0s autopkgtest [16:01:23]: starting date: 2024-03-05 0s autopkgtest [16:01:23]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [16:01:23]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k2wlyj3f/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@bos01-arm64-44.secgroup --name adt-noble-arm64-mdtraj-20240305-154649-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-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://us.ports.ubuntu.com/ubuntu-ports/ 149s autopkgtest [16:03:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 149s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 150s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [3976 B] 150s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [24.5 kB] 150s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [320 kB] 150s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [1778 kB] 150s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [426 kB] 150s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 150s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 150s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 150s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2075 kB] 150s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 150s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [14.3 kB] 150s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 151s Fetched 4791 kB in 1s (3847 kB/s) 152s Reading package lists... 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Calculating upgrade... 156s The following packages will be upgraded: 156s dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common 156s dbus-user-session gcc-13-base libdbus-1-3 libksba8 python3-rich zlib1g 157s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 977 kB of archives. 157s After this operation, 65.5 kB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 zlib1g arm64 1:1.3.dfsg-3.1ubuntu1 [61.7 kB] 157s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-base arm64 13.2.0-17ubuntu2 [47.4 kB] 157s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-system-bus-common all 1.14.10-4ubuntu1 [81.4 kB] 157s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-session-bus-common all 1.14.10-4ubuntu1 [80.2 kB] 157s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-user-session arm64 1.14.10-4ubuntu1 [9958 B] 157s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-daemon arm64 1.14.10-4ubuntu1 [115 kB] 157s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 dbus-bin arm64 1.14.10-4ubuntu1 [38.8 kB] 157s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 dbus arm64 1.14.10-4ubuntu1 [23.9 kB] 157s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libdbus-1-3 arm64 1.14.10-4ubuntu1 [210 kB] 157s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 python3-rich all 13.7.1-1 [189 kB] 157s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libksba8 arm64 1.6.6-1 [119 kB] 157s Fetched 977 kB in 1s (1673 kB/s) 157s (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 ... 74627 files and directories currently installed.) 157s Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu1_arm64.deb ... 157s Unpacking zlib1g:arm64 (1:1.3.dfsg-3.1ubuntu1) over (1:1.3.dfsg-3ubuntu1) ... 157s Setting up zlib1g:arm64 (1:1.3.dfsg-3.1ubuntu1) ... 157s (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 ... 74627 files and directories currently installed.) 158s Preparing to unpack .../0-gcc-13-base_13.2.0-17ubuntu2_arm64.deb ... 158s Unpacking gcc-13-base:arm64 (13.2.0-17ubuntu2) over (13.2.0-16ubuntu1) ... 158s Preparing to unpack .../1-dbus-system-bus-common_1.14.10-4ubuntu1_all.deb ... 158s Unpacking dbus-system-bus-common (1.14.10-4ubuntu1) over (1.14.10-3ubuntu1) ... 158s Preparing to unpack .../2-dbus-session-bus-common_1.14.10-4ubuntu1_all.deb ... 158s Unpacking dbus-session-bus-common (1.14.10-4ubuntu1) over (1.14.10-3ubuntu1) ... 158s Preparing to unpack .../3-dbus-user-session_1.14.10-4ubuntu1_arm64.deb ... 158s Unpacking dbus-user-session (1.14.10-4ubuntu1) over (1.14.10-3ubuntu1) ... 158s Preparing to unpack .../4-dbus-daemon_1.14.10-4ubuntu1_arm64.deb ... 158s Unpacking dbus-daemon (1.14.10-4ubuntu1) over (1.14.10-3ubuntu1) ... 158s Preparing to unpack .../5-dbus-bin_1.14.10-4ubuntu1_arm64.deb ... 158s Unpacking dbus-bin (1.14.10-4ubuntu1) over (1.14.10-3ubuntu1) ... 158s Preparing to unpack .../6-dbus_1.14.10-4ubuntu1_arm64.deb ... 158s Unpacking dbus (1.14.10-4ubuntu1) over (1.14.10-3ubuntu1) ... 158s Preparing to unpack .../7-libdbus-1-3_1.14.10-4ubuntu1_arm64.deb ... 158s Unpacking libdbus-1-3:arm64 (1.14.10-4ubuntu1) over (1.14.10-3ubuntu1) ... 158s Preparing to unpack .../8-python3-rich_13.7.1-1_all.deb ... 158s Unpacking python3-rich (13.7.1-1) over (13.7.0-1) ... 158s Preparing to unpack .../9-libksba8_1.6.6-1_arm64.deb ... 158s Unpacking libksba8:arm64 (1.6.6-1) over (1.6.5-2) ... 158s Setting up libksba8:arm64 (1.6.6-1) ... 158s Setting up python3-rich (13.7.1-1) ... 158s Setting up gcc-13-base:arm64 (13.2.0-17ubuntu2) ... 158s Setting up libdbus-1-3:arm64 (1.14.10-4ubuntu1) ... 158s Setting up dbus-session-bus-common (1.14.10-4ubuntu1) ... 158s Setting up dbus-system-bus-common (1.14.10-4ubuntu1) ... 158s Setting up dbus-bin (1.14.10-4ubuntu1) ... 158s Setting up dbus-daemon (1.14.10-4ubuntu1) ... 158s Setting up dbus-user-session (1.14.10-4ubuntu1) ... 158s Setting up dbus (1.14.10-4ubuntu1) ... 158s A reboot is required to replace the running dbus-daemon. 158s Please reboot the system when convenient. 158s Processing triggers for man-db (2.12.0-3) ... 159s Processing triggers for libc-bin (2.39-0ubuntu2) ... 160s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s 160s 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 160s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 160s 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 160s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 160s 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 160s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 160s 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 160s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 160s 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 160s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 160s 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 160s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 160s 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 160s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 160s 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 160s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 160s 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 160s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 160s 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 160s sh: Attempting to set up Debian/Ubuntu apt sources automatically 160s sh: Distribution appears to be Ubuntu 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 164s eatmydata is already the newest version (131-1). 164s dbus is already the newest version (1.14.10-4ubuntu1). 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s Reading package lists... 164s 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 164s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 164s 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 164s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s 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 164s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s 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 164s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s 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 164s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s 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 164s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s 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 164s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s 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 164s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s 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 164s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 164s 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 164s Building dependency tree... 164s Reading state information... 165s rng-tools-debian is already the newest version (2.4). 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s haveged is already the newest version (1.9.14-1ubuntu1). 165s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 165s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s The following packages will be REMOVED: 166s cloud-init* python3-configobj* python3-debconf* 166s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 166s After this operation, 3248 kB disk space will be freed. 166s (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 ... 74627 files and directories currently installed.) 166s Removing cloud-init (24.1-0ubuntu1) ... 167s Removing python3-configobj (5.0.8-3) ... 167s Removing python3-debconf (1.5.86) ... 167s Processing triggers for man-db (2.12.0-3) ... 167s (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 ... 74238 files and directories currently installed.) 167s Purging configuration files for cloud-init (24.1-0ubuntu1) ... 168s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 168s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 168s Reading package lists... 168s Building dependency tree... 168s Reading state information... 169s linux-generic is already the newest version (6.8.0-11.11+1). 169s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 169s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 169s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 169s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 169s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 169s Hit:5 http://ftpmaster.internal/ubuntu noble-backports InRelease 172s Reading package lists... 172s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2Reading package lists... 172s 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 172s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 172s 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 172s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 172s 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 172s 173s Building dependency tree... 173s Reading state information... 173s Calculating upgrade... 173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s autopkgtest [16:04:17]: rebooting testbed after setup commands that affected boot 327s autopkgtest [16:06:50]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 327s autopkgtest [16:06:50]: testbed dpkg architecture: arm64 329s autopkgtest [16:06:52]: @@@@@@@@@@@@@@@@@@@@ apt-source mdtraj 329s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:1 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:2 and /etc/apt/sources.list.d/ubuntu.sources:1 329s 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 329s W: Target Packages (main/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 329s 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 329s W: Target CNF (main/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 329s 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 329s W: Target Packages (universe/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 329s 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 329s W: Target CNF (universe/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 329s 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 329s W: Target Packages (restricted/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 329s 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 329s W: Target CNF (restricted/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 329s 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 329s W: Target Packages (multiverse/binary-arm64/Packages) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 329s 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 329s W: Target CNF (multiverse/cnf/Commands-arm64) is configured multiple times in /etc/apt/sources.list:3 and /etc/apt/sources.list.d/ubuntu.sources:2 329s 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 331s Get:1 http://ftpmaster.internal/ubuntu noble/universe mdtraj 1.9.9-1 (dsc) [2619 B] 331s Get:2 http://ftpmaster.internal/ubuntu noble/universe mdtraj 1.9.9-1 (tar) [21.7 MB] 331s Get:3 http://ftpmaster.internal/ubuntu noble/universe mdtraj 1.9.9-1 (diff) [299 kB] 331s gpgv: Signature made Tue Jan 16 11:10:34 2024 UTC 331s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 331s gpgv: issuer "tille@debian.org" 331s gpgv: Can't check signature: No public key 331s dpkg-source: warning: cannot verify inline signature for ./mdtraj_1.9.9-1.dsc: no acceptable signature found 332s autopkgtest [16:06:55]: testing package mdtraj version 1.9.9-1 332s autopkgtest [16:06:55]: build not needed 337s autopkgtest [16:07:00]: test command1: preparing testbed 341s Reading package lists... 341s Building dependency tree... 341s Reading state information... 341s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 341s Starting 2 pkgProblemResolver with broken count: 0 341s Done 341s Done 342s Starting pkgProblemResolver with broken count: 0 342s Starting 2 pkgProblemResolver with broken count: 0 342s Done 342s The following additional packages will be installed: 342s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 342s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-2 libdebuginfod-common 342s libdebuginfod1 libdeflate0 libdw1 libfontconfig1 libgfortran5 libgomp1 342s libgraphite2-3 libharfbuzz0b libhdf5-103-1 libimagequant0 libjbig0 342s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 342s liblcms2-2 liblerc4 libnorm1 libopenjp2-7 libpgm-5.3-0 libpython3.11-minimal 342s libpython3.11-stdlib libpython3.12 libqhull-r8.0 libraqm0 libsharpyuv0 342s libsnappy1v5 libsodium23 libsource-highlight-common libsource-highlight4v5 342s libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 342s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 python-matplotlib-data 342s python-tables-data python3-appdirs python3-asttokens python3-astunparse 342s python3-brotli python3-bytecode python3-comm python3-contourpy 342s python3-coverage python3-cpuinfo python3-cycler python3-dateutil 342s python3-debugpy python3-decorator python3-distutils python3-entrypoints 342s python3-executing python3-fastjsonschema python3-fonttools python3-fs 342s python3-iniconfig python3-ipykernel python3-ipython python3-jedi 342s python3-joblib python3-jupyter-client python3-jupyter-core 342s python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 342s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 342s python3-nbformat python3-nest-asyncio python3-networkx python3-numexpr 342s python3-numpy python3-packaging python3-pandas python3-pandas-lib 342s python3-parso python3-pexpect python3-pil python3-pil.imagetk 342s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 342s python3-ptyprocess python3-pure-eval python3-py python3-pydevd 342s python3-pytest python3-scipy python3-setuptools python3-sklearn 342s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 342s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 342s python3-traitlets python3-ufolib2 python3-unicodedata2 python3-wcwidth 342s python3-zmq python3.11 python3.11-minimal tk8.6-blt2.5 unicode-data 342s x11-common 342s Suggested packages: 342s blt-demo gdb-doc gdbserver libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 342s python-bytecode-doc python-coverage-doc python-cycler-doc 342s python-fastjsonschema-doc python-ipython-doc python3-pip python-lxml-doc 342s cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 342s inkscape ipython3 librsvg2-common python3-cairocffi python3-gi-cairo 342s python3-gobject python3-pyqt5 python3-sip texlive-extra-utils 342s texlive-latex-extra python-mdtraj-doc python-mpmath-doc python3-gmpy2 342s python-networkx-doc python3-gdal python3-pydot python3-pygraphviz gcc 342s gfortran python3-dev python-pandas-doc python3-statsmodels 342s python-pexpect-doc python-pil-doc subversion pydevd python-scipy-doc 342s python-setuptools-doc python3-dap python-sklearn-doc texlive-fonts-extra 342s python-sympy-doc python3-netcdf4 python-tables-doc vitables tix 342s python3-tk-dbg python3-pycurl python-tornado-doc python3-twisted 342s python3.11-venv python3.11-doc binfmt-support 342s Recommended packages: 342s libc-dbg javascript-common python3-simplejson python3-bs4 python3-cssselect 342s python3-html5lib python3-bottleneck python3-odf python3-openpyxl 342s python3-olefile g++ | c++-compiler isympy-common 342s The following NEW packages will be installed: 342s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gdb 342s libaec0 libbabeltrace1 libblas3 libblosc1 libblosc2-2 libdebuginfod-common 342s libdebuginfod1 libdeflate0 libdw1 libfontconfig1 libgfortran5 libgomp1 342s libgraphite2-3 libharfbuzz0b libhdf5-103-1 libimagequant0 libjbig0 342s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 342s liblcms2-2 liblerc4 libnorm1 libopenjp2-7 libpgm-5.3-0 libpython3.11-minimal 342s libpython3.11-stdlib libpython3.12 libqhull-r8.0 libraqm0 libsharpyuv0 342s libsnappy1v5 libsodium23 libsource-highlight-common libsource-highlight4v5 342s libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 342s libxft2 libxrender1 libxslt1.1 libxss1 libzmq5 python-matplotlib-data 342s python-tables-data python3-appdirs python3-asttokens python3-astunparse 342s python3-brotli python3-bytecode python3-comm python3-contourpy 342s python3-coverage python3-cpuinfo python3-cycler python3-dateutil 342s python3-debugpy python3-decorator python3-distutils python3-entrypoints 342s python3-executing python3-fastjsonschema python3-fonttools python3-fs 342s python3-iniconfig python3-ipykernel python3-ipython python3-jedi 342s python3-joblib python3-jupyter-client python3-jupyter-core 342s python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 342s python3-matplotlib python3-matplotlib-inline python3-mdtraj python3-mpmath 342s python3-nbformat python3-nest-asyncio python3-networkx python3-numexpr 342s python3-numpy python3-packaging python3-pandas python3-pandas-lib 342s python3-parso python3-pexpect python3-pil python3-pil.imagetk 342s python3-platformdirs python3-pluggy python3-prompt-toolkit python3-psutil 342s python3-ptyprocess python3-pure-eval python3-py python3-pydevd 342s python3-pytest python3-scipy python3-setuptools python3-sklearn 342s python3-sklearn-lib python3-stack-data python3-sympy python3-tables 342s python3-tables-lib python3-threadpoolctl python3-tk python3-tornado 342s python3-traitlets python3-ufolib2 python3-unicodedata2 python3-wcwidth 342s python3-zmq python3.11 python3.11-minimal tk8.6-blt2.5 unicode-data 342s x11-common 342s 0 upgraded, 134 newly installed, 0 to remove and 0 not upgraded. 342s 1 not fully installed or removed. 342s Need to get 108 MB of archives. 