0s autopkgtest [05:57:36]: starting date and time: 2025-05-02 05:57:36+0000 1s autopkgtest [05:57:36]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 1s autopkgtest [05:57:36]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6xfqa_53/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pyopengl --apt-upgrade pymol --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=pyopengl/3.1.9+dfsg-1.1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-9.secgroup --name adt-questing-arm64-pymol-20250502-055736-juju-7f2275-prod-proposed-migration-environment-15-faac9dc5-1370-4867-b88b-53a2d1f9d680 --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 51s autopkgtest [05:58:27]: testbed dpkg architecture: arm64 51s autopkgtest [05:58:27]: testbed apt version: 3.0.0 51s autopkgtest [05:58:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [05:58:27]: testbed release detected to be: None 52s autopkgtest [05:58:28]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 52s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 52s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 52s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 52s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [184 kB] 52s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [57.4 kB] 52s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2202 kB] 53s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [227 kB] 53s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1472 kB] 53s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [16.5 kB] 53s Fetched 4269 kB in 1s (5111 kB/s) 54s Reading package lists... 54s autopkgtest [05:58:30]: upgrading testbed (apt dist-upgrade and autopurge) 54s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 55s Starting 2 pkgProblemResolver with broken count: 0 55s Done 56s Entering ResolveByKeep 56s 56s Calculating upgrade... 57s The following packages will be upgraded: 57s libperl5.40 perl perl-base perl-modules-5.40 57s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 10.0 MB of archives. 57s After this operation, 0 B of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libperl5.40 arm64 5.40.1-3 [4780 kB] 57s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl arm64 5.40.1-3 [262 kB] 57s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-base arm64 5.40.1-3 [1786 kB] 57s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-modules-5.40 all 5.40.1-3 [3217 kB] 58s Fetched 10.0 MB in 1s (17.6 MB/s) 58s (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 ... 85224 files and directories currently installed.) 58s Preparing to unpack .../libperl5.40_5.40.1-3_arm64.deb ... 58s Unpacking libperl5.40:arm64 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 58s Preparing to unpack .../perl_5.40.1-3_arm64.deb ... 58s Unpacking perl (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 58s Preparing to unpack .../perl-base_5.40.1-3_arm64.deb ... 58s Unpacking perl-base (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 58s Setting up perl-base (5.40.1-3) ... 58s (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 ... 85224 files and directories currently installed.) 58s Preparing to unpack .../perl-modules-5.40_5.40.1-3_all.deb ... 58s Unpacking perl-modules-5.40 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 58s Setting up perl-modules-5.40 (5.40.1-3) ... 58s Setting up libperl5.40:arm64 (5.40.1-3) ... 58s Setting up perl (5.40.1-3) ... 58s Processing triggers for man-db (2.13.0-1) ... 59s Processing triggers for libc-bin (2.41-6ubuntu1) ... 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Starting pkgProblemResolver with broken count: 0 60s Starting 2 pkgProblemResolver with broken count: 0 60s Done 60s Solving dependencies... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s autopkgtest [05:58:39]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 63s autopkgtest [05:58:39]: @@@@@@@@@@@@@@@@@@@@ apt-source pymol 66s Get:1 http://ftpmaster.internal/ubuntu questing/universe pymol 3.1.0+dfsg-1 (dsc) [2307 B] 66s Get:2 http://ftpmaster.internal/ubuntu questing/universe pymol 3.1.0+dfsg-1 (tar) [22.0 MB] 66s Get:3 http://ftpmaster.internal/ubuntu questing/universe pymol 3.1.0+dfsg-1 (diff) [57.9 kB] 66s gpgv: Signature made Mon Mar 17 08:37:43 2025 UTC 66s gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 66s gpgv: Can't check signature: No public key 66s dpkg-source: warning: cannot verify inline signature for ./pymol_3.1.0+dfsg-1.dsc: no acceptable signature found 67s autopkgtest [05:58:43]: testing package pymol version 3.1.0+dfsg-1 68s autopkgtest [05:58:44]: build not needed 81s autopkgtest [05:58:57]: test command1: preparing testbed 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Starting pkgProblemResolver with broken count: 0 82s Starting 2 pkgProblemResolver with broken count: 0 82s Done 83s The following NEW packages will be installed: 83s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libaec0 83s libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libcups2t64 83s libdouble-conversion3 libegl-mesa0 libegl1 libfontconfig1 libgbm1 83s libgfortran5 libgl1 libgl1-mesa-dri libglew2.2 libglu1-mesa libglut3.12 83s libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libharfbuzz0b 83s libhdf5-310 libhdf5-hl-310 libice6 libinput-bin libinput10 libjpeg-turbo8 83s libjpeg8 liblapack3 libmd4c0 libmtdev1t64 libnetcdf22 libopengl0 83s libpcre2-16-0 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 83s libqt5help5 libqt5network5t64 libqt5opengl5t64 libqt5printsupport5t64 83s libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libsm6 libsz2 83s libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-server0 83s libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 83s libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 83s libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 83s libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxi6 83s libxkbcommon-x11-0 libxrender1 libxshmfence1 libxxf86vm1 mesa-libgallium 83s pymol pymol-data python3-legacy-cgi python3-numpy python3-numpy-dev 83s python3-opengl python3-pymol python3-pyqt5 python3-pyqt5.qtopengl 83s python3-pyqt5.sip x11-common 83s 0 upgraded, 94 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 45.5 MB of archives. 