack .../026-python3-traitlets_5.5.0-2_all.deb ... 386s Unpacking python3-traitlets (5.5.0-2) ... 386s Selecting previously unselected package python3-comm. 386s Preparing to unpack .../027-python3-comm_0.2.1-1_all.deb ... 386s Unpacking python3-comm (0.2.1-1) ... 386s Selecting previously unselected package libdw1:amd64. 386s Preparing to unpack .../028-libdw1_0.190-1_amd64.deb ... 386s Unpacking libdw1:amd64 (0.190-1) ... 386s Selecting previously unselected package libbabeltrace1:amd64. 386s Preparing to unpack .../029-libbabeltrace1_1.5.11-3build1_amd64.deb ... 386s Unpacking libbabeltrace1:amd64 (1.5.11-3build1) ... 386s Selecting previously unselected package libdebuginfod-common. 386s Preparing to unpack .../030-libdebuginfod-common_0.190-1_all.deb ... 386s Unpacking libdebuginfod-common (0.190-1) ... 386s Selecting previously unselected package libdebuginfod1:amd64. 386s Preparing to unpack .../031-libdebuginfod1_0.190-1_amd64.deb ... 386s Unpacking libdebuginfod1:amd64 (0.190-1) ... 386s Selecting previously unselected package libipt2. 386s Preparing to unpack .../032-libipt2_2.0.6-1_amd64.deb ... 386s Unpacking libipt2 (2.0.6-1) ... 386s Selecting previously unselected package libpython3.12:amd64. 386s Preparing to unpack .../033-libpython3.12_3.12.2-1_amd64.deb ... 386s Unpacking libpython3.12:amd64 (3.12.2-1) ... 386s Selecting previously unselected package libsource-highlight-common. 386s Preparing to unpack .../034-libsource-highlight-common_3.1.9-4.3_all.deb ... 386s Unpacking libsource-highlight-common (3.1.9-4.3) ... 386s Selecting previously unselected package libsource-highlight4v5:amd64. 386s Preparing to unpack .../035-libsource-highlight4v5_3.1.9-4.2build2_amd64.deb ... 386s Unpacking libsource-highlight4v5:amd64 (3.1.9-4.2build2) ... 386s Selecting previously unselected package gdb. 386s Preparing to unpack .../036-gdb_15.0.50.20240219-0ubuntu1_amd64.deb ... 386s Unpacking gdb (15.0.50.20240219-0ubuntu1) ... 387s Selecting previously unselected package python3-bytecode. 387s Preparing to unpack .../037-python3-bytecode_0.15.1-3_all.deb ... 387s Unpacking python3-bytecode (0.15.1-3) ... 387s Selecting previously unselected package python3-coverage. 387s Preparing to unpack .../038-python3-coverage_7.3.2-0ubuntu1_amd64.deb ... 387s Unpacking python3-coverage (7.3.2-0ubuntu1) ... 387s Selecting previously unselected package python3-pydevd. 387s Preparing to unpack .../039-python3-pydevd_2.10.0+ds-10ubuntu1_amd64.deb ... 387s Unpacking python3-pydevd (2.10.0+ds-10ubuntu1) ... 387s Selecting previously unselected package python3-debugpy. 387s Preparing to unpack .../040-python3-debugpy_1.8.0+ds-4ubuntu1_all.deb ... 387s Unpacking python3-debugpy (1.8.0+ds-4ubuntu1) ... 387s Selecting previously unselected package python3-parso. 387s Preparing to unpack .../041-python3-parso_0.8.3-1_all.deb ... 387s Unpacking python3-parso (0.8.3-1) ... 387s Selecting previously unselected package python3-jedi. 387s Preparing to unpack .../042-python3-jedi_0.18.2-1ubuntu1_all.deb ... 387s Unpacking python3-jedi (0.18.2-1ubuntu1) ... 387s Selecting previously unselected package python3-matplotlib-inline. 387s Preparing to unpack .../043-python3-matplotlib-inline_0.1.6-2_all.deb ... 387s Unpacking python3-matplotlib-inline (0.1.6-2) ... 387s Selecting previously unselected package python3-ptyprocess. 387s Preparing to unpack .../044-python3-ptyprocess_0.7.0-5_all.deb ... 387s Unpacking python3-ptyprocess (0.7.0-5) ... 387s Selecting previously unselected package python3-pexpect. 387s Preparing to unpack .../045-python3-pexpect_4.9-2_all.deb ... 387s Unpacking python3-pexpect (4.9-2) ... 387s Selecting previously unselected package python3-wcwidth. 387s Preparing to unpack .../046-python3-wcwidth_0.2.5+dfsg1-1.1ubuntu1_all.deb ... 387s Unpacking python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 387s Selecting previously unselected package python3-prompt-toolkit. 387s Preparing to unpack .../047-python3-prompt-toolkit_3.0.43-1_all.deb ... 387s Unpacking python3-prompt-toolkit (3.0.43-1) ... 387s Selecting previously unselected package python3-asttokens. 387s Preparing to unpack .../048-python3-asttokens_2.4.1-1_all.deb ... 387s Unpacking python3-asttokens (2.4.1-1) ... 387s Selecting previously unselected package python3-executing. 387s Preparing to unpack .../049-python3-executing_2.0.1-0.1_all.deb ... 387s Unpacking python3-executing (2.0.1-0.1) ... 387s Selecting previously unselected package python3-pure-eval. 387s Preparing to unpack .../050-python3-pure-eval_0.2.2-1_all.deb ... 387s Unpacking python3-pure-eval (0.2.2-1) ... 387s Selecting previously unselected package python3-stack-data. 387s Preparing to unpack .../051-python3-stack-data_0.6.3-1_all.deb ... 387s Unpacking python3-stack-data (0.6.3-1) ... 387s Selecting previously unselected package python3-ipython. 387s Preparing to unpack .../052-python3-ipython_8.20.0-1_all.deb ... 387s Unpacking python3-ipython (8.20.0-1) ... 387s Selecting previously unselected package python3-platformdirs. 387s Preparing to unpack .../053-python3-platformdirs_4.2.0-1_all.deb ... 387s Unpacking python3-platformdirs (4.2.0-1) ... 387s Selecting previously unselected package python3-jupyter-core. 387s Preparing to unpack .../054-python3-jupyter-core_5.3.2-1_all.deb ... 387s Unpacking python3-jupyter-core (5.3.2-1) ... 387s Selecting previously unselected package python3-entrypoints. 387s Preparing to unpack .../055-python3-entrypoints_0.4-2_all.deb ... 387s Unpacking python3-entrypoints (0.4-2) ... 387s Selecting previously unselected package python3-nest-asyncio. 387s Preparing to unpack .../056-python3-nest-asyncio_1.5.4-1_all.deb ... 387s Unpacking python3-nest-asyncio (1.5.4-1) ... 387s Selecting previously unselected package python3-tornado. 387s Preparing to unpack .../057-python3-tornado_6.4.0-1_amd64.deb ... 387s Unpacking python3-tornado (6.4.0-1) ... 387s Selecting previously unselected package python3-py. 387s Preparing to unpack .../058-python3-py_1.11.0-2_all.deb ... 387s Unpacking python3-py (1.11.0-2) ... 387s Selecting previously unselected package libnorm1:amd64. 387s Preparing to unpack .../059-libnorm1_1.5.9+dfsg-3_amd64.deb ... 387s Unpacking libnorm1:amd64 (1.5.9+dfsg-3) ... 388s Selecting previously unselected package libpgm-5.3-0:amd64. 388s Preparing to unpack .../060-libpgm-5.3-0_5.3.128~dfsg-2_amd64.deb ... 388s Unpacking libpgm-5.3-0:amd64 (5.3.128~dfsg-2) ... 388s Selecting previously unselected package libsodium23:amd64. 388s Preparing to unpack .../061-libsodium23_1.0.18-1build2_amd64.deb ... 388s Unpacking libsodium23:amd64 (1.0.18-1build2) ... 388s Selecting previously unselected package libzmq5:amd64. 388s Preparing to unpack .../062-libzmq5_4.3.5-1_amd64.deb ... 388s Unpacking libzmq5:amd64 (4.3.5-1) ... 388s Selecting previously unselected package python3-zmq. 388s Preparing to unpack .../063-python3-zmq_24.0.1-5_amd64.deb ... 388s Unpacking python3-zmq (24.0.1-5) ... 388s Selecting previously unselected package python3-jupyter-client. 388s Preparing to unpack .../064-python3-jupyter-client_7.4.9-2ubuntu1_all.deb ... 388s Unpacking python3-jupyter-client (7.4.9-2ubuntu1) ... 388s Selecting previously unselected package python3-psutil. 388s Preparing to unpack .../065-python3-psutil_5.9.8-1_amd64.deb ... 388s Unpacking python3-psutil (5.9.8-1) ... 388s Selecting previously unselected package python3-ipykernel. 388s Preparing to unpack .../066-python3-ipykernel_6.24.0-3_all.deb 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package python-matplotlib-data. 388s Preparing to unpack .../072-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ... 388s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ... 388s Selecting previously unselected package libimagequant0:amd64. 388s Preparing to unpack .../073-libimagequant0_2.18.0-1_amd64.deb ... 388s Unpacking libimagequant0:amd64 (2.18.0-1) ... 388s Selecting previously unselected package libjpeg-turbo8:amd64. 388s Preparing to unpack .../074-libjpeg-turbo8_2.1.5-2ubuntu1_amd64.deb ... 388s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 388s Selecting previously unselected package libjpeg8:amd64. 388s Preparing to unpack .../075-libjpeg8_8c-2ubuntu11_amd64.deb ... 388s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 388s Selecting previously unselected package liblcms2-2:amd64. 388s Preparing to unpack .../076-liblcms2-2_2.14-2_amd64.deb ... 388s Unpacking liblcms2-2:amd64 (2.14-2) ... 388s Selecting previously unselected package libopenjp2-7:amd64. 388s Preparing to unpack .../077-libopenjp2-7_2.5.0-2_amd64.deb ... 388s Unpacking libopenjp2-7:amd64 (2.5.0-2) ... 388s Selecting previously unselected package libgraphite2-3:amd64. 388s Preparing to unpack .../078-libgraphite2-3_1.3.14-2_amd64.deb ... 388s Unpacking libgraphite2-3:amd64 (1.3.14-2) ... 388s Selecting previously unselected package libharfbuzz0b:amd64. 388s Preparing to unpack .../079-libharfbuzz0b_8.3.0-2_amd64.deb ... 388s Unpacking libharfbuzz0b:amd64 (8.3.0-2) ... 388s Selecting previously unselected package libraqm0:amd64. 388s Preparing to unpack .../080-libraqm0_0.10.1-1_amd64.deb ... 388s Unpacking libraqm0:amd64 (0.10.1-1) ... 388s Selecting previously unselected package libdeflate0:amd64. 388s Preparing to unpack .../081-libdeflate0_1.19-1_amd64.deb ... 388s Unpacking libdeflate0:amd64 (1.19-1) ... 388s Selecting previously unselected package libjbig0:amd64. 388s Preparing to unpack .../082-libjbig0_2.1-6.1ubuntu1_amd64.deb ... 388s Unpacking libjbig0:amd64 (2.1-6.1ubuntu1) ... 388s Selecting previously unselected package liblerc4:amd64. 388s Preparing to unpack .../083-liblerc4_4.0.0+ds-4ubuntu1_amd64.deb ... 388s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 388s Selecting previously unselected package libsharpyuv0:amd64. 388s Preparing to unpack .../084-libsharpyuv0_1.3.2-0.4_amd64.deb ... 388s Unpacking libsharpyuv0:amd64 (1.3.2-0.4) ... 388s Selecting previously unselected package libwebp7:amd64. 388s Preparing to unpack .../085-libwebp7_1.3.2-0.4_amd64.deb ... 388s Unpacking libwebp7:amd64 (1.3.2-0.4) ... 388s Selecting previously unselected package libtiff6:amd64. 388s Preparing to unpack .../086-libtiff6_4.5.1+git230720-3ubuntu1_amd64.deb ... 388s Unpacking libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 388s Selecting previously unselected package libwebpdemux2:amd64. 388s Preparing to unpack .../087-libwebpdemux2_1.3.2-0.4_amd64.deb ... 388s Unpacking libwebpdemux2:amd64 (1.3.2-0.4) ... 389s Selecting previously unselected package libwebpmux3:amd64. 389s Preparing to unpack .../088-libwebpmux3_1.3.2-0.4_amd64.deb ... 389s Unpacking libwebpmux3:amd64 (1.3.2-0.4) ... 389s Selecting previously unselected package python3-pil:amd64. 389s Preparing to unpack .../089-python3-pil_10.2.0-1_amd64.deb ... 389s Unpacking python3-pil:amd64 (10.2.0-1) ... 389s Selecting previously unselected package libtcl8.6:amd64. 389s Preparing to unpack .../090-libtcl8.6_8.6.13+dfsg-2_amd64.deb ... 389s Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ... 389s Selecting previously unselected package fontconfig-config. 389s Preparing to unpack .../091-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ... 389s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 389s Selecting previously unselected package libfontconfig1:amd64. 389s Preparing to unpack .../092-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ... 389s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 389s Selecting previously unselected package libxrender1:amd64. 389s Preparing to unpack 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previously unselected package blt. 389s Preparing to unpack .../099-blt_2.5.3+dfsg-7_amd64.deb ... 389s Unpacking blt (2.5.3+dfsg-7) ... 389s Selecting previously unselected package python3-tk:amd64. 389s Preparing to unpack .../100-python3-tk_3.11.5-1_amd64.deb ... 389s Unpacking python3-tk:amd64 (3.11.5-1) ... 389s Selecting previously unselected package python3-pil.imagetk:amd64. 389s Preparing to unpack .../101-python3-pil.imagetk_10.2.0-1_amd64.deb ... 389s Unpacking python3-pil.imagetk:amd64 (10.2.0-1) ... 389s Selecting previously unselected package python3-contourpy. 389s Preparing to unpack .../102-python3-contourpy_1.0.7-1build2_amd64.deb ... 389s Unpacking python3-contourpy (1.0.7-1build2) ... 389s Selecting previously unselected package python3-cycler. 389s Preparing to unpack .../103-python3-cycler_0.11.0-2_all.deb ... 389s Unpacking python3-cycler (0.11.0-2) ... 389s Selecting previously unselected package python3-brotli. 389s Preparing to unpack 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package libxslt1.1:amd64. 390s Preparing to unpack .../110-libxslt1.1_1.1.35-1_amd64.deb ... 390s Unpacking libxslt1.1:amd64 (1.1.35-1) ... 390s Selecting previously unselected package python3-lxml:amd64. 