342s After this operation, 525 MB of additional disk space will be used. 342s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-astunparse all 1.6.3-2 [13.5 kB] 343s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 343s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 343s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 343s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 343s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 343s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240221-2.1ubuntu1 [443 kB] 343s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 343s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 343s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 343s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 343s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 344s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240221-2.1ubuntu1 [144 kB] 344s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 344s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 344s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] 344s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 344s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 344s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 344s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cpuinfo all 9.0.0-1 [21.2 kB] 344s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 344s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-numexpr arm64 2.9.0-1 [87.9 kB] 344s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 python-tables-data all 3.9.2-1 [56.7 kB] 344s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libsnappy1v5 arm64 1.1.10-1 [28.2 kB] 344s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 libblosc1 arm64 1.21.5+ds-1 [25.5 kB] 344s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libblosc2-2 arm64 2.13.1+ds-1ubuntu1 [147 kB] 344s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 344s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 345s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 345s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tables-lib arm64 3.9.2-1 [1068 kB] 345s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tables all 3.9.2-1 [467 kB] 345s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mdtraj arm64 1.9.9-1 [1768 kB] 345s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-traitlets all 5.5.0-2 [85.0 kB] 345s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-comm all 0.2.1-1 [7016 B] 345s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libdw1 arm64 0.190-1 [254 kB] 345s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libbabeltrace1 arm64 1.5.11-3build1 [158 kB] 345s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libdebuginfod-common all 0.190-1 [14.0 kB] 345s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libdebuginfod1 arm64 0.190-1 [16.0 kB] 345s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.12 arm64 3.12.2-1 [2291 kB] 345s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libsource-highlight-common all 3.1.9-4.3 [64.1 kB] 345s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libsource-highlight4v5 arm64 3.1.9-4.2build2 [243 kB] 345s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 gdb arm64 15.0.50.20240219-0ubuntu1 [4881 kB] 345s Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-bytecode all 0.15.1-3 [44.7 kB] 345s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-coverage arm64 7.3.2-0ubuntu1 [147 kB] 345s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pydevd arm64 2.10.0+ds-10ubuntu1 [600 kB] 345s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-debugpy all 1.8.0+ds-4ubuntu1 [652 kB] 345s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-parso all 0.8.3-1 [67.2 kB] 345s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jedi all 0.18.2-1ubuntu1 [692 kB] 345s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 345s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 345s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pexpect all 4.9-2 [48.1 kB] 345s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 345s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-prompt-toolkit all 3.0.43-1 [256 kB] 345s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-asttokens all 2.4.1-1 [20.9 kB] 345s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-executing all 2.0.1-0.1 [23.3 kB] 345s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pure-eval all 0.2.2-1 [11.3 kB] 345s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 345s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2 [396 kB] 345s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ipython all 8.20.0-1 [561 kB] 345s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-platformdirs all 4.2.0-1 [16.1 kB] 345s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jupyter-core all 5.3.2-1 [25.4 kB] 345s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-entrypoints all 0.4-2 [7146 B] 345s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-nest-asyncio all 1.5.4-1 [6256 B] 345s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tornado arm64 6.4.0-1 [297 kB] 345s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-py all 1.11.0-2 [72.7 kB] 345s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 libnorm1 arm64 1.5.9+dfsg-3 [176 kB] 345s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 libpgm-5.3-0 arm64 5.3.128~dfsg-2 [151 kB] 345s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libsodium23 arm64 1.0.18-1build2 [123 kB] 345s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 libzmq5 arm64 4.3.5-1 [246 kB] 345s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-zmq arm64 24.0.1-5 [363 kB] 345s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jupyter-client all 7.4.9-2ubuntu1 [90.5 kB] 345s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 python3-psutil arm64 5.9.8-1 [196 kB] 345s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ipykernel all 6.24.0-3 [105 kB] 345s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 345s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 345s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 345s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 345s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC3-1 [170 kB] 345s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 345s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 345s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 345s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 345s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 345s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 345s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 345s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 345s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 345s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 346s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 346s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 346s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 346s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 346s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 346s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 346s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 346s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 346s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 346s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 346s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 346s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 346s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 346s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 346s Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 346s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB] 347s Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB] 347s Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B] 347s Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB] 347s Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B] 347s Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB] 347s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B] 347s Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB] 347s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 348s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] 348s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB] 349s Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 349s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB] 349s Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.35-1 [161 kB] 349s Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB] 349s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB] 349s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1 [362 kB] 349s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 350s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB] 350s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-1build2 [65.4 kB] 350s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] 350s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB] 351s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fastjsonschema all 2.19.0-1 [19.6 kB] 351s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 351s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 351s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 351s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 351s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-joblib all 1.3.2-1 [207 kB] 351s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 351s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sklearn-lib arm64 1.4.1.post1+dfsg-1 [6663 kB] 351s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sklearn all 1.4.1.post1+dfsg-1 [2261 kB] 352s Preconfiguring packages ... 352s Fetched 108 MB in 9s (12.6 MB/s) 352s Selecting previously unselected package python3-astunparse. 352s (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 ... 74183 files and directories currently installed.) 352s Preparing to unpack .../000-python3-astunparse_1.6.3-2_all.deb ... 352s Unpacking python3-astunparse (1.6.3-2) ... 352s Selecting previously unselected package libpython3.11-minimal:arm64. 352s Preparing to unpack .../001-libpython3.11-minimal_3.11.8-1_arm64.deb ... 352s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 352s Selecting previously unselected package python3.11-minimal. 352s Preparing to unpack .../002-python3.11-minimal_3.11.8-1_arm64.deb ... 352s Unpacking python3.11-minimal (3.11.8-1) ... 352s Selecting previously unselected package libpython3.11-stdlib:arm64. 352s Preparing to unpack .../003-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 352s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 352s Selecting previously unselected package python3.11. 352s Preparing to unpack .../004-python3.11_3.11.8-1_arm64.deb ... 352s Unpacking python3.11 (3.11.8-1) ... 352s Selecting previously unselected package libblas3:arm64. 352s Preparing to unpack .../005-libblas3_3.12.0-3_arm64.deb ... 352s Unpacking libblas3:arm64 (3.12.0-3) ... 352s Selecting previously unselected package libgfortran5:arm64. 352s Preparing to unpack .../006-libgfortran5_14-20240221-2.1ubuntu1_arm64.deb ... 352s Unpacking libgfortran5:arm64 (14-20240221-2.1ubuntu1) ... 352s Selecting previously unselected package liblapack3:arm64. 352s Preparing to unpack .../007-liblapack3_3.12.0-3_arm64.deb ... 352s Unpacking liblapack3:arm64 (3.12.0-3) ... 352s Selecting previously unselected package python3-numpy. 352s Preparing to unpack .../008-python3-numpy_1%3a1.24.2-2_arm64.deb ... 352s Unpacking python3-numpy (1:1.24.2-2) ... 352s Selecting previously unselected package python3-decorator. 352s Preparing to unpack .../009-python3-decorator_5.1.1-5_all.deb ... 352s Unpacking python3-decorator (5.1.1-5) ... 352s Selecting previously unselected package liblbfgsb0:arm64. 352s Preparing to unpack .../010-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 352s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 352s Selecting previously unselected package python3-scipy. 352s Preparing to unpack .../011-python3-scipy_1.11.4-6_arm64.deb ... 352s Unpacking python3-scipy (1.11.4-6) ... 353s Selecting previously unselected package libgomp1:arm64. 353s Preparing to unpack .../012-libgomp1_14-20240221-2.1ubuntu1_arm64.deb ... 353s Unpacking libgomp1:arm64 (14-20240221-2.1ubuntu1) ... 353s Selecting previously unselected package python3-lib2to3. 353s Preparing to unpack .../013-python3-lib2to3_3.11.5-1_all.deb ... 353s Unpacking python3-lib2to3 (3.11.5-1) ... 353s Selecting previously unselected package python3-distutils. 353s Preparing to unpack .../014-python3-distutils_3.11.5-1_all.deb ... 353s Unpacking python3-distutils (3.11.5-1) ... 353s Selecting previously unselected package python3-networkx. 353s Preparing to unpack .../015-python3-networkx_2.8.8-1ubuntu1_all.deb ... 353s Unpacking python3-networkx (2.8.8-1ubuntu1) ... 353s Selecting previously unselected package python3-dateutil. 353s Preparing to unpack .../016-python3-dateutil_2.8.2-3_all.deb ... 353s Unpacking python3-dateutil (2.8.2-3) ... 353s Selecting previously unselected package python3-pandas-lib:arm64. 353s Preparing to unpack .../017-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 353s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 354s Selecting previously unselected package python3-pandas. 354s Preparing to unpack .../018-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 354s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 354s Selecting previously unselected package python3-cpuinfo. 354s Preparing to unpack .../019-python3-cpuinfo_9.0.0-1_all.deb ... 354s Unpacking python3-cpuinfo (9.0.0-1) ... 354s Selecting previously unselected package python3-packaging. 354s Preparing to unpack .../020-python3-packaging_23.2-1_all.deb ... 354s Unpacking python3-packaging (23.2-1) ... 354s Selecting previously unselected package python3-numexpr. 354s Preparing to unpack .../021-python3-numexpr_2.9.0-1_arm64.deb ... 354s Unpacking python3-numexpr (2.9.0-1) ... 354s Selecting previously unselected package python-tables-data. 354s Preparing to unpack .../022-python-tables-data_3.9.2-1_all.deb ... 354s Unpacking python-tables-data (3.9.2-1) ... 354s Selecting previously unselected package libsnappy1v5:arm64. 354s Preparing to unpack .../023-libsnappy1v5_1.1.10-1_arm64.deb ... 354s Unpacking libsnappy1v5:arm64 (1.1.10-1) ... 354s Selecting previously unselected package libblosc1:arm64. 354s Preparing to unpack .../024-libblosc1_1.21.5+ds-1_arm64.deb ... 354s Unpacking libblosc1:arm64 (1.21.5+ds-1) ... 354s Selecting previously unselected package libblosc2-2:arm64. 354s Preparing to unpack .../025-libblosc2-2_2.13.1+ds-1ubuntu1_arm64.deb ... 354s Unpacking libblosc2-2:arm64 (2.13.1+ds-1ubuntu1) ... 354s Selecting previously unselected package libaec0:arm64. 354s Preparing to unpack .../026-libaec0_1.1.2-1_arm64.deb ... 354s Unpacking libaec0:arm64 (1.1.2-1) ... 354s Selecting previously unselected package libsz2:arm64. 354s Preparing to unpack .../027-libsz2_1.1.2-1_arm64.deb ... 354s Unpacking libsz2:arm64 (1.1.2-1) ... 354s Selecting previously unselected package libhdf5-103-1:arm64. 354s Preparing to unpack .../028-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 354s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 354s Selecting previously unselected package python3-tables-lib. 354s Preparing to unpack .../029-python3-tables-lib_3.9.2-1_arm64.deb ... 354s Unpacking python3-tables-lib (3.9.2-1) ... 354s Selecting previously unselected package python3-tables. 354s Preparing to unpack .../030-python3-tables_3.9.2-1_all.deb ... 354s Unpacking python3-tables (3.9.2-1) ... 354s Selecting previously unselected package python3-mdtraj. 354s Preparing to unpack .../031-python3-mdtraj_1.9.9-1_arm64.deb ... 354s Unpacking python3-mdtraj (1.9.9-1) ... 354s Selecting previously unselected package python3-traitlets. 354s Preparing to unpack .../032-python3-traitlets_5.5.0-2_all.deb ... 354s Unpacking python3-traitlets (5.5.0-2) ... 354s Selecting previously unselected package python3-comm. 354s Preparing to unpack .../033-python3-comm_0.2.1-1_all.deb ... 354s Unpacking python3-comm (0.2.1-1) ... 354s Selecting previously unselected package libdw1:arm64. 354s Preparing to unpack .../034-libdw1_0.190-1_arm64.deb ... 354s Unpacking libdw1:arm64 (0.190-1) ... 354s Selecting previously unselected package libbabeltrace1:arm64. 354s Preparing to unpack .../035-libbabeltrace1_1.5.11-3build1_arm64.deb ... 354s Unpacking libbabeltrace1:arm64 (1.5.11-3build1) ... 354s Selecting previously unselected package libdebuginfod-common. 354s Preparing to unpack .../036-libdebuginfod-common_0.190-1_all.deb ... 354s Unpacking libdebuginfod-common (0.190-1) ... 354s Selecting previously unselected package libdebuginfod1:arm64. 354s Preparing to unpack .../037-libdebuginfod1_0.190-1_arm64.deb ... 354s Unpacking libdebuginfod1:arm64 (0.190-1) ... 354s Selecting previously unselected package libpython3.12:arm64. 354s Preparing to unpack .../038-libpython3.12_3.12.2-1_arm64.deb ... 354s Unpacking libpython3.12:arm64 (3.12.2-1) ... 354s Selecting previously unselected package libsource-highlight-common. 354s Preparing to unpack .../039-libsource-highlight-common_3.1.9-4.3_all.deb ... 354s Unpacking libsource-highlight-common (3.1.9-4.3) ... 354s Selecting previously unselected package libsource-highlight4v5:arm64. 354s Preparing to unpack .../040-libsource-highlight4v5_3.1.9-4.2build2_arm64.deb ... 354s Unpacking libsource-highlight4v5:arm64 (3.1.9-4.2build2) ... 354s Selecting previously unselected package gdb. 354s Preparing to unpack .../041-gdb_15.0.50.20240219-0ubuntu1_arm64.deb ... 354s Unpacking gdb (15.0.50.20240219-0ubuntu1) ... 355s Selecting previously unselected package python3-bytecode. 355s Preparing to unpack .../042-python3-bytecode_0.15.1-3_all.deb ... 355s Unpacking python3-bytecode (0.15.1-3) ... 355s Selecting previously unselected package python3-coverage. 355s Preparing to unpack .../043-python3-coverage_7.3.2-0ubuntu1_arm64.deb ... 355s Unpacking python3-coverage (7.3.2-0ubuntu1) ... 355s Selecting previously unselected package python3-pydevd. 355s Preparing to unpack .../044-python3-pydevd_2.10.0+ds-10ubuntu1_arm64.deb ... 355s Unpacking python3-pydevd (2.10.0+ds-10ubuntu1) ... 355s Selecting previously unselected package python3-debugpy. 355s Preparing to unpack .../045-python3-debugpy_1.8.0+ds-4ubuntu1_all.deb ... 355s Unpacking python3-debugpy (1.8.0+ds-4ubuntu1) ... 355s Selecting previously unselected package python3-parso. 355s Preparing to unpack .../046-python3-parso_0.8.3-1_all.deb ... 355s Unpacking python3-parso (0.8.3-1) ... 355s Selecting previously unselected package python3-jedi. 355s Preparing to unpack .../047-python3-jedi_0.18.2-1ubuntu1_all.deb ... 355s Unpacking python3-jedi (0.18.2-1ubuntu1) ... 355s Selecting previously unselected package python3-matplotlib-inline. 355s Preparing to unpack .../048-python3-matplotlib-inline_0.1.6-2_all.deb ... 355s Unpacking python3-matplotlib-inline (0.1.6-2) ... 355s Selecting previously unselected package python3-ptyprocess. 355s Preparing to unpack .../049-python3-ptyprocess_0.7.0-5_all.deb ... 355s Unpacking python3-ptyprocess (0.7.0-5) ... 355s Selecting previously unselected package python3-pexpect. 355s Preparing to unpack .../050-python3-pexpect_4.9-2_all.deb ... 355s Unpacking python3-pexpect (4.9-2) ... 355s Selecting previously unselected package python3-wcwidth. 355s Preparing to unpack .../051-python3-wcwidth_0.2.5+dfsg1-1.1ubuntu1_all.deb ... 355s Unpacking python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 355s Selecting previously unselected package python3-prompt-toolkit. 355s Preparing to unpack .../052-python3-prompt-toolkit_3.0.43-1_all.deb ... 355s Unpacking python3-prompt-toolkit (3.0.43-1) ... 355s Selecting previously unselected package python3-asttokens. 355s Preparing to unpack .../053-python3-asttokens_2.4.1-1_all.deb ... 355s Unpacking python3-asttokens (2.4.1-1) ... 355s Selecting previously unselected package python3-executing. 355s Preparing to unpack .../054-python3-executing_2.0.1-0.1_all.deb ... 355s Unpacking python3-executing (2.0.1-0.1) ... 355s Selecting previously unselected package python3-pure-eval. 355s Preparing to unpack .../055-python3-pure-eval_0.2.2-1_all.deb ... 355s Unpacking python3-pure-eval (0.2.2-1) ... 355s Selecting previously unselected package python3-stack-data. 355s Preparing to unpack .../056-python3-stack-data_0.6.3-1_all.deb ... 