83s After this operation, 184 MB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 83s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 83s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15-20250404-0ubuntu1 [444 kB] 83s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 83s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 83s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 83s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 83s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 83s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 83s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig arm64 2.15.0-2.2ubuntu1 [191 kB] 83s Get:11 http://ftpmaster.internal/ubuntu questing/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 83s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-common-data arm64 0.8-16ubuntu2 [31.0 kB] 83s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-common3 arm64 0.8-16ubuntu2 [22.9 kB] 83s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libavahi-client3 arm64 0.8-16ubuntu2 [26.9 kB] 83s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libcups2t64 arm64 2.4.12-0ubuntu1 [272 kB] 83s Get:16 http://ftpmaster.internal/ubuntu questing/universe arm64 libdouble-conversion3 arm64 3.3.1-1 [38.8 kB] 83s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 libwayland-server0 arm64 1.23.1-3 [36.1 kB] 83s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libx11-xcb1 arm64 2:1.8.10-2 [8020 B] 83s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-dri3-0 arm64 1.17.0-2 [7606 B] 83s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-present0 arm64 1.17.0-2 [6224 B] 83s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-randr0 arm64 1.17.0-2 [18.5 kB] 83s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-sync1 arm64 1.17.0-2 [9688 B] 83s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-xfixes0 arm64 1.17.0-2 [10.6 kB] 83s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 libxshmfence1 arm64 1.3-1build5 [4938 B] 83s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 mesa-libgallium arm64 25.0.3-1ubuntu2 [9455 kB] 83s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libgbm1 arm64 25.0.3-1ubuntu2 [33.7 kB] 83s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libwayland-client0 arm64 1.23.1-3 [27.0 kB] 83s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 83s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 libegl-mesa0 arm64 25.0.3-1ubuntu2 [122 kB] 83s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 libvulkan1 arm64 1.4.304.0-1 [158 kB] 83s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 libgl1-mesa-dri arm64 25.0.3-1ubuntu2 [35.4 kB] 83s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libglvnd0 arm64 1.7.0-1build1 [60.6 kB] 83s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-glx0 arm64 1.17.0-2 [25.5 kB] 83s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libxxf86vm1 arm64 1:1.1.4-1build4 [9130 B] 83s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 libglx-mesa0 arm64 25.0.3-1ubuntu2 [151 kB] 83s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 libglx0 arm64 1.7.0-1build1 [33.2 kB] 83s Get:37 http://ftpmaster.internal/ubuntu questing/main arm64 libgl1 arm64 1.7.0-1build1 [106 kB] 83s Get:38 http://ftpmaster.internal/ubuntu questing/universe arm64 libglew2.2 arm64 2.2.0-4build1 [191 kB] 83s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 libxi6 arm64 2:1.8.2-1 [32.4 kB] 83s Get:40 http://ftpmaster.internal/ubuntu questing/universe arm64 libglut3.12 arm64 3.4.0-4 [97.1 kB] 83s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 83s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 83s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 83s Get:44 http://ftpmaster.internal/ubuntu questing/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 83s Get:45 http://ftpmaster.internal/ubuntu questing/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 84s Get:46 http://ftpmaster.internal/ubuntu questing/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 84s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 84s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 84s Get:49 http://ftpmaster.internal/ubuntu questing/main arm64 libwacom-common all 2.14.0-1 [103 kB] 84s Get:50 http://ftpmaster.internal/ubuntu questing/main arm64 libwacom9 arm64 2.14.0-1 [26.7 kB] 84s Get:51 http://ftpmaster.internal/ubuntu questing/main arm64 libinput-bin arm64 1.27.1-1 [23.5 kB] 84s Get:52 http://ftpmaster.internal/ubuntu questing/main arm64 libmtdev1t64 arm64 1.1.7-1 [14.6 kB] 84s Get:53 http://ftpmaster.internal/ubuntu questing/main arm64 libinput10 arm64 1.27.1-1 [136 kB] 84s Get:54 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 84s Get:55 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 84s Get:56 http://ftpmaster.internal/ubuntu questing/universe arm64 libmd4c0 arm64 0.5.2-2 [42.4 kB] 84s Get:57 http://ftpmaster.internal/ubuntu questing/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB] 84s Get:58 http://ftpmaster.internal/ubuntu questing/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 84s Get:59 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5core5t64 arm64 5.15.15+dfsg-4ubuntu1 [1999 kB] 84s Get:60 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5dbus5t64 arm64 5.15.15+dfsg-4ubuntu1 [222 kB] 84s Get:61 http://ftpmaster.internal/ubuntu questing/main arm64 libegl1 arm64 1.7.0-1build1 [29.5 kB] 84s Get:62 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5network5t64 arm64 5.15.15+dfsg-4ubuntu1 [735 kB] 84s Get:63 http://ftpmaster.internal/ubuntu questing/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 84s Get:64 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-icccm4 arm64 0.4.2-1 [10.9 kB] 84s Get:65 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-util1 arm64 0.4.1-1 [10.9 kB] 84s Get:66 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-image0 arm64 0.4.0-2build1 [10.8 kB] 84s Get:67 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-keysyms1 arm64 0.4.1-1 [8802 B] 84s Get:68 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 84s Get:69 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render-util0 arm64 0.3.10-1 [10.5 kB] 84s Get:70 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shape0 arm64 1.17.0-2 [6246 B] 84s Get:71 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-xinerama0 arm64 1.17.0-2 [5590 B] 84s Get:72 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-xinput0 arm64 1.17.0-2 [34.2 kB] 84s Get:73 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-xkb1 arm64 1.17.0-2 [32.5 kB] 84s Get:74 http://ftpmaster.internal/ubuntu questing/main arm64 libxkbcommon-x11-0 arm64 1.7.0-2 [13.8 kB] 84s Get:75 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 84s Get:76 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5gui5t64 arm64 5.15.15+dfsg-4ubuntu1 [3680 kB] 84s Get:77 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5widgets5t64 arm64 