0s autopkgtest [18:23:56]: starting date and time: 2025-05-03 18:23:56+0000 0s autopkgtest [18:23:56]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [18:23:56]: host juju-7f2275-prod-proposed-migration-environment-21; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o6ndpl0v/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:matplotlib --apt-upgrade openstructure --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=matplotlib/3.10.1+dfsg1-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-21@bos03-9.secgroup --name adt-questing-amd64-openstructure-20250503-182356-juju-7f2275-prod-proposed-migration-environment-21-266b2306-5f53-4d55-bdc8-72c64bab9159 --image adt/ubuntu-questing-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-21 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 54s autopkgtest [18:24:50]: testbed dpkg architecture: amd64 55s autopkgtest [18:24:51]: testbed apt version: 3.0.0 55s autopkgtest [18:24:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 55s autopkgtest [18:24:51]: testbed release detected to be: None 56s autopkgtest [18:24:52]: updating testbed package index (apt update) 56s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 56s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 56s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 57s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 57s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1457 kB] 57s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.7 kB] 57s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [147 kB] 57s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [197 kB] 57s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [141 kB] 57s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [570 kB] 57s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1416 kB] 57s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [48.3 kB] 57s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [23.1 kB] 57s Fetched 4144 kB in 1s (2950 kB/s) 58s Reading package lists... 59s autopkgtest [18:24:55]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 60s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 60s Starting 2 pkgProblemResolver with broken count: 0 60s Done 60s Entering ResolveByKeep 61s 61s Calculating upgrade... 61s The following packages will be upgraded: 61s cloud-init cloud-init-base debianutils libmbim-glib4 libmbim-proxy 61s libnftnl11 libqmi-glib5 libqmi-proxy python3-lazr.restfulclient sos 61s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Need to get 2366 kB of archives. 61s After this operation, 113 kB disk space will be freed. 61s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 debianutils amd64 5.22 [93.0 kB] 61s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libnftnl11 amd64 1.2.9-1 [69.1 kB] 61s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init-base all 25.2~1g7a0265d3-0ubuntu1 [619 kB] 61s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-proxy amd64 1.32.0-1 [6276 B] 61s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-glib4 amd64 1.32.0-1 [233 kB] 61s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-proxy amd64 1.36.0-1 [6220 B] 61s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-glib5 amd64 1.36.0-1 [920 kB] 62s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 python3-lazr.restfulclient all 0.14.6-3 [51.0 kB] 62s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 sos all 4.9.1-1 [367 kB] 62s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init all 25.2~1g7a0265d3-0ubuntu1 [2106 B] 62s Preconfiguring packages ... 62s Fetched 2366 kB in 1s (3131 kB/s) 62s (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 ... 80514 files and directories currently installed.) 62s Preparing to unpack .../debianutils_5.22_amd64.deb ... 62s Unpacking debianutils (5.22) over (5.21) ... 62s Setting up debianutils (5.22) ... 62s (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 ... 80514 files and directories currently installed.) 62s Preparing to unpack .../0-libnftnl11_1.2.9-1_amd64.deb ... 62s Unpacking libnftnl11:amd64 (1.2.9-1) over (1.2.8-1) ... 62s Preparing to unpack .../1-cloud-init-base_25.2~1g7a0265d3-0ubuntu1_all.deb ... 63s Unpacking cloud-init-base (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 63s Preparing to unpack .../2-libmbim-proxy_1.32.0-1_amd64.deb ... 63s Unpacking libmbim-proxy (1.32.0-1) over (1.31.2-0ubuntu4) ... 63s Preparing to unpack .../3-libmbim-glib4_1.32.0-1_amd64.deb ... 63s Unpacking libmbim-glib4:amd64 (1.32.0-1) over (1.31.2-0ubuntu4) ... 63s Preparing to unpack .../4-libqmi-proxy_1.36.0-1_amd64.deb ... 63s Unpacking libqmi-proxy (1.36.0-1) over (1.35.6-1) ... 63s Preparing to unpack .../5-libqmi-glib5_1.36.0-1_amd64.deb ... 63s Unpacking libqmi-glib5:amd64 (1.36.0-1) over (1.35.6-1) ... 63s Preparing to unpack .../6-python3-lazr.restfulclient_0.14.6-3_all.deb ... 63s Unpacking python3-lazr.restfulclient (0.14.6-3) over (0.14.6-2) ... 63s Preparing to unpack .../7-sos_4.9.1-1_all.deb ... 64s Unpacking sos (4.9.1-1) over (4.9.0-6) ... 64s Preparing to unpack .../8-cloud-init_25.2~1g7a0265d3-0ubuntu1_all.deb ... 64s Unpacking cloud-init (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 64s Setting up sos (4.9.1-1) ... 64s Setting up libnftnl11:amd64 (1.2.9-1) ... 64s Setting up cloud-init-base (25.2~1g7a0265d3-0ubuntu1) ... 66s Setting up python3-lazr.restfulclient (0.14.6-3) ... 66s Setting up libmbim-glib4:amd64 (1.32.0-1) ... 66s Setting up cloud-init (25.2~1g7a0265d3-0ubuntu1) ... 66s Setting up libmbim-proxy (1.32.0-1) ... 66s Setting up libqmi-glib5:amd64 (1.36.0-1) ... 66s Setting up libqmi-proxy (1.36.0-1) ... 66s Processing triggers for libc-bin (2.41-6ubuntu1) ... 66s Processing triggers for rsyslog (8.2412.0-2ubuntu2) ... 66s Processing triggers for man-db (2.13.0-1) ... 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 69s Starting pkgProblemResolver with broken count: 0 69s Starting 2 pkgProblemResolver with broken count: 0 69s Done 69s Solving dependencies... 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s autopkgtest [18:25:05]: rebooting testbed after setup commands that affected boot 92s autopkgtest [18:25:28]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 15:05:05 UTC 2025 95s autopkgtest [18:25:31]: @@@@@@@@@@@@@@@@@@@@ apt-source openstructure 120s Get:1 http://ftpmaster.internal/ubuntu questing/universe openstructure 2.9.2-2 (dsc) [4847 B] 120s Get:2 http://ftpmaster.internal/ubuntu questing/universe openstructure 2.9.2-2 (tar) [27.8 MB] 120s Get:3 http://ftpmaster.internal/ubuntu questing/universe openstructure 2.9.2-2 (diff) [92.4 MB] 120s gpgv: Signature made Fri Mar 7 12:43:35 2025 UTC 120s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 120s gpgv: issuer "merkys@debian.org" 120s gpgv: Can't check signature: No public key 120s dpkg-source: warning: cannot verify inline signature for ./openstructure_2.9.2-2.dsc: no acceptable signature found 123s autopkgtest [18:25:59]: testing package openstructure version 2.9.2-2 129s autopkgtest [18:26:05]: build not needed 137s autopkgtest [18:26:13]: test python: preparing testbed 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Starting pkgProblemResolver with broken count: 0 138s Starting 2 pkgProblemResolver with broken count: 0 138s Done 139s The following NEW packages will be installed: 139s blt clustalw dssp fontconfig fontconfig-config fonts-dejavu-core 139s fonts-dejavu-mono fonts-lyx libavahi-client3 libavahi-common-data 139s libavahi-common3 libblas3 libboost-filesystem1.83.0 libboost-iostreams1.83.0 139s libboost-program-options1.83.0 libboost-python1.83.0 libboost-thread1.83.0 139s libcifpp-data libcifpp7 libcups2t64 libdeflate0 libdouble-conversion3 139s libdrm-intel1 libegl-mesa0 libegl1 