390s Preparing to unpack .../111-python3-lxml_5.1.0-1_amd64.deb ... 390s Unpacking python3-lxml:amd64 (5.1.0-1) ... 390s Selecting previously unselected package python3-lz4. 390s Preparing to unpack .../112-python3-lz4_4.0.2+dfsg-1build2_amd64.deb ... 390s Unpacking python3-lz4 (4.0.2+dfsg-1build2) ... 390s Selecting previously unselected package python3-unicodedata2. 390s Preparing to unpack .../113-python3-unicodedata2_15.1.0+ds-1_amd64.deb ... 390s Unpacking python3-unicodedata2 (15.1.0+ds-1) ... 390s Selecting previously unselected package unicode-data. 390s Preparing to unpack .../114-unicode-data_15.1.0-1_all.deb ... 390s Unpacking unicode-data (15.1.0-1) ... 390s Selecting previously unselected package python3-fonttools. 390s Preparing to unpack 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392s Setting up python3-py (1.11.0-2) ... 392s Setting up libdebuginfod-common (0.190-1) ... 392s Setting up python3-joblib (1.3.2-1) ... 393s Setting up python3-parso (0.8.3-1) ... 393s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 393s Setting up python3-asttokens (2.4.1-1) ... 393s Setting up python3-unicodedata2 (15.1.0+ds-1) ... 393s Setting up libpgm-5.3-0:amd64 (5.3.128~dfsg-2) ... 393s Setting up fonts-lyx (2.4.0~RC3-1) ... 393s Setting up libdebuginfod1:amd64 (0.190-1) ... 393s Setting up python3-threadpoolctl (3.1.0-1) ... 393s Setting up libnorm1:amd64 (1.5.9+dfsg-3) ... 393s Setting up x11-common (1:7.7+23ubuntu2) ... 393s Setting up libdeflate0:amd64 (1.19-1) ... 393s Setting up libqhull-r8.0:amd64 (2020.2-6) ... 393s Setting up python3-coverage (7.3.2-0ubuntu1) ... 394s Setting up libblosc2-2:amd64 (2.13.1+ds-1ubuntu1) ... 394s Setting up libgomp1:amd64 (14-20240221-2.1ubuntu1) ... 394s Setting up python3-networkx (2.8.8-1ubuntu1) ... 395s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 395s "graph [edge [ source u'u\4200' target u'u\4200' ] " 395s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 395s + "node [ id u'u\4200' label b ] ]" 395s Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ... 395s Setting up libaec0:amd64 (1.1.2-1) ... 395s Setting up python3-platformdirs (4.2.0-1) ... 395s Setting up python3-psutil (5.9.8-1) ... 395s Setting up libsource-highlight-common (3.1.9-4.3) ... 395s Setting up libsnappy1v5:amd64 (1.1.10-1) ... 395s Setting up unicode-data (15.1.0-1) ... 395s Setting up python3-decorator (5.1.1-5) ... 395s Setting up libblas3:amd64 (3.12.0-3) ... 395s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 395s Setting up python3-packaging 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python3-traitlets (5.5.0-2) ... 397s Setting up libxslt1.1:amd64 (1.1.35-1) ... 397s Setting up libblosc1:amd64 (1.21.5+ds-1) ... 397s Setting up libopenjp2-7:amd64 (2.5.0-2) ... 397s Setting up libharfbuzz0b:amd64 (8.3.0-2) ... 397s Setting up python3-dateutil (2.8.2-3) ... 397s Setting up libxss1:amd64 (1:1.2.3-1build2) ... 397s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 397s Setting up python3-mpmath (1.2.1-3) ... 397s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... 397s Setting up libwebpmux3:amd64 (1.3.2-0.4) ... 397s Setting up python3-appdirs (1.4.4-4) ... 397s Setting up python3-stack-data (0.6.3-1) ... 397s Setting up python-tables-data (3.9.2-1) ... 397s Setting up libpython3.12:amd64 (3.12.2-1) ... 397s Setting up python3-jupyter-core (5.3.2-1) ... 397s Setting up libsz2:amd64 (1.1.2-1) ... 397s Setting up libsource-highlight4v5:amd64 (3.1.9-4.2build2) ... 397s Setting up python3-ptyprocess (0.7.0-5) ... 398s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 398s Setting up python3-prompt-toolkit (3.0.43-1) ... 398s Setting up python3-sympy (1.12-7) ... 402s Setting up liblapack3:amd64 (3.12.0-3) ... 402s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 402s Setting up libzmq5:amd64 (4.3.5-1) ... 402s Setting up python3-jedi (0.18.2-1ubuntu1) ... 403s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 403s Setting up python3-pytest (7.4.4-1) ... 403s Setting up libwebpdemux2:amd64 (1.3.2-0.4) ... 403s Setting up python3-nbformat (5.9.1-1) ... 403s Setting up python3-matplotlib-inline (0.1.6-2) ... 403s Setting up python3-comm (0.2.1-1) ... 403s Setting up python3-fs (2.4.16-3) ... 404s Setting up gdb (15.0.50.20240219-0ubuntu1) ... 404s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 404s Setting up python3-pexpect (4.9-2) ... 404s Setting up python3-zmq (24.0.1-5) ... 404s Setting up libraqm0:amd64 (0.10.1-1) ... 404s Setting up python3-numpy (1:1.24.2-2) ... 406s Setting up libhdf5-103-1:amd64 (1.10.10+repack-3ubuntu1) ... 406s Setting up python3-lxml:amd64 (5.1.0-1) ... 406s Setting up libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 406s Setting up python3-jupyter-client (7.4.9-2ubuntu1) ... 406s Setting up python3-contourpy (1.0.7-1build2) ... 406s Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 406s Setting up python3-pydevd (2.10.0+ds-10ubuntu1) ... 406s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... 406s Setting up libxft2:amd64 (2.3.6-1) ... 406s Setting up python3-scipy (1.11.4-6) ... 409s Setting up python3-tables-lib (3.9.2-1) ... 409s Setting up libtk8.6:amd64 (8.6.13-2) ... 409s Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-4ubuntu2) ... 409s Setting up python3-sklearn-lib:amd64 (1.4.1.post1+dfsg-1) ... 409s Setting up python3-debugpy (1.8.0+ds-4ubuntu1) ... 409s Setting up python3-pil:amd64 (10.2.0-1) ... 410s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 413s Setting up python3-ipython (8.20.0-1) ... 414s Setting up python3-ipykernel (6.24.0-3) ... 414s Setting up python3-sklearn (1.4.1.post1+dfsg-1) ... 416s Setting up python3-numexpr (2.9.0-1) ... 416s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 416s Setting up blt (2.5.3+dfsg-7) ... 416s Setting up python3-tk:amd64 (3.11.5-1) ... 416s Setting up python3-tables (3.9.2-1) ... 417s Setting up python3-mdtraj (1.9.9-1) ... 417s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:271: SyntaxWarning: invalid escape sequence '\g' 417s """Read data from an AMBER ASCII restart file 417s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:534: SyntaxWarning: invalid escape sequence '\g' 417s """Read data from an AMBER NetCDF restart file 417s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:394: SyntaxWarning: invalid escape sequence '\d' 417s time = float(findall('t= *(\d+\.\d+)',comment)[-1]) 417s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:500: SyntaxWarning: invalid escape sequence '\.' 417s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 417s /usr/lib/python3/dist-packages/mdtraj/formats/gsd.py:228: SyntaxWarning: invalid escape sequence '\g' 417s """Write one or more frames of data to a gsd file. 417s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:237: SyntaxWarning: invalid escape sequence '\g' 417s """Read data from a lammpstrj file. 417s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:429: SyntaxWarning: invalid escape sequence '\g' 417s """Write the box lines in the header of a frame. 417s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:476: SyntaxWarning: invalid escape sequence '\g' 417s """Write one or more frames of data to a lammpstrj file. 417s /usr/lib/python3/dist-packages/mdtraj/formats/mol2.py:215: SyntaxWarning: invalid escape sequence '\s' 417s index_col=0, header=None, sep="\s+", engine='python') 417s /usr/lib/python3/dist-packages/mdtraj/formats/mol2.py:222: SyntaxWarning: invalid escape sequence '\s' 417s atoms_frame = pd.read_csv(csv, sep="\s+", engine='python', header=None) 417s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:217: SyntaxWarning: invalid escape sequence '\g' 417s """Read data from a molecular dynamics trajectory in the AMBER NetCDF 417s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:323: SyntaxWarning: invalid escape sequence '\g' 417s """Write one or more frames of a molecular dynamics trajectory to disk 417s /usr/lib/python3/dist-packages/mdtraj/formats/prmtop.py:63: SyntaxWarning: invalid escape sequence '\.' 417s FORMAT_RE_PATTERN = re.compile("([0-9]+)([a-zA-Z]+)([0-9]+)\.?([0-9]*)") 417s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:44: SyntaxWarning: invalid escape sequence '\s' 417s """Compute the distance between pairs of residues in a trajectory. 417s /usr/lib/python3/dist-packages/mdtraj/geometry/hbond.py:251: SyntaxWarning: invalid escape sequence '\c' 417s """Compute the Kabsch-Sander hydrogen bond energy between each pair 417s /usr/lib/python3/dist-packages/mdtraj/geometry/internal.py:370: SyntaxWarning: invalid escape sequence '\p' 417s """Calculate the Wilson B matrix, which collects the derivatives of the 417s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:80: SyntaxWarning: invalid escape sequence '\l' 417s """Compute the asphericity of a trajectory. 417s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:105: SyntaxWarning: invalid escape sequence '\l' 417s """Compute the acylindricity of a trajectory. 417s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:130: SyntaxWarning: invalid escape sequence '\k' 417s """Compute the relative shape anisotropy of a trajectory. 417s /usr/lib/python3/dist-packages/mdtraj/nmr/shift_wrappers.py:214: SyntaxWarning: invalid escape sequence '\s' 417s d = pd.read_table("./bb_details.dat", index_col=False, header=None, sep="\s+").drop([3], axis=1) 417s /usr/lib/python3/dist-packages/mdtraj/nmr/shift_wrappers.py:292: SyntaxWarning: invalid escape sequence '\s' 417s d = pd.read_table("./trj%d_pred.tab" % i, names=names, header=None, sep="\s+", skiprows=lines_to_skip) 417s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:305: SyntaxWarning: invalid escape sequence '\w' 417s if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str): 417s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:345: SyntaxWarning: invalid escape sequence '\*' 417s return [self['Signature'].replace('*','\*')] + [''] 417s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:464: SyntaxWarning: invalid escape sequence '\*' 417s argspec = argspec.replace('*','\*') 417s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:482: SyntaxWarning: invalid escape sequence '\*' 417s signature = self['Signature'].replace('*', '\*') 417s /usr/lib/python3/dist-packages/mdtraj/testing/docstrings.py:126: SyntaxWarning: invalid escape sequence '\d' 417s m = re.search('takes at most (\d+) positional arguments', str(e)) 417s Setting up python3-pil.imagetk:amd64 (10.2.0-1) ... 417s Setting up python3-fonttools (4.46.0-1) ... 418s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 418s Setting up python3-matplotlib (3.6.3-1ubuntu3) ... 419s Setting up autopkgtest-satdep (0) ... 419s Processing triggers for libc-bin (2.39-0ubuntu2) ... 419s Processing triggers for man-db (2.12.0-3) ... 424s (Reading database ... 87096 files and directories currently installed.) 424s Removing autopkgtest-satdep (0) ... 425s autopkgtest [14:03:43]: test command1: pytest-3 -k 'not nmr.ipynb and not test_image_molecules' 425s autopkgtest [14:03:43]: test command1: [----------------------- 425s ============================= test session starts ============================== 425s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3 425s cachedir: .pytest_cache 425s rootdir: /tmp/autopkgtest.t6mPHq/build.lYa/src 425s configfile: pytest.ini 425s testpaths: tests, examples 428s collecting ... collected 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[ 10%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.scalar_couplings] PASSED [ 10%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.shift_wrappers] PASSED [ 10%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.basereporter] PASSED [ 10%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.dcdreporter] PASSED [ 10%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.hdf5reporter] PASSED [ 10%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.netcdfreporter] PASSED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.xtcreporter] PASSED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdconvert] SKIPPED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdinspect] SKIPPED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docscrape] SKIPPED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docstrings] PASSED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.testing.testing] PASSED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.contextmanagers] PASSED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.delay_import] PASSED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.rotation] PASSED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.singleton] PASSED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.six] SKIPPED [ 