5.15.15+dfsg-4ubuntu1 [2568 kB] 84s Get:78 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5xml5t64 arm64 5.15.15+dfsg-4ubuntu1 [124 kB] 84s Get:79 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5designer5 arm64 5.15.15-6build1 [2840 kB] 84s Get:80 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5sql5t64 arm64 5.15.15+dfsg-4ubuntu1 [123 kB] 84s Get:81 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5help5 arm64 5.15.15-6build1 [165 kB] 84s Get:82 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5opengl5t64 arm64 5.15.15+dfsg-4ubuntu1 [149 kB] 84s Get:83 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5printsupport5t64 arm64 5.15.15+dfsg-4ubuntu1 [209 kB] 84s Get:84 http://ftpmaster.internal/ubuntu questing/universe arm64 libqt5test5t64 arm64 5.15.15+dfsg-4ubuntu1 [144 kB] 84s Get:85 http://ftpmaster.internal/ubuntu questing/main arm64 python3-legacy-cgi all 2.6.2-1 [16.6 kB] 84s Get:86 http://ftpmaster.internal/ubuntu questing/main arm64 libopengl0 arm64 1.7.0-1build1 [35.1 kB] 84s Get:87 http://ftpmaster.internal/ubuntu questing/main arm64 libglu1-mesa arm64 9.0.2-1.1build1 [139 kB] 84s Get:88 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 python3-opengl all 3.1.9+dfsg-1.1 [631 kB] 84s Get:89 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-pyqt5.sip arm64 12.17.0-1build1 [67.6 kB] 84s Get:90 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-pyqt5 arm64 5.15.11+dfsg-2 [2580 kB] 84s Get:91 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-pyqt5.qtopengl arm64 5.15.11+dfsg-2 [119 kB] 84s Get:92 http://ftpmaster.internal/ubuntu questing/universe arm64 pymol-data all 3.1.0+dfsg-1 [1394 kB] 84s Get:93 http://ftpmaster.internal/ubuntu questing/universe arm64 python3-pymol arm64 3.1.0+dfsg-1 [3999 kB] 84s Get:94 http://ftpmaster.internal/ubuntu questing/universe arm64 pymol all 3.1.0+dfsg-1 [126 kB] 85s Fetched 45.5 MB in 2s (28.8 MB/s) 85s Selecting previously unselected package python3-numpy-dev:arm64. 85s (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 ... 85224 files and directories currently installed.) 85s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 85s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 85s Selecting previously unselected package libblas3:arm64. 85s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 85s Unpacking libblas3:arm64 (3.12.1-2) ... 85s Selecting previously unselected package libgfortran5:arm64. 85s Preparing to unpack .../02-libgfortran5_15-20250404-0ubuntu1_arm64.deb ... 85s Unpacking libgfortran5:arm64 (15-20250404-0ubuntu1) ... 85s Selecting previously unselected package liblapack3:arm64. 85s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 85s Unpacking liblapack3:arm64 (3.12.1-2) ... 85s Selecting previously unselected package python3-numpy. 85s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 85s Unpacking python3-numpy (1:2.2.3+ds-5) ... 85s Selecting previously unselected package fonts-dejavu-mono. 85s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ... 85s Unpacking fonts-dejavu-mono (2.37-8) ... 85s Selecting previously unselected package fonts-dejavu-core. 85s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ... 85s Unpacking fonts-dejavu-core (2.37-8) ... 85s Selecting previously unselected package fontconfig-config. 85s Preparing to unpack .../07-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 85s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 85s Selecting previously unselected package libfontconfig1:arm64. 85s Preparing to unpack .../08-libfontconfig1_2.15.0-2.2ubuntu1_arm64.deb ... 85s Unpacking libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 85s Selecting previously unselected package fontconfig. 85s Preparing to unpack .../09-fontconfig_2.15.0-2.2ubuntu1_arm64.deb ... 85s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 85s Selecting previously unselected package libaec0:arm64. 85s Preparing to unpack .../10-libaec0_1.1.3-1_arm64.deb ... 85s Unpacking libaec0:arm64 (1.1.3-1) ... 85s Selecting previously unselected package libavahi-common-data:arm64. 85s Preparing to unpack .../11-libavahi-common-data_0.8-16ubuntu2_arm64.deb ... 85s Unpacking libavahi-common-data:arm64 (0.8-16ubuntu2) ... 86s Selecting previously unselected package libavahi-common3:arm64. 86s Preparing to unpack .../12-libavahi-common3_0.8-16ubuntu2_arm64.deb ... 86s Unpacking libavahi-common3:arm64 (0.8-16ubuntu2) ... 86s Selecting previously unselected package libavahi-client3:arm64. 86s Preparing to unpack .../13-libavahi-client3_0.8-16ubuntu2_arm64.deb ... 86s Unpacking libavahi-client3:arm64 (0.8-16ubuntu2) ... 86s Selecting previously unselected package libcups2t64:arm64. 86s Preparing to unpack .../14-libcups2t64_2.4.12-0ubuntu1_arm64.deb ... 86s Unpacking libcups2t64:arm64 (2.4.12-0ubuntu1) ... 86s Selecting previously unselected package libdouble-conversion3:arm64. 86s Preparing to unpack .../15-libdouble-conversion3_3.3.1-1_arm64.deb ... 86s Unpacking libdouble-conversion3:arm64 (3.3.1-1) ... 86s Selecting previously unselected package libwayland-server0:arm64. 86s Preparing to unpack .../16-libwayland-server0_1.23.1-3_arm64.deb ... 86s Unpacking libwayland-server0:arm64 (1.23.1-3) ... 86s Selecting previously unselected package libx11-xcb1:arm64. 86s Preparing to unpack .../17-libx11-xcb1_2%3a1.8.10-2_arm64.deb ... 86s Unpacking libx11-xcb1:arm64 (2:1.8.10-2) ... 86s Selecting previously unselected package libxcb-dri3-0:arm64. 86s Preparing to unpack .../18-libxcb-dri3-0_1.17.0-2_arm64.deb ... 86s Unpacking libxcb-dri3-0:arm64 (1.17.0-2) ... 86s Selecting previously unselected package libxcb-present0:arm64. 86s Preparing to unpack .../19-libxcb-present0_1.17.0-2_arm64.deb ... 86s Unpacking libxcb-present0:arm64 (1.17.0-2) ... 86s Selecting previously unselected package libxcb-randr0:arm64. 86s Preparing to unpack .../20-libxcb-randr0_1.17.0-2_arm64.deb ... 86s Unpacking libxcb-randr0:arm64 (1.17.0-2) ... 86s Selecting previously unselected package libxcb-sync1:arm64. 86s Preparing to unpack .../21-libxcb-sync1_1.17.0-2_arm64.deb ... 86s Unpacking libxcb-sync1:arm64 (1.17.0-2) ... 86s Selecting previously unselected package libxcb-xfixes0:arm64. 86s Preparing to unpack .../22-libxcb-xfixes0_1.17.0-2_arm64.deb ... 86s Unpacking libxcb-xfixes0:arm64 (1.17.0-2) ... 86s Selecting previously unselected package libxshmfence1:arm64. 86s Preparing to unpack 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Unpacking libegl-mesa0:arm64 (25.0.3-1ubuntu2) ... 86s Selecting previously unselected package libvulkan1:arm64. 86s Preparing to unpack .../29-libvulkan1_1.4.304.0-1_arm64.deb ... 