libfftw3-single3 libfontconfig1 libgbm1 139s libgfortran5 libgl1 libgl1-mesa-dri libglu1-mesa libglvnd0 libglx-mesa0 139s libglx0 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libimagequant0 139s libinput-bin libinput10 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 139s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libmbedcrypto16 139s libmbedtls21 libmbedx509-7 libmd4c0 libmtdev1t64 libopengl0 libopenjp2-7 139s libopenmm8.1 libost-base-dev libost-base2.9 libost-bindings-dev 139s libost-bindings2.9 libost-conop-dev libost-conop2.9 libost-db-dev 139s libost-db2.9 libost-geom-dev libost-geom2.9 libost-gfx-dev libost-gfx2.9 139s libost-gui-dev libost-gui2.9 libost-img-alg-dev libost-img-alg2.9 139s libost-img-dev libost-img2.9 libost-info-dev libost-info2.9 libost-io-dev 139s libost-io2.9 libost-mol-alg-dev libost-mol-alg2.9 libost-mol-dev 139s libost-mol-mm-dev libost-mol-mm2.9 libost-mol2.9 libost-seq-alg-dev 139s libost-seq-alg2.9 libost-seq-dev libost-seq2.9 libparasail8t64 libpciaccess0 139s libpcre2-16-0 libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5designer5 139s libqt5gui5t64 libqt5help5 libqt5network5t64 libqt5printsupport5t64 139s libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libraqm0 139s libsharpyuv0 libsm6 libtcl8.6 libtiff6 libtk8.6 libvulkan1 libwacom-common 139s libwacom9 libwayland-client0 libwayland-server0 libwebp7 libwebpdemux2 139s libwebpmux3 libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 139s libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 139s libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 139s libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 139s libxft2 libxkbcommon-x11-0 libxrender1 libxshmfence1 libxslt1.1 libxss1 139s libxxf86vm1 mesa-libgallium ncbi-blast+ ncbi-data openstructure 139s python-matplotlib-data python3-brotli python3-contourpy python3-cycler 139s python3-decorator python3-fonttools python3-fs python3-kiwisolver 139s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy 139s python3-numpy-dev python3-ost python3-pil python3-pil.imagetk 139s python3-platformdirs python3-pyqt5 python3-pyqt5.sip python3-scipy 139s python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 python3.13-tk 139s tk8.6-blt2.5 unicode-data voronota x11-common 139s 0 upgraded, 179 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 238 MB of archives. 139s After this operation, 701 MB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 139s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 139s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran5 amd64 15-20250404-0ubuntu1 [926 kB] 140s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 140s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 140s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 140s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 140s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 140s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig-config amd64 2.15.0-2.2ubuntu1 [37.8 kB] 140s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 libfontconfig1 amd64 2.15.0-2.2ubuntu1 [164 kB] 140s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 140s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 140s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 140s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 140s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 140s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 140s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 140s Get:18 http://ftpmaster.internal/ubuntu questing/universe amd64 clustalw amd64 2.1+lgpl-7 [275 kB] 140s Get:19 http://ftpmaster.internal/ubuntu questing/universe amd64 libcifpp-data all 7.0.9-1 [481 kB] 140s Get:20 http://ftpmaster.internal/ubuntu questing/universe amd64 libcifpp7 amd64 7.0.9-1 [1144 kB] 140s Get:21 http://ftpmaster.internal/ubuntu questing/universe amd64 dssp amd64 4.4.10-1 [786 kB] 140s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig amd64 2.15.0-2.2ubuntu1 [180 kB] 140s Get:23 http://ftpmaster.internal/ubuntu questing/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 140s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 libavahi-common-data amd64 0.8-16ubuntu2 [31.0 kB] 140s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 libavahi-common3 amd64 0.8-16ubuntu2 [23.6 kB] 140s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 libavahi-client3 amd64 0.8-16ubuntu2 [27.5 kB] 140s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.2ubuntu1 [287 kB] 140s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-4.2ubuntu1 [260 kB] 140s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.2ubuntu1 [323 kB] 140s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 libboost-python1.83.0 amd64 1.83.0-4.2ubuntu1 [314 kB] 140s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.2ubuntu1 [278 kB] 140s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 libcups2t64 amd64 2.4.12-0ubuntu1 [292 kB] 140s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 140s Get:34 http://ftpmaster.internal/ubuntu questing/universe amd64 libdouble-conversion3 amd64 3.3.1-1 [41.7 kB] 140s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 140s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 libdrm-intel1 amd64 2.4.124-2 [68.9 kB] 140s Get:37 http://ftpmaster.internal/ubuntu questing/main amd64 libwayland-server0 amd64 1.23.1-3 [37.2 kB] 140s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [7944 B] 140s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [7508 B] 140s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-present0 amd64 1.17.0-2 [6064 B] 140s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-randr0 amd64 1.17.0-2 [17.9 kB] 140s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-sync1 amd64 1.17.0-2 [9312 B] 140s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [10.2 kB] 140s Get:44 http://ftpmaster.internal/ubuntu questing/main amd64 libxshmfence1 amd64 1.3.3-1 [5262 B] 140s Get:45 http://ftpmaster.internal/ubuntu questing/main amd64 mesa-libgallium amd64 25.0.3-1ubuntu2 [12.1 MB] 141s Get:46 http://ftpmaster.internal/ubuntu questing/main amd64 libgbm1 amd64 25.0.3-1ubuntu2 [33.4 kB] 141s Get:47 http://ftpmaster.internal/ubuntu questing/main amd64 libwayland-client0 amd64 1.23.1-3 [29.7 kB] 141s Get:48 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 141s Get:49 http://ftpmaster.internal/ubuntu questing/main amd64 libegl-mesa0 amd64 25.0.3-1ubuntu2 [136 kB] 141s Get:50 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 141s Get:51 http://ftpmaster.internal/ubuntu questing/main amd64 libfftw3-single3 amd64 3.3.10-2fakesync1build1 [871 kB] 141s Get:52 http://ftpmaster.internal/ubuntu questing/main amd64 libvulkan1 amd64 1.4.304.0-1 [147 kB] 141s Get:53 http://ftpmaster.internal/ubuntu questing/main amd64 libgl1-mesa-dri amd64 25.0.3-1ubuntu2 [35.7 kB] 141s Get:54 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-glx0 amd64 1.17.0-2 [24.8 kB] 141s Get:55 http://ftpmaster.internal/ubuntu questing/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B] 141s Get:56 http://ftpmaster.internal/ubuntu questing/main amd64 libglx-mesa0 amd64 25.0.3-1ubuntu2 [146 kB] 141s Get:57 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 141s Get:58 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 141s Get:59 http://ftpmaster.internal/ubuntu questing/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 141s Get:60 http://ftpmaster.internal/ubuntu questing/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 141s Get:61 http://ftpmaster.internal/ubuntu questing/main amd64 libwacom-common all 2.14.0-1 [103 kB] 141s Get:62 http://ftpmaster.internal/ubuntu questing/main amd64 libwacom9 amd64 2.14.0-1 [27.3 kB] 141s Get:63 