11%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.basedimension] PASSED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.baseunit] SKIPPED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.constants] PASSED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.mymatrix] SKIPPED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.prefix] SKIPPED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.quantity] SKIPPED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.standard_dimensions] PASSED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit] SKIPPED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_definitions] SKIPPED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_math] SKIPPED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_operators] SKIPPED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unitcell] PASSED [ 12%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.validation] PASSED [ 13%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.utils.zipped] PASSED [ 13%] 438s tests/test_docstrings.py::test_docstrings[mdtraj.version] PASSED [ 13%] 438s tests/test_drid.py::test_drid_1 PASSED [ 13%] 438s tests/test_drid.py::test_drid_2 PASSED [ 13%] 438s tests/test_dssp.py::test_1 SKIPPED (This test requires mkdssp to be ...) [ 13%] 438s tests/test_dssp.py::test_2 SKIPPED (This test requires mkdssp to be ...) [ 13%] 438s tests/test_dssp.py::test_3 SKIPPED (This test requires mkdssp to be ...) [ 13%] 438s tests/test_dssp.py::test_4 PASSED [ 13%] 438s tests/test_dssp.py::test_5 PASSED [ 13%] 438s tests/test_dssp.py::test_7 PASSED [ 13%] 438s tests/test_dtr.py::test_read PASSED [ 13%] 438s tests/test_dtr.py::test_read_1 PASSED [ 14%] 438s tests/test_dtr.py::test_read_2 PASSED [ 14%] 438s tests/test_dtr.py::test_read_3 PASSED [ 14%] 438s tests/test_dtr.py::test_read_stride PASSED [ 14%] 438s tests/test_dtr.py::test_read_4 PASSED [ 14%] 438s tests/test_dtr.py::test_read_5 PASSED [ 14%] 438s tests/test_dtr.py::test_read_6 PASSED [ 14%] 438s tests/test_dtr.py::test_read_7 PASSED [ 14%] 438s tests/test_dtr.py::test_read_8 PASSED [ 14%] 439s tests/test_dtr.py::test_write_1 PASSED [ 14%] 440s tests/test_dtr.py::test_write_2 PASSED [ 14%] 440s tests/test_dtr.py::test_write_3 PASSED [ 14%] 440s tests/test_dtr.py::test_write_4 PASSED [ 15%] 440s tests/test_dtr.py::test_seek PASSED [ 15%] 440s tests/test_dtr.py::test_read_closed PASSED [ 15%] 440s tests/test_dtr.py::test_tell PASSED [ 15%] 440s tests/test_element.py::test_immutable PASSED [ 15%] 440s tests/test_element.py::test_element_0 PASSED [ 15%] 440s tests/test_element.py::test_element_pickle PASSED [ 15%] 440s tests/test_geometry.py::test_rg PASSED [ 15%] 440s tests/test_geometry.py::test_distances PASSED [ 15%] 440s tests/test_geometry.py::test_center_of_mass PASSED [ 15%] 440s tests/test_geometry.py::test_center_of_geometry PASSED [ 15%] 440s tests/test_geometry.py::test_dihedral_indices PASSED [ 15%] 440s tests/test_geometry.py::test_dihedral_index_offset_generation PASSED [ 15%] 441s tests/test_geometry.py::test_dihedral_0 PASSED [ 16%] 441s tests/test_geometry.py::test_dihedral_1 PASSED [ 16%] 441s tests/test_geometry.py::test_dihedral_triclinic PASSED [ 16%] 441s tests/test_geometry.py::test_angle_0 PASSED [ 16%] 441s tests/test_geometry.py::test_angle_periodic_0 PASSED [ 16%] 441s tests/test_geometry.py::test_angle_triclinic_0 PASSED [ 16%] 441s tests/test_geometry.py::test_angle_1 PASSED [ 16%] 441s tests/test_geometry.py::test_dihedral_performance SKIPPED (Not doing...) [ 16%] 441s tests/test_geometry.py::test_angle_performance SKIPPED (Not doing pe...) [ 16%] 441s tests/test_geometry.py::test_angle_nan PASSED [ 16%] 442s tests/test_geometry.py::test_angle_pbc PASSED [ 16%] 444s tests/test_geometry.py::test_dihedral_pbc PASSED [ 16%] 445s tests/test_geometry.py::test_dihedral_pbc_fails1 PASSED [ 17%] 445s tests/test_geometry.py::test_dihedral_pbc_fails2 PASSED [ 17%] 445s tests/test_geometry.py::test_angle_pbc_fails1 PASSED [ 17%] 445s tests/test_geometry.py::test_no_indices PASSED [ 17%] 446s tests/test_gro.py::test_read_write PASSED [ 17%] 446s tests/test_gro.py::test_read_write_precision PASSED [ 17%] 446s tests/test_gro.py::test_no_whitespace_gro PASSED [ 17%] 446s tests/test_gro.py::test_load PASSED [ 17%] 446s tests/test_gro.py::test_load_with_given_top PASSED [ 17%] 447s tests/test_gro.py::test_against_gmx PASSED [ 17%] 447s tests/test_gsd.py::test_read SKIPPED (gsd module is not available) [ 17%] 447s tests/test_gsd.py::test_read_start SKIPPED (gsd module is not available) [ 17%] 447s tests/test_gsd.py::test_read_frame SKIPPED (gsd module is not available) [ 18%] 447s tests/test_gsd.py::test_read_stride SKIPPED (gsd module is not avail...) [ 18%] 447s tests/test_gsd.py::test_read_variable_top_error SKIPPED (gsd module ...) [ 18%] 447s tests/test_gsd.py::test_write SKIPPED (gsd module is not available) [ 18%] 447s tests/test_gsd.py::test_write_frame SKIPPED (gsd module is not avail...) [ 18%] 447s tests/test_hbonds.py::test_hbonds PASSED [ 18%] 447s tests/test_hbonds.py::test_hbonds_against_dssp SKIPPED (This test re...) [ 18%] 447s tests/test_hbonds.py::test_baker_hubbard_0 PASSED [ 18%] 447s tests/test_hbonds.py::test_baker_hubbard_1 PASSED [ 18%] 448s tests/test_hbonds.py::test_baker_hubbard_2 PASSED [ 18%] 448s tests/test_hbonds.py::test_baker_hubbard_3 PASSED [ 18%] 448s tests/test_hbonds.py::test_wernet_nilsson_0 PASSED [ 18%] 448s tests/test_hbonds.py::test_wernet_nilsson_1 PASSED [ 19%] 448s tests/test_hdf5.py::test_write_coordinates PASSED [ 19%] 448s tests/test_hdf5.py::test_write_coordinates_reshape PASSED [ 19%] 448s tests/test_hdf5.py::test_write_multiple PASSED [ 19%] 448s tests/test_hdf5.py::test_write_inconsistent PASSED [ 19%] 448s tests/test_hdf5.py::test_write_inconsistent_2 PASSED [ 19%] 448s tests/test_hdf5.py::test_write_units SKIPPED (requires openmm.units) [ 19%] 448s tests/test_hdf5.py::test_write_units2 PASSED [ 19%] 448s tests/test_hdf5.py::test_write_units_mismatch SKIPPED (requires open...) [ 19%] 448s tests/test_hdf5.py::test_topology PASSED [ 19%] 448s tests/test_hdf5.py::test_constraints PASSED [ 19%] 448s tests/test_hdf5.py::test_constraints2 PASSED [ 19%] 448s tests/test_hdf5.py::test_read_0 PASSED [ 20%] 448s tests/test_hdf5.py::test_read_1 SKIPPED (requires openmm.units) [ 20%] 448s tests/test_hdf5.py::test_read_slice_0 PASSED [ 20%] 448s tests/test_hdf5.py::test_read_slice_1 PASSED [ 20%] 448s tests/test_hdf5.py::test_read_slice_2 PASSED [ 20%] 448s tests/test_hdf5.py::test_read_slice_3 PASSED [ 20%] 448s tests/test_hdf5.py::test_do_overwrite PASSED [ 20%] 449s tests/test_hdf5.py::test_vsite_elements PASSED [ 20%] 449s tests/test_hdf5.py::test_dont_overwrite PASSED [ 20%] 449s tests/test_hdf5.py::test_attributes PASSED [ 20%] 449s tests/test_hdf5.py::test_append PASSED [ 20%] 451s tests/test_hoomdxml.py::test_load PASSED [ 20%] 451s tests/test_hoomdxml.py::test_load_no_chains PASSED [ 21%] 451s tests/test_hoomdxml.py::test_load_no_ions PASSED [ 21%] 451s tests/test_hoomdxml.py::test_correct_ordering PASSED [ 21%] 451s tests/test_io.py::test_overwrite_1 PASSED [ 21%] 451s tests/test_io.py::test_overwrite_2 PASSED [ 21%] 451s tests/test_io.py::test_io::test_load_1 PASSED [ 21%] 451s tests/test_io.py::test_io::test_load_2 PASSED [ 21%] 451s tests/test_io.py::test_io::test_load_3 PASSED [ 21%] 451s tests/test_io.py::test_io::test_save PASSED [ 21%] 451s tests/test_io.py::test_io_int::test_load_1 PASSED [ 21%] 451s tests/test_io.py::test_io_int::test_load_2 PASSED [ 21%] 451s tests/test_io.py::test_io_int::test_load_3 PASSED [ 21%] 451s tests/test_io.py::test_io_int::test_save PASSED [ 21%] 451s tests/test_io.py::test_groups PASSED [ 22%] 451s tests/test_lammpstrj.py::test_read_0 PASSED [ 22%] 451s tests/test_lammpstrj.py::test_read_1 PASSED [ 22%] 451s tests/test_lammpstrj.py::test_read_write_0 PASSED [ 22%] 451s tests/test_lammpstrj.py::test_mdwrite PASSED [ 22%] 451s tests/test_lammpstrj.py::test_multiread PASSED [ 22%] 451s tests/test_lammpstrj.py::test_seek PASSED [ 22%] 451s tests/test_lammpstrj.py::test_custom PASSED [ 22%] 451s tests/test_lh5.py::test_write_coordinates PASSED [ 22%] 451s tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 22%] 451s tests/test_lh5.py::test_write_multiple PASSED [ 22%] 451s tests/test_lh5.py::test_topology PASSED [ 22%] 451s tests/test_lh5.py::test_read_slice_0 PASSED [ 23%] 451s tests/test_lh5.py::test_vsite_elements PASSED [ 23%] 451s tests/test_lh5.py::test_do_overwrite_0 PASSED [ 23%] 451s tests/test_lh5.py::test_do_overwrite_1 PASSED [ 23%] 452s tests/test_load.py::test_load_single PASSED [ 23%] 452s tests/test_load.py::test_load_single_list PASSED [ 23%] 453s tests/test_load.py::test_load_many_list PASSED [ 23%] 453s tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 23%] 453s tests/test_lprmsd.py::test_munkres_0 PASSED [ 23%] 453s tests/test_lprmsd.py::test_lprmsd_null PASSED [ 23%] 453s tests/test_lprmsd.py::test_lprmsd_0 PASSED [ 23%] 453s tests/test_lprmsd.py::test_lprmsd_1 PASSED [ 23%] 453s tests/test_lprmsd.py::test_lprmsd_2 PASSED [ 24%] 453s tests/test_lprmsd.py::test_lprmsd_3 PASSED [ 24%] 453s tests/test_lprmsd.py::test_lprmsd_4 PASSED [ 24%] 453s tests/test_lprmsd.py::test_lprmsd_5 PASSED [ 24%] 455s tests/test_mdconvert.py::test_index PASSED [ 24%] 456s tests/test_mdconvert.py::test_slice PASSED [ 24%] 476s tests/test_mdconvert.py::test_pairwise[from-xtc] PASSED [ 24%] 495s tests/test_mdconvert.py::test_pairwise[from-dcd] PASSED [ 24%] 515s tests/test_mdconvert.py::test_pairwise[from-binpos] PASSED [ 24%] 534s tests/test_mdconvert.py::test_pairwise[from-trr] PASSED [ 24%] 554s tests/test_mdconvert.py::test_pairwise[from-nc] PASSED [ 24%] 573s tests/test_mdconvert.py::test_pairwise[from-pdb] PASSED [ 24%] 618s tests/test_mdconvert.py::test_pairwise[from-h5] PASSED [ 25%] 663s tests/test_mdconvert.py::test_pairwise[from-lh5] PASSED [ 25%] 682s tests/test_mdconvert.py::test_pairwise[from-netcdf] PASSED [ 25%] 683s tests/test_mdconvert.py::test_mdconvert_alanine PASSED [ 25%] 683s tests/test_mdcrd.py::test_read_0 PASSED [ 25%] 683s tests/test_mdcrd.py::test_read_1 PASSED [ 25%] 683s tests/test_mdcrd.py::test_read_write_0 PASSED [ 25%] 683s tests/test_mdcrd.py::test_read_write_1 PASSED [ 25%] 683s tests/test_mdcrd.py::test_read_write_2 PASSED [ 25%] 683s tests/test_mdcrd.py::test_multiread PASSED [ 25%] 683s tests/test_mdcrd.py::test_seek PASSED [ 25%] 683s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 25%] 683s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 683s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 683s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 26%] 683s tests/test_mol2.py::test_mol2_dataframe PASSED [ 26%] 683s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 26%] 683s tests/test_mol2.py::test_mol2_warnings PASSED [ 26%] 683s tests/test_mol2.py::test_mol2_status_bits PASSED [ 26%] 683s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 26%] 683s tests/test_mol2.py::test_mol2_element_name PASSED [ 26%] 683s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 26%] 683s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 26%] 683s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 26%] 683s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 26%] 683s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 683s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 27%] 683s tests/test_mol2.py::test_mol2_n_residues PASSED [ 27%] 683s tests/test_neighborlist.py::test_nonperiodic PASSED [ 27%] 683s tests/test_neighborlist.py::test_periodic PASSED [ 27%] 684s tests/test_neighborlist.py::test_triclinic PASSED [ 27%] 684s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 27%] 685s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 27%] 686s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 27%] 686s tests/test_netcdf.py::test_read_after_close PASSED [ 27%] 686s tests/test_netcdf.py::test_shape PASSED [ 27%] 686s tests/test_netcdf.py::test_read_chunk_1 PASSED [ 27%] 686s tests/test_netcdf.py::test_read_chunk_2 PASSED [ 28%] 686s tests/test_netcdf.py::test_read_chunk_3 PASSED [ 28%] 686s tests/test_netcdf.py::test_read_write_1 PASSED [ 28%] 686s tests/test_netcdf.py::test_read_write_2 PASSED [ 28%] 686s tests/test_netcdf.py::test_ragged_1 PASSED [ 28%] 686s tests/test_netcdf.py::test_ragged_2 PASSED [ 28%] 686s tests/test_netcdf.py::test_read_write_25 PASSED [ 28%] 686s tests/test_netcdf.py::test_write_3 PASSED [ 28%] 686s tests/test_netcdf.py::test_n_atoms PASSED [ 28%] 686s tests/test_netcdf.py::test_do_overwrite PASSED [ 28%] 686s tests/test_netcdf.py::test_trajectory_save_load PASSED [ 28%] 686s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 28%] 686s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 29%] 686s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 29%] 686s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 29%] 686s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 29%] 686s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 29%] 686s tests/test_order.py::test_nematic_order PASSED [ 29%] 686s tests/test_order.py::test_director PASSED [ 29%] 686s tests/test_order.py::test_inertia PASSED [ 29%] 686s tests/test_order.py::test_nematic_order_args PASSED [ 29%] 686s tests/test_order.py::test_order_from_traj PASSED [ 29%] 686s tests/test_order.py::test_directors_angle_from_traj PASSED [ 29%] 686s tests/test_pdb.py::test_pdbread PASSED [ 29%] 686s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 30%] 686s tests/test_pdb.py::test_pdbwrite PASSED [ 30%] 686s tests/test_pdb.py::test_load_multiframe PASSED [ 30%] 686s tests/test_pdb.py::test_4ZUO PASSED [ 30%] 687s tests/test_pdb.py::test_2EQQ_0 PASSED [ 30%] 689s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 30%] 689s tests/test_pdb.py::test_write_large PASSED [ 30%] 689s tests/test_pdb.py::test_write_large_2 PASSED [ 30%] 689s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 30%] 689s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 30%] 689s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 30%] 689s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 30%] 691s tests/test_pdb.py::test_pdb_from_url PASSED [ 31%] 692s tests/test_pdb.py::test_3nch_conect PASSED [ 31%] 694s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 31%] 694s tests/test_pdb.py::test_1ncw PASSED [ 31%] 696s tests/test_pdb.py::test_1vii_url_and_gz PASSED [ 31%] 696s tests/test_pdb.py::test_segment_id PASSED [ 31%] 696s tests/test_pdb.py::test_bfactors PASSED [ 31%] 699s tests/test_pdb.py::test_hex PASSED [ 31%] 700s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 31%] 700s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 31%] 700s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 31%] 700s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 31%] 700s tests/test_prmtop.py::test_load_prmtop PASSED [ 31%] 700s tests/test_prmtop.py::test_load_binpos_w_prmtop PASSED [ 32%] 700s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 32%] 700s tests/test_psf.py::test_load_psf PASSED [ 32%] 705s tests/test_psf.py::test_multichain_psf PASSED [ 32%] 705s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 32%] 705s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 32%] 705s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 32%] 705s tests/test_quaternion.py::test_quaternion_0 PASSED [ 32%] 705s tests/test_quaternion.py::test_quaternion_1 PASSED [ 32%] 705s tests/test_quaternion.py::test_quaternion_2 PASSED [ 32%] 708s tests/test_rdf.py::test_rdf_norm PASSED [ 32%] 708s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 32%] 708s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 33%] 713s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 33%] 713s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 33%] 713s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 33%] 714s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 33%] 715s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 33%] 715s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 33%] 715s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 33%] 716s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 33%] 716s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 33%] 716s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 33%] 717s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 33%] 717s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 34%] 717s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 34%] 717s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 34%] 717s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 34%] 717s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 34%] 718s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 34%] 718s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 34%] 718s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 34%] 718s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 34%] 718s tests/test_restart.py::test_read_after_close PASSED [ 34%] 718s tests/test_restart.py::test_shape PASSED [ 34%] 718s tests/test_restart.py::test_shape_2 PASSED [ 34%] 718s tests/test_restart.py::test_read_write_1 PASSED [ 35%] 718s tests/test_restart.py::test_read_write_2 PASSED [ 35%] 718s tests/test_restart.py::test_read_write_3 PASSED [ 35%] 718s tests/test_restart.py::test_read_write_4 PASSED [ 35%] 718s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 35%] 718s tests/test_rmsd.py::test_precentered_1 PASSED [ 35%] 718s tests/test_rmsd.py::test_precentered_2 PASSED [ 35%] 719s tests/test_rmsd.py::test_superpose_0 PASSED [ 35%] 719s tests/test_rmsd.py::test_superpose_1 PASSED [ 35%] 719s tests/test_rmsd.py::test_superpose_2 PASSED [ 35%] 719s tests/test_rmsd.py::test_superpose_refinds PASSED [ 35%] 719s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 35%] 719s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 36%] 719s tests/test_rmsd.py::test_average_structure PASSED [ 36%] 719s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 36%] 719s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 36%] 719s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 36%] 719s tests/test_rmsd_memmap.py::test_1 PASSED [ 36%] 719s tests/test_rmsd_memmap.py::test_2 PASSED [ 36%] 719s tests/test_sasa.py::test_sasa_0 PASSED [ 36%] 719s tests/test_sasa.py::test_sasa_1 PASSED [ 36%] 719s tests/test_sasa.py::test_sasa_2 PASSED [ 36%] 720s tests/test_sasa.py::test_sasa_3 PASSED [ 36%] 721s tests/test_sasa.py::test_sasa_4 PASSED [ 36%] 721s tests/test_sasa.py::test_sasa_5 PASSED [ 36%] 721s tests/test_selection.py::test_range PASSED [ 37%] 721s tests/test_selection.py::test_unary_2 PASSED [ 37%] 721s tests/test_selection.py::test_unary_3 PASSED [ 37%] 721s tests/test_selection.py::test_binary_1 PASSED [ 37%] 721s tests/test_selection.py::test_binary_2 PASSED [ 37%] 721s tests/test_selection.py::test_simple PASSED [ 37%] 721s tests/test_selection.py::test_alias PASSED [ 37%] 721s tests/test_selection.py::test_unary_1 PASSED [ 37%] 721s tests/test_selection.py::test_binary_selection_operator PASSED [ 37%] 721s tests/test_selection.py::test_raises PASSED [ 37%] 721s tests/test_selection.py::test_raises2 PASSED [ 37%] 721s tests/test_selection.py::test_bool PASSED [ 37%] 721s tests/test_selection.py::test_nested_bool PASSED [ 38%] 721s tests/test_selection.py::test_values PASSED [ 38%] 721s tests/test_selection.py::test_element PASSED [ 38%] 721s tests/test_selection.py::test_not PASSED [ 38%] 721s tests/test_selection.py::test_re PASSED [ 38%] 721s tests/test_selection.py::test_quotes PASSED [ 38%] 721s tests/test_selection.py::test_top PASSED [ 38%] 721s tests/test_selection.py::test_top_2 PASSED [ 38%] 722s tests/test_selection.py::test_backbone PASSED [ 38%] 722s tests/test_selection.py::test_sidechain PASSED [ 38%] 722s tests/test_selection.py::test_literal PASSED [ 38%] 722s tests/test_selection.py::test_in PASSED [ 38%] 722s tests/test_shape.py::test_gyration PASSED [ 39%] 722s tests/test_shape.py::test_principal_moments PASSED [ 39%] 723s tests/test_shape.py::test_asphericity PASSED [ 39%] 723s tests/test_shape.py::test_shape_metrics PASSED [ 39%] 723s tests/test_thermodynamic_properties.py::test_volume PASSED [ 39%] 723s tests/test_thermodynamic_properties.py::test_density PASSED [ 39%] 723s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 39%] 723s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 39%] 723s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 39%] 723s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 39%] 723s tests/test_tng.py::test_load_trajectory PASSED [ 39%] 723s tests/test_tng.py::test_load_topology SKIPPED (Fails on macOS + Pyth...) [ 39%] 723s tests/test_tng.py::test_write PASSED [ 40%] 723s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 40%] 723s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 40%] 723s tests/test_topology.py::test_topology_pandas PASSED [ 40%] 724s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 40%] 724s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 40%] 724s tests/test_topology.py::test_topology_numbers PASSED [ 40%] 724s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 40%] 724s tests/test_topology.py::test_chain PASSED [ 40%] 724s tests/test_topology.py::test_residue PASSED [ 40%] 724s tests/test_topology.py::test_segment_id PASSED [ 40%] 724s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 40%] 724s tests/test_topology.py::test_pickle PASSED [ 41%] 724s tests/test_topology.py::test_atoms_by_name PASSED [ 41%] 724s tests/test_topology.py::test_select_atom_indices PASSED [ 41%] 724s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 41%] 724s tests/test_topology.py::test_n_bonds PASSED [ 41%] 724s tests/test_topology.py::test_load_unknown_topology PASSED [ 41%] 724s tests/test_topology.py::test_unique_pairs PASSED [ 41%] 725s tests/test_topology.py::test_select_pairs PASSED [ 41%] 725s tests/test_topology.py::test_to_fasta PASSED [ 41%] 725s tests/test_topology.py::test_subset PASSED [ 41%] 726s tests/test_topology.py::test_subset_re_index_residues PASSED [ 41%] 726s tests/test_topology.py::test_molecules PASSED [ 41%] 726s tests/test_topology.py::test_copy_and_hash PASSED [ 42%] 726s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 42%] 726s tests/test_topology.py::test_topology_join PASSED [ 42%] 726s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 42%] 726s tests/test_trajectory.py::test_mismatch PASSED [ 42%] 726s tests/test_trajectory.py::test_box PASSED [ 42%] 726s tests/test_trajectory.py::test_load_pdb_box PASSED [ 42%] 727s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 42%] 727s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 42%] 727s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 42%] 727s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 42%] 727s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 42%] 727s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 42%] 727s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 43%] 727s tests/test_trajectory.py::test_box_load_save[binpos] SKIPPED (binpos...) [ 43%] 727s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 43%] 727s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 43%] 727s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 43%] 727s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 43%] 727s tests/test_trajectory.py::test_box_load_save[tng] PASSED [ 43%] 727s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 43%] 727s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 43%] 727s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 43%] 727s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 43%] 727s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 43%] 727s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 44%] 727s tests/test_trajectory.py::test_slice PASSED [ 44%] 727s tests/test_trajectory.py::test_slice2 PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[nc] PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[h5] PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[trr] PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[binpos] PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 44%] 727s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 45%] 727s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 45%] 727s tests/test_trajectory.py::test_read_path[tng] PASSED [ 45%] 727s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 45%] 727s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 45%] 727s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 45%] 727s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 45%] 727s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 45%] 727s tests/test_trajectory.py::test_read_path[gro] PASSED [ 45%] 727s tests/test_trajectory.py::test_write_path[nc] PASSED [ 45%] 727s tests/test_trajectory.py::test_write_path[h5] PASSED [ 45%] 727s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 45%] 727s tests/test_trajectory.py::test_write_path[trr] PASSED [ 46%] 727s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 46%] 727s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 46%] 727s tests/test_trajectory.py::test_write_path[binpos] PASSED [ 46%] 728s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 46%] 728s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 46%] 728s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 46%] 728s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 46%] 728s tests/test_trajectory.py::test_write_path[tng] PASSED [ 46%] 728s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 46%] 728s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 46%] 728s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 46%] 728s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 47%] 728s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 47%] 728s tests/test_trajectory.py::test_write_path[gro] PASSED [ 47%] 728s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 