86s Unpacking libvulkan1:arm64 (1.4.304.0-1) ... 86s Selecting previously unselected package libgl1-mesa-dri:arm64. 86s Preparing to unpack .../30-libgl1-mesa-dri_25.0.3-1ubuntu2_arm64.deb ... 86s Unpacking libgl1-mesa-dri:arm64 (25.0.3-1ubuntu2) ... 86s Selecting previously unselected package libglvnd0:arm64. 86s Preparing to unpack .../31-libglvnd0_1.7.0-1build1_arm64.deb ... 86s Unpacking libglvnd0:arm64 (1.7.0-1build1) ... 86s Selecting previously unselected package libxcb-glx0:arm64. 86s Preparing to unpack .../32-libxcb-glx0_1.17.0-2_arm64.deb ... 86s Unpacking libxcb-glx0:arm64 (1.17.0-2) ... 86s Selecting previously unselected package libxxf86vm1:arm64. 86s Preparing to unpack .../33-libxxf86vm1_1%3a1.1.4-1build4_arm64.deb ... 86s Unpacking libxxf86vm1:arm64 (1:1.1.4-1build4) ... 86s Selecting previously unselected package libglx-mesa0:arm64. 86s Preparing to unpack .../34-libglx-mesa0_25.0.3-1ubuntu2_arm64.deb ... 86s Unpacking libglx-mesa0:arm64 (25.0.3-1ubuntu2) ... 86s Selecting previously unselected package libglx0:arm64. 86s Preparing to unpack .../35-libglx0_1.7.0-1build1_arm64.deb ... 86s Unpacking libglx0:arm64 (1.7.0-1build1) ... 86s Selecting previously unselected package libgl1:arm64. 86s Preparing to unpack .../36-libgl1_1.7.0-1build1_arm64.deb ... 86s Unpacking libgl1:arm64 (1.7.0-1build1) ... 86s Selecting previously unselected package libglew2.2:arm64. 86s Preparing to unpack .../37-libglew2.2_2.2.0-4build1_arm64.deb ... 86s Unpacking libglew2.2:arm64 (2.2.0-4build1) ... 86s Selecting previously unselected package libxi6:arm64. 87s Preparing to unpack .../38-libxi6_2%3a1.8.2-1_arm64.deb ... 87s Unpacking libxi6:arm64 (2:1.8.2-1) ... 87s Selecting previously unselected package libglut3.12:arm64. 87s Preparing to unpack .../39-libglut3.12_3.4.0-4_arm64.deb ... 87s Unpacking libglut3.12:arm64 (3.4.0-4) ... 87s Selecting previously unselected package libgomp1:arm64. 87s Preparing to unpack .../40-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 87s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 87s Selecting previously unselected package libgraphite2-3:arm64. 87s Preparing to unpack .../41-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 87s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 87s Selecting previously unselected package libharfbuzz0b:arm64. 87s Preparing to unpack .../42-libharfbuzz0b_10.2.0-1_arm64.deb ... 87s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 87s Selecting previously unselected package libsz2:arm64. 87s Preparing to unpack .../43-libsz2_1.1.3-1_arm64.deb ... 87s Unpacking libsz2:arm64 (1.1.3-1) ... 87s Selecting previously unselected package libhdf5-310:arm64. 87s Preparing to unpack .../44-libhdf5-310_1.14.5+repack-3_arm64.deb ... 87s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 87s Selecting previously 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Setting up libxcb-shape0:arm64 (1.17.0-2) ... 89s Setting up x11-common (1:7.7+23ubuntu4) ... 89s Setting up libxcb-render-util0:arm64 (0.3.10-1) ... 89s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 89s Setting up libxcb-icccm4:arm64 (0.4.2-1) ... 89s Setting up libgomp1:arm64 (15-20250404-0ubuntu1) ... 89s Setting up libpcre2-16-0:arm64 (10.45-1) ... 89s Setting up libaec0:arm64 (1.1.3-1) ... 89s Setting up libopengl0:arm64 (1.7.0-1build1) ... 89s Setting up libxcb-util1:arm64 (0.4.1-1) ... 89s Setting up libxxf86vm1:arm64 (1:1.1.4-1build4) ... 89s Setting up libxcb-xkb1:arm64 (1.17.0-2) ... 89s Setting up libxcb-image0:arm64 (0.4.0-2build1) ... 89s Setting up libxcb-present0:arm64 (1.17.0-2) ... 89s Setting up libqt5core5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 89s Setting up libblas3:arm64 (3.12.1-2) ... 89s 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 89s Setting up libxcb-xinerama0:arm64 (1.17.0-2) ... 89s Setting up libxcb-sync1:arm64 (1.17.0-2) ... 89s Setting up libavahi-common-data:arm64 (0.8-16ubuntu2) ... 89s Setting up pymol-data (3.1.0+dfsg-1) ... 89s Setting up libxkbcommon-x11-0:arm64 (1.7.0-2) ... 89s Setting up fonts-dejavu-mono (2.37-8) ... 89s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 89s Setting up fonts-dejavu-core (2.37-8) ... 89s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 89s Setting up libgfortran5:arm64 (15-20250404-0ubuntu1) ... 89s Setting up libvulkan1:arm64 (1.4.304.0-1) ... 89s Setting up python3-legacy-cgi (2.6.2-1) ... 90s Setting up python3-pyqt5.sip (12.17.0-1build1) ... 90s Setting up libmtdev1t64:arm64 (1.1.7-1) ... 90s Setting up libxshmfence1:arm64 (1.3-1build5) ... 90s Setting up libxcb-randr0:arm64 (1.17.0-2) ... 90s Setting up libqt5sql5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 90s Setting up libmd4c0:arm64 (0.5.2-2) ... 90s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 90s Setting up libglu1-mesa:arm64 (9.0.2-1.1build1) ... 90s Setting up libsz2:arm64 (1.1.3-1) ... 90s Setting up libwacom-common (2.14.0-1) ... 90s Setting up libwayland-client0:arm64 (1.23.1-3) ... 90s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 90s Setting up libice6:arm64 (2:1.1.1-1) ... 90s Setting up mesa-libgallium:arm64 (25.0.3-1ubuntu2) ... 90s Setting up liblapack3:arm64 (3.12.1-2) ... 90s 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 90s Setting up libqt5dbus5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 90s Setting up libgbm1:arm64 (25.0.3-1ubuntu2) ... 90s Setting up libwacom9:arm64 (2.14.0-1) ... 90s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 90s Setting up libgl1-mesa-dri:arm64 (25.0.3-1ubuntu2) ... 90s Setting up libqt5network5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 90s Setting up libavahi-common3:arm64 (0.8-16ubuntu2) ... 90s Setting up libqt5xml5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 90s Setting up libqt5test5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 90s Setting up libinput-bin (1.27.1-1) ... 90s Setting up libegl-mesa0:arm64 (25.0.3-1ubuntu2) ... 90s Setting up python3-numpy (1:2.2.3+ds-5) ... 91s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 91s Setting up libegl1:arm64 (1.7.0-1build1) ... 91s Setting up libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 91s Setting up libsm6:arm64 (2:1.2.4-1) ... 91s Setting up libavahi-client3:arm64 (0.8-16ubuntu2) ... 91s Setting up libinput10:arm64 (1.27.1-1) ... 91s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 91s Setting up fontconfig (2.15.0-2.2ubuntu1) ... 93s Regenerating fonts cache... done. 93s Setting up libglx-mesa0:arm64 (25.0.3-1ubuntu2) ... 93s Setting up libglx0:arm64 (1.7.0-1build1) ... 93s Setting up libnetcdf22:arm64 (1:4.9.3-1) ... 