http://ftpmaster.internal/ubuntu questing/main amd64 libinput-bin amd64 1.27.1-1 [23.4 kB] 141s Get:64 http://ftpmaster.internal/ubuntu questing/main amd64 libmtdev1t64 amd64 1.1.7-1 [16.3 kB] 141s Get:65 http://ftpmaster.internal/ubuntu questing/main amd64 libinput10 amd64 1.27.1-1 [155 kB] 141s Get:66 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 141s Get:67 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 141s Get:68 http://ftpmaster.internal/ubuntu questing/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 141s Get:69 http://ftpmaster.internal/ubuntu questing/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 141s Get:70 http://ftpmaster.internal/ubuntu questing/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 141s Get:71 http://ftpmaster.internal/ubuntu questing/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 141s Get:72 http://ftpmaster.internal/ubuntu questing/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 141s Get:73 http://ftpmaster.internal/ubuntu questing/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB] 141s Get:74 http://ftpmaster.internal/ubuntu questing/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB] 141s Get:75 http://ftpmaster.internal/ubuntu questing/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB] 141s Get:76 http://ftpmaster.internal/ubuntu questing/universe amd64 libmd4c0 amd64 0.5.2-2 [50.1 kB] 141s Get:77 http://ftpmaster.internal/ubuntu questing/universe amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1120 kB] 141s Get:78 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-base2.9 amd64 2.9.2-2 [25.3 kB] 141s Get:79 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-base-dev amd64 2.9.2-2 [17.9 kB] 141s Get:80 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-geom2.9 amd64 2.9.2-2 [57.7 kB] 141s Get:81 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-mol2.9 amd64 2.9.2-2 [328 kB] 141s Get:82 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 141s Get:83 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5core5t64 amd64 5.15.15+dfsg-4ubuntu1 [2038 kB] 141s Get:84 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5xml5t64 amd64 5.15.15+dfsg-4ubuntu1 [124 kB] 141s Get:85 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-info2.9 amd64 2.9.2-2 [146 kB] 141s Get:86 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-seq2.9 amd64 2.9.2-2 [63.8 kB] 141s Get:87 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-bindings2.9 amd64 2.9.2-2 [199 kB] 141s Get:88 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-bindings-dev amd64 2.9.2-2 [5208 B] 141s Get:89 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-conop2.9 amd64 2.9.2-2 [176 kB] 141s Get:90 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-conop-dev amd64 2.9.2-2 [12.2 kB] 141s Get:91 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-db2.9 amd64 2.9.2-2 [34.5 kB] 141s Get:92 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-db-dev amd64 2.9.2-2 [7602 B] 141s Get:93 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-geom-dev amd64 2.9.2-2 [19.2 kB] 141s Get:94 http://ftpmaster.internal/ubuntu questing/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 141s Get:95 http://ftpmaster.internal/ubuntu questing/main amd64 libopengl0 amd64 1.7.0-1build1 [32.8 kB] 141s Get:96 http://ftpmaster.internal/ubuntu questing/main amd64 libglu1-mesa amd64 9.0.2-1.1build1 [152 kB] 141s Get:97 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-img2.9 amd64 2.9.2-2 [135 kB] 141s Get:98 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-img-alg2.9 amd64 2.9.2-2 [146 kB] 141s Get:99 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-gfx2.9 amd64 2.9.2-2 [404 kB] 141s Get:100 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-gfx-dev amd64 2.9.2-2 [56.6 kB] 141s Get:101 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-mol-alg2.9 amd64 2.9.2-2 [325 kB] 141s Get:102 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 141s Get:103 http://ftpmaster.internal/ubuntu questing/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 141s Get:104 http://ftpmaster.internal/ubuntu questing/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 142s Get:105 http://ftpmaster.internal/ubuntu questing/main amd64 libtiff6 amd64 4.7.0-3ubuntu1 [204 kB] 142s Get:106 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-io2.9 amd64 2.9.2-2 [757 kB] 142s Get:107 http://ftpmaster.internal/ubuntu questing/universe amd64 libparasail8t64 amd64 2.6.2+dfsg-1ubuntu2 [1990 kB] 142s Get:108 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-seq-alg2.9 amd64 2.9.2-2 [264 kB] 142s Get:109 http://ftpmaster.internal/ubuntu questing/main amd64 libegl1 amd64 1.7.0-1build1 [28.7 kB] 142s Get:110 http://ftpmaster.internal/ubuntu questing/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB] 142s Get:111 http://ftpmaster.internal/ubuntu questing/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB] 142s Get:112 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5dbus5t64 amd64 5.15.15+dfsg-4ubuntu1 [221 kB] 142s Get:113 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5network5t64 amd64 5.15.15+dfsg-4ubuntu1 [725 kB] 142s Get:114 http://ftpmaster.internal/ubuntu questing/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 142s Get:115 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-icccm4 amd64 0.4.2-1 [11.1 kB] 142s Get:116 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-util1 amd64 0.4.1-1 [11.2 kB] 142s Get:117 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-image0 amd64 0.4.0-2build1 [10.8 kB] 142s Get:118 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-keysyms1 amd64 0.4.1-1 [8738 B] 142s Get:119 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 142s Get:120 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render-util0 amd64 0.3.10-1 [10.8 kB] 142s Get:121 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shape0 amd64 1.17.0-2 [6092 B] 142s Get:122 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-xinerama0 amd64 1.17.0-2 [5412 B] 142s Get:123 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-xinput0 amd64 1.17.0-2 [33.2 kB] 142s Get:124 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-xkb1 amd64 1.17.0-2 [32.3 kB] 142s Get:125 http://ftpmaster.internal/ubuntu questing/main amd64 libxkbcommon-x11-0 amd64 1.7.0-2 [15.2 kB] 142s Get:126 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5gui5t64 amd64 5.15.15+dfsg-4ubuntu1 [3791 kB] 142s Get:127 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5widgets5t64 amd64 5.15.15+dfsg-4ubuntu1 [2560 kB] 142s Get:128 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-gui2.9 amd64 2.9.2-2 [454 kB] 142s Get:129 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-gui-dev amd64 2.9.2-2 [43.9 kB] 142s Get:130 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-img-alg-dev amd64 2.9.2-2 [19.7 kB] 142s Get:131 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-img-dev amd64 2.9.2-2 [33.8 kB] 142s Get:132 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-info-dev amd64 2.9.2-2 [10.5 kB] 142s Get:133 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-io-dev amd64 2.9.2-2 [43.2 kB] 142s Get:134 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-mol-alg-dev amd64 2.9.2-2 [21.6 kB] 142s Get:135 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-mol-dev amd64 2.9.2-2 [48.7 kB] 142s Get:136 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-mol-mm2.9 amd64 2.9.2-2 [253 kB] 142s Get:137 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-mol-mm-dev amd64 2.9.2-2 [18.6 kB] 142s Get:138 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-seq-alg-dev amd64 2.9.2-2 [182 kB] 142s Get:139 http://ftpmaster.internal/ubuntu questing/universe amd64 libost-seq-dev