47%] 728s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 47%] 728s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 47%] 728s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 47%] 728s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 47%] 728s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 47%] 728s tests/test_trajectory.py::test_read_write[nc-binpos] PASSED [ 47%] 728s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 47%] 728s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 47%] 729s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 47%] 729s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 48%] 729s tests/test_trajectory.py::test_read_write[nc-tng] PASSED [ 48%] 729s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 48%] 729s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 48%] 730s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 48%] 730s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 48%] 730s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 48%] 730s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 48%] 730s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 48%] 730s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 48%] 730s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 48%] 730s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 48%] 730s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 49%] 730s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 49%] 730s tests/test_trajectory.py::test_read_write[h5-binpos] PASSED [ 49%] 730s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 49%] 730s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 49%] 731s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 49%] 731s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 49%] 731s tests/test_trajectory.py::test_read_write[h5-tng] PASSED [ 49%] 731s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 49%] 731s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 49%] 732s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 49%] 732s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 49%] 732s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 50%] 732s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 50%] 732s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 50%] 732s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 50%] 732s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 50%] 732s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 50%] 732s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 50%] 732s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 50%] 732s tests/test_trajectory.py::test_read_write[xtc-binpos] PASSED [ 50%] 732s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 50%] 733s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 50%] 733s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 50%] 733s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 51%] 733s tests/test_trajectory.py::test_read_write[xtc-tng] PASSED [ 51%] 733s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 51%] 733s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 51%] 734s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 51%] 734s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 51%] 734s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 51%] 734s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 51%] 734s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 51%] 734s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 51%] 734s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 51%] 734s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 51%] 734s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 52%] 734s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 52%] 734s tests/test_trajectory.py::test_read_write[trr-binpos] PASSED [ 52%] 735s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 52%] 735s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 52%] 735s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 52%] 735s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 52%] 735s tests/test_trajectory.py::test_read_write[trr-tng] PASSED [ 52%] 735s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 52%] 735s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 52%] 736s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 52%] 736s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 52%] 736s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 52%] 736s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 53%] 736s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 53%] 736s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 53%] 736s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 53%] 736s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 53%] 736s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 53%] 736s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 53%] 736s tests/test_trajectory.py::test_read_write[dcd-binpos] PASSED [ 53%] 737s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 53%] 737s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 53%] 737s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 53%] 737s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 53%] 737s tests/test_trajectory.py::test_read_write[dcd-tng] PASSED [ 54%] 737s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 54%] 738s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 54%] 738s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 54%] 738s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 54%] 738s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 54%] 738s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 54%] 738s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 54%] 738s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 54%] 738s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 54%] 738s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 54%] 738s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 54%] 738s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 55%] 738s tests/test_trajectory.py::test_read_write[mdcrd-binpos] PASSED [ 55%] 738s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 55%] 739s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 55%] 739s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 55%] 739s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 55%] 739s tests/test_trajectory.py::test_read_write[mdcrd-tng] PASSED [ 55%] 739s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 55%] 740s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 55%] 741s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 55%] 741s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 55%] 741s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 55%] 741s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-nc] PASSED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-h5] PASSED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-xtc] PASSED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-trr] PASSED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-dcd] PASSED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-mdcrd] SKIPPED (mdc...) [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-binpos] PASSED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-dtr] SKIPPED (dtr n...) [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-xyz] PASSED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-xyz.gz] PASSED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-lammpstrj] SKIPPED [ 56%] 741s tests/test_trajectory.py::test_read_write[binpos-tng] PASSED [ 57%] 741s tests/test_trajectory.py::test_read_write[binpos-lh5] PASSED [ 57%] 742s tests/test_trajectory.py::test_read_write[binpos-pdb] PASSED [ 57%] 742s tests/test_trajectory.py::test_read_write[binpos-pdb.gz] PASSED [ 57%] 742s tests/test_trajectory.py::test_read_write[binpos-ncrst] SKIPPED (ncr...) [ 57%] 742s tests/test_trajectory.py::test_read_write[binpos-rst7] SKIPPED (rst7...) [ 57%] 742s tests/test_trajectory.py::test_read_write[binpos-gro] PASSED [ 57%] 742s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 57%] 742s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 57%] 742s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 57%] 742s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 57%] 742s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 57%] 742s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 57%] 742s tests/test_trajectory.py::test_read_write[dtr-binpos] PASSED [ 58%] 743s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 58%] 743s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 58%] 743s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 58%] 743s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 58%] 743s tests/test_trajectory.py::test_read_write[dtr-tng] PASSED [ 58%] 743s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 58%] 744s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 58%] 744s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 58%] 744s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 58%] 744s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 58%] 744s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 58%] 744s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-binpos] PASSED [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-tng] PASSED [ 59%] 745s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 60%] 745s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 60%] 746s tests/test_trajectory.py::test_read_write[xyz.gz-binpos] PASSED [ 61%] 746s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 61%] 746s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 61%] 747s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 61%] 747s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 61%] 747s tests/test_trajectory.py::test_read_write[xyz.gz-tng] PASSED [ 61%] 747s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 61%] 747s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 61%] 748s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 61%] 748s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 61%] 748s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 61%] 748s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 61%] 748s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 62%] 748s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 62%] 748s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 62%] 748s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 62%] 748s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 62%] 748s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 62%] 748s tests/test_trajectory.py::test_read_write[lammpstrj-binpos] PASSED [ 62%] 749s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 62%] 749s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 62%] 749s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 62%] 749s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 62%] 749s tests/test_trajectory.py::test_read_write[lammpstrj-tng] PASSED [ 62%] 749s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 63%] 750s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 63%] 750s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 63%] 750s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 63%] 750s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 63%] 750s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 63%] 750s tests/test_trajectory.py::test_read_write[tng-nc] PASSED [ 63%] 750s tests/test_trajectory.py::test_read_write[tng-h5] PASSED [ 63%] 750s tests/test_trajectory.py::test_read_write[tng-xtc] PASSED [ 63%] 750s tests/test_trajectory.py::test_read_write[tng-trr] PASSED [ 63%] 750s tests/test_trajectory.py::test_read_write[tng-dcd] PASSED [ 63%] 750s tests/test_trajectory.py::test_read_write[tng-mdcrd] SKIPPED (mdcrd ...) [ 63%] 750s tests/test_trajectory.py::test_read_write[tng-binpos] PASSED [ 63%] 754s tests/test_trajectory.py::test_read_write[tng-dtr] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-xyz] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-xyz.gz] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-lammpstrj] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-tng] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-lh5] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-pdb] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-pdb.gz] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-ncrst] SKIPPED (ncrst ...) [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-rst7] SKIPPED (rst7 ca...) [ 64%] 754s tests/test_trajectory.py::test_read_write[tng-gro] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 64%] 754s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-binpos] PASSED [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-tng] PASSED [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 