93s Setting up libgl1:arm64 (1.7.0-1build1) ... 93s Setting up libglut3.12:arm64 (3.4.0-4) ... 93s Setting up libglew2.2:arm64 (2.2.0-4build1) ... 93s Setting up libcups2t64:arm64 (2.4.12-0ubuntu1) ... 93s Setting up python3-opengl (3.1.9+dfsg-1.1) ... 94s /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:30: SyntaxWarning: invalid escape sequence '\ ' 94s |\ |\ 95s Setting up libqt5gui5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 95s Setting up libqt5widgets5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 95s Setting up libqt5help5:arm64 (5.15.15-6build1) ... 95s Setting up libqt5opengl5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 95s Setting up libqt5printsupport5t64:arm64 (5.15.15+dfsg-4ubuntu1) ... 95s Setting up libqt5designer5:arm64 (5.15.15-6build1) ... 95s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 95s Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ... 95s Setting up python3-pymol (3.1.0+dfsg-1) ... 96s Setting up pymol (3.1.0+dfsg-1) ... 96s Processing triggers for libc-bin (2.41-6ubuntu1) ... 96s Processing triggers for man-db (2.13.0-1) ... 96s Processing triggers for udev (257.4-1ubuntu3) ... 97s autopkgtest [05:59:13]: test command1: sh debian/tests/call-pymol-scripts examples/ \ "(start_pymol)|(xmlrpc01)|(sd_annotate)|(povray01)|(contact)|(dali)|(density)|(groel_es)|(packing)|(packsurf)|(ref_frame)|(ribosome)|(scenes2movie)|(ss_xfer)|(multiclip_ray)|(tkwindow)|(importing)" 97s autopkgtest [05:59:13]: test command1: [----------------------- 98s Search pymol scripts in /tmp/autopkgtest.7rYsm3/build.L3c/src/examples... 98s Processing new directory /tmp/autopkgtest.7rYsm3/build.L3c/src/examples 98s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/chempy/generate_amber.py'... 98s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/chempy/generate_mmff.py'... 98s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/area_diff.pml'... 99s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/build_peptide.py'... 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/contact.pml 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/dali.py 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/density.pml 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/groel_es.pml 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/multiclip_ray.pml 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/packing.pml 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/packsurf.pml 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/ref_frame.pml 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/ribosome.pml 99s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/scenes2movie.pml 99s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/seq_match_sele.pml'... 100s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/ss_xfer.pml 100s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/symsph.py'... 100s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/brick01.py'... 101s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo01.py'... 101s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo02.py'... 104s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo03.py'... 107s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo04.py'... 107s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo05.py'... 108s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo06.py'... 109s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo07.py'... 109s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo08.py'... 109s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo_3Dtext01.py'... 109s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo_axes.py'... 109s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo_label_hack.py'... 113s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo_plane.py'... 113s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/chempy_model01.py'... 113s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/chempy_model02.py'... 113s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/chempy_model03.py'... 116s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/click_ordered_list.py'... 117s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/count_molecules.py'... 117s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/extend_demo01.py'... 117s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/gl01.py'... 117s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/gl02.py'... 118s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/gl03.py'... 121s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/importing.py 121s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/link_demo.py'... 121s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/membrane.py'... 122s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/mutate01.pml'... 122s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/mutate02.py'... 123s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/my_ext_gui.py'... 124s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/particle01.py'... 124s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/particle02.py'... 124s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/pick_wiz.py'... 124s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/povray01.py 124s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/scenes_to_movie01.pml'... 125s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/sd_annotate.pml 125s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/sele_wiz.py'... 125s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/start_pymol.py 125s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/syncmol.py'... 125s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/tkwindow.py 125s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/webgui01.py'... 125s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/webgui02.py'... 127s /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/webgui02.py:161: SyntaxWarning: invalid escape sequence '\=' 127s mo = re.search("molid\=([A-Z0-9]+)",self.path) 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/xmlrpc01.py 127s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/xmlrpc02.py'... 127s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/launching/launch_demo.py'... 127s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/launching/launch_viewer1.py'... 127s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/launching/launch_viewer2.py'... 127s Processing new directory /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/chempy 127s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/chempy/generate_amber.py'... 