amd64 2.9.2-2 [14.8 kB] 142s Get:140 http://ftpmaster.internal/ubuntu questing/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 142s Get:141 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5designer5 amd64 5.15.15-6build1 [2827 kB] 143s Get:142 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5sql5t64 amd64 5.15.15+dfsg-4ubuntu1 [122 kB] 143s Get:143 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5help5 amd64 5.15.15-6build1 [162 kB] 143s Get:144 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5printsupport5t64 amd64 5.15.15+dfsg-4ubuntu1 [208 kB] 143s Get:145 http://ftpmaster.internal/ubuntu questing/universe amd64 libqt5test5t64 amd64 5.15.15+dfsg-4ubuntu1 [149 kB] 143s Get:146 http://ftpmaster.internal/ubuntu questing/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 143s Get:147 http://ftpmaster.internal/ubuntu questing/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 143s Get:148 http://ftpmaster.internal/ubuntu questing/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 143s Get:149 http://ftpmaster.internal/ubuntu questing/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu4 [176 kB] 143s Get:150 http://ftpmaster.internal/ubuntu questing/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 143s Get:151 http://ftpmaster.internal/ubuntu questing/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6build1 [15.8 MB] 144s Get:152 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 python-matplotlib-data all 3.10.1+dfsg1-3 [2936 kB] 144s Get:153 http://ftpmaster.internal/ubuntu questing/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 144s Get:154 http://ftpmaster.internal/ubuntu questing/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 144s Get:155 http://ftpmaster.internal/ubuntu questing/main amd64 python3.13-tk amd64 3.13.3-1 [107 kB] 144s Get:156 http://ftpmaster.internal/ubuntu questing/main amd64 python3-tk amd64 3.13.3-1 [9856 B] 144s Get:157 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 144s Get:158 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 144s Get:159 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 144s Get:160 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 144s Get:161 http://ftpmaster.internal/ubuntu questing/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 144s Get:162 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 144s Get:163 http://ftpmaster.internal/ubuntu questing/main amd64 python3-lxml amd64 5.3.2-1 [1407 kB] 144s Get:164 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 144s Get:165 http://ftpmaster.internal/ubuntu questing/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 144s Get:166 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 145s Get:167 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 145s Get:168 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 145s Get:169 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 145s Get:170 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build3 [360 kB] 145s Get:171 http://ftpmaster.internal/ubuntu questing/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 146s Get:172 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 146s Get:173 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 146s Get:174 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 python3-matplotlib amd64 3.10.1+dfsg1-3 [18.1 MB] 147s Get:175 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-pyqt5.sip amd64 12.17.0-1build1 [76.5 kB] 147s Get:176 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-pyqt5 amd64 5.15.11+dfsg-2 [2725 kB] 147s Get:177 http://ftpmaster.internal/ubuntu questing/universe amd64 python3-ost amd64 2.9.2-2 [3674 kB] 147s Get:178 http://ftpmaster.internal/ubuntu questing/universe amd64 openstructure amd64 2.9.2-2 [92.4 MB] 151s Get:179 http://ftpmaster.internal/ubuntu questing/universe amd64 voronota amd64 1.29.4307+ds-1 [2459 kB] 152s Preconfiguring packages ... 152s Fetched 238 MB in 13s (18.8 MB/s) 152s Selecting previously unselected package python3-numpy-dev:amd64. 153s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80518 files and directories currently installed.) 153s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 153s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 153s Selecting previously unselected package libblas3:amd64. 153s Preparing to unpack .../001-libblas3_3.12.1-2_amd64.deb ... 153s Unpacking libblas3:amd64 (3.12.1-2) ... 153s Selecting previously unselected package libgfortran5:amd64. 153s Preparing to unpack .../002-libgfortran5_15-20250404-0ubuntu1_amd64.deb ... 153s Unpacking libgfortran5:amd64 (15-20250404-0ubuntu1) ... 153s Selecting previously unselected package liblapack3:amd64. 153s Preparing to unpack .../003-liblapack3_3.12.1-2_amd64.deb ... 153s Unpacking liblapack3:amd64 (3.12.1-2) ... 153s Selecting previously unselected package python3-numpy. 153s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 153s Unpacking python3-numpy (1:2.2.3+ds-5) ... 153s Selecting previously unselected package libtcl8.6:amd64. 153s Preparing to unpack .../005-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 153s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 153s Selecting previously unselected package fonts-dejavu-mono. 153s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 153s Unpacking fonts-dejavu-mono (2.37-8) ... 153s Selecting previously unselected package fonts-dejavu-core. 153s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 153s Unpacking fonts-dejavu-core (2.37-8) ... 153s Selecting previously unselected package fontconfig-config. 153s Preparing to unpack .../008-fontconfig-config_2.15.0-2.2ubuntu1_amd64.deb ... 154s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 154s Selecting previously unselected package libfontconfig1:amd64. 154s Preparing to unpack .../009-libfontconfig1_2.15.0-2.2ubuntu1_amd64.deb ... 154s Unpacking libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 154s Selecting previously unselected package libxrender1:amd64. 154s Preparing to unpack .../010-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 154s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 154s Selecting previously unselected package libxft2:amd64. 154s Preparing to unpack .../011-libxft2_2.3.6-1build1_amd64.deb ... 154s Unpacking libxft2:amd64 (2.3.6-1build1) ... 154s Selecting previously unselected package x11-common. 154s Preparing to unpack .../012-x11-common_1%3a7.7+23ubuntu4_all.deb ... 154s Unpacking x11-common (1:7.7+23ubuntu4) ... 154s Selecting previously unselected package libxss1:amd64. 154s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_amd64.deb ... 154s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 154s Selecting previously unselected package libtk8.6:amd64. 154s Preparing to unpack .../014-libtk8.6_8.6.16-1_amd64.deb ... 154s Unpacking libtk8.6:amd64 (8.6.16-1) ... 154s Selecting previously unselected package tk8.6-blt2.5. 154s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 154s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 154s Selecting previously unselected package blt. 154s Preparing to unpack .../016-blt_2.5.3+dfsg-8_amd64.deb ... 154s Unpacking blt (2.5.3+dfsg-8) ... 154s Selecting previously unselected package clustalw. 154s Preparing to unpack .../017-clustalw_2.1+lgpl-7_amd64.deb ... 154s Unpacking clustalw (2.1+lgpl-7) ... 154s Selecting previously unselected package libcifpp-data. 154s Preparing to unpack .../018-libcifpp-data_7.0.9-1_all.deb ... 154s Unpacking libcifpp-data (7.0.9-1) ... 154s Selecting previously unselected package libcifpp7:amd64. 154s Preparing to unpack .../019-libcifpp7_7.0.9-1_amd64.deb ... 154s Unpacking libcifpp7:amd64 (7.0.9-1) ... 154s Selecting previously unselected package dssp. 154s Preparing to unpack .../020-dssp_4.4.10-1_amd64.deb ... 