65%] 754s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 754s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 754s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 754s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 754s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 754s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 754s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 755s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 755s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 755s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 755s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 66%] 755s tests/test_trajectory.py::test_read_write[pdb-binpos] PASSED [ 66%] 756s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 756s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 757s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 757s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 757s tests/test_trajectory.py::test_read_write[pdb-tng] PASSED [ 67%] 757s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 758s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 758s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 758s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 758s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 759s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 759s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 67%] 759s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 759s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 759s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 760s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 760s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 760s tests/test_trajectory.py::test_read_write[pdb.gz-binpos] PASSED [ 68%] 762s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 762s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 762s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 762s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 762s tests/test_trajectory.py::test_read_write[pdb.gz-tng] PASSED [ 68%] 762s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 762s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 68%] 763s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 763s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 763s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 763s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 763s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 763s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 763s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 763s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 763s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 763s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 763s tests/test_trajectory.py::test_read_write[ncrst-binpos] XFAIL (These...) [ 69%] 763s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 763s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 764s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 764s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 764s tests/test_trajectory.py::test_read_write[ncrst-tng] XFAIL (These re...) [ 70%] 764s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 764s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 764s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 764s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 764s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 764s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 764s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 764s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 764s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-binpos] XFAIL (These ...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-tng] XFAIL (These ref...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 764s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 72%] 764s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 764s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 764s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 764s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 764s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 764s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 764s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 764s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 764s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 764s tests/test_trajectory.py::test_read_write[gro-binpos] PASSED [ 72%] 765s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 765s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 73%] 765s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 73%] 765s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 765s tests/test_trajectory.py::test_read_write[gro-tng] PASSED [ 73%] 765s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 766s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 766s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 766s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 766s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 766s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 766s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 766s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 766s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 767s tests/test_trajectory.py::test_load[trr] PASSED [ 74%] 767s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 767s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 767s tests/test_trajectory.py::test_load[binpos] PASSED [ 74%] 767s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 767s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 767s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 767s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 768s tests/test_trajectory.py::test_load[tng] PASSED [ 74%] 768s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 769s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 770s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 770s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 75%] 770s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 75%] 771s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 771s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 771s tests/test_trajectory.py::test_center PASSED [ 75%] 771s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[binpos] PASSED [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[tng] PASSED [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 771s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 771s tests/test_trajectory.py::test_restrict_atoms PASSED [ 77%] 771s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 77%] 771s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 77%] 771s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 771s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 771s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 771s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 771s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 771s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 771s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 771s tests/test_trajectory.py::test_load_combination[binpos] PASSED [ 77%] 771s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 771s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 78%] 771s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 78%] 771s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 78%] 771s tests/test_trajectory.py::test_load_combination[tng] PASSED [ 78%] 771s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 772s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 772s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 772s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 772s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 772s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 772s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 772s tests/test_trajectory.py::test_join PASSED [ 78%] 772s tests/test_trajectory.py::test_md_join PASSED [ 78%] 772s tests/test_trajectory.py::test_stack_1 PASSED [ 79%] 772s tests/test_trajectory.py::test_stack_2 PASSED [ 79%] 772s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 79%] 772s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 772s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 772s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 772s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 773s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 773s tests/test_trajectory.py::test_seek_read_mode[binpos] PASSED [ 79%] 773s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 773s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 773s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 773s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 80%] 773s tests/test_trajectory.py::test_seek_read_mode[tng] PASSED [ 80%] 773s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 80%] 773s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 80%] 773s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 773s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 773s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 773s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 773s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 773s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 773s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 773s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 773s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 81%] 773s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 81%] 773s tests/test_trajectory.py::test_load_frame[binpos] PASSED [ 81%] 773s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 81%] 773s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 773s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 773s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 773s tests/test_trajectory.py::test_load_frame[tng] PASSED [ 81%] 773s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 774s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 774s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 774s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 774s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 82%] 774s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 82%] 774s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 82%] 774s tests/test_trajectory.py::test_iterload[nc] PASSED [ 82%] 774s tests/test_trajectory.py::test_iterload[h5] PASSED [ 82%] 774s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 774s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 775s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 775s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 775s tests/test_trajectory.py::test_iterload[binpos] PASSED [ 82%] 775s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 775s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 775s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 83%] 775s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 83%] 775s tests/test_trajectory.py::test_iterload[tng] PASSED [ 83%] 775s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 83%] 775s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 83%] 775s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 83%] 775s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 775s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 775s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 776s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 778s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 779s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 780s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 84%] 781s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 84%] 783s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 84%] 783s tests/test_trajectory.py::test_iterload_skip[binpos] PASSED [ 84%] 783s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 84%] 784s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 84%] 786s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 787s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 788s tests/test_trajectory.py::test_iterload_skip[tng] PASSED [ 84%] 789s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 789s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 789s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 789s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 789s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 85%] 789s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 85%] 789s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 85%] 789s tests/test_trajectory.py::test_save_load[nc] PASSED [ 85%] 789s tests/test_trajectory.py::test_save_load[h5] PASSED [ 85%] 