355s Unpacking python3-stack-data (0.6.3-1) ... 355s Selecting previously unselected package python3-setuptools. 355s Preparing to unpack .../057-python3-setuptools_68.1.2-2_all.deb ... 355s Unpacking python3-setuptools (68.1.2-2) ... 355s Selecting previously unselected package python3-ipython. 355s Preparing to unpack .../058-python3-ipython_8.20.0-1_all.deb ... 355s Unpacking python3-ipython (8.20.0-1) ... 355s Selecting previously unselected package python3-platformdirs. 355s Preparing to unpack .../059-python3-platformdirs_4.2.0-1_all.deb ... 355s Unpacking python3-platformdirs (4.2.0-1) ... 355s Selecting previously unselected package python3-jupyter-core. 355s Preparing to unpack .../060-python3-jupyter-core_5.3.2-1_all.deb ... 355s Unpacking python3-jupyter-core (5.3.2-1) ... 355s Selecting previously unselected package python3-entrypoints. 355s Preparing to unpack .../061-python3-entrypoints_0.4-2_all.deb ... 355s Unpacking python3-entrypoints (0.4-2) ... 355s Selecting previously unselected package python3-nest-asyncio. 355s Preparing to unpack .../062-python3-nest-asyncio_1.5.4-1_all.deb ... 355s Unpacking python3-nest-asyncio (1.5.4-1) ... 355s Selecting previously unselected package python3-tornado. 355s Preparing to unpack .../063-python3-tornado_6.4.0-1_arm64.deb ... 355s Unpacking python3-tornado (6.4.0-1) ... 355s Selecting previously unselected package python3-py. 355s Preparing to unpack .../064-python3-py_1.11.0-2_all.deb ... 355s Unpacking python3-py (1.11.0-2) ... 355s Selecting previously unselected package libnorm1:arm64. 355s Preparing to unpack .../065-libnorm1_1.5.9+dfsg-3_arm64.deb ... 355s Unpacking libnorm1:arm64 (1.5.9+dfsg-3) ... 355s Selecting previously unselected package libpgm-5.3-0:arm64. 355s Preparing to unpack .../066-libpgm-5.3-0_5.3.128~dfsg-2_arm64.deb ... 355s Unpacking libpgm-5.3-0:arm64 (5.3.128~dfsg-2) ... 355s Selecting previously unselected package libsodium23:arm64. 355s Preparing to unpack .../067-libsodium23_1.0.18-1build2_arm64.deb ... 355s Unpacking libsodium23:arm64 (1.0.18-1build2) ... 355s Selecting previously unselected package libzmq5:arm64. 355s Preparing to unpack .../068-libzmq5_4.3.5-1_arm64.deb ... 355s Unpacking libzmq5:arm64 (4.3.5-1) ... 355s Selecting previously unselected package python3-zmq. 356s Preparing to unpack .../069-python3-zmq_24.0.1-5_arm64.deb ... 356s Unpacking python3-zmq (24.0.1-5) ... 356s Selecting previously unselected package python3-jupyter-client. 356s Preparing to unpack .../070-python3-jupyter-client_7.4.9-2ubuntu1_all.deb ... 356s Unpacking python3-jupyter-client (7.4.9-2ubuntu1) ... 356s Selecting previously unselected package python3-psutil. 356s Preparing to unpack .../071-python3-psutil_5.9.8-1_arm64.deb ... 356s Unpacking python3-psutil (5.9.8-1) ... 356s Selecting previously unselected package python3-ipykernel. 356s Preparing to unpack .../072-python3-ipykernel_6.24.0-3_all.deb ... 356s Unpacking python3-ipykernel (6.24.0-3) ... 356s Selecting previously unselected package libjs-jquery. 356s Preparing to unpack .../073-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 356s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 356s Selecting previously unselected package libjs-jquery-ui. 356s Preparing to unpack .../074-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 356s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 356s Selecting previously unselected package fonts-dejavu-mono. 356s Preparing to unpack .../075-fonts-dejavu-mono_2.37-8_all.deb ... 356s Unpacking fonts-dejavu-mono (2.37-8) ... 356s Selecting previously unselected package fonts-dejavu-core. 356s Preparing to unpack .../076-fonts-dejavu-core_2.37-8_all.deb ... 356s Unpacking fonts-dejavu-core (2.37-8) ... 356s Selecting previously unselected package fonts-lyx. 356s Preparing to unpack .../077-fonts-lyx_2.4.0~RC3-1_all.deb ... 356s Unpacking fonts-lyx (2.4.0~RC3-1) ... 356s Selecting previously unselected package python-matplotlib-data. 356s Preparing to unpack .../078-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ... 356s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ... 356s Selecting previously unselected package libimagequant0:arm64. 356s Preparing to unpack .../079-libimagequant0_2.18.0-1_arm64.deb ... 356s Unpacking libimagequant0:arm64 (2.18.0-1) ... 356s Selecting previously unselected package libjpeg-turbo8:arm64. 356s Preparing to unpack .../080-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 356s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 356s Selecting previously unselected package libjpeg8:arm64. 356s Preparing to unpack .../081-libjpeg8_8c-2ubuntu11_arm64.deb ... 356s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 356s Selecting previously unselected package liblcms2-2:arm64. 356s Preparing to unpack .../082-liblcms2-2_2.14-2_arm64.deb ... 356s Unpacking liblcms2-2:arm64 (2.14-2) ... 356s Selecting previously unselected package libopenjp2-7:arm64. 356s Preparing to unpack .../083-libopenjp2-7_2.5.0-2_arm64.deb ... 356s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 356s Selecting previously unselected package libgraphite2-3:arm64. 356s Preparing to unpack .../084-libgraphite2-3_1.3.14-2_arm64.deb ... 356s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 356s Selecting previously unselected package libharfbuzz0b:arm64. 356s Preparing to unpack .../085-libharfbuzz0b_8.3.0-2_arm64.deb ... 356s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 356s Selecting previously unselected package libraqm0:arm64. 356s Preparing to unpack .../086-libraqm0_0.10.1-1_arm64.deb ... 356s Unpacking libraqm0:arm64 (0.10.1-1) ... 356s Selecting previously unselected package libdeflate0:arm64. 356s Preparing to unpack .../087-libdeflate0_1.19-1_arm64.deb ... 356s Unpacking libdeflate0:arm64 (1.19-1) ... 356s Selecting previously unselected package libjbig0:arm64. 356s Preparing to unpack .../088-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 356s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 356s Selecting previously unselected package liblerc4:arm64. 356s Preparing to unpack .../089-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 356s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 356s Selecting previously unselected package libsharpyuv0:arm64. 356s Preparing to unpack .../090-libsharpyuv0_1.3.2-0.4_arm64.deb ... 356s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 356s Selecting previously unselected package libwebp7:arm64. 356s Preparing to unpack .../091-libwebp7_1.3.2-0.4_arm64.deb ... 356s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 356s Selecting previously unselected package libtiff6:arm64. 356s Preparing to unpack .../092-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 356s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 356s Selecting previously unselected package libwebpdemux2:arm64. 356s Preparing to unpack .../093-libwebpdemux2_1.3.2-0.4_arm64.deb ... 356s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 356s Selecting previously unselected package libwebpmux3:arm64. 356s Preparing to unpack .../094-libwebpmux3_1.3.2-0.4_arm64.deb ... 356s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 356s Selecting previously unselected package python3-pil:arm64. 356s Preparing to unpack .../095-python3-pil_10.2.0-1_arm64.deb ... 356s Unpacking python3-pil:arm64 (10.2.0-1) ... 356s Selecting previously unselected package libtcl8.6:arm64. 356s Preparing to unpack .../096-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 356s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 356s Selecting previously unselected package fontconfig-config. 356s Preparing to unpack .../097-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 356s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 356s Selecting previously unselected package libfontconfig1:arm64. 357s Preparing to unpack .../098-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 357s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 357s Selecting previously unselected package libxrender1:arm64. 357s Preparing to unpack .../099-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 357s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 357s Selecting previously unselected package libxft2:arm64. 357s Preparing to unpack .../100-libxft2_2.3.6-1_arm64.deb ... 357s Unpacking libxft2:arm64 (2.3.6-1) ... 357s Selecting previously unselected package x11-common. 357s Preparing to unpack .../101-x11-common_1%3a7.7+23ubuntu2_all.deb ... 357s Unpacking x11-common (1:7.7+23ubuntu2) ... 357s Selecting previously unselected package libxss1:arm64. 357s Preparing to unpack .../102-libxss1_1%3a1.2.3-1build2_arm64.deb ... 357s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 357s Selecting previously unselected package libtk8.6:arm64. 357s Preparing to unpack .../103-libtk8.6_8.6.13-2_arm64.deb ... 357s Unpacking libtk8.6:arm64 (8.6.13-2) ... 357s Selecting previously unselected package tk8.6-blt2.5. 357s Preparing to unpack .../104-tk8.6-blt2.5_2.5.3+dfsg-7_arm64.deb ... 357s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... 357s Selecting previously unselected package blt. 357s Preparing to unpack .../105-blt_2.5.3+dfsg-7_arm64.deb ... 357s Unpacking blt (2.5.3+dfsg-7) ... 357s Selecting previously unselected package python3-tk:arm64. 357s Preparing to unpack .../106-python3-tk_3.11.5-1_arm64.deb ... 357s Unpacking python3-tk:arm64 (3.11.5-1) ... 357s Selecting previously unselected package python3-pil.imagetk:arm64. 357s Preparing to unpack .../107-python3-pil.imagetk_10.2.0-1_arm64.deb ... 357s Unpacking python3-pil.imagetk:arm64 (10.2.0-1) ... 357s Selecting previously unselected package python3-contourpy. 357s Preparing to unpack .../108-python3-contourpy_1.0.7-1build2_arm64.deb ... 357s Unpacking python3-contourpy (1.0.7-1build2) ... 357s Selecting previously unselected package python3-cycler. 357s Preparing to unpack .../109-python3-cycler_0.11.0-2_all.deb ... 357s Unpacking python3-cycler (0.11.0-2) ... 357s Selecting previously unselected package python3-brotli. 357s Preparing to unpack .../110-python3-brotli_1.1.0-2_arm64.deb ... 357s Unpacking python3-brotli (1.1.0-2) ... 357s Selecting previously unselected package python3-ufolib2. 357s Preparing to unpack .../111-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 357s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 357s Selecting previously unselected package python3-mpmath. 357s Preparing to unpack .../112-python3-mpmath_1.2.1-3_all.deb ... 357s Unpacking python3-mpmath (1.2.1-3) ... 357s Selecting previously unselected package python3-sympy. 357s Preparing to unpack .../113-python3-sympy_1.12-7_all.deb ... 357s Unpacking python3-sympy (1.12-7) ... 357s Selecting previously unselected package python3-appdirs. 357s Preparing to unpack .../114-python3-appdirs_1.4.4-4_all.deb ... 357s Unpacking python3-appdirs (1.4.4-4) ... 357s Selecting previously unselected package python3-fs. 357s Preparing to unpack .../115-python3-fs_2.4.16-3_all.deb ... 357s Unpacking python3-fs (2.4.16-3) ... 357s Selecting previously unselected package libxslt1.1:arm64. 357s Preparing to unpack .../116-libxslt1.1_1.1.35-1_arm64.deb ... 357s Unpacking libxslt1.1:arm64 (1.1.35-1) ... 357s Selecting previously unselected package python3-lxml:arm64. 357s Preparing to unpack .../117-python3-lxml_5.1.0-1_arm64.deb ... 357s Unpacking python3-lxml:arm64 (5.1.0-1) ... 357s Selecting previously unselected package python3-lz4. 357s Preparing to unpack .../118-python3-lz4_4.0.2+dfsg-1build2_arm64.deb ... 357s Unpacking python3-lz4 (4.0.2+dfsg-1build2) ... 357s Selecting previously unselected package python3-unicodedata2. 357s Preparing to unpack .../119-python3-unicodedata2_15.1.0+ds-1_arm64.deb ... 357s Unpacking python3-unicodedata2 (15.1.0+ds-1) ... 357s Selecting previously unselected package unicode-data. 357s Preparing to unpack .../120-unicode-data_15.1.0-1_all.deb ... 357s Unpacking unicode-data (15.1.0-1) 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(4.0.0+ds-4ubuntu1) ... 360s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 360s Setting up python3-py (1.11.0-2) ... 360s Setting up libdebuginfod-common (0.190-1) ... 360s Setting up python3-joblib (1.3.2-1) ... 360s Setting up python3-parso (0.8.3-1) ... 360s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 360s Setting up python3-asttokens (2.4.1-1) ... 360s Setting up python3-unicodedata2 (15.1.0+ds-1) ... 360s Setting up libpgm-5.3-0:arm64 (5.3.128~dfsg-2) ... 360s Setting up fonts-lyx (2.4.0~RC3-1) ... 360s Setting up libdebuginfod1:arm64 (0.190-1) ... 360s Setting up python3-threadpoolctl (3.1.0-1) ... 361s Setting up libnorm1:arm64 (1.5.9+dfsg-3) ... 361s Setting up x11-common (1:7.7+23ubuntu2) ... 361s Setting up libdeflate0:arm64 (1.19-1) ... 361s Setting up libqhull-r8.0:arm64 (2020.2-6) ... 361s Setting up libblosc2-2:arm64 (2.13.1+ds-1ubuntu1) ... 361s Setting up libgomp1:arm64 (14-20240221-2.1ubuntu1) ... 361s Setting up python3-networkx (2.8.8-1ubuntu1) ... 362s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' 362s "graph [edge [ source u'u\4200' target u'u\4200' ] " 362s /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' 362s + "node [ id u'u\4200' label b ] ]" 362s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 362s Setting up libaec0:arm64 (1.1.2-1) ... 362s Setting up python3-platformdirs (4.2.0-1) ... 362s Setting up python3-psutil (5.9.8-1) ... 362s Setting up libsource-highlight-common (3.1.9-4.3) ... 362s Setting up libsnappy1v5:arm64 (1.1.10-1) ... 362s Setting up unicode-data (15.1.0-1) ... 362s Setting up python3-decorator (5.1.1-5) ... 362s Setting up libblas3:arm64 (3.12.0-3) ... 362s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 362s Setting up python3-packaging (23.2-1) ... 363s Setting up python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 363s Setting up python3-executing (2.0.1-0.1) ... 363s Setting up python3-nest-asyncio (1.5.4-1) ... 363s Setting up python3-brotli (1.1.0-2) ... 363s Setting up python3-cycler (0.11.0-2) ... 363s Setting up libimagequant0:arm64 (2.18.0-1) ... 363s Setting up python3-bytecode (0.15.1-3) ... 363s Setting up fonts-dejavu-mono (2.37-8) ... 363s Setting up python3-kiwisolver (1.4.4-1build2) ... 364s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... 364s Setting up fonts-dejavu-core (2.37-8) ... 364s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 364s Setting up python3-cpuinfo (9.0.0-1) ... 364s Setting up libbabeltrace1:arm64 (1.5.11-3build1) ... 364s Setting up libgfortran5:arm64 (14-20240221-2.1ubuntu1) ... 364s Setting up python3-pluggy (1.4.0-1) ... 364s Setting up libwebp7:arm64 (1.3.2-0.4) ... 364s Setting up python3-fastjsonschema (2.19.0-1) ... 364s Setting up python3-traitlets (5.5.0-2) ... 364s Setting up libxslt1.1:arm64 (1.1.35-1) ... 364s Setting up libblosc1:arm64 (1.21.5+ds-1) ... 364s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 364s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 364s Setting up python3-dateutil (2.8.2-3) ... 364s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 364s Setting up libxss1:arm64 (1:1.2.3-1build2) ... 364s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 364s Setting up python3-mpmath (1.2.1-3) ... 365s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ... 365s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 365s Setting up python3-lib2to3 (3.11.5-1) ... 365s Setting up python3-appdirs (1.4.4-4) ... 365s Setting up python3-stack-data (0.6.3-1) ... 365s Setting up python-tables-data (3.9.2-1) ... 365s Setting up libpython3.12:arm64 (3.12.2-1) ... 365s Setting up libsz2:arm64 (1.1.2-1) ... 365s Setting up libsource-highlight4v5:arm64 (3.1.9-4.2build2) ... 365s Setting up python3-ptyprocess (0.7.0-5) ... 365s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 365s Setting up python3-prompt-toolkit (3.0.43-1) ... 366s Setting up python3-distutils (3.11.5-1) ... 367s python3.12: can't get files for byte-compilation 367s Setting up python3.11-minimal (3.11.8-1) ... 367s Setting up python3-sympy (1.12-7) ... 371s Setting up liblapack3:arm64 (3.12.0-3) ... 371s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 371s Setting up libzmq5:arm64 (4.3.5-1) ... 371s Setting up python3-setuptools (68.1.2-2) ... 372s Setting up python3-jedi (0.18.2-1ubuntu1) ... 372s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 372s Setting up python3-pytest (7.4.4-1) ... 372s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 372s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 372s Setting up python3-matplotlib-inline (0.1.6-2) ... 372s Setting up python3-comm (0.2.1-1) ... 372s Setting up python3-fs (2.4.16-3) ... 373s Setting up gdb (15.0.50.20240219-0ubuntu1) ... 373s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 373s Setting up python3-pexpect (4.9-2) ... 373s Setting up python3-zmq (24.0.1-5) ... 373s Setting up libraqm0:arm64 (0.10.1-1) ... 373s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 373s Setting up python3-lxml:arm64 (5.1.0-1) ... 373s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 373s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 373s Setting up python3-jupyter-core (5.3.2-1) ... 373s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 373s Setting up python3.11 (3.11.8-1) ... 374s Setting up libxft2:arm64 (2.3.6-1) ... 374s Setting up libtk8.6:arm64 (8.6.13-2) ... 374s Setting up python3-coverage (7.3.2-0ubuntu1) ... 374s Setting up python3-nbformat (5.9.1-1) ... 374s Setting up python3-pil:arm64 (10.2.0-1) ... 375s Setting up python3-ipython (8.20.0-1) ... 375s Setting up python3-numpy (1:1.24.2-2) ... 377s Setting up python3-jupyter-client (7.4.9-2ubuntu1) ... 377s Setting up python3-contourpy (1.0.7-1build2) ... 377s Setting up python3-pydevd (2.10.0+ds-10ubuntu1) ... 378s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 378s Setting up python3-scipy (1.11.4-6) ... 380s Setting up python3-tables-lib (3.9.2-1) ... 380s Setting up blt (2.5.3+dfsg-7) ... 380s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 380s Setting up python3-sklearn-lib:arm64 (1.4.1.post1+dfsg-1) ... 380s Setting up python3-tk:arm64 (3.11.5-1) ... 380s Setting up python3-debugpy (1.8.0+ds-4ubuntu1) ... 381s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 385s Setting up python3-pil.imagetk:arm64 (10.2.0-1) ... 385s Setting up python3-ipykernel (6.24.0-3) ... 385s Setting up python3-sklearn (1.4.1.post1+dfsg-1) ... 387s Setting up python3-numexpr (2.9.0-1) ... 387s Setting up python3-tables (3.9.2-1) ... 387s Setting up python3-mdtraj (1.9.9-1) ... 387s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:271: SyntaxWarning: invalid escape sequence '\g' 387s """Read data from an AMBER ASCII restart file 387s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:534: SyntaxWarning: invalid escape sequence '\g' 387s """Read data from an AMBER NetCDF restart file 387s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:394: SyntaxWarning: invalid escape sequence '\d' 388s time = float(findall('t= *(\d+\.\d+)',comment)[-1]) 388s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:500: SyntaxWarning: invalid escape sequence '\.' 388s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 388s /usr/lib/python3/dist-packages/mdtraj/formats/gsd.py:228: SyntaxWarning: invalid escape sequence '\g' 388s """Write one or more frames of data to a gsd file. 388s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:237: SyntaxWarning: invalid escape sequence '\g' 388s """Read data from a lammpstrj file. 388s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:429: SyntaxWarning: invalid escape sequence '\g' 388s """Write the box lines in the header of a frame. 