127s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/chempy/generate_mmff.py'... 127s Processing new directory /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook 127s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/area_diff.pml'... 127s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/build_peptide.py'... 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/contact.pml 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/dali.py 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/density.pml 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/groel_es.pml 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/multiclip_ray.pml 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/packing.pml 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/packsurf.pml 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/ref_frame.pml 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/ribosome.pml 127s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/scenes2movie.pml 127s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/seq_match_sele.pml'... 129s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/ss_xfer.pml 129s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/cookbook/symsph.py'... 129s Processing new directory /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel 129s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/brick01.py'... 129s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo01.py'... 129s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo02.py'... 132s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo03.py'... 136s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo04.py'... 136s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo05.py'... 136s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo06.py'... 137s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo07.py'... 137s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo08.py'... 137s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo_3Dtext01.py'... 138s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo_axes.py'... 138s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo_label_hack.py'... 141s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/cgo_plane.py'... 141s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/chempy_model01.py'... 141s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/chempy_model02.py'... 142s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/chempy_model03.py'... 145s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/click_ordered_list.py'... 145s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/count_molecules.py'... 145s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/extend_demo01.py'... 145s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/gl01.py'... 146s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/gl02.py'... 146s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/gl03.py'... 150s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/importing.py 150s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/link_demo.py'... 150s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/membrane.py'... 150s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/mutate01.pml'... 150s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/mutate02.py'... 152s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/my_ext_gui.py'... 152s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/particle01.py'... 152s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/particle02.py'... 153s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/pick_wiz.py'... 153s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/povray01.py 153s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/scenes_to_movie01.pml'... 153s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/sd_annotate.pml 153s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/sele_wiz.py'... 153s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/start_pymol.py 153s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/syncmol.py'... 153s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/tkwindow.py 153s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/webgui01.py'... 154s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/webgui02.py'... 154s /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/webgui02.py:161: SyntaxWarning: invalid escape sequence '\=' 154s mo = re.search("molid\=([A-Z0-9]+)",self.path) 154s Skip /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/xmlrpc01.py 154s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/devel/xmlrpc02.py'... 154s Processing new directory /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/launching 154s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/launching/launch_demo.py'... 154s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/launching/launch_viewer1.py'... 154s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/examples/launching/launch_viewer2.py'... 155s autopkgtest [06:00:11]: test command1: -----------------------] 155s command1 PASS (superficial) 155s autopkgtest [06:00:11]: test command1: - - - - - - - - - - results - - - - - - - - - - 155s autopkgtest [06:00:11]: test command2: preparing testbed 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Starting pkgProblemResolver with broken count: 0 156s Starting 2 pkgProblemResolver with broken count: 0 156s Done 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s autopkgtest [06:00:14]: test command2: sh debian/tests/call-pymol-scripts data/demo 158s autopkgtest [06:00:14]: test command2: [----------------------- 158s Search pymol scripts in /tmp/autopkgtest.7rYsm3/build.L3c/src/data/demo... 158s Processing new directory /tmp/autopkgtest.7rYsm3/build.L3c/src/data/demo 158s Run 'pymol -c /tmp/autopkgtest.7rYsm3/build.L3c/src/data/demo/cgo03.py'... 161s autopkgtest [06:00:17]: test command2: -----------------------] 162s command2 PASS (superficial) 162s autopkgtest [06:00:18]: test command2: - - - - - - - - - - results - - - - - - - - - - 162s autopkgtest [06:00:18]: test command3: preparing testbed 162s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Starting pkgProblemResolver with broken count: 0 163s Starting 2 pkgProblemResolver with broken count: 0 163s Done 164s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s autopkgtest [06:00:20]: test command3: sh debian/tests/call-pymol-scripts /usr/share/pymol/examples \ "(cookbook/)|(xmlrpc01)|(sd_annotate)|(povray01)|(tkwindow)|(importing)" 164s autopkgtest [06:00:20]: test command3: [----------------------- 165s Search pymol scripts in /usr/share/pymol/examples... 