154s Unpacking dssp (4.4.10-1) ... 154s Selecting previously unselected package fontconfig. 154s Preparing to unpack .../021-fontconfig_2.15.0-2.2ubuntu1_amd64.deb ... 154s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 154s Selecting previously unselected package fonts-lyx. 154s Preparing to unpack .../022-fonts-lyx_2.4.3-1_all.deb ... 154s Unpacking fonts-lyx (2.4.3-1) ... 154s Selecting previously unselected package libavahi-common-data:amd64. 154s Preparing to unpack .../023-libavahi-common-data_0.8-16ubuntu2_amd64.deb ... 154s Unpacking libavahi-common-data:amd64 (0.8-16ubuntu2) ... 154s Selecting previously unselected package libavahi-common3:amd64. 154s Preparing to unpack .../024-libavahi-common3_0.8-16ubuntu2_amd64.deb ... 154s Unpacking libavahi-common3:amd64 (0.8-16ubuntu2) ... 154s Selecting previously unselected package libavahi-client3:amd64. 154s Preparing to unpack .../025-libavahi-client3_0.8-16ubuntu2_amd64.deb ... 154s Unpacking libavahi-client3:amd64 (0.8-16ubuntu2) ... 154s Selecting previously unselected package libboost-filesystem1.83.0:amd64. 154s Preparing to unpack .../026-libboost-filesystem1.83.0_1.83.0-4.2ubuntu1_amd64.deb ... 154s Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-4.2ubuntu1) ... 154s Selecting previously unselected package libboost-iostreams1.83.0:amd64. 154s Preparing to unpack .../027-libboost-iostreams1.83.0_1.83.0-4.2ubuntu1_amd64.deb ... 154s Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-4.2ubuntu1) ... 154s Selecting previously unselected package libboost-program-options1.83.0:amd64. 154s Preparing to unpack .../028-libboost-program-options1.83.0_1.83.0-4.2ubuntu1_amd64.deb ... 154s Unpacking libboost-program-options1.83.0:amd64 (1.83.0-4.2ubuntu1) ... 154s Selecting previously unselected package libboost-python1.83.0. 154s Preparing to unpack .../029-libboost-python1.83.0_1.83.0-4.2ubuntu1_amd64.deb ... 154s Unpacking libboost-python1.83.0 (1.83.0-4.2ubuntu1) ... 154s Selecting previously unselected package libboost-thread1.83.0:amd64. 154s Preparing to unpack .../030-libboost-thread1.83.0_1.83.0-4.2ubuntu1_amd64.deb ... 154s Unpacking libboost-thread1.83.0:amd64 (1.83.0-4.2ubuntu1) ... 154s Selecting previously unselected package libcups2t64:amd64. 154s Preparing to unpack .../031-libcups2t64_2.4.12-0ubuntu1_amd64.deb ... 154s Unpacking libcups2t64:amd64 (2.4.12-0ubuntu1) ... 154s Selecting previously unselected package libdeflate0:amd64. 154s Preparing to unpack .../032-libdeflate0_1.23-2_amd64.deb ... 154s Unpacking libdeflate0:amd64 (1.23-2) ... 154s Selecting previously unselected package libdouble-conversion3:amd64. 154s Preparing to unpack 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libxshmfence1:amd64 (1.3.3-1) ... 155s Selecting previously unselected package mesa-libgallium:amd64. 155s Preparing to unpack .../044-mesa-libgallium_25.0.3-1ubuntu2_amd64.deb ... 155s Unpacking mesa-libgallium:amd64 (25.0.3-1ubuntu2) ... 155s Selecting previously unselected package libgbm1:amd64. 155s Preparing to unpack .../045-libgbm1_25.0.3-1ubuntu2_amd64.deb ... 155s Unpacking libgbm1:amd64 (25.0.3-1ubuntu2) ... 155s Selecting previously unselected package libwayland-client0:amd64. 155s Preparing to unpack .../046-libwayland-client0_1.23.1-3_amd64.deb ... 155s Unpacking libwayland-client0:amd64 (1.23.1-3) ... 155s Selecting previously unselected package libxcb-shm0:amd64. 155s Preparing to unpack .../047-libxcb-shm0_1.17.0-2_amd64.deb ... 155s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 155s Selecting previously unselected package libegl-mesa0:amd64. 155s Preparing to unpack .../048-libegl-mesa0_25.0.3-1ubuntu2_amd64.deb ... 155s Unpacking libegl-mesa0:amd64 (25.0.3-1ubuntu2) ... 155s Selecting previously unselected package libgomp1:amd64. 155s Preparing to unpack .../049-libgomp1_15-20250404-0ubuntu1_amd64.deb ... 155s Unpacking libgomp1:amd64 (15-20250404-0ubuntu1) ... 155s Selecting previously unselected package libfftw3-single3:amd64. 155s Preparing to unpack .../050-libfftw3-single3_3.3.10-2fakesync1build1_amd64.deb ... 155s Unpacking libfftw3-single3:amd64 (3.3.10-2fakesync1build1) ... 155s Selecting previously unselected package libvulkan1:amd64. 155s Preparing to unpack .../051-libvulkan1_1.4.304.0-1_amd64.deb ... 155s Unpacking libvulkan1:amd64 (1.4.304.0-1) ... 155s Selecting previously unselected package libgl1-mesa-dri:amd64. 155s Preparing to unpack .../052-libgl1-mesa-dri_25.0.3-1ubuntu2_amd64.deb ... 155s Unpacking libgl1-mesa-dri:amd64 (25.0.3-1ubuntu2) ... 155s Selecting previously unselected package libxcb-glx0:amd64. 155s Preparing to unpack .../053-libxcb-glx0_1.17.0-2_amd64.deb ... 155s Unpacking libxcb-glx0:amd64 (1.17.0-2) ... 155s 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libimagequant0:amd64. 155s Preparing to unpack .../059-libimagequant0_2.18.0-1build1_amd64.deb ... 155s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 155s Selecting previously unselected package libwacom-common. 155s Preparing to unpack .../060-libwacom-common_2.14.0-1_all.deb ... 155s Unpacking libwacom-common (2.14.0-1) ... 155s Selecting previously unselected package libwacom9:amd64. 155s Preparing to unpack .../061-libwacom9_2.14.0-1_amd64.deb ... 155s Unpacking libwacom9:amd64 (2.14.0-1) ... 155s Selecting previously unselected package libinput-bin. 155s Preparing to unpack .../062-libinput-bin_1.27.1-1_amd64.deb ... 155s Unpacking libinput-bin (1.27.1-1) ... 156s Selecting previously unselected package libmtdev1t64:amd64. 156s Preparing to unpack .../063-libmtdev1t64_1.1.7-1_amd64.deb ... 156s Unpacking libmtdev1t64:amd64 (1.1.7-1) ... 156s Selecting previously unselected package libinput10:amd64. 156s Preparing to unpack .../064-libinput10_1.27.1-1_amd64.deb ... 156s 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156s Selecting previously unselected package liblcms2-2:amd64. 156s Preparing to unpack .../070-liblcms2-2_2.16-2_amd64.deb ... 156s Unpacking liblcms2-2:amd64 (2.16-2) ... 156s Selecting previously unselected package liblerc4:amd64. 156s Preparing to unpack .../071-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 156s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 156s Selecting previously unselected package libmbedcrypto16:amd64. 156s Preparing to unpack .../072-libmbedcrypto16_3.6.2-3ubuntu1_amd64.deb ... 156s Unpacking libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 156s Selecting previously unselected package libmbedx509-7:amd64. 156s Preparing to unpack .../073-libmbedx509-7_3.6.2-3ubuntu1_amd64.deb ... 156s Unpacking libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 156s Selecting previously unselected package libmbedtls21:amd64. 156s Preparing to unpack .../074-libmbedtls21_3.6.2-3ubuntu1_amd64.deb ... 156s Unpacking libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 156s Selecting previously unselected package libmd4c0:amd64. 156s Preparing to unpack .../075-libmd4c0_0.5.2-2_amd64.deb ... 156s Unpacking libmd4c0:amd64 (0.5.2-2) ... 156s Selecting previously unselected package libopenmm8.1. 156s Preparing to unpack .../076-libopenmm8.1_8.1.2+dfsg-11_amd64.deb ... 156s Unpacking libopenmm8.1 (8.1.2+dfsg-11) ... 156s Selecting previously unselected package libost-base2.9:amd64. 156s Preparing to unpack .../077-libost-base2.9_2.9.2-2_amd64.deb ... 156s Unpacking libost-base2.9:amd64 (2.9.2-2) ... 156s Selecting previously unselected package libost-base-dev. 156s Preparing to unpack .../078-libost-base-dev_2.9.2-2_amd64.deb ... 156s Unpacking libost-base-dev (2.9.2-2) ... 156s Selecting previously unselected package libost-geom2.9:amd64. 156s Preparing to unpack .../079-libost-geom2.9_2.9.2-2_amd64.deb ... 