388s /usr/lib/python3/dist-packages/mdtraj/formats/lammpstrj.py:476: SyntaxWarning: invalid escape sequence '\g' 388s """Write one or more frames of data to a lammpstrj file. 388s /usr/lib/python3/dist-packages/mdtraj/formats/mol2.py:215: SyntaxWarning: invalid escape sequence '\s' 388s index_col=0, header=None, sep="\s+", engine='python') 388s /usr/lib/python3/dist-packages/mdtraj/formats/mol2.py:222: SyntaxWarning: invalid escape sequence '\s' 388s atoms_frame = pd.read_csv(csv, sep="\s+", engine='python', header=None) 388s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:217: SyntaxWarning: invalid escape sequence '\g' 388s """Read data from a molecular dynamics trajectory in the AMBER NetCDF 388s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:323: SyntaxWarning: invalid escape sequence '\g' 388s """Write one or more frames of a molecular dynamics trajectory to disk 388s /usr/lib/python3/dist-packages/mdtraj/formats/prmtop.py:63: SyntaxWarning: invalid escape sequence '\.' 388s FORMAT_RE_PATTERN = re.compile("([0-9]+)([a-zA-Z]+)([0-9]+)\.?([0-9]*)") 388s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:44: SyntaxWarning: invalid escape sequence '\s' 388s """Compute the distance between pairs of residues in a trajectory. 388s /usr/lib/python3/dist-packages/mdtraj/geometry/hbond.py:251: SyntaxWarning: invalid escape sequence '\c' 388s """Compute the Kabsch-Sander hydrogen bond energy between each pair 388s /usr/lib/python3/dist-packages/mdtraj/geometry/internal.py:370: SyntaxWarning: invalid escape sequence '\p' 388s """Calculate the Wilson B matrix, which collects the derivatives of the 388s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:80: SyntaxWarning: invalid escape sequence '\l' 388s """Compute the asphericity of a trajectory. 388s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:105: SyntaxWarning: invalid escape sequence '\l' 388s """Compute the acylindricity of a trajectory. 388s /usr/lib/python3/dist-packages/mdtraj/geometry/shape.py:130: SyntaxWarning: invalid escape sequence '\k' 388s """Compute the relative shape anisotropy of a trajectory. 388s /usr/lib/python3/dist-packages/mdtraj/nmr/shift_wrappers.py:214: SyntaxWarning: invalid escape sequence '\s' 388s d = pd.read_table("./bb_details.dat", index_col=False, header=None, sep="\s+").drop([3], axis=1) 388s /usr/lib/python3/dist-packages/mdtraj/nmr/shift_wrappers.py:292: SyntaxWarning: invalid escape sequence '\s' 388s d = pd.read_table("./trj%d_pred.tab" % i, names=names, header=None, sep="\s+", skiprows=lines_to_skip) 388s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:305: SyntaxWarning: invalid escape sequence '\w' 388s if re.compile('^([\w., ]+=)?\s*[\w\.]+\(.*\)$').match(summary_str): 388s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:345: SyntaxWarning: invalid escape sequence '\*' 388s return [self['Signature'].replace('*','\*')] + [''] 388s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:464: SyntaxWarning: invalid escape sequence '\*' 388s argspec = argspec.replace('*','\*') 388s /usr/lib/python3/dist-packages/mdtraj/testing/docscrape.py:482: SyntaxWarning: invalid escape sequence '\*' 388s signature = self['Signature'].replace('*', '\*') 388s /usr/lib/python3/dist-packages/mdtraj/testing/docstrings.py:126: SyntaxWarning: invalid escape sequence '\d' 388s m = re.search('takes at most (\d+) positional arguments', str(e)) 388s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 388s Setting up python3-fonttools (4.46.0-1) ... 388s Setting up python3-matplotlib (3.6.3-1ubuntu3) ... 390s Setting up autopkgtest-satdep (0) ... 390s Processing triggers for libc-bin (2.39-0ubuntu2) ... 390s Processing triggers for systemd (255.2-3ubuntu2) ... 390s Processing triggers for man-db (2.12.0-3) ... 396s (Reading database ... 91023 files and directories currently installed.) 396s Removing autopkgtest-satdep (0) ... 398s autopkgtest [16:08:01]: test command1: pytest-3 -k 'not nmr.ipynb and not test_image_molecules' 398s autopkgtest [16:08:01]: test command1: [----------------------- 398s ============================= test session starts ============================== 398s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3 398s cachedir: .pytest_cache 398s rootdir: /tmp/autopkgtest.QpWX0U/build.RuN/src 398s configfile: pytest.ini 398s testpaths: tests, examples 400s collecting ... collected 1221 items / 2 deselected / 1219 selected 400s 400s tests/test_alignment.py::test_rmsd_zero PASSED [ 0%] 400s tests/test_alignment.py::test_rmsd_nonzero PASSED [ 0%] 400s tests/test_alignment.py::test_transform PASSED [ 0%] 400s tests/test_alignment.py::test_transform2 PASSED [ 0%] 400s tests/test_angles.py::test_angle_pbc_0 PASSED [ 0%] 400s tests/test_angles.py::test_generator PASSED [ 0%] 400s tests/test_arc.py::test_read_0 PASSED [ 0%] 401s tests/test_arc.py::test_read_arctraj PASSED 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[ 10%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.scalar_couplings] PASSED [ 10%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.nmr.shift_wrappers] PASSED [ 10%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.basereporter] PASSED [ 10%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.dcdreporter] PASSED [ 10%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.hdf5reporter] PASSED [ 10%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.netcdfreporter] PASSED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.reporters.xtcreporter] PASSED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdconvert] SKIPPED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.scripts.mdinspect] SKIPPED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docscrape] SKIPPED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.testing.docstrings] PASSED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.testing.testing] PASSED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.contextmanagers] PASSED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.delay_import] PASSED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.rotation] PASSED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.singleton] PASSED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.six] SKIPPED [ 11%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.basedimension] PASSED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.baseunit] SKIPPED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.constants] PASSED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.mymatrix] SKIPPED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.prefix] SKIPPED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.quantity] SKIPPED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.standard_dimensions] PASSED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit] SKIPPED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_definitions] SKIPPED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_math] SKIPPED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unit.unit_operators] SKIPPED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.unitcell] PASSED [ 12%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.validation] PASSED [ 13%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.utils.zipped] PASSED [ 13%] 410s tests/test_docstrings.py::test_docstrings[mdtraj.version] PASSED [ 13%] 410s tests/test_drid.py::test_drid_1 PASSED [ 13%] 410s tests/test_drid.py::test_drid_2 PASSED [ 13%] 410s tests/test_dssp.py::test_1 SKIPPED (This test requires mkdssp to be ...) [ 13%] 410s tests/test_dssp.py::test_2 SKIPPED (This test requires mkdssp to be ...) [ 13%] 410s tests/test_dssp.py::test_3 SKIPPED (This test requires mkdssp to be ...) [ 13%] 410s tests/test_dssp.py::test_4 PASSED [ 13%] 410s tests/test_dssp.py::test_5 PASSED [ 13%] 411s tests/test_dssp.py::test_7 PASSED [ 13%] 411s tests/test_dtr.py::test_read PASSED [ 13%] 411s tests/test_dtr.py::test_read_1 PASSED [ 14%] 411s tests/test_dtr.py::test_read_2 PASSED [ 14%] 411s tests/test_dtr.py::test_read_3 PASSED [ 14%] 411s tests/test_dtr.py::test_read_stride PASSED [ 14%] 411s tests/test_dtr.py::test_read_4 PASSED [ 14%] 411s tests/test_dtr.py::test_read_5 PASSED [ 14%] 411s tests/test_dtr.py::test_read_6 PASSED [ 14%] 411s tests/test_dtr.py::test_read_7 PASSED [ 14%] 411s tests/test_dtr.py::test_read_8 PASSED [ 14%] 411s tests/test_dtr.py::test_write_1 PASSED [ 14%] 412s tests/test_dtr.py::test_write_2 PASSED [ 14%] 412s tests/test_dtr.py::test_write_3 PASSED [ 14%] 412s tests/test_dtr.py::test_write_4 PASSED [ 15%] 412s tests/test_dtr.py::test_seek PASSED [ 15%] 412s tests/test_dtr.py::test_read_closed PASSED [ 15%] 412s tests/test_dtr.py::test_tell PASSED [ 15%] 412s tests/test_element.py::test_immutable PASSED [ 15%] 412s tests/test_element.py::test_element_0 PASSED [ 15%] 412s tests/test_element.py::test_element_pickle PASSED [ 15%] 412s tests/test_geometry.py::test_rg PASSED [ 15%] 412s tests/test_geometry.py::test_distances PASSED [ 15%] 412s tests/test_geometry.py::test_center_of_mass PASSED [ 15%] 412s tests/test_geometry.py::test_center_of_geometry PASSED [ 15%] 412s tests/test_geometry.py::test_dihedral_indices PASSED [ 15%] 412s tests/test_geometry.py::test_dihedral_index_offset_generation PASSED [ 15%] 412s tests/test_geometry.py::test_dihedral_0 PASSED [ 16%] 412s tests/test_geometry.py::test_dihedral_1 PASSED [ 16%] 412s tests/test_geometry.py::test_dihedral_triclinic PASSED [ 16%] 412s tests/test_geometry.py::test_angle_0 PASSED [ 16%] 412s tests/test_geometry.py::test_angle_periodic_0 PASSED [ 16%] 412s tests/test_geometry.py::test_angle_triclinic_0 PASSED [ 16%] 412s tests/test_geometry.py::test_angle_1 PASSED [ 16%] 412s tests/test_geometry.py::test_dihedral_performance SKIPPED (Not doing...) [ 16%] 412s tests/test_geometry.py::test_angle_performance SKIPPED (Not doing pe...) [ 16%] 412s tests/test_geometry.py::test_angle_nan PASSED [ 16%] 413s tests/test_geometry.py::test_angle_pbc PASSED [ 16%] 416s tests/test_geometry.py::test_dihedral_pbc PASSED [ 16%] 416s tests/test_geometry.py::test_dihedral_pbc_fails1 PASSED [ 17%] 416s tests/test_geometry.py::test_dihedral_pbc_fails2 PASSED [ 17%] 416s tests/test_geometry.py::test_angle_pbc_fails1 PASSED [ 17%] 417s tests/test_geometry.py::test_no_indices PASSED [ 17%] 417s tests/test_gro.py::test_read_write PASSED [ 17%] 417s tests/test_gro.py::test_read_write_precision PASSED [ 17%] 417s tests/test_gro.py::test_no_whitespace_gro PASSED [ 17%] 417s tests/test_gro.py::test_load PASSED [ 17%] 418s tests/test_gro.py::test_load_with_given_top PASSED [ 17%] 418s tests/test_gro.py::test_against_gmx PASSED [ 17%] 418s tests/test_gsd.py::test_read SKIPPED (gsd module is not available) [ 17%] 418s tests/test_gsd.py::test_read_start SKIPPED (gsd module is not available) [ 17%] 418s tests/test_gsd.py::test_read_frame SKIPPED (gsd module is not available) [ 18%] 418s tests/test_gsd.py::test_read_stride SKIPPED (gsd module is not avail...) [ 18%] 418s tests/test_gsd.py::test_read_variable_top_error SKIPPED (gsd module ...) [ 18%] 418s tests/test_gsd.py::test_write SKIPPED (gsd module is not available) [ 18%] 418s tests/test_gsd.py::test_write_frame SKIPPED (gsd module is not avail...) [ 18%] 418s tests/test_hbonds.py::test_hbonds PASSED [ 18%] 418s tests/test_hbonds.py::test_hbonds_against_dssp SKIPPED (This test re...) [ 18%] 418s tests/test_hbonds.py::test_baker_hubbard_0 PASSED [ 18%] 419s tests/test_hbonds.py::test_baker_hubbard_1 PASSED [ 18%] 419s tests/test_hbonds.py::test_baker_hubbard_2 PASSED [ 18%] 419s tests/test_hbonds.py::test_baker_hubbard_3 PASSED [ 18%] 419s tests/test_hbonds.py::test_wernet_nilsson_0 PASSED [ 18%] 420s tests/test_hbonds.py::test_wernet_nilsson_1 PASSED [ 19%] 420s tests/test_hdf5.py::test_write_coordinates PASSED [ 19%] 420s tests/test_hdf5.py::test_write_coordinates_reshape PASSED [ 19%] 420s tests/test_hdf5.py::test_write_multiple PASSED [ 19%] 420s tests/test_hdf5.py::test_write_inconsistent PASSED [ 19%] 420s tests/test_hdf5.py::test_write_inconsistent_2 PASSED [ 19%] 420s tests/test_hdf5.py::test_write_units SKIPPED (requires openmm.units) [ 19%] 420s tests/test_hdf5.py::test_write_units2 PASSED [ 19%] 420s tests/test_hdf5.py::test_write_units_mismatch SKIPPED (requires open...) [ 19%] 420s tests/test_hdf5.py::test_topology PASSED [ 19%] 420s tests/test_hdf5.py::test_constraints PASSED [ 19%] 420s tests/test_hdf5.py::test_constraints2 PASSED [ 19%] 420s tests/test_hdf5.py::test_read_0 PASSED [ 20%] 420s tests/test_hdf5.py::test_read_1 SKIPPED (requires openmm.units) [ 20%] 420s tests/test_hdf5.py::test_read_slice_0 PASSED [ 20%] 420s tests/test_hdf5.py::test_read_slice_1 PASSED [ 20%] 420s tests/test_hdf5.py::test_read_slice_2 PASSED [ 20%] 420s tests/test_hdf5.py::test_read_slice_3 PASSED [ 20%] 420s tests/test_hdf5.py::test_do_overwrite PASSED [ 20%] 420s tests/test_hdf5.py::test_vsite_elements PASSED [ 20%] 420s tests/test_hdf5.py::test_dont_overwrite PASSED [ 20%] 420s tests/test_hdf5.py::test_attributes PASSED [ 20%] 420s tests/test_hdf5.py::test_append PASSED [ 20%] 422s tests/test_hoomdxml.py::test_load PASSED [ 20%] 422s tests/test_hoomdxml.py::test_load_no_chains PASSED [ 21%] 422s tests/test_hoomdxml.py::test_load_no_ions PASSED [ 21%] 422s tests/test_hoomdxml.py::test_correct_ordering PASSED [ 21%] 422s tests/test_io.py::test_overwrite_1 PASSED [ 21%] 422s tests/test_io.py::test_overwrite_2 PASSED [ 21%] 422s tests/test_io.py::test_io::test_load_1 PASSED [ 21%] 422s tests/test_io.py::test_io::test_load_2 PASSED [ 21%] 422s tests/test_io.py::test_io::test_load_3 PASSED [ 21%] 422s tests/test_io.py::test_io::test_save PASSED [ 21%] 422s tests/test_io.py::test_io_int::test_load_1 PASSED [ 21%] 422s tests/test_io.py::test_io_int::test_load_2 PASSED [ 21%] 422s tests/test_io.py::test_io_int::test_load_3 PASSED [ 21%] 422s tests/test_io.py::test_io_int::test_save PASSED [ 21%] 422s tests/test_io.py::test_groups PASSED [ 22%] 422s tests/test_lammpstrj.py::test_read_0 PASSED [ 22%] 422s tests/test_lammpstrj.py::test_read_1 PASSED [ 22%] 422s tests/test_lammpstrj.py::test_read_write_0 PASSED [ 22%] 423s tests/test_lammpstrj.py::test_mdwrite PASSED [ 22%] 423s tests/test_lammpstrj.py::test_multiread PASSED [ 22%] 423s tests/test_lammpstrj.py::test_seek PASSED [ 22%] 423s tests/test_lammpstrj.py::test_custom PASSED [ 22%] 423s tests/test_lh5.py::test_write_coordinates PASSED [ 22%] 423s tests/test_lh5.py::test_write_coordinates_reshape PASSED [ 22%] 423s tests/test_lh5.py::test_write_multiple PASSED [ 22%] 423s tests/test_lh5.py::test_topology PASSED [ 22%] 423s tests/test_lh5.py::test_read_slice_0 PASSED [ 23%] 423s tests/test_lh5.py::test_vsite_elements PASSED [ 23%] 423s tests/test_lh5.py::test_do_overwrite_0 PASSED [ 23%] 423s tests/test_lh5.py::test_do_overwrite_1 PASSED [ 23%] 423s tests/test_load.py::test_load_single PASSED [ 23%] 423s tests/test_load.py::test_load_single_list PASSED [ 23%] 424s tests/test_load.py::test_load_many_list PASSED [ 23%] 424s tests/test_load.py::test_load_atom_indices_multiple_files PASSED [ 23%] 424s tests/test_lprmsd.py::test_munkres_0 PASSED [ 23%] 424s tests/test_lprmsd.py::test_lprmsd_null PASSED [ 23%] 424s tests/test_lprmsd.py::test_lprmsd_0 PASSED [ 23%] 424s tests/test_lprmsd.py::test_lprmsd_1 PASSED [ 23%] 424s tests/test_lprmsd.py::test_lprmsd_2 PASSED [ 24%] 424s tests/test_lprmsd.py::test_lprmsd_3 PASSED [ 24%] 425s tests/test_lprmsd.py::test_lprmsd_4 PASSED [ 24%] 425s tests/test_lprmsd.py::test_lprmsd_5 PASSED [ 24%] 425s tests/test_mdconvert.py::test_index PASSED [ 24%] 426s tests/test_mdconvert.py::test_slice PASSED [ 24%] 442s tests/test_mdconvert.py::test_pairwise[from-xtc] PASSED [ 24%] 459s tests/test_mdconvert.py::test_pairwise[from-dcd] PASSED [ 24%] 475s tests/test_mdconvert.py::test_pairwise[from-binpos] PASSED [ 24%] 491s tests/test_mdconvert.py::test_pairwise[from-trr] PASSED [ 24%] 507s tests/test_mdconvert.py::test_pairwise[from-nc] PASSED [ 24%] 523s tests/test_mdconvert.py::test_pairwise[from-pdb] PASSED [ 24%] 542s tests/test_mdconvert.py::test_pairwise[from-h5] PASSED [ 25%] 561s tests/test_mdconvert.py::test_pairwise[from-lh5] PASSED [ 25%] 578s tests/test_mdconvert.py::test_pairwise[from-netcdf] PASSED [ 25%] 578s tests/test_mdconvert.py::test_mdconvert_alanine PASSED [ 25%] 578s tests/test_mdcrd.py::test_read_0 PASSED [ 25%] 578s tests/test_mdcrd.py::test_read_1 PASSED [ 25%] 578s tests/test_mdcrd.py::test_read_write_0 PASSED [ 25%] 578s tests/test_mdcrd.py::test_read_write_1 PASSED [ 25%] 578s tests/test_mdcrd.py::test_read_write_2 PASSED [ 25%] 578s tests/test_mdcrd.py::test_multiread PASSED [ 25%] 578s tests/test_mdcrd.py::test_seek PASSED [ 25%] 578s tests/test_mdcrd.py::test_atom_indices_0 PASSED [ 25%] 578s tests/test_mdcrd.py::test_atom_indices_1 PASSED [ 26%] 578s tests/test_mol2.py::test_load_mol2 PASSED [ 26%] 578s tests/test_mol2.py::test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb SKIPPED [ 26%] 578s tests/test_mol2.py::test_mol2_dataframe PASSED [ 26%] 578s tests/test_mol2.py::test_mol2_dataframe_status PASSED [ 26%] 578s tests/test_mol2.py::test_mol2_warnings PASSED [ 26%] 578s tests/test_mol2.py::test_mol2_status_bits PASSED [ 26%] 578s tests/test_mol2.py::test_mol2_without_bonds PASSED [ 26%] 578s tests/test_mol2.py::test_mol2_element_name PASSED [ 26%] 578s tests/test_mol2.py::test_load_all_mol2[li.mol2] PASSED [ 26%] 578s tests/test_mol2.py::test_load_all_mol2[lysozyme-ligand-tripos.mol2] PASSED [ 26%] 578s tests/test_mol2.py::test_load_all_mol2[imatinib.mol2] PASSED [ 26%] 578s tests/test_mol2.py::test_load_all_mol2[status-bits.mol2] PASSED [ 26%] 578s tests/test_mol2.py::test_load_all_mol2[adp.mol2] PASSED [ 27%] 578s tests/test_mol2.py::test_load_all_mol2[water_acn.mol2] PASSED [ 27%] 578s tests/test_mol2.py::test_mol2_n_residues PASSED [ 27%] 579s tests/test_neighborlist.py::test_nonperiodic PASSED [ 27%] 579s tests/test_neighborlist.py::test_periodic PASSED [ 27%] 580s tests/test_neighborlist.py::test_triclinic PASSED [ 27%] 580s tests/test_neighbors.py::test_compute_neighbors_1 PASSED [ 27%] 580s tests/test_neighbors.py::test_compute_neighbors_2 PASSED [ 27%] 581s tests/test_neighbors.py::test_compute_neighbors_3 PASSED [ 27%] 581s tests/test_netcdf.py::test_read_after_close PASSED [ 27%] 581s tests/test_netcdf.py::test_shape PASSED [ 27%] 581s tests/test_netcdf.py::test_read_chunk_1 PASSED [ 27%] 581s tests/test_netcdf.py::test_read_chunk_2 PASSED [ 28%] 581s tests/test_netcdf.py::test_read_chunk_3 PASSED [ 28%] 581s tests/test_netcdf.py::test_read_write_1 PASSED [ 28%] 581s tests/test_netcdf.py::test_read_write_2 PASSED [ 28%] 581s tests/test_netcdf.py::test_ragged_1 PASSED [ 28%] 581s tests/test_netcdf.py::test_ragged_2 PASSED [ 28%] 581s tests/test_netcdf.py::test_read_write_25 PASSED [ 28%] 581s tests/test_netcdf.py::test_write_3 PASSED [ 28%] 581s tests/test_netcdf.py::test_n_atoms PASSED [ 28%] 581s tests/test_netcdf.py::test_do_overwrite PASSED [ 28%] 581s tests/test_netcdf.py::test_trajectory_save_load PASSED [ 28%] 581s tests/test_netcdf.py::test_cpptraj SKIPPED (This test requires cpptr...) [ 28%] 581s tests/test_nmr.py::test_spartaplus SKIPPED (SPARTA+ binary not found) [ 29%] 581s tests/test_nmr.py::test_ppm SKIPPED (PPM binary not found) [ 29%] 581s tests/test_nmr.py::test_shiftx2 SKIPPED (SHIFTX2 binary not found or...) [ 29%] 581s tests/test_nmr.py::test_2_scalar_couplings PASSED [ 29%] 581s tests/test_nmr.py::test_3_scalar_couplings PASSED [ 29%] 581s tests/test_order.py::test_nematic_order PASSED [ 29%] 581s tests/test_order.py::test_director PASSED [ 29%] 581s tests/test_order.py::test_inertia PASSED [ 29%] 581s tests/test_order.py::test_nematic_order_args PASSED [ 29%] 