165s Processing new directory /usr/share/pymol/examples 165s Run 'pymol -c /usr/share/pymol/examples/chempy/generate_amber.py'... 165s Run 'pymol -c /usr/share/pymol/examples/chempy/generate_mmff.py'... 165s Skip /usr/share/pymol/examples/cookbook/area_diff.pml 165s Skip /usr/share/pymol/examples/cookbook/contact.pml 165s Skip /usr/share/pymol/examples/cookbook/multiclip_ray.pml 165s Skip /usr/share/pymol/examples/cookbook/packing.pml 165s Skip /usr/share/pymol/examples/cookbook/packsurf.pml 165s Skip /usr/share/pymol/examples/cookbook/ref_frame.pml 165s Skip /usr/share/pymol/examples/cookbook/scenes2movie.pml 165s Skip /usr/share/pymol/examples/cookbook/seq_match_sele.pml 165s Skip /usr/share/pymol/examples/cookbook/ss_xfer.pml 165s Run 'pymol -c /usr/share/pymol/examples/devel/brick01.py'... 165s Run 'pymol -c /usr/share/pymol/examples/devel/cgo01.py'... 165s Run 'pymol -c /usr/share/pymol/examples/devel/cgo02.py'... 169s Run 'pymol -c /usr/share/pymol/examples/devel/cgo03.py'... 172s Run 'pymol -c /usr/share/pymol/examples/devel/cgo04.py'... 172s Run 'pymol -c /usr/share/pymol/examples/devel/cgo05.py'... 172s Run 'pymol -c /usr/share/pymol/examples/devel/cgo06.py'... 173s Run 'pymol -c /usr/share/pymol/examples/devel/cgo07.py'... 173s Run 'pymol -c /usr/share/pymol/examples/devel/cgo08.py'... 174s Run 'pymol -c /usr/share/pymol/examples/devel/cgo_3Dtext01.py'... 174s Run 'pymol -c /usr/share/pymol/examples/devel/cgo_axes.py'... 174s Run 'pymol -c /usr/share/pymol/examples/devel/cgo_label_hack.py'... 177s Run 'pymol -c /usr/share/pymol/examples/devel/cgo_plane.py'... 177s Run 'pymol -c /usr/share/pymol/examples/devel/chempy_model01.py'... 177s Run 'pymol -c /usr/share/pymol/examples/devel/chempy_model02.py'... 178s Run 'pymol -c /usr/share/pymol/examples/devel/chempy_model03.py'... 181s Run 'pymol -c /usr/share/pymol/examples/devel/click_ordered_list.py'... 181s Run 'pymol -c /usr/share/pymol/examples/devel/count_molecules.py'... 181s Run 'pymol -c /usr/share/pymol/examples/devel/extend_demo01.py'... 182s Run 'pymol -c /usr/share/pymol/examples/devel/gl01.py'... 182s Run 'pymol -c /usr/share/pymol/examples/devel/gl02.py'... 182s Run 'pymol -c /usr/share/pymol/examples/devel/gl03.py'... 186s Skip /usr/share/pymol/examples/devel/importing.py 186s Run 'pymol -c /usr/share/pymol/examples/devel/link_demo.py'... 186s Run 'pymol -c /usr/share/pymol/examples/devel/membrane.py'... 186s Run 'pymol -c /usr/share/pymol/examples/devel/mutate01.pml'... 187s Run 'pymol -c /usr/share/pymol/examples/devel/mutate02.py'... 188s Run 'pymol -c /usr/share/pymol/examples/devel/my_ext_gui.py'... 188s Run 'pymol -c /usr/share/pymol/examples/devel/particle01.py'... 189s Run 'pymol -c /usr/share/pymol/examples/devel/particle02.py'... 189s Run 'pymol -c /usr/share/pymol/examples/devel/pick_wiz.py'... 189s Run 'pymol -c /usr/share/pymol/examples/devel/scenes_to_movie01.pml'... 189s Skip /usr/share/pymol/examples/devel/sd_annotate.pml 189s Run 'pymol -c /usr/share/pymol/examples/devel/sele_wiz.py'... 190s Run 'pymol -c /usr/share/pymol/examples/devel/syncmol.py'... 190s Skip /usr/share/pymol/examples/devel/tkwindow.py 190s Run 'pymol -c /usr/share/pymol/examples/devel/webgui01.py'... 190s Run 'pymol -c /usr/share/pymol/examples/devel/webgui02.py'... 190s /usr/share/pymol/examples/devel/webgui02.py:161: SyntaxWarning: invalid escape sequence '\=' 190s mo = re.search("molid\=([A-Z0-9]+)",self.path) 190s Skip /usr/share/pymol/examples/devel/xmlrpc01.py 190s Run 'pymol -c /usr/share/pymol/examples/devel/xmlrpc02.py'... 190s Run 'pymol -c /usr/share/pymol/examples/launching/launch_demo.py'... 190s Run 'pymol -c /usr/share/pymol/examples/launching/launch_viewer1.py'... 191s Run 'pymol -c /usr/share/pymol/examples/launching/launch_viewer2.py'... 191s Processing new directory /usr/share/pymol/examples/chempy 191s Run 'pymol -c /usr/share/pymol/examples/chempy/generate_amber.py'... 191s Run 'pymol -c /usr/share/pymol/examples/chempy/generate_mmff.py'... 191s Processing new directory /usr/share/pymol/examples/cookbook 191s Skip /usr/share/pymol/examples/cookbook/area_diff.pml 191s Skip /usr/share/pymol/examples/cookbook/contact.pml 191s Skip /usr/share/pymol/examples/cookbook/multiclip_ray.pml 191s Skip /usr/share/pymol/examples/cookbook/packing.pml 191s Skip /usr/share/pymol/examples/cookbook/packsurf.pml 191s Skip /usr/share/pymol/examples/cookbook/ref_frame.pml 191s Skip /usr/share/pymol/examples/cookbook/scenes2movie.pml 191s Skip /usr/share/pymol/examples/cookbook/seq_match_sele.pml 191s Skip /usr/share/pymol/examples/cookbook/ss_xfer.pml 191s Processing new directory /usr/share/pymol/examples/devel 191s Run 'pymol -c /usr/share/pymol/examples/devel/brick01.py'... 191s Run 'pymol -c /usr/share/pymol/examples/devel/cgo01.py'... 192s Run 'pymol -c /usr/share/pymol/examples/devel/cgo02.py'... 195s Run 'pymol -c /usr/share/pymol/examples/devel/cgo03.py'... 198s Run 'pymol -c /usr/share/pymol/examples/devel/cgo04.py'... 198s Run 'pymol -c /usr/share/pymol/examples/devel/cgo05.py'... 198s Run 'pymol -c /usr/share/pymol/examples/devel/cgo06.py'... 200s Run 'pymol -c /usr/share/pymol/examples/devel/cgo07.py'... 200s Run 'pymol -c /usr/share/pymol/examples/devel/cgo08.py'... 200s Run 'pymol -c /usr/share/pymol/examples/devel/cgo_3Dtext01.py'... 200s Run 'pymol -c /usr/share/pymol/examples/devel/cgo_axes.py'... 200s Run 'pymol -c /usr/share/pymol/examples/devel/cgo_label_hack.py'... 203s Run 'pymol -c /usr/share/pymol/examples/devel/cgo_plane.py'... 204s Run 'pymol -c /usr/share/pymol/examples/devel/chempy_model01.py'... 204s Run 'pymol -c /usr/share/pymol/examples/devel/chempy_model02.py'... 204s Run 'pymol -c /usr/share/pymol/examples/devel/chempy_model03.py'... 207s Run 'pymol -c /usr/share/pymol/examples/devel/click_ordered_list.py'... 207s Run 'pymol -c /usr/share/pymol/examples/devel/count_molecules.py'... 208s Run 'pymol -c /usr/share/pymol/examples/devel/extend_demo01.py'... 208s Run 'pymol -c /usr/share/pymol/examples/devel/gl01.py'... 208s Run 'pymol -c /usr/share/pymol/examples/devel/gl02.py'... 208s Run 'pymol -c /usr/share/pymol/examples/devel/gl03.py'... 212s Skip /usr/share/pymol/examples/devel/importing.py 212s Run 'pymol -c /usr/share/pymol/examples/devel/link_demo.py'... 212s Run 'pymol -c /usr/share/pymol/examples/devel/membrane.py'... 212s Run 'pymol -c /usr/share/pymol/examples/devel/mutate01.pml'... 213s Run 'pymol -c /usr/share/pymol/examples/devel/mutate02.py'... 214s Run 'pymol -c /usr/share/pymol/examples/devel/my_ext_gui.py'... 214s Run 'pymol -c /usr/share/pymol/examples/devel/particle01.py'... 215s Run 'pymol -c /usr/share/pymol/examples/devel/particle02.py'... 