156s Unpacking libost-geom2.9:amd64 (2.9.2-2) ... 156s Selecting previously unselected package libost-mol2.9. 156s Preparing to unpack .../080-libost-mol2.9_2.9.2-2_amd64.deb ... 156s Unpacking libost-mol2.9 (2.9.2-2) ... 156s Selecting previously unselected package libpcre2-16-0:amd64. 156s Preparing to unpack .../081-libpcre2-16-0_10.45-1_amd64.deb ... 156s Unpacking libpcre2-16-0:amd64 (10.45-1) ... 156s Selecting previously unselected package libqt5core5t64:amd64. 156s Preparing to unpack .../082-libqt5core5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 156s Unpacking libqt5core5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 156s Selecting previously unselected package libqt5xml5t64:amd64. 156s Preparing to unpack .../083-libqt5xml5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 156s Unpacking libqt5xml5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 156s Selecting previously unselected package libost-info2.9. 156s Preparing to unpack .../084-libost-info2.9_2.9.2-2_amd64.deb ... 156s Unpacking libost-info2.9 (2.9.2-2) ... 156s Selecting previously unselected package libost-seq2.9. 156s Preparing to unpack .../085-libost-seq2.9_2.9.2-2_amd64.deb ... 156s Unpacking libost-seq2.9 (2.9.2-2) ... 156s 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libost-seq-alg2.9 (2.9.2-2) ... 157s Selecting previously unselected package libegl1:amd64. 157s Preparing to unpack .../108-libegl1_1.7.0-1build1_amd64.deb ... 157s Unpacking libegl1:amd64 (1.7.0-1build1) ... 157s Selecting previously unselected package libglx0:amd64. 157s Preparing to unpack .../109-libglx0_1.7.0-1build1_amd64.deb ... 157s Unpacking libglx0:amd64 (1.7.0-1build1) ... 157s Selecting previously unselected package libgl1:amd64. 157s Preparing to unpack .../110-libgl1_1.7.0-1build1_amd64.deb ... 157s Unpacking libgl1:amd64 (1.7.0-1build1) ... 157s Selecting previously unselected package libqt5dbus5t64:amd64. 157s Preparing to unpack .../111-libqt5dbus5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 157s Unpacking libqt5dbus5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 157s Selecting previously unselected package libqt5network5t64:amd64. 157s Preparing to unpack .../112-libqt5network5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 157s Unpacking libqt5network5t64:amd64 (5.15.15+dfsg-4ubuntu1) 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Preparing to unpack .../118-libxcb-render0_1.17.0-2_amd64.deb ... 157s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 157s Selecting previously unselected package libxcb-render-util0:amd64. 157s Preparing to unpack .../119-libxcb-render-util0_0.3.10-1_amd64.deb ... 157s Unpacking libxcb-render-util0:amd64 (0.3.10-1) ... 157s Selecting previously unselected package libxcb-shape0:amd64. 157s Preparing to unpack .../120-libxcb-shape0_1.17.0-2_amd64.deb ... 157s Unpacking libxcb-shape0:amd64 (1.17.0-2) ... 157s Selecting previously unselected package libxcb-xinerama0:amd64. 157s Preparing to unpack .../121-libxcb-xinerama0_1.17.0-2_amd64.deb ... 157s Unpacking libxcb-xinerama0:amd64 (1.17.0-2) ... 157s Selecting previously unselected package libxcb-xinput0:amd64. 157s Preparing to unpack .../122-libxcb-xinput0_1.17.0-2_amd64.deb ... 157s Unpacking libxcb-xinput0:amd64 (1.17.0-2) ... 157s Selecting previously unselected package libxcb-xkb1:amd64. 157s Preparing to unpack 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package libqt5test5t64:amd64. 158s Preparing to unpack .../144-libqt5test5t64_5.15.15+dfsg-4ubuntu1_amd64.deb ... 158s Unpacking libqt5test5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 158s Selecting previously unselected package libraqm0:amd64. 158s Preparing to unpack .../145-libraqm0_0.10.2-1_amd64.deb ... 158s Unpacking libraqm0:amd64 (0.10.2-1) ... 158s Selecting previously unselected package libwebpdemux2:amd64. 158s Preparing to unpack .../146-libwebpdemux2_1.5.0-0.1_amd64.deb ... 158s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 158s Selecting previously unselected package libwebpmux3:amd64. 158s Preparing to unpack .../147-libwebpmux3_1.5.0-0.1_amd64.deb ... 158s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 158s Selecting previously unselected package libxslt1.1:amd64. 158s Preparing to unpack .../148-libxslt1.1_1.1.39-0exp1ubuntu4_amd64.deb ... 158s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu4) ... 158s Selecting previously unselected package ncbi-data. 158s Preparing to unpack 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... 169s Setting up python3-numpy (1:2.2.3+ds-5) ... 171s Setting up libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 171s Setting up python3-lxml:amd64 (5.3.2-1) ... 171s Setting up libtiff6:amd64 (4.7.0-3ubuntu1) ... 171s Setting up libegl1:amd64 (1.7.0-1build1) ... 171s Setting up python3-contourpy (1.3.1-1build1) ... 171s Setting up libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 171s Setting up libost-geom-dev (2.9.2-2) ... 171s Setting up libsm6:amd64 (2:1.2.4-1) ... 171s Setting up libavahi-client3:amd64 (0.8-16ubuntu2) ... 171s Setting up libost-conop2.9 (2.9.2-2) ... 171s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 171s Setting up libinput10:amd64 (1.27.1-1) ... 171s Setting up fontconfig (2.15.0-2.2ubuntu1) ... 173s Regenerating fonts cache... done. 173s Setting up libxft2:amd64 (2.3.6-1build1) ... 173s Setting up libost-info2.9 (2.9.2-2) ... 173s Setting up libglx-mesa0:amd64 (25.0.3-1ubuntu2) ... 173s Setting up python3-scipy (1.14.1-4ubuntu2) ... 176s Setting up libglx0:amd64 (1.7.0-1build1) ... 176s Setting up libost-info-dev (2.9.2-2) ... 176s Setting up libost-seq2.9 (2.9.2-2) ... 176s Setting up libtk8.6:amd64 (8.6.16-1) ... 176s Setting up libost-mol-dev (2.9.2-2) ... 176s Setting up libost-img2.9 (2.9.2-2) ... 176s Setting up libost-seq-dev (2.9.2-2) ... 176s Setting up python3.13-tk (3.13.3-1) ... 176s Setting up libost-conop-dev (2.9.2-2) ... 176s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 176s Setting up python3-pil:amd64 (11.1.0-5build1) ... 177s Setting up libgl1:amd64 (1.7.0-1build1) ... 177s Setting up libost-img-alg2.9 (2.9.2-2) ... 177s Setting up libost-seq-alg2.9 (2.9.2-2) ... 177s Setting up libost-bindings2.9 (2.9.2-2) ... 177s Setting up libost-db2.9 (2.9.2-2) ... 177s Setting up libcups2t64:amd64 (2.4.12-0ubuntu1) ... 177s Setting up libost-img-dev (2.9.2-2) ... 177s Setting up libost-db-dev (2.9.2-2) ... 177s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 177s Setting up libost-mol-alg2.9 (2.9.2-2) ... 177s Setting up blt (2.5.3+dfsg-8) ... 177s Setting up python3-tk:amd64 (3.13.3-1) ... 177s Setting up libost-seq-alg-dev (2.9.2-2) ... 177s Setting up libost-img-alg-dev (2.9.2-2) ... 177s Setting up libost-gfx2.9 (2.9.2-2) ... 177s Setting up libqt5gui5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 177s Setting up python3-pil.imagetk:amd64 (11.1.0-5build1) ... 177s Setting up libost-bindings-dev (2.9.2-2) ... 177s Setting up libost-mol-alg-dev (2.9.2-2) ... 177s Setting up libost-io2.9 (2.9.2-2) ... 177s Setting up libost-gfx-dev (2.9.2-2) ... 177s Setting up libqt5widgets5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 177s Setting up libost-mol-mm2.9 (2.9.2-2) ... 177s Setting up libost-mol-mm-dev (2.9.2-2) ... 177s Setting up libqt5help5:amd64 (5.15.15-6build1) ... 177s Setting up libost-gui2.9 (2.9.2-2) ... 177s Setting up libost-io-dev (2.9.2-2) ... 177s Setting up libqt5printsupport5t64:amd64 (5.15.15+dfsg-4ubuntu1) ... 177s Setting up libqt5designer5:amd64 (5.15.15-6build1) ... 177s Setting up libost-gui-dev (2.9.2-2) ... 177s Setting up python3-pyqt5 (5.15.11+dfsg-2) ... 177s Setting up python3-fonttools (4.55.3-2build1) ... 178s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 178s Setting up python3-matplotlib (3.10.1+dfsg1-3) ... 