581s tests/test_order.py::test_order_from_traj PASSED [ 29%] 582s tests/test_order.py::test_directors_angle_from_traj PASSED [ 29%] 582s tests/test_pdb.py::test_pdbread PASSED [ 29%] 582s tests/test_pdb.py::test_pdbread_with_input_top PASSED [ 30%] 582s tests/test_pdb.py::test_pdbwrite PASSED [ 30%] 582s tests/test_pdb.py::test_load_multiframe PASSED [ 30%] 582s tests/test_pdb.py::test_4ZUO PASSED [ 30%] 582s tests/test_pdb.py::test_2EQQ_0 PASSED [ 30%] 584s tests/test_pdb.py::test_1vii_solvated_with_ligand PASSED [ 30%] 584s tests/test_pdb.py::test_write_large PASSED [ 30%] 584s tests/test_pdb.py::test_write_large_2 PASSED [ 30%] 584s tests/test_pdb.py::test_pdbstructure_0 PASSED [ 30%] 584s tests/test_pdb.py::test_pdbstructure_1 PASSED [ 30%] 584s tests/test_pdb.py::test_pdbstructure_2 PASSED [ 30%] 584s tests/test_pdb.py::test_pdbstructure_3 PASSED [ 30%] 589s tests/test_pdb.py::test_pdb_from_url PASSED [ 31%] 589s tests/test_pdb.py::test_3nch_conect PASSED [ 31%] 591s tests/test_pdb.py::test_3nch_serial_resSeq PASSED [ 31%] 591s tests/test_pdb.py::test_1ncw PASSED [ 31%] 593s tests/test_pdb.py::test_1vii_url_and_gz PASSED [ 31%] 593s tests/test_pdb.py::test_segment_id PASSED [ 31%] 593s tests/test_pdb.py::test_bfactors PASSED [ 31%] 598s tests/test_pdb.py::test_hex PASSED [ 31%] 598s tests/test_pdb.py::test_dummy_pdb_box_detection PASSED [ 31%] 598s tests/test_pdb.py::test_multichain_load_cycle PASSED [ 31%] 598s tests/test_pdb.py::test_load_pdb_input_top PASSED [ 31%] 598s tests/test_pdbx.py::test_convert SKIPPED (test_pdbx.py needs OpenMM.) [ 31%] 598s tests/test_prmtop.py::test_load_prmtop PASSED [ 31%] 598s tests/test_prmtop.py::test_load_binpos_w_prmtop PASSED [ 32%] 598s tests/test_prmtop.py::test_load_chamber_prmtop PASSED [ 32%] 598s tests/test_psf.py::test_load_psf PASSED [ 32%] 603s tests/test_psf.py::test_multichain_psf PASSED [ 32%] 603s tests/test_psf.py::test_load_mdcrd_with_psf PASSED [ 32%] 603s tests/test_psf.py::test_against_vmd[1vii.pdb] SKIPPED (This test req...) [ 32%] 603s tests/test_psf.py::test_against_vmd[2EQQ.pdb] SKIPPED (This test req...) [ 32%] 603s tests/test_quaternion.py::test_quaternion_0 PASSED [ 32%] 603s tests/test_quaternion.py::test_quaternion_1 PASSED [ 32%] 603s tests/test_quaternion.py::test_quaternion_2 PASSED [ 32%] 606s tests/test_rdf.py::test_rdf_norm PASSED [ 32%] 606s tests/test_rdf.py::test_compare_rdf_to_gromacs SKIPPED (Binning does...) [ 32%] 606s tests/test_rdf.py::test_rdf_t[True-True] PASSED [ 33%] 611s tests/test_rdf.py::test_rdf_t[True-False] PASSED [ 33%] 611s tests/test_rdf.py::test_rdf_t[False-True] PASSED [ 33%] 611s tests/test_rdf.py::test_rdf_t[False-False] PASSED [ 33%] 612s tests/test_rdf.py::test_rdf_t_norm[0] PASSED [ 33%] 612s tests/test_rdf.py::test_rdf_t_norm[2] PASSED [ 33%] 613s tests/test_rdf.py::test_rdf_t_norm[4] PASSED [ 33%] 613s tests/test_rdf.py::test_compare_rdf_t_at_0[True-True] PASSED [ 33%] 614s tests/test_rdf.py::test_compare_rdf_t_at_0[True-False] PASSED [ 33%] 614s tests/test_rdf.py::test_compare_rdf_t_at_0[False-True] PASSED [ 33%] 614s tests/test_rdf.py::test_compare_rdf_t_at_0[False-False] PASSED [ 33%] 615s tests/test_rdf.py::test_amber_rdf_t[True-True] PASSED [ 33%] 615s tests/test_rdf.py::test_amber_rdf_t[True-False] PASSED [ 34%] 615s tests/test_rdf.py::test_amber_rdf_t[False-True] PASSED [ 34%] 615s tests/test_rdf.py::test_amber_rdf_t[False-False] PASSED [ 34%] 615s tests/test_rdf.py::test_compare_gromacs_rdf_t SKIPPED (Binning does ...) [ 34%] 615s tests/test_rdf.py::test_compare_rdf_t_master PASSED [ 34%] 616s tests/test_rdf.py::test_compare_n_concurrent_pairs PASSED [ 34%] 616s tests/test_reporter.py::test_reporter SKIPPED (test_reporter.py need...) [ 34%] 616s tests/test_reporter.py::test_reporter_subset SKIPPED (test_reporter....) [ 34%] 616s tests/test_reporter.py::test_xtc_reporter_append SKIPPED (test_repor...) [ 34%] 616s tests/test_restart.py::test_read_after_close PASSED [ 34%] 616s tests/test_restart.py::test_shape PASSED [ 34%] 616s tests/test_restart.py::test_shape_2 PASSED [ 34%] 616s tests/test_restart.py::test_read_write_1 PASSED [ 35%] 616s tests/test_restart.py::test_read_write_2 PASSED [ 35%] 616s tests/test_restart.py::test_read_write_3 PASSED [ 35%] 616s tests/test_restart.py::test_read_write_4 PASSED [ 35%] 616s tests/test_rmsd.py::test_trajectory_rmsd PASSED [ 35%] 616s tests/test_rmsd.py::test_precentered_1 PASSED [ 35%] 616s tests/test_rmsd.py::test_precentered_2 PASSED [ 35%] 616s tests/test_rmsd.py::test_superpose_0 PASSED [ 35%] 616s tests/test_rmsd.py::test_superpose_1 PASSED [ 35%] 616s tests/test_rmsd.py::test_superpose_2 PASSED [ 35%] 616s tests/test_rmsd.py::test_superpose_refinds PASSED [ 35%] 616s tests/test_rmsd.py::test_rmsd_atom_indices PASSED [ 35%] 616s tests/test_rmsd.py::test_rmsd_ref_ainds PASSED [ 36%] 617s tests/test_rmsd.py::test_average_structure PASSED [ 36%] 617s tests/test_rmsd.py::test_trajectory_rmsf PASSED [ 36%] 617s tests/test_rmsd.py::test_trajectory_rmsf_aligned PASSED [ 36%] 617s tests/test_rmsd.py::test_rmsd_atom_indices_vs_ref_indices PASSED [ 36%] 617s tests/test_rmsd_memmap.py::test_1 PASSED [ 36%] 617s tests/test_rmsd_memmap.py::test_2 PASSED [ 36%] 617s tests/test_sasa.py::test_sasa_0 PASSED [ 36%] 617s tests/test_sasa.py::test_sasa_1 PASSED [ 36%] 617s tests/test_sasa.py::test_sasa_2 PASSED [ 36%] 618s tests/test_sasa.py::test_sasa_3 PASSED [ 36%] 619s tests/test_sasa.py::test_sasa_4 PASSED [ 36%] 619s tests/test_sasa.py::test_sasa_5 PASSED [ 36%] 619s tests/test_selection.py::test_range PASSED [ 37%] 619s tests/test_selection.py::test_unary_2 PASSED [ 37%] 619s tests/test_selection.py::test_unary_3 PASSED [ 37%] 619s tests/test_selection.py::test_binary_1 PASSED [ 37%] 619s tests/test_selection.py::test_binary_2 PASSED [ 37%] 619s tests/test_selection.py::test_simple PASSED [ 37%] 619s tests/test_selection.py::test_alias PASSED [ 37%] 619s tests/test_selection.py::test_unary_1 PASSED [ 37%] 619s tests/test_selection.py::test_binary_selection_operator PASSED [ 37%] 619s tests/test_selection.py::test_raises PASSED [ 37%] 619s tests/test_selection.py::test_raises2 PASSED [ 37%] 619s tests/test_selection.py::test_bool PASSED [ 37%] 619s tests/test_selection.py::test_nested_bool PASSED [ 38%] 619s tests/test_selection.py::test_values PASSED [ 38%] 619s tests/test_selection.py::test_element PASSED [ 38%] 619s tests/test_selection.py::test_not PASSED [ 38%] 619s tests/test_selection.py::test_re PASSED [ 38%] 620s tests/test_selection.py::test_quotes PASSED [ 38%] 620s tests/test_selection.py::test_top PASSED [ 38%] 620s tests/test_selection.py::test_top_2 PASSED [ 38%] 620s tests/test_selection.py::test_backbone PASSED [ 38%] 620s tests/test_selection.py::test_sidechain PASSED [ 38%] 621s tests/test_selection.py::test_literal PASSED [ 38%] 621s tests/test_selection.py::test_in PASSED [ 38%] 621s tests/test_shape.py::test_gyration PASSED [ 39%] 621s tests/test_shape.py::test_principal_moments PASSED [ 39%] 621s tests/test_shape.py::test_asphericity PASSED [ 39%] 621s tests/test_shape.py::test_shape_metrics PASSED [ 39%] 621s tests/test_thermodynamic_properties.py::test_volume PASSED [ 39%] 622s tests/test_thermodynamic_properties.py::test_density PASSED [ 39%] 622s tests/test_thermodynamic_properties.py::test_dipole_moments PASSED [ 39%] 622s tests/test_thermodynamic_properties.py::test_static_dielectric PASSED [ 39%] 622s tests/test_thermodynamic_properties.py::test_kappa PASSED [ 39%] 622s tests/test_thermodynamic_properties.py::test_alpha SKIPPED (Thermal ...) [ 39%] 622s tests/test_tng.py::test_load_trajectory PASSED [ 39%] 622s tests/test_tng.py::test_load_topology SKIPPED (Fails on macOS + Pyth...) [ 39%] 622s tests/test_tng.py::test_write PASSED [ 40%] 622s tests/test_topology.py::test_topology_openmm SKIPPED (needs OpenMM) [ 40%] 622s tests/test_topology.py::test_topology_openmm_boxes SKIPPED (needs Op...) [ 40%] 622s tests/test_topology.py::test_topology_pandas PASSED [ 40%] 622s tests/test_topology.py::test_topology_pandas_TIP4PEW PASSED [ 40%] 622s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq PASSED [ 40%] 622s tests/test_topology.py::test_topology_numbers PASSED [ 40%] 622s tests/test_topology.py::test_topology_unique_elements_bpti PASSED [ 40%] 622s tests/test_topology.py::test_chain PASSED [ 40%] 622s tests/test_topology.py::test_residue PASSED [ 40%] 622s tests/test_topology.py::test_segment_id PASSED [ 40%] 622s tests/test_topology.py::test_nonconsective_resSeq PASSED [ 40%] 622s tests/test_topology.py::test_pickle PASSED [ 41%] 622s tests/test_topology.py::test_atoms_by_name PASSED [ 41%] 622s tests/test_topology.py::test_select_atom_indices PASSED [ 41%] 622s tests/test_topology.py::test_top_dataframe_openmm_roundtrip SKIPPED [ 41%] 623s tests/test_topology.py::test_n_bonds PASSED [ 41%] 623s tests/test_topology.py::test_load_unknown_topology PASSED [ 41%] 623s tests/test_topology.py::test_unique_pairs PASSED [ 41%] 624s tests/test_topology.py::test_select_pairs PASSED [ 41%] 624s tests/test_topology.py::test_to_fasta PASSED [ 41%] 624s tests/test_topology.py::test_subset PASSED [ 41%] 625s tests/test_topology.py::test_subset_re_index_residues PASSED [ 41%] 625s tests/test_topology.py::test_molecules PASSED [ 41%] 625s tests/test_topology.py::test_copy_and_hash PASSED [ 42%] 625s tests/test_topology.py::test_topology_sliced_residue_indices PASSED [ 42%] 625s tests/test_topology.py::test_topology_join PASSED [ 42%] 625s tests/test_topology.py::test_topology_join_keep_resSeq PASSED [ 42%] 625s tests/test_trajectory.py::test_mismatch PASSED [ 42%] 625s tests/test_trajectory.py::test_box PASSED [ 42%] 625s tests/test_trajectory.py::test_load_pdb_box PASSED [ 42%] 625s tests/test_trajectory.py::test_load_pdb_gz PASSED [ 42%] 625s tests/test_trajectory.py::test_box_load_save[nc] PASSED [ 42%] 625s tests/test_trajectory.py::test_box_load_save[h5] PASSED [ 42%] 625s tests/test_trajectory.py::test_box_load_save[xtc] PASSED [ 42%] 625s tests/test_trajectory.py::test_box_load_save[trr] PASSED [ 42%] 625s tests/test_trajectory.py::test_box_load_save[dcd] PASSED [ 42%] 625s tests/test_trajectory.py::test_box_load_save[mdcrd] PASSED [ 43%] 625s tests/test_trajectory.py::test_box_load_save[binpos] SKIPPED (binpos...) [ 43%] 625s tests/test_trajectory.py::test_box_load_save[dtr] PASSED [ 43%] 625s tests/test_trajectory.py::test_box_load_save[xyz] SKIPPED (xyz does ...) [ 43%] 625s tests/test_trajectory.py::test_box_load_save[xyz.gz] SKIPPED (xyz.gz...) [ 43%] 625s tests/test_trajectory.py::test_box_load_save[lammpstrj] PASSED [ 43%] 625s tests/test_trajectory.py::test_box_load_save[tng] PASSED [ 43%] 625s tests/test_trajectory.py::test_box_load_save[lh5] SKIPPED (lh5 does ...) [ 43%] 625s tests/test_trajectory.py::test_box_load_save[pdb] SKIPPED (pdb does ...) [ 43%] 625s tests/test_trajectory.py::test_box_load_save[pdb.gz] SKIPPED (pdb.gz...) [ 43%] 625s tests/test_trajectory.py::test_box_load_save[ncrst] PASSED [ 43%] 625s tests/test_trajectory.py::test_box_load_save[rst7] PASSED [ 43%] 625s tests/test_trajectory.py::test_box_load_save[gro] PASSED [ 44%] 625s tests/test_trajectory.py::test_slice PASSED [ 44%] 625s tests/test_trajectory.py::test_slice2 PASSED [ 44%] 625s tests/test_trajectory.py::test_read_path[nc] PASSED [ 44%] 625s tests/test_trajectory.py::test_read_path[h5] PASSED [ 44%] 625s tests/test_trajectory.py::test_read_path[xtc] PASSED [ 44%] 625s tests/test_trajectory.py::test_read_path[trr] PASSED [ 44%] 625s tests/test_trajectory.py::test_read_path[dcd] PASSED [ 44%] 625s tests/test_trajectory.py::test_read_path[mdcrd] PASSED [ 44%] 625s tests/test_trajectory.py::test_read_path[binpos] PASSED [ 44%] 625s tests/test_trajectory.py::test_read_path[dtr] PASSED [ 44%] 625s tests/test_trajectory.py::test_read_path[xyz] PASSED [ 44%] 626s tests/test_trajectory.py::test_read_path[xyz.gz] PASSED [ 45%] 626s tests/test_trajectory.py::test_read_path[lammpstrj] PASSED [ 45%] 626s tests/test_trajectory.py::test_read_path[tng] PASSED [ 45%] 626s tests/test_trajectory.py::test_read_path[lh5] PASSED [ 45%] 626s tests/test_trajectory.py::test_read_path[pdb] PASSED [ 45%] 626s tests/test_trajectory.py::test_read_path[pdb.gz] PASSED [ 45%] 626s tests/test_trajectory.py::test_read_path[ncrst] XFAIL (These referen...) [ 45%] 626s tests/test_trajectory.py::test_read_path[rst7] XFAIL (These referenc...) [ 45%] 626s tests/test_trajectory.py::test_read_path[gro] PASSED [ 45%] 626s tests/test_trajectory.py::test_write_path[nc] PASSED [ 45%] 626s tests/test_trajectory.py::test_write_path[h5] PASSED [ 45%] 626s tests/test_trajectory.py::test_write_path[xtc] PASSED [ 45%] 626s tests/test_trajectory.py::test_write_path[trr] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[dcd] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[mdcrd] SKIPPED (mdcrd can ...) [ 46%] 626s tests/test_trajectory.py::test_write_path[binpos] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[dtr] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[xyz] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[xyz.gz] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[lammpstrj] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[tng] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[lh5] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[pdb] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[pdb.gz] PASSED [ 46%] 626s tests/test_trajectory.py::test_write_path[ncrst] SKIPPED (ncrst can ...) [ 47%] 626s tests/test_trajectory.py::test_write_path[rst7] SKIPPED (rst7 can on...) [ 47%] 626s tests/test_trajectory.py::test_write_path[gro] PASSED [ 47%] 626s tests/test_trajectory.py::test_read_write[nc-nc] PASSED [ 47%] 626s tests/test_trajectory.py::test_read_write[nc-h5] PASSED [ 47%] 627s tests/test_trajectory.py::test_read_write[nc-xtc] PASSED [ 47%] 627s tests/test_trajectory.py::test_read_write[nc-trr] PASSED [ 47%] 627s tests/test_trajectory.py::test_read_write[nc-dcd] PASSED [ 47%] 627s tests/test_trajectory.py::test_read_write[nc-mdcrd] SKIPPED (mdcrd c...) [ 47%] 627s tests/test_trajectory.py::test_read_write[nc-binpos] PASSED [ 47%] 627s tests/test_trajectory.py::test_read_write[nc-dtr] PASSED [ 47%] 627s tests/test_trajectory.py::test_read_write[nc-xyz] PASSED [ 47%] 627s tests/test_trajectory.py::test_read_write[nc-xyz.gz] PASSED [ 47%] 627s tests/test_trajectory.py::test_read_write[nc-lammpstrj] PASSED [ 48%] 627s tests/test_trajectory.py::test_read_write[nc-tng] PASSED [ 48%] 627s tests/test_trajectory.py::test_read_write[nc-lh5] PASSED [ 48%] 627s tests/test_trajectory.py::test_read_write[nc-pdb] PASSED [ 48%] 628s tests/test_trajectory.py::test_read_write[nc-pdb.gz] PASSED [ 48%] 628s tests/test_trajectory.py::test_read_write[nc-ncrst] SKIPPED (ncrst c...) [ 48%] 628s tests/test_trajectory.py::test_read_write[nc-rst7] SKIPPED (rst7 can...) [ 48%] 628s tests/test_trajectory.py::test_read_write[nc-gro] PASSED [ 48%] 628s tests/test_trajectory.py::test_read_write[h5-nc] PASSED [ 48%] 628s tests/test_trajectory.py::test_read_write[h5-h5] PASSED [ 48%] 628s tests/test_trajectory.py::test_read_write[h5-xtc] PASSED [ 48%] 628s tests/test_trajectory.py::test_read_write[h5-trr] PASSED [ 48%] 628s tests/test_trajectory.py::test_read_write[h5-dcd] PASSED [ 49%] 628s tests/test_trajectory.py::test_read_write[h5-mdcrd] SKIPPED (mdcrd c...) [ 49%] 628s tests/test_trajectory.py::test_read_write[h5-binpos] PASSED [ 49%] 628s tests/test_trajectory.py::test_read_write[h5-dtr] PASSED [ 49%] 628s tests/test_trajectory.py::test_read_write[h5-xyz] PASSED [ 49%] 629s tests/test_trajectory.py::test_read_write[h5-xyz.gz] PASSED [ 49%] 629s tests/test_trajectory.py::test_read_write[h5-lammpstrj] PASSED [ 49%] 629s tests/test_trajectory.py::test_read_write[h5-tng] PASSED [ 49%] 629s tests/test_trajectory.py::test_read_write[h5-lh5] PASSED [ 49%] 629s tests/test_trajectory.py::test_read_write[h5-pdb] PASSED [ 49%] 630s tests/test_trajectory.py::test_read_write[h5-pdb.gz] PASSED [ 49%] 630s tests/test_trajectory.py::test_read_write[h5-ncrst] SKIPPED (ncrst c...) [ 49%] 630s tests/test_trajectory.py::test_read_write[h5-rst7] SKIPPED (rst7 can...) [ 50%] 630s tests/test_trajectory.py::test_read_write[h5-gro] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-nc] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-h5] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-xtc] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-trr] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-dcd] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-mdcrd] SKIPPED (mdcrd ...) [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-binpos] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-dtr] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-xyz] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-xyz.gz] PASSED [ 50%] 630s tests/test_trajectory.py::test_read_write[xtc-lammpstrj] PASSED [ 51%] 630s tests/test_trajectory.py::test_read_write[xtc-tng] PASSED [ 51%] 630s tests/test_trajectory.py::test_read_write[xtc-lh5] PASSED [ 51%] 631s tests/test_trajectory.py::test_read_write[xtc-pdb] PASSED [ 51%] 631s tests/test_trajectory.py::test_read_write[xtc-pdb.gz] PASSED [ 51%] 631s tests/test_trajectory.py::test_read_write[xtc-ncrst] SKIPPED (ncrst ...) [ 51%] 631s tests/test_trajectory.py::test_read_write[xtc-rst7] SKIPPED (rst7 ca...) [ 51%] 631s tests/test_trajectory.py::test_read_write[xtc-gro] PASSED [ 51%] 631s tests/test_trajectory.py::test_read_write[trr-nc] PASSED [ 51%] 631s tests/test_trajectory.py::test_read_write[trr-h5] PASSED [ 51%] 632s tests/test_trajectory.py::test_read_write[trr-xtc] PASSED [ 51%] 632s tests/test_trajectory.py::test_read_write[trr-trr] PASSED [ 51%] 632s tests/test_trajectory.py::test_read_write[trr-dcd] PASSED [ 52%] 632s tests/test_trajectory.py::test_read_write[trr-mdcrd] SKIPPED (mdcrd ...) [ 52%] 632s tests/test_trajectory.py::test_read_write[trr-binpos] PASSED [ 52%] 632s tests/test_trajectory.py::test_read_write[trr-dtr] PASSED [ 52%] 632s tests/test_trajectory.py::test_read_write[trr-xyz] PASSED [ 52%] 632s tests/test_trajectory.py::test_read_write[trr-xyz.gz] PASSED [ 52%] 632s tests/test_trajectory.py::test_read_write[trr-lammpstrj] PASSED [ 52%] 632s tests/test_trajectory.py::test_read_write[trr-tng] PASSED [ 52%] 632s tests/test_trajectory.py::test_read_write[trr-lh5] PASSED [ 52%] 633s tests/test_trajectory.py::test_read_write[trr-pdb] PASSED [ 52%] 633s tests/test_trajectory.py::test_read_write[trr-pdb.gz] PASSED [ 52%] 633s tests/test_trajectory.py::test_read_write[trr-ncrst] SKIPPED (ncrst ...) [ 52%] 633s tests/test_trajectory.py::test_read_write[trr-rst7] SKIPPED (rst7 ca...) [ 52%] 633s tests/test_trajectory.py::test_read_write[trr-gro] PASSED [ 53%] 633s tests/test_trajectory.py::test_read_write[dcd-nc] PASSED [ 53%] 633s tests/test_trajectory.py::test_read_write[dcd-h5] PASSED [ 53%] 633s tests/test_trajectory.py::test_read_write[dcd-xtc] PASSED [ 53%] 633s tests/test_trajectory.py::test_read_write[dcd-trr] PASSED [ 53%] 633s tests/test_trajectory.py::test_read_write[dcd-dcd] PASSED [ 53%] 633s tests/test_trajectory.py::test_read_write[dcd-mdcrd] SKIPPED (mdcrd ...) [ 53%] 633s tests/test_trajectory.py::test_read_write[dcd-binpos] PASSED [ 53%] 633s tests/test_trajectory.py::test_read_write[dcd-dtr] PASSED [ 53%] 633s tests/test_trajectory.py::test_read_write[dcd-xyz] PASSED [ 53%] 634s tests/test_trajectory.py::test_read_write[dcd-xyz.gz] PASSED [ 53%] 634s tests/test_trajectory.py::test_read_write[dcd-lammpstrj] PASSED [ 53%] 634s tests/test_trajectory.py::test_read_write[dcd-tng] PASSED [ 54%] 634s tests/test_trajectory.py::test_read_write[dcd-lh5] PASSED [ 54%] 634s tests/test_trajectory.py::test_read_write[dcd-pdb] PASSED [ 54%] 635s tests/test_trajectory.py::test_read_write[dcd-pdb.gz] PASSED [ 54%] 635s tests/test_trajectory.py::test_read_write[dcd-ncrst] SKIPPED (ncrst ...) [ 54%] 635s tests/test_trajectory.py::test_read_write[dcd-rst7] SKIPPED (rst7 ca...) [ 54%] 635s tests/test_trajectory.py::test_read_write[dcd-gro] PASSED [ 54%] 635s tests/test_trajectory.py::test_read_write[mdcrd-nc] PASSED [ 54%] 635s tests/test_trajectory.py::test_read_write[mdcrd-h5] PASSED [ 54%] 635s tests/test_trajectory.py::test_read_write[mdcrd-xtc] PASSED [ 54%] 635s tests/test_trajectory.py::test_read_write[mdcrd-trr] PASSED [ 54%] 635s tests/test_trajectory.py::test_read_write[mdcrd-dcd] PASSED [ 54%] 635s tests/test_trajectory.py::test_read_write[mdcrd-mdcrd] SKIPPED (mdcr...) [ 55%] 635s tests/test_trajectory.py::test_read_write[mdcrd-binpos] PASSED [ 55%] 635s tests/test_trajectory.py::test_read_write[mdcrd-dtr] SKIPPED (dtr ne...) [ 55%] 635s tests/test_trajectory.py::test_read_write[mdcrd-xyz] PASSED [ 55%] 636s tests/test_trajectory.py::test_read_write[mdcrd-xyz.gz] PASSED [ 55%] 636s tests/test_trajectory.py::test_read_write[mdcrd-lammpstrj] SKIPPED (...) [ 55%] 636s tests/test_trajectory.py::test_read_write[mdcrd-tng] PASSED [ 55%] 636s tests/test_trajectory.py::test_read_write[mdcrd-lh5] PASSED [ 55%] 637s tests/test_trajectory.py::test_read_write[mdcrd-pdb] PASSED [ 55%] 638s tests/test_trajectory.py::test_read_write[mdcrd-pdb.gz] PASSED [ 55%] 638s tests/test_trajectory.py::test_read_write[mdcrd-ncrst] SKIPPED (ncrs...) [ 55%] 638s tests/test_trajectory.py::test_read_write[mdcrd-rst7] SKIPPED (rst7 ...) [ 55%] 638s tests/test_trajectory.py::test_read_write[mdcrd-gro] PASSED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-nc] PASSED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-h5] PASSED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-xtc] PASSED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-trr] PASSED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-dcd] PASSED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-mdcrd] SKIPPED (mdc...) [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-binpos] PASSED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-dtr] SKIPPED (dtr n...) [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-xyz] PASSED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-xyz.gz] PASSED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-lammpstrj] SKIPPED [ 56%] 638s tests/test_trajectory.py::test_read_write[binpos-tng] PASSED [ 57%] 638s tests/test_trajectory.py::test_read_write[binpos-lh5] PASSED [ 57%] 638s tests/test_trajectory.py::test_read_write[binpos-pdb] PASSED [ 57%] 639s tests/test_trajectory.py::test_read_write[binpos-pdb.gz] PASSED [ 57%] 639s tests/test_trajectory.py::test_read_write[binpos-ncrst] SKIPPED (ncr...) [ 57%] 639s tests/test_trajectory.py::test_read_write[binpos-rst7] SKIPPED (rst7...) [ 57%] 639s tests/test_trajectory.py::test_read_write[binpos-gro] PASSED [ 57%] 639s tests/test_trajectory.py::test_read_write[dtr-nc] PASSED [ 57%] 639s tests/test_trajectory.py::test_read_write[dtr-h5] PASSED [ 57%] 639s tests/test_trajectory.py::test_read_write[dtr-xtc] PASSED [ 57%] 639s tests/test_trajectory.py::test_read_write[dtr-trr] PASSED [ 57%] 639s tests/test_trajectory.py::test_read_write[dtr-dcd] PASSED [ 57%] 639s tests/test_trajectory.py::test_read_write[dtr-mdcrd] SKIPPED (mdcrd ...) [ 57%] 639s tests/test_trajectory.py::test_read_write[dtr-binpos] PASSED [ 58%] 639s tests/test_trajectory.py::test_read_write[dtr-dtr] PASSED [ 58%] 639s tests/test_trajectory.py::test_read_write[dtr-xyz] PASSED [ 58%] 640s tests/test_trajectory.py::test_read_write[dtr-xyz.gz] PASSED [ 58%] 640s tests/test_trajectory.py::test_read_write[dtr-lammpstrj] PASSED [ 58%] 640s tests/test_trajectory.py::test_read_write[dtr-tng] PASSED [ 58%] 640s tests/test_trajectory.py::test_read_write[dtr-lh5] PASSED [ 58%] 640s tests/test_trajectory.py::test_read_write[dtr-pdb] PASSED [ 58%] 641s tests/test_trajectory.py::test_read_write[dtr-pdb.gz] PASSED [ 58%] 641s tests/test_trajectory.py::test_read_write[dtr-ncrst] SKIPPED (ncrst ...) [ 58%] 641s tests/test_trajectory.py::test_read_write[dtr-rst7] SKIPPED (rst7 ca...) [ 58%] 641s tests/test_trajectory.py::test_read_write[dtr-gro] PASSED [ 58%] 641s tests/test_trajectory.py::test_read_write[xyz-nc] PASSED [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-h5] PASSED [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-xtc] PASSED [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-trr] PASSED [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-dcd] PASSED [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-mdcrd] SKIPPED (mdcrd ...) [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-binpos] PASSED [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-dtr] SKIPPED (dtr need...) [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-xyz] PASSED [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-xyz.gz] PASSED [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-lammpstrj] SKIPPED (la...) [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-tng] PASSED [ 59%] 641s tests/test_trajectory.py::test_read_write[xyz-lh5] PASSED [ 60%] 642s tests/test_trajectory.py::test_read_write[xyz-pdb] PASSED [ 60%] 642s tests/test_trajectory.py::test_read_write[xyz-pdb.gz] PASSED [ 60%] 642s tests/test_trajectory.py::test_read_write[xyz-ncrst] SKIPPED (ncrst ...) [ 60%] 642s tests/test_trajectory.py::test_read_write[xyz-rst7] SKIPPED (rst7 ca...) [ 60%] 642s tests/test_trajectory.py::test_read_write[xyz-gro] PASSED [ 60%] 642s tests/test_trajectory.py::test_read_write[xyz.gz-nc] PASSED [ 60%] 642s tests/test_trajectory.py::test_read_write[xyz.gz-h5] PASSED [ 60%] 642s tests/test_trajectory.py::test_read_write[xyz.gz-xtc] PASSED [ 60%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-trr] PASSED [ 60%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-dcd] PASSED [ 60%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-mdcrd] SKIPPED (mdc...) [ 60%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-binpos] PASSED [ 61%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-dtr] SKIPPED (dtr n...) [ 61%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-xyz] PASSED [ 61%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-xyz.gz] PASSED [ 61%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-lammpstrj] SKIPPED [ 61%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-tng] PASSED [ 61%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-lh5] PASSED [ 61%] 643s tests/test_trajectory.py::test_read_write[xyz.gz-pdb] PASSED [ 61%] 644s tests/test_trajectory.py::test_read_write[xyz.gz-pdb.gz] PASSED [ 61%] 644s tests/test_trajectory.py::test_read_write[xyz.gz-ncrst] SKIPPED (ncr...) [ 61%] 644s tests/test_trajectory.py::test_read_write[xyz.gz-rst7] SKIPPED (rst7...) [ 61%] 644s tests/test_trajectory.py::test_read_write[xyz.gz-gro] PASSED [ 61%] 644s tests/test_trajectory.py::test_read_write[lammpstrj-nc] PASSED [ 62%] 644s tests/test_trajectory.py::test_read_write[lammpstrj-h5] PASSED [ 62%] 644s tests/test_trajectory.py::test_read_write[lammpstrj-xtc] PASSED [ 62%] 644s tests/test_trajectory.py::test_read_write[lammpstrj-trr] PASSED [ 62%] 644s tests/test_trajectory.py::test_read_write[lammpstrj-dcd] PASSED [ 62%] 644s tests/test_trajectory.py::test_read_write[lammpstrj-mdcrd] SKIPPED (...) [ 62%] 644s tests/test_trajectory.py::test_read_write[lammpstrj-binpos] PASSED [ 62%] 644s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] PASSED [ 62%] 645s tests/test_trajectory.py::test_read_write[lammpstrj-xyz] PASSED [ 62%] 645s tests/test_trajectory.py::test_read_write[lammpstrj-xyz.gz] PASSED [ 62%] 645s tests/test_trajectory.py::test_read_write[lammpstrj-lammpstrj] PASSED [ 62%] 645s tests/test_trajectory.py::test_read_write[lammpstrj-tng] PASSED [ 62%] 645s tests/test_trajectory.py::test_read_write[lammpstrj-lh5] PASSED [ 63%] 645s tests/test_trajectory.py::test_read_write[lammpstrj-pdb] PASSED [ 63%] 646s tests/test_trajectory.py::test_read_write[lammpstrj-pdb.gz] PASSED [ 63%] 646s tests/test_trajectory.py::test_read_write[lammpstrj-ncrst] SKIPPED (...) [ 63%] 646s tests/test_trajectory.py::test_read_write[lammpstrj-rst7] SKIPPED (r...) [ 63%] 646s tests/test_trajectory.py::test_read_write[lammpstrj-gro] PASSED [ 63%] 646s tests/test_trajectory.py::test_read_write[tng-nc] PASSED [ 63%] 646s tests/test_trajectory.py::test_read_write[tng-h5] PASSED [ 63%] 646s tests/test_trajectory.py::test_read_write[tng-xtc] PASSED [ 63%] 646s tests/test_trajectory.py::test_read_write[tng-trr] PASSED [ 63%] 646s tests/test_trajectory.py::test_read_write[tng-dcd] PASSED [ 63%] 646s tests/test_trajectory.py::test_read_write[tng-mdcrd] SKIPPED (mdcrd ...) [ 63%] 646s tests/test_trajectory.py::test_read_write[tng-binpos] PASSED [ 63%] 646s tests/test_trajectory.py::test_read_write[tng-dtr] PASSED [ 64%] 646s tests/test_trajectory.py::test_read_write[tng-xyz] PASSED [ 64%] 647s tests/test_trajectory.py::test_read_write[tng-xyz.gz] PASSED [ 64%] 647s tests/test_trajectory.py::test_read_write[tng-lammpstrj] PASSED [ 64%] 647s tests/test_trajectory.py::test_read_write[tng-tng] PASSED [ 64%] 647s tests/test_trajectory.py::test_read_write[tng-lh5] PASSED [ 64%] 647s tests/test_trajectory.py::test_read_write[tng-pdb] PASSED [ 64%] 648s tests/test_trajectory.py::test_read_write[tng-pdb.gz] PASSED [ 64%] 648s tests/test_trajectory.py::test_read_write[tng-ncrst] SKIPPED (ncrst ...) [ 64%] 648s tests/test_trajectory.py::test_read_write[tng-rst7] SKIPPED (rst7 ca...) [ 64%] 648s tests/test_trajectory.py::test_read_write[tng-gro] PASSED [ 64%] 648s tests/test_trajectory.py::test_read_write[lh5-nc] PASSED [ 64%] 648s tests/test_trajectory.py::test_read_write[lh5-h5] PASSED [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-xtc] PASSED [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-trr] PASSED [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-dcd] PASSED [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-mdcrd] SKIPPED (mdcrd ...) [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-binpos] PASSED [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-dtr] SKIPPED (dtr need...) [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-xyz] PASSED [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-xyz.gz] PASSED [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-lammpstrj] SKIPPED (la...) [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-tng] PASSED [ 65%] 648s tests/test_trajectory.py::test_read_write[lh5-lh5] PASSED [ 65%] 649s tests/test_trajectory.py::test_read_write[lh5-pdb] PASSED [ 66%] 649s tests/test_trajectory.py::test_read_write[lh5-pdb.gz] PASSED [ 66%] 649s tests/test_trajectory.py::test_read_write[lh5-ncrst] SKIPPED (ncrst ...) [ 66%] 649s tests/test_trajectory.py::test_read_write[lh5-rst7] SKIPPED (rst7 ca...) [ 66%] 649s tests/test_trajectory.py::test_read_write[lh5-gro] PASSED [ 66%] 650s tests/test_trajectory.py::test_read_write[pdb-nc] PASSED [ 66%] 650s tests/test_trajectory.py::test_read_write[pdb-h5] PASSED [ 66%] 650s tests/test_trajectory.py::test_read_write[pdb-xtc] PASSED [ 66%] 650s tests/test_trajectory.py::test_read_write[pdb-trr] PASSED [ 66%] 650s tests/test_trajectory.py::test_read_write[pdb-dcd] PASSED [ 66%] 650s tests/test_trajectory.py::test_read_write[pdb-mdcrd] SKIPPED (mdcrd ...) [ 66%] 650s tests/test_trajectory.py::test_read_write[pdb-binpos] PASSED [ 66%] 651s tests/test_trajectory.py::test_read_write[pdb-dtr] PASSED [ 67%] 651s tests/test_trajectory.py::test_read_write[pdb-xyz] PASSED [ 67%] 651s tests/test_trajectory.py::test_read_write[pdb-xyz.gz] PASSED [ 67%] 652s tests/test_trajectory.py::test_read_write[pdb-lammpstrj] PASSED [ 67%] 652s tests/test_trajectory.py::test_read_write[pdb-tng] PASSED [ 67%] 652s tests/test_trajectory.py::test_read_write[pdb-lh5] PASSED [ 67%] 653s tests/test_trajectory.py::test_read_write[pdb-pdb] PASSED [ 67%] 653s tests/test_trajectory.py::test_read_write[pdb-pdb.gz] PASSED [ 67%] 653s tests/test_trajectory.py::test_read_write[pdb-ncrst] SKIPPED (ncrst ...) [ 67%] 653s tests/test_trajectory.py::test_read_write[pdb-rst7] SKIPPED (rst7 ca...) [ 67%] 653s tests/test_trajectory.py::test_read_write[pdb-gro] PASSED [ 67%] 654s tests/test_trajectory.py::test_read_write[pdb.gz-nc] PASSED [ 67%] 654s tests/test_trajectory.py::test_read_write[pdb.gz-h5] PASSED [ 68%] 654s tests/test_trajectory.py::test_read_write[pdb.gz-xtc] PASSED [ 68%] 654s tests/test_trajectory.py::test_read_write[pdb.gz-trr] PASSED [ 68%] 654s tests/test_trajectory.py::test_read_write[pdb.gz-dcd] PASSED [ 68%] 654s tests/test_trajectory.py::test_read_write[pdb.gz-mdcrd] SKIPPED (mdc...) [ 68%] 655s tests/test_trajectory.py::test_read_write[pdb.gz-binpos] PASSED [ 68%] 655s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] PASSED [ 68%] 655s tests/test_trajectory.py::test_read_write[pdb.gz-xyz] PASSED [ 68%] 656s tests/test_trajectory.py::test_read_write[pdb.gz-xyz.gz] PASSED [ 68%] 656s tests/test_trajectory.py::test_read_write[pdb.gz-lammpstrj] PASSED [ 68%] 656s tests/test_trajectory.py::test_read_write[pdb.gz-tng] PASSED [ 68%] 656s tests/test_trajectory.py::test_read_write[pdb.gz-lh5] PASSED [ 68%] 657s tests/test_trajectory.py::test_read_write[pdb.gz-pdb] PASSED [ 68%] 657s tests/test_trajectory.py::test_read_write[pdb.gz-pdb.gz] PASSED [ 69%] 657s tests/test_trajectory.py::test_read_write[pdb.gz-ncrst] SKIPPED (ncr...) [ 69%] 657s tests/test_trajectory.py::test_read_write[pdb.gz-rst7] SKIPPED (rst7...) [ 69%] 658s tests/test_trajectory.py::test_read_write[pdb.gz-gro] PASSED [ 69%] 658s tests/test_trajectory.py::test_read_write[ncrst-nc] XFAIL (These ref...) [ 69%] 658s tests/test_trajectory.py::test_read_write[ncrst-h5] XFAIL (These ref...) [ 69%] 658s tests/test_trajectory.py::test_read_write[ncrst-xtc] XFAIL (These re...) [ 69%] 658s tests/test_trajectory.py::test_read_write[ncrst-trr] XFAIL (These re...) [ 69%] 658s tests/test_trajectory.py::test_read_write[ncrst-dcd] XFAIL (These re...) [ 69%] 658s tests/test_trajectory.py::test_read_write[ncrst-mdcrd] XFAIL (These ...) [ 69%] 658s tests/test_trajectory.py::test_read_write[ncrst-binpos] XFAIL (These...) [ 69%] 658s tests/test_trajectory.py::test_read_write[ncrst-dtr] XFAIL (These re...) [ 69%] 658s tests/test_trajectory.py::test_read_write[ncrst-xyz] XFAIL (These re...) [ 70%] 658s tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] XFAIL (These...) [ 70%] 658s tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] XFAIL (Th...) [ 70%] 658s tests/test_trajectory.py::test_read_write[ncrst-tng] XFAIL (These re...) [ 70%] 658s tests/test_trajectory.py::test_read_write[ncrst-lh5] XFAIL (These re...) [ 70%] 658s tests/test_trajectory.py::test_read_write[ncrst-pdb] XFAIL (These re...) [ 70%] 658s tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] XFAIL (These...) [ 70%] 658s tests/test_trajectory.py::test_read_write[ncrst-ncrst] XFAIL (These ...) [ 70%] 658s tests/test_trajectory.py::test_read_write[ncrst-rst7] XFAIL (These r...) [ 70%] 658s tests/test_trajectory.py::test_read_write[ncrst-gro] XFAIL (These re...) [ 70%] 658s tests/test_trajectory.py::test_read_write[rst7-nc] XFAIL (These refe...) [ 70%] 658s tests/test_trajectory.py::test_read_write[rst7-h5] XFAIL (These refe...) [ 70%] 658s tests/test_trajectory.py::test_read_write[rst7-xtc] XFAIL (These ref...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-trr] XFAIL (These ref...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-dcd] XFAIL (These ref...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-mdcrd] XFAIL (These r...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-binpos] XFAIL (These ...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-dtr] XFAIL (These ref...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-xyz] XFAIL (These ref...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-xyz.gz] XFAIL (These ...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-lammpstrj] XFAIL (The...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-tng] XFAIL (These ref...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-lh5] XFAIL (These ref...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-pdb] XFAIL (These ref...) [ 71%] 658s tests/test_trajectory.py::test_read_write[rst7-pdb.gz] XFAIL (These ...) [ 72%] 658s tests/test_trajectory.py::test_read_write[rst7-ncrst] XFAIL (These r...) [ 72%] 658s tests/test_trajectory.py::test_read_write[rst7-rst7] XFAIL (These re...) [ 72%] 658s tests/test_trajectory.py::test_read_write[rst7-gro] XFAIL (These ref...) [ 72%] 658s tests/test_trajectory.py::test_read_write[gro-nc] PASSED [ 72%] 658s tests/test_trajectory.py::test_read_write[gro-h5] PASSED [ 72%] 658s tests/test_trajectory.py::test_read_write[gro-xtc] PASSED [ 72%] 659s tests/test_trajectory.py::test_read_write[gro-trr] PASSED [ 72%] 659s tests/test_trajectory.py::test_read_write[gro-dcd] PASSED [ 72%] 659s tests/test_trajectory.py::test_read_write[gro-mdcrd] SKIPPED (mdcrd ...) [ 72%] 659s tests/test_trajectory.py::test_read_write[gro-binpos] PASSED [ 72%] 659s tests/test_trajectory.py::test_read_write[gro-dtr] PASSED [ 72%] 659s tests/test_trajectory.py::test_read_write[gro-xyz] PASSED [ 73%] 659s tests/test_trajectory.py::test_read_write[gro-xyz.gz] PASSED [ 73%] 659s tests/test_trajectory.py::test_read_write[gro-lammpstrj] PASSED [ 73%] 659s tests/test_trajectory.py::test_read_write[gro-tng] PASSED [ 73%] 659s tests/test_trajectory.py::test_read_write[gro-lh5] PASSED [ 73%] 660s tests/test_trajectory.py::test_read_write[gro-pdb] PASSED [ 73%] 660s tests/test_trajectory.py::test_read_write[gro-pdb.gz] PASSED [ 73%] 660s tests/test_trajectory.py::test_read_write[gro-ncrst] SKIPPED (ncrst ...) [ 73%] 660s tests/test_trajectory.py::test_read_write[gro-rst7] SKIPPED (rst7 ca...) [ 73%] 660s tests/test_trajectory.py::test_read_write[gro-gro] PASSED [ 73%] 660s tests/test_trajectory.py::test_load[nc] PASSED [ 73%] 660s tests/test_trajectory.py::test_load[h5] PASSED [ 73%] 661s tests/test_trajectory.py::test_load[xtc] PASSED [ 73%] 661s tests/test_trajectory.py::test_load[trr] PASSED [ 74%] 661s tests/test_trajectory.py::test_load[dcd] PASSED [ 74%] 661s tests/test_trajectory.py::test_load[mdcrd] PASSED [ 74%] 661s tests/test_trajectory.py::test_load[binpos] PASSED [ 74%] 661s tests/test_trajectory.py::test_load[dtr] PASSED [ 74%] 661s tests/test_trajectory.py::test_load[xyz] PASSED [ 74%] 661s tests/test_trajectory.py::test_load[xyz.gz] PASSED [ 74%] 661s tests/test_trajectory.py::test_load[lammpstrj] PASSED [ 74%] 661s tests/test_trajectory.py::test_load[tng] PASSED [ 74%] 661s tests/test_trajectory.py::test_load[lh5] PASSED [ 74%] 663s tests/test_trajectory.py::test_load[pdb] PASSED [ 74%] 664s tests/test_trajectory.py::test_load[pdb.gz] PASSED [ 74%] 664s tests/test_trajectory.py::test_load[ncrst] XFAIL (These reference fi...) [ 75%] 664s tests/test_trajectory.py::test_load[rst7] XFAIL (These reference fil...) [ 75%] 665s tests/test_trajectory.py::test_load[gro] PASSED [ 75%] 665s tests/test_trajectory.py::test_hdf5 PASSED [ 75%] 665s tests/test_trajectory.py::test_center PASSED [ 75%] 665s tests/test_trajectory.py::test_center_aind PASSED [ 75%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[nc] PASSED [ 75%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[h5] PASSED [ 75%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[xtc] PASSED [ 75%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[trr] PASSED [ 75%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[dcd] PASSED [ 75%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[mdcrd] PASSED [ 75%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[binpos] PASSED [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[dtr] PASSED [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[xyz] PASSED [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[xyz.gz] PASSED [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[lammpstrj] PASSED [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[tng] PASSED [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[lh5] PASSED [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[pdb] PASSED [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[pdb.gz] PASSED [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] XFAIL [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[rst7] XFAIL [ 76%] 665s tests/test_trajectory.py::test_float_atom_indices_exception[gro] PASSED [ 76%] 665s tests/test_trajectory.py::test_restrict_atoms PASSED [ 77%] 665s tests/test_trajectory.py::test_restrict_atoms_not_inplace PASSED [ 77%] 665s tests/test_trajectory.py::test_array_vs_matrix PASSED [ 77%] 665s tests/test_trajectory.py::test_pdb_unitcell_loadsave PASSED [ 77%] 665s tests/test_trajectory.py::test_load_combination[nc] PASSED [ 77%] 665s tests/test_trajectory.py::test_load_combination[h5] PASSED [ 77%] 665s tests/test_trajectory.py::test_load_combination[xtc] PASSED [ 77%] 665s tests/test_trajectory.py::test_load_combination[trr] PASSED [ 77%] 665s tests/test_trajectory.py::test_load_combination[dcd] PASSED [ 77%] 665s tests/test_trajectory.py::test_load_combination[mdcrd] PASSED [ 77%] 665s tests/test_trajectory.py::test_load_combination[binpos] PASSED [ 77%] 665s tests/test_trajectory.py::test_load_combination[dtr] PASSED [ 77%] 665s tests/test_trajectory.py::test_load_combination[xyz] PASSED [ 78%] 665s tests/test_trajectory.py::test_load_combination[xyz.gz] PASSED [ 78%] 665s tests/test_trajectory.py::test_load_combination[lammpstrj] PASSED [ 78%] 665s tests/test_trajectory.py::test_load_combination[tng] PASSED [ 78%] 665s tests/test_trajectory.py::test_load_combination[lh5] PASSED [ 78%] 666s tests/test_trajectory.py::test_load_combination[pdb] PASSED [ 78%] 666s tests/test_trajectory.py::test_load_combination[pdb.gz] PASSED [ 78%] 666s tests/test_trajectory.py::test_load_combination[ncrst] XFAIL (These ...) [ 78%] 666s tests/test_trajectory.py::test_load_combination[rst7] XFAIL (These r...) [ 78%] 667s tests/test_trajectory.py::test_load_combination[gro] PASSED [ 78%] 667s tests/test_trajectory.py::test_no_topology PASSED [ 78%] 667s tests/test_trajectory.py::test_join PASSED [ 78%] 667s tests/test_trajectory.py::test_md_join PASSED [ 78%] 667s tests/test_trajectory.py::test_stack_1 PASSED [ 79%] 667s tests/test_trajectory.py::test_stack_2 PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[nc] PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[h5] PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[xtc] PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[trr] PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[dcd] PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[mdcrd] PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[binpos] PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[dtr] PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[xyz] PASSED [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[xyz.gz] XFAIL (This is...) [ 79%] 667s tests/test_trajectory.py::test_seek_read_mode[lammpstrj] PASSED [ 80%] 667s tests/test_trajectory.py::test_seek_read_mode[tng] PASSED [ 80%] 667s tests/test_trajectory.py::test_seek_read_mode[lh5] PASSED [ 80%] 667s tests/test_trajectory.py::test_seek_read_mode[pdb] XFAIL (PDB Files ...) [ 80%] 667s tests/test_trajectory.py::test_seek_read_mode[pdb.gz] XFAIL (PDB Fil...) [ 80%] 667s tests/test_trajectory.py::test_seek_read_mode[ncrst] XFAIL (These re...) [ 80%] 667s tests/test_trajectory.py::test_seek_read_mode[rst7] XFAIL (These ref...) [ 80%] 667s tests/test_trajectory.py::test_seek_read_mode[gro] XFAIL (This is br...) [ 80%] 667s tests/test_trajectory.py::test_load_frame[nc] PASSED [ 80%] 667s tests/test_trajectory.py::test_load_frame[h5] PASSED [ 80%] 667s tests/test_trajectory.py::test_load_frame[xtc] PASSED [ 80%] 667s tests/test_trajectory.py::test_load_frame[trr] PASSED [ 80%] 667s tests/test_trajectory.py::test_load_frame[dcd] PASSED [ 81%] 667s tests/test_trajectory.py::test_load_frame[mdcrd] PASSED [ 81%] 667s tests/test_trajectory.py::test_load_frame[binpos] PASSED [ 81%] 667s tests/test_trajectory.py::test_load_frame[dtr] XFAIL (DTR doesn't lo...) [ 81%] 667s tests/test_trajectory.py::test_load_frame[xyz] PASSED [ 81%] 667s tests/test_trajectory.py::test_load_frame[xyz.gz] PASSED [ 81%] 667s tests/test_trajectory.py::test_load_frame[lammpstrj] PASSED [ 81%] 667s tests/test_trajectory.py::test_load_frame[tng] PASSED [ 81%] 667s tests/test_trajectory.py::test_load_frame[lh5] PASSED [ 81%] 668s tests/test_trajectory.py::test_load_frame[pdb] PASSED [ 81%] 668s tests/test_trajectory.py::test_load_frame[pdb.gz] PASSED [ 81%] 668s tests/test_trajectory.py::test_load_frame[ncrst] XFAIL (These refere...) [ 81%] 668s tests/test_trajectory.py::test_load_frame[rst7] XFAIL (These referen...) [ 82%] 668s tests/test_trajectory.py::test_load_frame[gro] XFAIL (Gro doesn't im...) [ 82%] 668s tests/test_trajectory.py::test_load_frame_2eqq PASSED [ 82%] 668s tests/test_trajectory.py::test_iterload[nc] PASSED [ 82%] 668s tests/test_trajectory.py::test_iterload[h5] PASSED [ 82%] 668s tests/test_trajectory.py::test_iterload[xtc] PASSED [ 82%] 668s tests/test_trajectory.py::test_iterload[trr] PASSED [ 82%] 668s tests/test_trajectory.py::test_iterload[dcd] PASSED [ 82%] 668s tests/test_trajectory.py::test_iterload[mdcrd] PASSED [ 82%] 668s tests/test_trajectory.py::test_iterload[binpos] PASSED [ 82%] 668s tests/test_trajectory.py::test_iterload[dtr] XFAIL (This is broken w...) [ 82%] 669s tests/test_trajectory.py::test_iterload[xyz] PASSED [ 82%] 669s tests/test_trajectory.py::test_iterload[xyz.gz] PASSED [ 83%] 669s tests/test_trajectory.py::test_iterload[lammpstrj] PASSED [ 83%] 669s tests/test_trajectory.py::test_iterload[tng] PASSED [ 83%] 669s tests/test_trajectory.py::test_iterload[lh5] PASSED [ 83%] 669s tests/test_trajectory.py::test_iterload[pdb] PASSED [ 83%] 669s tests/test_trajectory.py::test_iterload[pdb.gz] PASSED [ 83%] 669s tests/test_trajectory.py::test_iterload[ncrst] SKIPPED (Only 1 frame...) [ 83%] 669s tests/test_trajectory.py::test_iterload[rst7] SKIPPED (Only 1 frame ...) [ 83%] 669s tests/test_trajectory.py::test_iterload[gro] PASSED [ 83%] 669s tests/test_trajectory.py::test_iterload_skip[nc] PASSED [ 83%] 672s tests/test_trajectory.py::test_iterload_skip[h5] PASSED [ 83%] 673s tests/test_trajectory.py::test_iterload_skip[xtc] PASSED [ 83%] 674s tests/test_trajectory.py::test_iterload_skip[trr] PASSED [ 84%] 674s tests/test_trajectory.py::test_iterload_skip[dcd] PASSED [ 84%] 676s tests/test_trajectory.py::test_iterload_skip[mdcrd] PASSED [ 84%] 676s tests/test_trajectory.py::test_iterload_skip[binpos] PASSED [ 84%] 677s tests/test_trajectory.py::test_iterload_skip[dtr] PASSED [ 84%] 677s tests/test_trajectory.py::test_iterload_skip[xyz] PASSED [ 84%] 678s tests/test_trajectory.py::test_iterload_skip[xyz.gz] PASSED [ 84%] 679s tests/test_trajectory.py::test_iterload_skip[lammpstrj] PASSED [ 84%] 680s tests/test_trajectory.py::test_iterload_skip[tng] PASSED [ 84%] 682s tests/test_trajectory.py::test_iterload_skip[lh5] PASSED [ 84%] 682s tests/test_trajectory.py::test_iterload_skip[pdb] XFAIL (PDB Iterloa...) [ 84%] 682s tests/test_trajectory.py::test_iterload_skip[pdb.gz] XFAIL (PDB Iter...) [ 84%] 682s tests/test_trajectory.py::test_iterload_skip[ncrst] XFAIL (These ref...) [ 84%] 682s tests/test_trajectory.py::test_iterload_skip[rst7] XFAIL (These refe...) [ 85%] 682s tests/test_trajectory.py::test_iterload_skip[gro] XFAIL (Not impleme...) [ 85%] 682s tests/test_trajectory.py::test_iterload_chunk_dcd PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[nc] PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[h5] PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[xtc] PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[trr] PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[dcd] PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[mdcrd] PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[binpos] PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[dtr] PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[xyz] PASSED [ 85%] 682s tests/test_trajectory.py::test_save_load[xyz.gz] PASSED [ 86%] 682s tests/test_trajectory.py::test_save_load[lammpstrj] PASSED [ 86%] 682s tests/test_trajectory.py::test_save_load[tng] PASSED [ 86%] 682s tests/test_trajectory.py::test_save_load[lh5] PASSED [ 86%] 682s tests/test_trajectory.py::test_save_load[pdb] PASSED [ 86%] 682s tests/test_trajectory.py::test_save_load[pdb.gz] PASSED [ 86%] 682s tests/test_trajectory.py::test_save_load[ncrst] PASSED [ 86%] 682s tests/test_trajectory.py::test_save_load[rst7] PASSED [ 86%] 682s tests/test_trajectory.py::test_save_load[gro] PASSED [ 86%] 682s tests/test_trajectory.py::test_force_overwrite[nc] PASSED [ 86%] 682s tests/test_trajectory.py::test_force_overwrite[h5] PASSED [ 86%] 682s tests/test_trajectory.py::test_force_overwrite[xtc] PASSED [ 86%] 682s tests/test_trajectory.py::test_force_overwrite[trr] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[dcd] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[mdcrd] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[binpos] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[dtr] XFAIL (This is b...) [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[xyz] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[xyz.gz] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[lammpstrj] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[tng] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[lh5] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[pdb] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[pdb.gz] PASSED [ 87%] 682s tests/test_trajectory.py::test_force_overwrite[ncrst] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_overwrite[rst7] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_overwrite[gro] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[nc] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[h5] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[xtc] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[trr] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[dcd] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[mdcrd] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[binpos] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[dtr] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[xyz] PASSED [ 88%] 682s tests/test_trajectory.py::test_force_noverwrite[xyz.gz] PASSED [ 89%] 682s tests/test_trajectory.py::test_force_noverwrite[lammpstrj] PASSED [ 89%] 682s tests/test_trajectory.py::test_force_noverwrite[tng] PASSED [ 89%] 682s tests/test_trajectory.py::test_force_noverwrite[lh5] PASSED [ 89%] 682s tests/test_trajectory.py::test_force_noverwrite[pdb] PASSED [ 89%] 682s tests/test_trajectory.py::test_force_noverwrite[pdb.gz] PASSED [ 89%] 682s tests/test_trajectory.py::test_force_noverwrite[ncrst] PASSED [ 89%] 682s tests/test_trajectory.py::test_force_noverwrite[rst7] PASSED [ 89%] 682s tests/test_trajectory.py::test_force_noverwrite[gro] PASSED [ 89%] 682s tests/test_trajectory.py::test_open_and_load PASSED [ 89%] 683s tests/test_trajectory.py::test_length PASSED [ 89%] 683s tests/test_trajectory.py::test_unitcell[nc] PASSED [ 89%] 683s tests/test_trajectory.py::test_unitcell[h5] PASSED [ 89%] 683s tests/test_trajectory.py::test_unitcell[xtc] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[trr] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[dcd] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[mdcrd] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[binpos] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[dtr] XFAIL (dtr seems to nee...) [ 90%] 683s tests/test_trajectory.py::test_unitcell[xyz] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[xyz.gz] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[lammpstrj] XFAIL (lammpstrj ...) [ 90%] 683s tests/test_trajectory.py::test_unitcell[tng] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[lh5] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[pdb] PASSED [ 90%] 683s tests/test_trajectory.py::test_unitcell[pdb.gz] PASSED [ 91%] 683s tests/test_trajectory.py::test_unitcell[ncrst] XFAIL (ncrst seems to...) [ 91%] 683s tests/test_trajectory.py::test_unitcell[rst7] XFAIL (rst7 seems to n...) [ 91%] 683s tests/test_trajectory.py::test_unitcell[gro] PASSED [ 91%] 683s tests/test_trajectory.py::test_chunk0_iterload PASSED [ 91%] 683s tests/test_trajectory.py::test_hashing PASSED [ 91%] 683s tests/test_trajectory.py::test_smooth PASSED [ 91%] 683s tests/test_trajectory.py::test_load_pdb_no_standard_names PASSED [ 91%] 683s tests/test_trajectory.py::test_load_with_atom_indices PASSED [ 91%] 684s tests/test_trajectory.py::test_load_with_frame PASSED [ 91%] 684s tests/test_trajectory.py::test_add_remove_atoms PASSED [ 91%] 684s tests/test_trr.py::test_1 PASSED [ 91%] 684s tests/test_trr.py::test_read_stride PASSED [ 92%] 684s tests/test_trr.py::test_read_stride_n_frames PASSED [ 92%] 684s tests/test_trr.py::test_read_stride_offsets PASSED [ 92%] 684s tests/test_trr.py::test_read_stride_n_frames_offsets PASSED [ 92%] 684s tests/test_trr.py::test_read_stride_switching PASSED [ 92%] 684s tests/test_trr.py::test_write_read PASSED [ 92%] 684s tests/test_trr.py::test_read_atomindices_1 PASSED [ 92%] 684s tests/test_trr.py::test_read_atomindices_2 PASSED [ 92%] 684s tests/test_trr.py::test_deficient_shape PASSED [ 92%] 684s tests/test_trr.py::test_ragged_1 PASSED [ 92%] 684s tests/test_trr.py::test_ragged_2 PASSED [ 92%] 684s tests/test_trr.py::test_malformed PASSED [ 92%] 684s tests/test_trr.py::test_tell PASSED [ 93%] 684s tests/test_trr.py::test_seek PASSED [ 93%] 684s tests/test_trr.py::test_get_velocities PASSED [ 93%] 684s tests/test_trr.py::test_get_forces PASSED [ 93%] 684s tests/test_trr.py::test_get_velocities_and_forces PASSED [ 93%] 684s tests/test_trr.py::test_get_velocities_forces_atom_indices_1 PASSED [ 93%] 684s tests/test_trr.py::test_get_velocities_forces_atom_indices_2 PASSED [ 93%] 684s tests/test_trr.py::test_read_velocities_do_not_exist PASSED [ 93%] 684s tests/test_trr.py::test_read_forces_do_not_exist PASSED [ 93%] 684s tests/test_utils.py::test_unitcell_0 PASSED [ 93%] 684s tests/test_utils.py::test_unitcell_1 PASSED [ 93%] 684s tests/test_utils.py::test_ensure_type_1 PASSED [ 93%] 684s tests/test_utils.py::test_ensure_type_2 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_25 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_3 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_4 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_5 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_6 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_7 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_8 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_9 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_10 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_11 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_12 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_13 PASSED [ 94%] 684s tests/test_utils.py::test_ensure_type_14 PASSED [ 95%] 684s tests/test_utils.py::test_ensure_type_15 PASSED [ 95%] 684s tests/test_utils.py::test_delay_import_fail_1 PASSED [ 95%] 684s tests/test_utils.py::test_delay_import PASSED [ 95%] 684s tests/test_utils.py::test_unit_0 PASSED [ 95%] 684s tests/test_utils.py::test_unit_1 PASSED [ 95%] 684s tests/test_utils.py::test_unit_2 PASSED [ 95%] 684s tests/test_utils.py::test_unit_3 PASSED [ 95%] 684s tests/test_xml.py::test_xml PASSED [ 95%] 684s tests/test_xtc.py::test_read_chunk1 PASSED [ 95%] 684s tests/test_xtc.py::test_read_stride PASSED [ 95%] 684s tests/test_xtc.py::test_read_stride_n_frames PASSED [ 95%] 684s tests/test_xtc.py::test_read_stride_offsets PASSED [ 96%] 684s tests/test_xtc.py::test_read_stride_n_frames_offsets PASSED [ 96%] 684s tests/test_xtc.py::test_read_stride_switching_offsets PASSED [ 96%] 684s tests/test_xtc.py::test_read_atomindices_1 PASSED [ 96%] 684s tests/test_xtc.py::test_read_atomindices_w_stride PASSED [ 96%] 684s tests/test_xtc.py::test_read_atomindices_2 PASSED [ 96%] 684s tests/test_xtc.py::test_read_chunk2 PASSED [ 96%] 684s tests/test_xtc.py::test_read_chunk3 PASSED [ 96%] 684s tests/test_xtc.py::test_write_0 PASSED [ 96%] 684s tests/test_xtc.py::test_write_1 PASSED [ 96%] 684s tests/test_xtc.py::test_write_2 PASSED [ 96%] 684s tests/test_xtc.py::test_read_error_0 PASSED [ 96%] 684s tests/test_xtc.py::test_write_error_0 PASSED [ 97%] 684s tests/test_xtc.py::test_read_error_1 PASSED [ 97%] 684s tests/test_xtc.py::test_read_error_2 PASSED [ 97%] 684s tests/test_xtc.py::test_xtc_write_wierd_0 PASSED [ 97%] 684s tests/test_xtc.py::test_tell PASSED [ 97%] 684s tests/test_xtc.py::test_seek PASSED [ 97%] 684s tests/test_xtc.py::test_seek_natoms9 PASSED [ 97%] 684s tests/test_xtc.py::test_seek_out_of_bounds PASSED [ 97%] 684s tests/test_xtc.py::test_ragged_1 PASSED [ 97%] 684s tests/test_xtc.py::test_ragged_2 PASSED [ 97%] 684s tests/test_xtc.py::test_short_traj PASSED [ 97%] 684s tests/test_xtc.py::test_flush PASSED [ 97%] 684s tests/test_xyz.py::test_read_0 PASSED [ 98%] 684s tests/test_xyz.py::test_read_1 PASSED [ 98%] 684s tests/test_xyz.py::test_read_gz PASSED [ 98%] 684s tests/test_xyz.py::test_read_write PASSED [ 98%] 684s tests/test_xyz.py::test_mdwrite PASSED [ 98%] 684s tests/test_xyz.py::test_multiread PASSED [ 98%] 684s tests/test_xyz.py::test_seek PASSED [ 98%] 684s tests/test_xyz.py::test_len PASSED [ 98%] 684s tests/test_zipped.py::test_read_gz PASSED [ 98%] 684s tests/test_zipped.py::test_write_gz PASSED [ 98%] 684s tests/test_zipped.py::test_read_bz2 PASSED [ 98%] 684s tests/test_zipped.py::test_write_bz2 PASSED [ 98%] 822s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] PASSED [ 99%] 956s examples/test_examples.py::test_example_notebook[hbonds.ipynb] SKIPPED [ 99%] 1093s examples/test_examples.py::test_example_notebook[iterload.ipynb] PASSED [ 99%] 1227s examples/test_examples.py::test_example_notebook[native-contact.ipynb] SKIPPED [ 99%] 1363s examples/test_examples.py::test_example_notebook[two-pass-clustering.ipynb] PASSED [ 99%] 1500s examples/test_examples.py::test_example_notebook[principal-components.ipynb] PASSED [ 99%] 1636s examples/test_examples.py::test_example_notebook[atom-selection.ipynb] PASSED [ 99%] 1772s examples/test_examples.py::test_example_notebook[ramachandran-plot.ipynb] PASSED [ 99%] 1909s examples/test_examples.py::test_example_notebook[clustering.ipynb] PASSED [ 99%] 2044s examples/test_examples.py::test_example_notebook[rmsd-drift.ipynb] PASSED [ 99%] 2179s examples/test_examples.py::test_example_notebook[rmsd-benchmark.ipynb] PASSED [ 99%] 2314s examples/test_examples.py::test_example_notebook[centroids.ipynb] PASSED [ 99%] 2314s examples/test_examples.py::test_example_notebook[simulation-with-openmm.ipynb] SKIPPED [100%] 2314s 2314s =============================== warnings summary =============================== 2314s ../../../../usr/lib/python3/dist-packages/mdtraj/utils/unit/__init__.py:57 2314s /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 2314s ast.Pow, ast.Div, ast.Mult, ast.Num] 2314s 2314s ../../../../usr/lib/python3/dist-packages/mdtraj/formats/__init__.py:6 2314s /usr/lib/python3/dist-packages/mdtraj/formats/__init__.py:6: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13 2314s from .xtc import XTCTrajectoryFile 2314s 2314s ../../../../usr/lib/python3/dist-packages/mdtraj/geometry/order.py:25 2314s /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 2314s from pkg_resources import parse_version 2314s 2314s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871 2314s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`. 