789s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] 790s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 790s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 790s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 790s tests/test_trajectory.py::test_save_load[binpos] PASSED [ 85%] 790s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 790s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 790s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 86%] 790s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 86%] 790s tests/test_trajectory.py::test_save_load[tng] PASSED [ 86%] 790s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 86%] 790s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 86%] 790s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 86%] 790s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 86%] 790s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 790s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 790s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 790s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 790s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 790s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[binpos] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[tng] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 790s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[binpos] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 790s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 89%] 790s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 89%] 790s tests/test_trajectory.py::test_force_noverwrite[tng] PASSED [ 89%] 790s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 89%] 790s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 89%] 790s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 89%] 790s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 89%] 790s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 89%] 790s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 89%] 790s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 790s tests/test_trajectory.py::test_length PASSED [ 89%] 790s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 790s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 790s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[binpos] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 90%] 790s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 790s tests/test_trajectory.py::test_unitcell[tng] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 790s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 91%] 790s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 91%] 790s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 91%] 790s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 91%] 790s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 91%] 791s tests/test_trajectory.py::test_hashing PASSED [ 91%] 791s tests/test_trajectory.py::test_smooth PASSED [ 91%] 791s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 91%] 791s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] 791s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 791s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 791s tests/test_trr.py::test_1 PASSED [ 91%] 791s tests/test_trr.py::test_read_stride PASSED [ 92%] 791s tests/test_trr.py::test_read_stride_n_frames PASSED [ 92%] 791s tests/test_trr.py::test_read_stride_offsets PASSED [ 92%] 791s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 92%] 791s tests/test_trr.py::test_read_stride_switching PASSED [ 92%] 791s tests/test_trr.py::test_write_read PASSED [ 92%] 791s tests/test_trr.py::test_read_atomindices_1 PASSED [ 92%] 791s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 791s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 791s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 791s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 791s tests/test_trr.py::test_malformed PASSED [ 92%] 791s tests/test_trr.py::test_tell PASSED [ 93%] 791s tests/test_trr.py::test_seek PASSED [ 93%] 791s tests/test_trr.py::test_get_velocities PASSED [ 93%] 791s tests/test_trr.py::test_get_forces PASSED [ 93%] 791s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 93%] 791s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 93%] 791s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 791s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 791s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 791s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 791s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 791s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 791s tests/test_utils.py::test_ensure_type_2 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_25 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_3 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_4 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_5 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_6 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 791s tests/test_utils.py::test_ensure_type_14 PASSED [ 95%] 791s tests/test_utils.py::test_ensure_type_15 PASSED [ 95%] 791s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 95%] 791s tests/test_utils.py::test_delay_import PASSED [ 95%] 791s tests/test_utils.py::test_unit_0 PASSED [ 95%] 791s tests/test_utils.py::test_unit_1 PASSED [ 95%] 791s tests/test_utils.py::test_unit_2 PASSED [ 95%] 791s tests/test_utils.py::test_unit_3 PASSED [ 95%] 791s tests/test_xml.py::test_xml PASSED [ 95%] 791s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 791s tests/test_xtc.py::test_read_stride PASSED [ 95%] 791s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 791s tests/test_xtc.py::test_read_stride_offsets PASSED [ 96%] 791s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 96%] 791s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 96%] 791s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 791s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 791s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 791s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 791s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 791s tests/test_xtc.py::test_write_0 PASSED [ 96%] 791s tests/test_xtc.py::test_write_1 PASSED [ 96%] 792s tests/test_xtc.py::test_write_2 PASSED [ 96%] 792s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 792s tests/test_xtc.py::test_write_error_0 PASSED [ 97%] 792s tests/test_xtc.py::test_read_error_1 PASSED [ 97%] 792s tests/test_xtc.py::test_read_error_2 PASSED [ 97%] 792s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 792s tests/test_xtc.py::test_tell PASSED [ 97%] 792s tests/test_xtc.py::test_seek PASSED [ 97%] 792s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 792s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 792s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 792s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 792s tests/test_xtc.py::test_short_traj PASSED [ 97%] 792s tests/test_xtc.py::test_flush PASSED [ 97%] 792s tests/test_xyz.py::test_read_0 PASSED [ 98%] 792s tests/test_xyz.py::test_read_1 PASSED [ 98%] 792s tests/test_xyz.py::test_read_gz PASSED [ 98%] 792s tests/test_xyz.py::test_read_write PASSED [ 98%] 792s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 792s tests/test_xyz.py::test_multiread PASSED [ 98%] 792s tests/test_xyz.py::test_seek PASSED [ 98%] 792s tests/test_xyz.py::test_len PASSED [ 98%] 792s tests/test_zipped.py::test_read_gz PASSED [ 98%] 792s tests/test_zipped.py::test_write_gz PASSED [ 98%] 792s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 792s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 931s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 1064s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 1064s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [ 99%] 1201s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 1338s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 1474s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 1612s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 1749s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 1886s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 2023s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 2158s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 2296s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 2432s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [100%] 2432s 2432s =============================== warnings summary =============================== 2432s ../../../../usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:57 2432s /usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:57: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead 2432s ast.Pow, ast.Div, ast.Mult, ast.Num] 2432s 2432s ../../../../usr/lib/python3/dist-packages/mdtraj/formats/__init__.py:6 2432s /usr/lib/python3/dist-packages/mdtraj/formats/__init__.py:6: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13 2432s from .xtc import XTCTrajectoryFile 2432s 2432s ../../../../usr/lib/python3/dist-packages/mdtraj/geometry/order.py:25 2432s /usr/lib/python3/dist-packages/mdtraj/geometry/order.py:25: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 2432s from pkg_resources import parse_version 2432s 2432s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871 2432s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`. 2432s Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages 2432s declare_namespace(pkg) 2432s 2432s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 2432s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 2432s EPOCH = datetime.datetime.utcfromtimestamp(0) 2432s 2432s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:27 2432s /usr/lib/python3/dist-packages/jupyter_client/connect.py:27: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 2432s given by the platformdirs library. To remove this warning and 2432s see the appropriate new directories, set the environment variable 2432s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 2432s The use of platformdirs will be the default in `jupyter_core` v6 2432s from jupyter_core.paths import jupyter_data_dir 2432s 2432s examples/test_examples.py:26 2432s /tmp/autopkgtest.t6mPHq/build.lYa/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 2432s examples = [pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 2432s 2432s tests/test_angles.py::test_angle_pbc_0 2432s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting unitcell_vectors dtype=float64 to 2432s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2432s 2432s tests/test_arc.py::test_read_arctraj 2432s tests/test_order.py::test_nematic_order 2432s tests/test_order.py::test_director 2432s tests/test_order.py::test_inertia 2432s tests/test_order.py::test_nematic_order_args 2432s tests/test_shape.py::test_gyration 2432s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:198: RuntimeWarning: divide by zero encountered in divide 2432s particle_density = traj.top.n_atoms / traj.unitcell_volumes[0] 2432s 2432s tests/test_arc.py: 1 warning 2432s tests/test_gro.py: 3 warnings 2432s tests/test_order.py: 4 warnings 2432s tests/test_pdb.py: 1 warning 2432s tests/test_shape.py: 4 warnings 2432s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:200: UserWarning: Unlikely unit cell vectors detected in PDB file likely resulting from a dummy CRYST1 record. Discarding unit cell vectors. 2432s warnings.warn('Unlikely unit cell vectors detected in PDB file likely ' 2432s 2432s tests/test_arc.py: 1 warning 2432s tests/test_dihedral.py: 1 warning 2432s tests/test_geometry.py: 2 warnings 2432s tests/test_hdf5.py: 1 warning 2432s tests/test_lprmsd.py: 1 warning 2432s tests/test_mdconvert.py: 9 warnings 2432s tests/test_mol2.py: 1 warning 2432s tests/test_nmr.py: 1 warning 2432s tests/test_rmsd.py: 8 warnings 2432s tests/test_rmsd_memmap.py: 2 warnings 2432s tests/test_sasa.py: 3 warnings 2432s tests/test_topology.py: 2 warnings 2432s tests/test_trajectory.py: 85 warnings 2432s /usr/lib/python3/dist-packages/mdtraj/core/trajectory.py:439: UserWarning: top= kwargs ignored since this file parser does not support it 2432s warnings.warn('top= kwargs ignored since this file parser does not support it') 2432s 2432s tests/test_contact.py::test_contact_0 2432s tests/test_contact.py::test_contact_4 2432s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:199: 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. 