179s Setting up python3-ost (2.9.2-2) ... 180s Setting up openstructure (2.9.2-2) ... 222s Building compounds library, this may take a while... 0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ 222s Processing triggers for man-db (2.13.0-1) ... 223s Processing triggers for udev (257.4-1ubuntu3) ... 223s Processing triggers for libc-bin (2.41-6ubuntu1) ... 230s autopkgtest [18:27:46]: test python: [----------------------- 230s Compound library not available. Some functionality may not work as expected. 231s .... 231s ---------------------------------------------------------------------- 231s Ran 4 tests in 0.000s 231s 231s OK 231s Compound library not available. Some functionality may not work as expected. 231s ...... 231s ---------------------------------------------------------------------- 231s Ran 6 tests in 0.000s 231s 231s OK 231s Compound library not available. Some functionality may not work as expected. 231s ...../usr/lib/python3/dist-packages/ost/table.py:2696: DeprecationWarning: `trapz` is deprecated. Use `trapezoid` instead, or one of the numerical integration functions in `scipy.integrate`. 231s return np.trapz(enr[1], enr[0]) 231s ../usr/lib/python3/dist-packages/ost/table.py:2807: DeprecationWarning: `trapz` is deprecated. Use `trapezoid` instead, or one of the numerical integration functions in `scipy.integrate`. 231s return np.trapz(roc[1], roc[0]) 232s ...................../usr/lib/python3/dist-packages/ost/table.py:2807: DeprecationWarning: `trapz` is deprecated. Use `trapezoid` instead, or one of the numerical integration functions in `scipy.integrate`. 232s return np.trapz(roc[1], roc[0]) 232s ........../usr/lib/python3.13/unittest/case.py:606: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/enrichment-out.png'> 232s if method() is not None: 232s ResourceWarning: Enable tracemalloc to get the object allocation traceback 232s ../usr/lib/python3.13/unittest/case.py:606: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-out.png'> 232s if method() is not None: 232s ResourceWarning: Enable tracemalloc to get the object allocation traceback 232s ./usr/lib/python3/dist-packages/matplotlib/text.py:508: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/logroc-out.png'> 232s return bbox, list(zip(lines, zip(ws, hs), *xys.T)), descent 232s ResourceWarning: Enable tracemalloc to get the object allocation traceback 232s /usr/lib/python3.13/unittest/case.py:606: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-same-val-out.png'> 232s if method() is not None: 232s ResourceWarning: Enable tracemalloc to get the object allocation traceback 232s .......................................... 232s ---------------------------------------------------------------------- 232s Ran 83 tests in 1.053s 232s 232s OK 233s /tmp/autopkgtest.26XI9m/build.c7m/src/modules/bindings/tests/test_blast.py:81: SyntaxWarning: invalid escape sequence '\d' 233s re_v = re.compile('\d+\.\d+\.\d+') 233s Compound library not available. Some functionality may not work as expected. 233s Could not find /I/do/not/exist 233s ...Could not find /I/do/not/exist 233s ... 233s ---------------------------------------------------------------------- 233s Ran 6 tests in 0.426s 233s 233s OK 233s Compound library not available. Some functionality may not work as expected. 245s s. 245s ---------------------------------------------------------------------- 245s Ran 2 tests in 11.949s 245s 245s OK (skipped=1) 245s Compound library not available. Some functionality may not work as expected. 246s .s..... 246s ---------------------------------------------------------------------- 246s Ran 7 tests in 0.168s 246s 246s OK (skipped=1) 246s Compound library not available. Some functionality may not work as expected. 246s Could not find DockQ.py, could not test binding... 246s Compound library not available. Some functionality may not work as expected. 246s Could not find hbplus, could not test binding... 246s Compound library not available. Some functionality may not work as expected. 246s No HHblits installation found: skip unit tests 246s Compound library not available. Some functionality may not work as expected. 246s .Could not find ialign master perl script: ignoring unit tests 246s 246s ---------------------------------------------------------------------- 246s Ran 1 test in 0.013s 246s 246s OK 246s Compound library not available. Some functionality may not work as expected. 246s Could not find kClust executable: ignoring unit tests 247s Compound library not available. Some functionality may not work as expected. 247s . 247s ---------------------------------------------------------------------- 247s Ran 1 test in 0.016s 247s 247s OK 247s Could not find lga executable: ignoring unit tests 247s Compound library not available. Some functionality may not work as expected. 247s Could not find msms executable: ignoring unit tests 247s Compound library not available. Some functionality may not work as expected. 247s Could not find NACCESS, could not test binding... 247s Compound library not available. Some functionality may not work as expected. 247s ...Could not find tmalign executable: ignoring unit tests 247s Could not find tmalign executable: ignoring unit tests 247s 247s ---------------------------------------------------------------------- 247s Ran 3 tests in 0.167s 247s 247s OK 247s Compound library not available. Some functionality may not work as expected. 247s No compound library available. Ignoring test_cleanup.py tests. 248s Compound library not available. Some functionality may not work as expected. 248s ../tmp/autopkgtest.26XI9m/build.c7m/src/modules/conop/tests/test_complib.py:71: UserWarning: Compound library not available. Some functionality may not work as expected. 248s warnings.warn("Compound library not available. Some functionality may not work as expected.") 248s ...... 248s ---------------------------------------------------------------------- 248s Ran 8 tests in 0.084s 248s 248s OK 248s Compound library not available. Some functionality may not work as expected. 248s No compound library available. Ignoring test_compound.py tests. 248s Compound library not available. Some functionality may not work as expected. 248s . 248s ---------------------------------------------------------------------- 248s Ran 1 test in 0.000s 248s 248s OK 248s Compound library not available. Some functionality may not work as expected. 248s ... 248s ---------------------------------------------------------------------- 248s Ran 3 tests in 0.002s 248s 248s OK 248s Compound library not available. Some functionality may not work as expected. 248s ........ 248s ---------------------------------------------------------------------- 248s Ran 8 tests in 0.002s 248s 248s OK 248s Traceback (most recent call last): 248s File "/tmp/autopkgtest.26XI9m/build.c7m/src/modules/gfx/tests/test_entity.py", line 1, in 248s eh=io.LoadPDB("1crn",remote=True) 248s ^^ 248s NameError: name 'io' is not defined. Did you mean: 'id'? Or did you forget to import 'io'? 248s Compound library not available. Some functionality may not work as expected. 248s ...... 248s ---------------------------------------------------------------------- 248s Ran 6 tests in 0.002s 248s 248s OK 249s Traceback (most recent call last): 249s File "/tmp/autopkgtest.26XI9m/build.c7m/src/modules/gfx/tests/test_gost_export.py", line 1, in 249s import desost_util as util 249s ModuleNotFoundError: No module named 'desost_util' 249s Traceback (most recent call last): 249s File "/tmp/autopkgtest.26XI9m/build.c7m/src/modules/gfx/tests/test_gost_import.py", line 3, in 249s with open("test.gost","rb") as gf: 249s ~~~~^^^^^^^^^^^^^^^^^^ 249s FileNotFoundError: [Errno 2] No such file or directory: 'test.gost' 249s Compound library not available. Some functionality may not work as expected. 