2314s 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 2314s declare_namespace(pkg) 2314s 2314s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 2314s /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). 2314s EPOCH = datetime.datetime.utcfromtimestamp(0) 2314s 2314s ../../../../usr/lib/python3/dist-packages/jupyter_client/connect.py:27 2314s /usr/lib/python3/dist-packages/jupyter_client/connect.py:27: DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs 2314s given by the platformdirs library. To remove this warning and 2314s see the appropriate new directories, set the environment variable 2314s `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. 2314s The use of platformdirs will be the default in `jupyter_core` v6 2314s from jupyter_core.paths import jupyter_data_dir 2314s 2314s examples/test_examples.py:26 2314s /tmp/autopkgtest.QpWX0U/build.RuN/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 2314s examples = [pytest.param(fn, marks=pytest.mark.flaky) if fn in FLAKEY_LIST else fn 2314s 2314s tests/test_angles.py::test_angle_pbc_0 2314s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting unitcell_vectors dtype=float64 to 2314s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2314s 2314s tests/test_arc.py::test_read_arctraj 2314s tests/test_order.py::test_nematic_order 2314s tests/test_order.py::test_director 2314s tests/test_order.py::test_inertia 2314s tests/test_order.py::test_nematic_order_args 2314s tests/test_shape.py::test_gyration 2314s /usr/lib/python3/dist-packages/mdtraj/formats/pdb/pdbfile.py:198: RuntimeWarning: divide by zero encountered in divide 2314s particle_density = traj.top.n_atoms / traj.unitcell_volumes[0] 2314s 2314s tests/test_arc.py: 1 warning 2314s tests/test_gro.py: 3 warnings 2314s tests/test_order.py: 4 warnings 2314s tests/test_pdb.py: 1 warning 2314s tests/test_shape.py: 4 warnings 2314s /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. 2314s warnings.warn('Unlikely unit cell vectors detected in PDB file likely ' 2314s 2314s tests/test_arc.py: 1 warning 2314s tests/test_dihedral.py: 1 warning 2314s tests/test_geometry.py: 2 warnings 2314s tests/test_hdf5.py: 1 warning 2314s tests/test_lprmsd.py: 1 warning 2314s tests/test_mdconvert.py: 9 warnings 2314s tests/test_mol2.py: 1 warning 2314s tests/test_nmr.py: 1 warning 2314s tests/test_rmsd.py: 8 warnings 2314s tests/test_rmsd_memmap.py: 2 warnings 2314s tests/test_sasa.py: 3 warnings 2314s tests/test_topology.py: 2 warnings 2314s tests/test_trajectory.py: 85 warnings 2314s /usr/lib/python3/dist-packages/mdtraj/core/trajectory.py:439: UserWarning: top= kwargs ignored since this file parser does not support it 2314s warnings.warn('top= kwargs ignored since this file parser does not support it') 2314s 2314s tests/test_contact.py::test_contact_0 2314s tests/test_contact.py::test_contact_4 2314s /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. 2314s warnings.warn('selected topology includes at least one glycine residue, which has no heavy atoms in its sidechain. The distances involving glycine residues ' 2314s 2314s tests/test_contact.py::test_contact_3 2314s /usr/lib/python3/dist-packages/mdtraj/geometry/contact.py:227: RuntimeWarning: overflow encountered in exp 2314s np.log(np.sum(np.exp(soft_min_beta/ 2314s 2314s tests/test_contact.py::test_contact_3 2314s /tmp/autopkgtest.QpWX0U/build.RuN/src/tests/test_contact.py:106: RuntimeWarning: divide by zero encountered in divide 2314s assert np.allclose(beta / np.log(np.sum(np.exp(beta / maps[t, r0, r1]))), dists[t, i]) 2314s 2314s tests/test_dcd.py::test_do_overwrite 2314s tests/test_dcd.py::test_ragged_1 2314s tests/test_dcd.py::test_ragged_2 2314s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting xyz dtype=float64 to 2314s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2314s 2314s tests/test_distance.py: 6 warnings 2314s tests/test_mdconvert.py: 112 warnings 2314s tests/test_neighbors.py: 2 warnings 2314s tests/test_netcdf.py: 46 warnings 2314s tests/test_rdf.py: 8 warnings 2314s tests/test_restart.py: 4 warnings 2314s tests/test_trajectory.py: 196 warnings 2314s /usr/lib/python3/dist-packages/mdtraj/formats/netcdf.py:130: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2314s if StrictVersion(import_('scipy.version').short_version) < StrictVersion('0.12.0'): 2314s 2314s tests/test_drid.py::test_drid_2 2314s /tmp/autopkgtest.QpWX0U/build.RuN/src/tests/test_drid.py:61: RuntimeWarning: divide by zero encountered in divide 2314s recip = 1 / squareform(pdist(t.xyz[i])) 2314s 2314s tests/test_geometry.py: 1 warning 2314s tests/test_hoomdxml.py: 1 warning 2314s tests/test_neighbors.py: 2 warnings 2314s tests/test_rdf.py: 38 warnings 2314s tests/test_selection.py: 73 warnings 2314s tests/test_topology.py: 17 warnings 2314s /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 2314s if isinstance(astnode, ast.Num) or isinstance(astnode, ast.Str): 2314s 2314s tests/test_geometry.py: 2 warnings 2314s tests/test_hoomdxml.py: 1 warning 2314s tests/test_neighbors.py: 2 warnings 2314s tests/test_rdf.py: 38 warnings 2314s tests/test_selection.py: 73 warnings 2314s tests/test_topology.py: 17 warnings 2314s /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 2314s if isinstance(astnode, ast.Num) or isinstance(astnode, ast.Str): 2314s 2314s tests/test_geometry.py::test_dihedral_indices 2314s tests/test_geometry.py::test_dihedral_indices 2314s /usr/lib/python3/dist-packages/mdtraj/geometry/dihedral.py:203: DeprecationWarning: Passing a Trajectory object to _atom_sequence isdeprecated. Please pass a Topology object 2314s warnings.warn("Passing a Trajectory object to _atom_sequence is" 2314s 2314s tests/test_gro.py::test_load 2314s tests/test_topology.py::test_topology_pandas_2residues_same_resSeq 2314s /usr/lib/python3/dist-packages/mdtraj/formats/gro.py:322: UserWarning: WARNING: two consecutive residues with same number (GST, HST) 2314s warnings.warn("WARNING: two consecutive residues with same number (%s, %s)" % (thisresname, old_resname)) 2314s 2314s tests/test_hdf5.py::test_read_0 2314s tests/test_hdf5.py::test_read_slice_0 2314s tests/test_hdf5.py::test_read_slice_2 2314s tests/test_hdf5.py::test_read_slice_3 2314s /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 2314s check_attribute_name(name) 2314s 2314s tests/test_rdf.py: 7 warnings 2314s tests/test_selection.py: 14 warnings 2314s tests/test_topology.py: 5 warnings 2314s /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 2314s return ast.NameConstant(value=_safe_names[node.id], kind=None) 2314s 2314s tests/test_rdf.py: 32 warnings 2314s tests/test_selection.py: 23 warnings 2314s tests/test_topology.py: 12 warnings 2314s /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 2314s return ast.Str(s=node.id, kind=None) 2314s 2314s tests/test_rdf.py: 32 warnings 2314s tests/test_selection.py: 23 warnings 2314s tests/test_topology.py: 12 warnings 2314s /usr/lib/python3.12/ast.py:587: DeprecationWarning: Attribute s is deprecated and will be removed in Python 3.14; use value instead 2314s return Constant(*args, **kwargs) 2314s 2314s tests/test_restart.py: 1014 warnings 2314s tests/test_trajectory.py: 12 warnings 2314s /usr/lib/python3/dist-packages/mdtraj/formats/amberrst.py:465: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. 2314s if StrictVersion(import_('scipy.version').short_version) < StrictVersion('0.12.0'): 2314s 2314s tests/test_trajectory.py::test_box_load_save[dtr] 2314s tests/test_trajectory.py::test_read_write[dcd-dtr] 2314s tests/test_trajectory.py::test_read_write[lammpstrj-dtr] 2314s tests/test_trajectory.py::test_read_write[pdb-dtr] 2314s tests/test_trajectory.py::test_read_write[pdb.gz-dtr] 2314s tests/test_trajectory.py::test_save_load[dtr] 2314s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=int64 to 2314s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2314s 2314s tests/test_trajectory.py::test_write_path[dtr] 2314s tests/test_trajectory.py::test_read_write[h5-dtr] 2314s tests/test_trajectory.py::test_read_write[xtc-dtr] 2314s tests/test_trajectory.py::test_read_write[trr-dtr] 2314s tests/test_trajectory.py::test_read_write[tng-dtr] 2314s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=float32 to 2314s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2314s 2314s tests/test_trajectory.py::test_read_write[nc-dtr] 2314s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting times dtype=>f4 to 2314s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2314s 2314s tests/test_trajectory.py::test_float_atom_indices_exception[gro] 2314s /usr/lib/python3/dist-packages/mdtraj/core/topology.py:91: UserWarning: atom_indices are not monotonically increasing 2314s warnings.warn('atom_indices are not monotonically increasing') 2314s 2314s tests/test_trajectory.py::test_array_vs_matrix 2314s /tmp/autopkgtest.QpWX0U/build.RuN/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. 2314s xyz_mat = np.matrix(xyz) 2314s 2314s tests/test_utils.py::test_ensure_type_8 2314s tests/test_utils.py::test_ensure_type_9 2314s tests/test_utils.py::test_ensure_type_13 2314s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting dtype=float64 to 2314s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2314s 2314s tests/test_utils.py::test_ensure_type_11 2314s /usr/lib/python3/dist-packages/mdtraj/utils/validation.py:115: TypeCastPerformanceWarning: Casting dtype=int64 to 2314s warnings.warn("Casting %s dtype=%s to %s " % (name, val.dtype, dtype), 2314s 2314s tests/test_utils.py::test_unit_3 2314s tests/test_utils.py::test_unit_3 2314s /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 2314s if not any(isinstance(node, a) for a in self.allowed_ops): 2314s 2314s examples/test_examples.py::test_example_notebook[solvent-accessible-surface-area.ipynb] 2314s /usr/lib/python3/dist-packages/jupyter_client/utils.py:18: DeprecationWarning: There is no current event loop 2314s loop = asyncio.get_event_loop_policy().get_event_loop() 2314s 2314s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 2314s =========================== short test summary info ============================ 2314s SKIPPED [1] tests/test_dihedral.py:48: pymol executable not found 2314s SKIPPED [1] tests/test_dihedral.py:149: pymol executable not found 2314s SKIPPED [16] tests/test_docstrings.py:36: Skip checking certain modules' docstrings 2314s SKIPPED [1] tests/test_dssp.py:44: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2314s SKIPPED [1] tests/test_dssp.py:52: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2314s SKIPPED [1] tests/test_dssp.py:59: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2314s SKIPPED [1] tests/test_geometry.py:243: Not doing performance testing 2314s SKIPPED [1] tests/test_geometry.py:261: Not doing performance testing 2314s SKIPPED [1] tests/test_gsd.py:30: gsd module is not available 2314s SKIPPED [1] tests/test_gsd.py:41: gsd module is not available 2314s SKIPPED [1] tests/test_gsd.py:51: gsd module is not available 2314s SKIPPED [1] tests/test_gsd.py:61: gsd module is not available 2314s SKIPPED [1] tests/test_gsd.py:75: gsd module is not available 2314s SKIPPED [1] tests/test_gsd.py:82: gsd module is not available 2314s SKIPPED [1] tests/test_gsd.py:94: gsd module is not available 2314s SKIPPED [1] tests/test_hbonds.py:43: This test requires mkdssp to be installed, from http://swift.cmbi.ru.nl/gv/dssp/ 2314s SKIPPED [1] tests/test_hdf5.py:99: requires openmm.units 2314s SKIPPED [1] tests/test_hdf5.py:133: requires openmm.units 2314s SKIPPED [1] tests/test_hdf5.py:186: requires openmm.units 2314s SKIPPED [1] tests/test_mol2.py:55: Requires obabel 2314s SKIPPED [1] tests/test_netcdf.py:248: This test requires cpptraj from AmberTools to be installed (http://ambermd.org) 2314s SKIPPED [1] tests/test_nmr.py:11: SPARTA+ binary not found 2314s SKIPPED [1] tests/test_nmr.py:24: PPM binary not found 2314s SKIPPED [1] tests/test_nmr.py:38: SHIFTX2 binary not found or Python 2 not found or runningn on travis. 2314s SKIPPED [1] tests/test_pdbx.py:39: test_pdbx.py needs OpenMM. 2314s SKIPPED [2] tests/test_psf.py:92: This test requires the VMD executable: http://www.ks.uiuc.edu/Research/vmd/ 2314s SKIPPED [1] tests/test_rdf.py:66: Binning does not match up with gromacs currently. 2314s SKIPPED [1] tests/test_rdf.py:153: Binning does not match up with gromacs currently. 2314s SKIPPED [1] tests/test_reporter.py:47: test_reporter.py needs OpenMM. 2314s SKIPPED [1] tests/test_reporter.py:121: test_reporter.py needs OpenMM. 2314s SKIPPED [1] tests/test_reporter.py:201: test_reporter.py needs OpenMM. 2314s SKIPPED [1] tests/test_thermodynamic_properties.py:154: Thermal expansion test doesn't work. 2314s SKIPPED [1] tests/test_tng.py:20: Fails on macOS + Python 3.11, need to investigate. 2314s SKIPPED [1] tests/test_topology.py:42: needs OpenMM 2314s SKIPPED [1] tests/test_topology.py:59: needs OpenMM 2314s SKIPPED [1] tests/test_topology.py:187: needs OpenMM 2314s SKIPPED [1] tests/test_trajectory.py:128: binpos does not store box information 2314s SKIPPED [1] tests/test_trajectory.py:128: xyz does not store box information 2314s SKIPPED [1] tests/test_trajectory.py:128: xyz.gz does not store box information 2314s SKIPPED [1] tests/test_trajectory.py:128: lh5 does not store box information 2314s SKIPPED [1] tests/test_trajectory.py:128: pdb does not store box information 2314s SKIPPED [1] tests/test_trajectory.py:128: pdb.gz does not store box information 2314s SKIPPED [1] tests/test_trajectory.py:200: mdcrd can only store rectilinear boxes 2314s SKIPPED [1] tests/test_trajectory.py:198: ncrst can only store 1 frame per file 2314s SKIPPED [1] tests/test_trajectory.py:198: rst7 can only store 1 frame per file 2314s SKIPPED [16] tests/test_trajectory.py:212: mdcrd can only store rectilinear boxes 2314s SKIPPED [16] tests/test_trajectory.py:210: ncrst can only store 1 frame per file 2314s SKIPPED [16] tests/test_trajectory.py:210: rst7 can only store 1 frame per file 2314s SKIPPED [5] tests/test_trajectory.py:219: dtr needs to write unitcells 2314s SKIPPED [5] tests/test_trajectory.py:219: lammpstrj needs to write unitcells 2314s SKIPPED [2] tests/test_trajectory.py:541: Only 1 frame per file format 2314s SKIPPED [2] examples/test_examples.py:71: Network access required 2314s SKIPPED [1] examples/test_examples.py:71: Openmm required for example notebook `simulation-with-openmm.ipynb` 2314s XFAIL tests/test_trajectory.py::test_read_path[ncrst] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_path[rst7] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-nc] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-h5] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xtc] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-trr] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dcd] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-mdcrd] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-binpos] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-dtr] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-xyz.gz] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lammpstrj] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-tng] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-lh5] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-pdb.gz] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-ncrst] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-rst7] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[ncrst-gro] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-nc] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-h5] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-xtc] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-trr] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-dcd] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-mdcrd] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-binpos] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-dtr] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-xyz.gz] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-lammpstrj] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-tng] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-lh5] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-pdb.gz] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-ncrst] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-rst7] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_read_write[rst7-gro] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_load[ncrst] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_load[rst7] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[ncrst] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_float_atom_indices_exception[rst7] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_load_combination[ncrst] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_load_combination[rst7] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_seek_read_mode[xyz.gz] - reason: This is broken 2314s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb] - reason: PDB Files don't support seeking 2314s XFAIL tests/test_trajectory.py::test_seek_read_mode[pdb.gz] - reason: PDB Files don't support seeking 2314s XFAIL tests/test_trajectory.py::test_seek_read_mode[ncrst] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_seek_read_mode[rst7] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_seek_read_mode[gro] - reason: This is broken 2314s XFAIL tests/test_trajectory.py::test_load_frame[dtr] - reason: DTR doesn't load a single frame properly 2314s XFAIL tests/test_trajectory.py::test_load_frame[ncrst] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_load_frame[rst7] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_load_frame[gro] - reason: Gro doesn't implement seek 2314s XFAIL tests/test_trajectory.py::test_iterload[dtr] - reason: This is broken with dtr 2314s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb] - reason: PDB Iterloads an extra frame!! 2314s XFAIL tests/test_trajectory.py::test_iterload_skip[pdb.gz] - reason: PDB Iterloads an extra frame!! 2314s XFAIL tests/test_trajectory.py::test_iterload_skip[ncrst] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_iterload_skip[rst7] - reason: These reference files don't exist yet 2314s XFAIL tests/test_trajectory.py::test_iterload_skip[gro] - reason: Not implemented for some reason 2314s XFAIL tests/test_trajectory.py::test_force_overwrite[dtr] - reason: This is broken with dtr 2314s XFAIL tests/test_trajectory.py::test_unitcell[dtr] - reason: dtr seems to need unit vectors 2314s XFAIL tests/test_trajectory.py::test_unitcell[lammpstrj] - reason: lammpstrj seems to need unit vectors 2314s XFAIL tests/test_trajectory.py::test_unitcell[ncrst] - reason: ncrst seems to need unit vectors 2314s XFAIL tests/test_trajectory.py::test_unitcell[rst7] - reason: rst7 seems to need unit vectors 2314s = 1030 passed, 124 skipped, 2 deselected, 65 xfailed, 2006 warnings in 1916.09s (0:31:56) = 2315s autopkgtest [16:39:58]: test command1: -----------------------] 2316s autopkgtest [16:39:59]: test command1: - - - - - - - - - - results - - - - - - - - - - 2316s command1 PASS 2316s autopkgtest [16:39:59]: @@@@@@@@@@@@@@@@@@@@ summary 2316s command1 PASS 2336s Creating nova instance adt-noble-arm64-mdtraj-20240305-154649-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240304.img (UUID 798e10ba-3c91-4aca-8041-56247acf271e)...