215s Run 'pymol -c /usr/share/pymol/examples/devel/pick_wiz.py'... 215s Run 'pymol -c /usr/share/pymol/examples/devel/scenes_to_movie01.pml'... 215s Skip /usr/share/pymol/examples/devel/sd_annotate.pml 215s Run 'pymol -c /usr/share/pymol/examples/devel/sele_wiz.py'... 216s Run 'pymol -c /usr/share/pymol/examples/devel/syncmol.py'... 216s Skip /usr/share/pymol/examples/devel/tkwindow.py 216s Run 'pymol -c /usr/share/pymol/examples/devel/webgui01.py'... 216s Run 'pymol -c /usr/share/pymol/examples/devel/webgui02.py'... 216s /usr/share/pymol/examples/devel/webgui02.py:161: SyntaxWarning: invalid escape sequence '\=' 216s mo = re.search("molid\=([A-Z0-9]+)",self.path) 216s Skip /usr/share/pymol/examples/devel/xmlrpc01.py 216s Run 'pymol -c /usr/share/pymol/examples/devel/xmlrpc02.py'... 216s Processing new directory /usr/share/pymol/examples/launching 216s Run 'pymol -c /usr/share/pymol/examples/launching/launch_demo.py'... 216s Run 'pymol -c /usr/share/pymol/examples/launching/launch_viewer1.py'... 217s Run 'pymol -c /usr/share/pymol/examples/launching/launch_viewer2.py'... 217s autopkgtest [06:01:13]: test command3: -----------------------] 217s command3 PASS (superficial) 217s autopkgtest [06:01:13]: test command3: - - - - - - - - - - results - - - - - - - - - - 218s autopkgtest [06:01:14]: test command4: preparing testbed 218s Reading package lists... 218s Building dependency tree... 218s Reading state information... 218s Starting pkgProblemResolver with broken count: 0 219s Starting 2 pkgProblemResolver with broken count: 0 219s Done 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 220s autopkgtest [06:01:16]: test command4: sh debian/tests/call-pymol-scripts /usr/share/pymol/examples/cookbook multiclip_ray 220s autopkgtest [06:01:16]: test command4: [----------------------- 220s Search pymol scripts in /usr/share/pymol/examples/cookbook... 220s Processing new directory /usr/share/pymol/examples/cookbook 220s Run 'pymol -c /usr/share/pymol/examples/cookbook/area_diff.pml'... 221s Run 'pymol -c /usr/share/pymol/examples/cookbook/contact.pml'... 222s Skip /usr/share/pymol/examples/cookbook/multiclip_ray.pml 222s Run 'pymol -c /usr/share/pymol/examples/cookbook/packing.pml'... 223s Run 'pymol -c /usr/share/pymol/examples/cookbook/packsurf.pml'... 250s Run 'pymol -c /usr/share/pymol/examples/cookbook/ref_frame.pml'... 251s Run 'pymol -c /usr/share/pymol/examples/cookbook/scenes2movie.pml'... 251s Run 'pymol -c /usr/share/pymol/examples/cookbook/seq_match_sele.pml'... 253s Run 'pymol -c /usr/share/pymol/examples/cookbook/ss_xfer.pml'... 254s autopkgtest [06:01:50]: test command4: -----------------------] 254s command4 PASS (superficial) 254s autopkgtest [06:01:50]: test command4: - - - - - - - - - - results - - - - - - - - - - 254s autopkgtest [06:01:50]: test command5: preparing testbed 255s Reading package lists... 255s Building dependency tree... 255s Reading state information... 255s Starting pkgProblemResolver with broken count: 0 255s Starting 2 pkgProblemResolver with broken count: 0 255s Done 256s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 257s autopkgtest [06:01:53]: test command5: (cd /usr/share/pymol/examples/devel/ && pymol -c sd_annotate.pml) 257s autopkgtest [06:01:53]: test command5: [----------------------- 257s PyMOL(TM) Molecular Graphics System, Version 3.1.0. 257s Copyright (c) Schrodinger, LLC. 257s All Rights Reserved. 257s 257s Created by Warren L. DeLano, Ph.D. 257s 257s PyMOL is user-supported open-source software. Although some versions 257s are freely available, PyMOL is not in the public domain. 257s 257s If PyMOL is helpful in your work or study, then please volunteer 257s support for our ongoing efforts to create open and affordable scientific 257s software by purchasing a PyMOL Maintenance and/or Support subscription. 257s 257s More information can be found at "http://www.pymol.org". 257s 257s Enter "help" for a list of commands. 257s Enter "help " for information on a specific command. 257s 257s Hit ESC anytime to toggle between text and graphics. 257s 257s Setting: wizard_prompt_mode set to 3. 257s Detected 2 CPU cores. Enabled multithreaded rendering. 257s PyMOL>from pymol.wizard.annotation import load_annotated_sdf 257s PyMOL>cmd.extend('load_annotated_sdf',load_annotated_sdf) 257s PyMOL>wizard annotation 257s PyMOL>set wizard_prompt_mode,3 257s PyMOL>load_annotated_sdf demo.sdf 257s HBA ['[1, 25, 26, 34]\n'] 257s HBD ['[20]\n'] 257s ACD_NUMBER ['MFCD02681585\n'] 257s SCORE ['-222.044\n'] 257s MOLID ['MFCD02681585\n'] 257s HBA ['[1, 21]\n'] 257s HBD ['[]\n'] 257s ACD_NUMBER ['MFCD01567969\n'] 257s SCORE ['-219.984\n'] 257s MOLID ['MFCD01567969\n'] 257s HBA ['[1, 24]\n'] 257s HBD ['[10, 22]\n'] 257s ACD_NUMBER ['MFCD00023789\n'] 257s SCORE ['-219.911\n'] 257s MOLID ['MFCD00023789\n'] 257s HBA ['[1, 11]\n'] 257s HBD ['[3]\n'] 257s ACD_NUMBER ['MFCD02579443\n'] 257s SCORE ['-219.769\n'] 257s MOLID ['MFCD02579443\n'] 257s HBA ['[1, 11]\n'] 257s HBD ['[9]\n'] 257s ACD_NUMBER ['MFCD02579410\n'] 257s SCORE ['-214.809\n'] 257s MOLID ['MFCD02579410\n'] 257s HBA ['[1, 20, 22, 27, 32]\n'] 257s HBD ['[10, 20]\n'] 257s ACD_NUMBER ['MFCD02579135\n'] 257s SCORE ['-213.630\n'] 257s MOLID ['MFCD02579135\n'] 257s HBA ['[1, 11, 14, 21]\n'] 257s HBD ['[]\n'] 257s ACD_NUMBER ['MFCD02681468\n'] 257s SCORE ['-213.462\n'] 257s MOLID ['MFCD02681468\n'] 257s HBA ['[1, 13, 14, 29]\n'] 257s HBD ['[]\n'] 257s ACD_NUMBER ['MFCD00141070\n'] 257s SCORE ['-213.240\n'] 257s MOLID ['MFCD00141070\n'] 257s HBA ['[1, 8]\n'] 257s HBD ['[]\n'] 257s ACD_NUMBER ['MFCD02983625\n'] 257s SCORE ['-211.422\n'] 257s MOLID ['MFCD02983625\n'] 257s HBA ['[1, 11]\n'] 257s HBD ['[3, 12]\n'] 257s ACD_NUMBER ['MFCD00115818\n'] 257s SCORE ['-210.482\n'] 257s MOLID ['MFCD00115818\n'] 257s autopkgtest [06:01:53]: test command5: -----------------------] 258s autopkgtest [06:01:54]: test command5: - - - - - - - - - - results - - - - - - - - - - 258s command5 PASS (superficial) 258s autopkgtest [06:01:54]: @@@@@@@@@@@@@@@@@@@@ summary 258s command1 PASS (superficial) 258s command2 PASS (superficial) 258s command3 PASS (superficial) 258s command4 PASS (superficial) 258s command5 PASS (superficial) 262s nova [W] Using flock in prodstack7-arm64 262s Creating nova instance adt-questing-arm64-pymol-20250502-055736-juju-7f2275-prod-proposed-migration-environment-15-faac9dc5-1370-4867-b88b-53a2d1f9d680 from image adt/ubuntu-questing-arm64-server-20250501.img (UUID 137c3127-57d2-4bf2-a106-d904ad6e43f4)... 262s nova [W] Timed out waiting for de9ea8f9-6c9d-43c5-aaf7-f89b1722cdeb to get deleted.