249s .No citation for identifier '1' found. Couldn't set author list. 249s SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 249s ..SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 249s .SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'LYZ' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s unknown residue 'HYP' in SEQRES record. Setting one-letter-code to 'X' 249s .SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 249s No SEQRES found for chain 'A'. Most likely the entity_poly_seq category was missing from the input file. 249s No SEQRES found for chain 'B'. Most likely the entity_poly_seq category was missing from the input file. 249s No SEQRES found for chain 'C'. Most likely the entity_poly_seq category was missing from the input file. 249s ......s 249s ---------------------------------------------------------------------- 249s Ran 12 tests in 0.521s 249s 249s OK (skipped=1) 249s Compound library not available. Some functionality may not work as expected. 250s No compound library available. Ignoring test_stereochemistry.py tests. 250s Compound library not available. Some functionality may not work as expected. 250s ....s 250s ---------------------------------------------------------------------- 250s Ran 5 tests in 0.003s 250s 250s OK (skipped=1) 250s Compound library not available. Some functionality may not work as expected. 250s ..... 250s ---------------------------------------------------------------------- 250s Ran 5 tests in 0.004s 250s 250s OK 250s Compound library not available. Some functionality may not work as expected. 252s s. 252s ---------------------------------------------------------------------- 252s Ran 2 tests in 1.921s 252s 252s OK (skipped=1) 252s Could not find NACCESS, could not compare Accessiblity function... 252s Compound library not available. Some functionality may not work as expected. 252s No compound lib available. Ignoring test_bblddt.py tests. 253s Compound library not available. Some functionality may not work as expected. 253s Ignoring struct_ref_seq_dif with missing data item seq_num 253s Ignoring struct_ref_seq_dif with missing data item seq_num 253s SEQRES requires a valid compound library to handle non standard compounds. Their One letter codes will be set to X. 253s unknown residue 'ACE' in SEQRES record. Setting one-letter-code to 'X' 253s . 253s ---------------------------------------------------------------------- 253s Ran 1 test in 0.093s 253s 253s OK 253s Compound library not available. Some functionality may not work as expected. 253s No compound lib available. Ignoring test_chain_mapping.py tests. 253s Compound library not available. Some functionality may not work as expected. 253s No compound lib available. Ignoring contact_score.py tests. 254s Compound library not available. Some functionality may not work as expected. 254s ......... 254s ---------------------------------------------------------------------- 254s Ran 9 tests in 0.653s 254s 254s OK 254s Compound library not available. Some functionality may not work as expected. 254s .. 254s ---------------------------------------------------------------------- 254s Ran 2 tests in 0.006s 254s 254s OK 254s Compound library not available. Some functionality may not work as expected. 255s No compound library available. Ignoring test_lddt.py tests. 255s Compound library not available. Some functionality may not work as expected. 255s Failed to import ligand_scoring.py. Happens when numpy, scipy or networkx is missing. Ignoring test_ligand_scoring.py tests. 255s Compound library not available. Some functionality may not work as expected. 255s No compound library available. Ignoring test_nonstandard.py tests. 255s Compound library not available. Some functionality may not work as expected. 256s . 256s ---------------------------------------------------------------------- 256s Ran 1 test in 0.154s 256s 256s OK 256s Compound library not available. Some functionality may not work as expected. 256s ........ 256s ---------------------------------------------------------------------- 256s Ran 8 tests in 0.004s 256s 256s OK 256s Compound library not available. Some functionality may not work as expected. 256s No compound lib available. Ignoring test_qsscore.py tests. 256s Compound library not available. Some functionality may not work as expected. 256s No compound library available. Ignoring test_qsscoring.py tests. 256s Compound library not available. Some functionality may not work as expected. 257s s 257s ---------------------------------------------------------------------- 257s Ran 1 test in 0.000s 257s 257s OK (skipped=1) 257s Compound library not available. Some functionality may not work as expected. 257s No compound library available. Ignoring test_stereochemistry.py tests. 257s Compound library not available. Some functionality may not work as expected. 257s ....... 257s ---------------------------------------------------------------------- 257s Ran 7 tests in 0.001s 257s 257s OK 257s Compound library not available. Some functionality may not work as expected. 257s ... 257s ---------------------------------------------------------------------- 257s Ran 3 tests in 0.018s 257s 257s OK 257s Compound library not available. Some functionality may not work as expected. 257s . 257s ---------------------------------------------------------------------- 257s Ran 1 test in 0.045s 257s 257s OK 257s Compound library not available. Some functionality may not work as expected. 257s . 257s ---------------------------------------------------------------------- 257s Ran 1 test in 0.001s 257s 257s OK 257s Compound library not available. Some functionality may not work as expected. 257s No compound library available. Ignoring test_aligntoseqres.py tests. 257s Compound library not available. Some functionality may not work as expected. 258s ... 258s ---------------------------------------------------------------------- 258s Ran 3 tests in 0.002s 258s 258s OK 258s Compound library not available. Some functionality may not work as expected. 258s ... 258s ---------------------------------------------------------------------- 258s Ran 3 tests in 0.002s 258s 258s OK 258s Compound library not available. Some functionality may not work as expected. 258s ........ 258s ---------------------------------------------------------------------- 258s Ran 8 tests in 0.033s 258s 258s OK 258s Compound library not available. Some functionality may not work as expected. 258s . 258s ---------------------------------------------------------------------- 258s Ran 1 test in 0.001s 258s 258s OK 258s Compound library not available. Some functionality may not work as expected. 259s .. 259s ---------------------------------------------------------------------- 259s Ran 2 tests in 0.000s 259s 259s OK 259s Compound library not available. Some functionality may not work as expected. 259s .............. 259s ---------------------------------------------------------------------- 259s Ran 14 tests in 0.005s 259s 259s OK 259s autopkgtest [18:28:15]: test python: -----------------------] 260s python PASS 260s autopkgtest [18:28:16]: test python: - - - - - - - - - - results - - - - - - - - - - 260s autopkgtest [18:28:16]: @@@@@@@@@@@@@@@@@@@@ summary 260s python PASS 412s nova [W] Skipping flock for amd64 412s Creating nova instance adt-questing-amd64-openstructure-20250503-182356-juju-7f2275-prod-proposed-migration-environment-21-266b2306-5f53-4d55-bdc8-72c64bab9159 from image adt/ubuntu-questing-amd64-server-20250503.img (UUID 57b7c1b6-ad80-4bdb-b031-36f045f7f3b3)... 412s nova [W] Timed out waiting for d083dacd-dd4b-44bc-8cfd-69b87897ce18 to get deleted.