2432s warnings.warn('selected topology includes at least one glycine residue, which has no heavy atoms in its sidechain. The distances involving glycine residues ' 2432s 2432s tests/test_contact.py::test_contact_3 2432s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:227: RuntimeWarning: overflow encountered in exp 2432s np.log(np.sum(np.exp(soft_min_beta/ 2432s 2432s tests/test_contact.py::test_contact_3 2432s /tmp/autopkgtest.t6mPHq/build.lYa/src/tests/test_contact.py:106: RuntimeWarning: divide by zero encountered in divide 2432s assert np.allclose(beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), dists[t, i]) 2432s 2432s tests/test_dcd.py::test_do_overwrite 2432s tests/test_dcd.py::test_ragged_1 2432s tests/test_dcd.py::test_ragged_2 2432s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 2432s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2432s 2432s tests/test_distance.py: 6 warnings 2432s tests/test_mdconvert.py: 112 warnings 2432s tests/test_neighbors.py: 2 warnings 2432s tests/test_netcdf.py: 46 warnings 2432s tests/test_rdf.py: 8 warnings 2432s tests/test_restart.py: 4 warnings 2432s tests/test_trajectory.py: 196 warnings 2432s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:130: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2432s if StrictVersion(import_('scipy.version').short_version) < StrictVersion('0.12.0'): 2432s 2432s tests/test_drid.py::test_drid_2 2432s /tmp/autopkgtest.t6mPHq/build.lYa/src/tests/test_drid.py:61: RuntimeWarning: divide by zero encountered in divide 2432s recip = 1 / squareform(pdist(t.xyz[i])) 2432s 2432s tests/test_geometry.py: 1 warning 2432s tests/test_hoomdxml.py: 1 warning 2432s tests/test_neighbors.py: 2 warnings 2432s tests/test_rdf.py: 38 warnings 2432s tests/test_selection.py: 73 warnings 2432s tests/test_topology.py: 17 warnings 2432s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:385: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead 2432s if isinstance(astnode, ast.Num) or isinstance(astnode, ast.Str): 2432s 2432s tests/test_geometry.py: 2 warnings 2432s tests/test_hoomdxml.py: 1 warning 2432s tests/test_neighbors.py: 2 warnings 2432s tests/test_rdf.py: 38 warnings 2432s tests/test_selection.py: 73 warnings 2432s tests/test_topology.py: 17 warnings 2432s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:385: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead 2432s if isinstance(astnode, ast.Num) or isinstance(astnode, ast.Str): 2432s 2432s tests/test_geometry.py::test_dihedral_indices 2432s tests/test_geometry.py::test_dihedral_indices 2432s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:203: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 2432s warnings.warn("Passing a Trajectory object to _atom_sequence is" 2432s 2432s tests/test_gro.py::test_load 2432s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 2432s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:322: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 2432s warnings.warn("WARNING: two consecutive residues with same number (%s, %s)" % (thisresname, old_resname)) 2432s 2432s tests/test_hdf5.py::test_read_0 2432s tests/test_hdf5.py::test_read_slice_0 2432s tests/test_hdf5.py::test_read_slice_2 2432s tests/test_hdf5.py::test_read_slice_3 2432s /usr/lib/python3/dist-packages/tables/path.py:137: NaturalNameWarning: object name is a Python keyword: 'lambda'; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though 2432s check_attribute_name(name) 2432s 2432s tests/test_rdf.py: 7 warnings 2432s tests/test_selection.py: 14 warnings 2432s tests/test_topology.py: 5 warnings 2432s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:62: DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead 2432s return ast.NameConstant(value=_safe_names[node.id], kind=None) 2432s 2432s tests/test_rdf.py: 32 warnings 2432s tests/test_selection.py: 23 warnings 2432s tests/test_topology.py: 12 warnings 2432s /usr/lib/python3/dist-packages/mdtraj/core/selection.py:68: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead 2432s return ast.Str(s=node.id, kind=None) 2432s 2432s tests/test_rdf.py: 32 warnings 2432s tests/test_selection.py: 23 warnings 2432s tests/test_topology.py: 12 warnings 2432s /usr/lib/python3.12/ast.py:587: DeprecationWarning: Attribute s is deprecated and will be removed in Python 3.14; use value instead 2432s return Constant(*args, **kwargs) 2432s 2432s tests/test_restart.py: 1014 warnings 2432s tests/test_trajectory.py: 12 warnings 2432s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:465: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2432s if StrictVersion(import_('scipy.version').short_version) < StrictVersion('0.12.0'): 2432s 2432s tests/test_trajectory.py::test_box_load_save[dtr] 2432s tests/test_trajectory.py::test_read_write[dcd-dtr] 2432s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] 2432s tests/test_trajectory.py::test_read_write[pdb-dtr] 2432s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] 2432s tests/test_trajectory.py::test_save_load[dtr] 2432s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=int64 to 2432s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2432s 2432s tests/test_trajectory.py::test_write_path[dtr] 2432s tests/test_trajectory.py::test_read_write[h5-dtr] 2432s tests/test_trajectory.py::test_read_write[xtc-dtr] 2432s tests/test_trajectory.py::test_read_write[trr-dtr] 2432s tests/test_trajectory.py::test_read_write[tng-dtr] 2432s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=float32 to 2432s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2432s 2432s tests/test_trajectory.py::test_read_write[nc-dtr] 2432s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=>f4 to 2432s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2432s 2432s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 2432s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:91: UserWarning: atom_indices are not monotonically increasing 2432s warnings.warn('atom_indices are not monotonically increasing') 2432s 2432s tests/test_trajectory.py::test_array_vs_matrix 2432s /tmp/autopkgtest.t6mPHq/build.lYa/src/tests/test_trajectory.py:352: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 2432s xyz_mat = np.matrix(xyz) 2432s 2432s tests/test_utils.py::test_ensure_type_8 2432s tests/test_utils.py::test_ensure_type_9 2432s tests/test_utils.py::test_ensure_type_13 2432s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting dtype=float64 to 2432s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2432s 2432s tests/test_utils.py::test_ensure_type_11 2432s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting dtype=int64 to 2432s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2432s 2432s tests/test_utils.py::test_unit_3 2432s tests/test_utils.py::test_unit_3 2432s /usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:60: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead 2432s if not any(isinstance(node, a) for a in self.allowed_ops): 2432s 2432s examples/test_examples.py::test_example_notebook[principal-components.ipynb] 2432s /usr/lib/python3/dist-packages/jupyter_client/utils.py:18: DeprecationWarning: There is no current event loop 2432s loop = asyncio.get_event_loop_policy().get_event_loop() 2432s 2432s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 2432s =========================== short test summary info ============================ 2432s SKIPPED [1] tests/test_dihedral.py:48: pymol executable not found 2432s SKIPPED [1] tests/test_dihedral.py:149: pymol executable not found 2432s SKIPPED [16] tests/test_docstrings.py:36: Skip checking certain modules' docstrings 2432s SKIPPED [1] tests/test_dssp.py:44: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2432s SKIPPED [1] tests/test_dssp.py:52: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2432s SKIPPED [1] tests/test_dssp.py:59: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2432s SKIPPED [1] tests/test_geometry.py:243: Not doing performance testing 2432s SKIPPED [1] tests/test_geometry.py:261: Not doing performance testing 2432s SKIPPED [1] tests/test_gsd.py:30: gsd module is not available 2432s SKIPPED [1] tests/test_gsd.py:41: gsd module is not available 2432s SKIPPED [1] tests/test_gsd.py:51: gsd module is not available 2432s SKIPPED [1] tests/test_gsd.py:61: gsd module is not available 2432s SKIPPED [1] tests/test_gsd.py:75: gsd module is not available 2432s SKIPPED [1] tests/test_gsd.py:82: gsd module is not available 2432s SKIPPED [1] tests/test_gsd.py:94: gsd module is not available 2432s SKIPPED [1] tests/test_hbonds.py:43: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2432s SKIPPED [1] tests/test_hdf5.py:99: requires openmm.units 2432s SKIPPED [1] tests/test_hdf5.py:133: requires openmm.units 2432s SKIPPED [1] tests/test_hdf5.py:186: requires openmm.units 2432s SKIPPED [1] tests/test_mol2.py:55: Requires obabel 2432s SKIPPED [1] tests/test_netcdf.py:248: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 2432s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 2432s SKIPPED [1] tests/test_nmr.py:24: PPM binary not found 2432s SKIPPED [1] tests/test_nmr.py:38: SHIFTX2 binary not found or Python 2 not found or runningn on travis. 2432s SKIPPED [1] tests/test_pdbx.py:39: test_pdbx.py needs OpenMM. 2432s SKIPPED [2] tests/test_psf.py:92: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 2432s SKIPPED [1] tests/test_rdf.py:66: Binning does not match up with gromacs currently. 2432s SKIPPED [1] tests/test_rdf.py:153: Binning does not match up with gromacs currently. 2432s SKIPPED [1] tests/test_reporter.py:47: test_reporter.py needs OpenMM. 2432s SKIPPED [1] tests/test_reporter.py:121: test_reporter.py needs OpenMM. 2432s SKIPPED [1] tests/test_reporter.py:201: test_reporter.py needs OpenMM. 2432s SKIPPED [1] tests/test_thermodynamic_properties.py:154: Thermal expansion test doesn't work. 2432s SKIPPED [1] tests/test_tng.py:20: Fails on macOS + Python 3.11, need to investigate. 2432s SKIPPED [1] tests/test_topology.py:42: needs OpenMM 2432s SKIPPED [1] tests/test_topology.py:59: needs OpenMM 2432s SKIPPED [1] tests/test_topology.py:187: needs OpenMM 2432s SKIPPED [1] tests/test_trajectory.py:128: binpos does not store box information 2432s SKIPPED [1] tests/test_trajectory.py:128: xyz does not store box information 2432s SKIPPED [1] tests/test_trajectory.py:128: xyz.gz does not store box information 2432s SKIPPED [1] tests/test_trajectory.py:128: lh5 does not store box information 2432s SKIPPED [1] tests/test_trajectory.py:128: pdb does not store box information 2432s SKIPPED [1] tests/test_trajectory.py:128: pdb.gz does not store box information 2432s SKIPPED [1] tests/test_trajectory.py:200: mdcrd can only store rectilinear boxes 2432s SKIPPED [1] tests/test_trajectory.py:198: ncrst can only store 1 frame per file 2432s SKIPPED [1] tests/test_trajectory.py:198: rst7 can only store 1 frame per file 2432s SKIPPED [16] tests/test_trajectory.py:212: mdcrd can only store rectilinear boxes 2432s SKIPPED [16] tests/test_trajectory.py:210: ncrst can only store 1 frame per file 2432s SKIPPED [16] tests/test_trajectory.py:210: rst7 can only store 1 frame per file 2432s SKIPPED [5] tests/test_trajectory.py:219: dtr needs to write unitcells 2432s SKIPPED [5] tests/test_trajectory.py:219: lammpstrj needs to write unitcells 2432s SKIPPED [2] tests/test_trajectory.py:541: Only 1 frame per file format 2432s SKIPPED [2] examples/test_examples.py:71: Network access required 2432s SKIPPED [1] examples/test_examples.py:71: Openmm required for example notebook `simulation-with-openmm.ipynb` 2432s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-binpos] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-tng] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-binpos] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-tng] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 2432s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 2432s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 2432s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 2432s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 2432s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 2432s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 2432s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 2432s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 2432s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 2432s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 2432s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 2432s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 2432s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 2432s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 2432s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 2432s = 1030 passed, 124 skipped, 2 deselected, 65 xfailed, 2006 warnings in 2007.27s (0:33:27) = 2433s autopkgtest [14:37:11]: test command1: -----------------------] 2433s autopkgtest [14:37:11]: test command1: - - - - - - - - - - results - - - - - - - - - - 2433s command1 PASS 2433s autopkgtest [14:37:11]: @@@@@@@@@@@@@@@@@@@@ summary 2433s command1 PASS 2443s Creating nova instance adt-noble-amd64-mdtraj-20240305-135638-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240304.img (UUID ae047650-70fb-43f4-8dd2-17d325c301dd)...