0s autopkgtest [09:34:40]: starting date and time: 2024-12-03 09:34:40+0000 0s autopkgtest [09:34:40]: git checkout: be626eda Fix armhf LXD image generation for plucky 0s autopkgtest [09:34:40]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9p4l1qm5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:rdkit --apt-upgrade coot --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=rdkit/202409.2-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-24.secgroup --name adt-plucky-amd64-coot-20241203-093439-juju-7f2275-prod-proposed-migration-environment-15-e7fbebe5-3e2b-472b-8295-c0ea477fc06c --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 64s autopkgtest [09:35:44]: testbed dpkg architecture: amd64 64s autopkgtest [09:35:44]: testbed apt version: 2.9.14ubuntu1 64s autopkgtest [09:35:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s autopkgtest [09:35:44]: testbed release detected to be: None 65s autopkgtest [09:35:45]: updating testbed package index (apt update) 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 66s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 66s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 66s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 66s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 66s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB] 66s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [65.3 kB] 66s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [781 kB] 66s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [153 kB] 66s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [104 kB] 66s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.6 kB] 66s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2572 B] 66s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [256 kB] 66s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [687 kB] 66s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [21.9 kB] 66s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [6364 B] 66s Fetched 2217 kB in 1s (2533 kB/s) 67s Reading package lists... 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Calculating upgrade... 68s The following packages will be upgraded: 68s gcc-14-base libatomic1 libgcc-s1 libstdc++6 68s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Need to get 928 kB of archives. 68s After this operation, 1024 B of additional disk space will be used. 68s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 14.2.0-9ubuntu1 [10.3 kB] 68s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-base amd64 14.2.0-9ubuntu1 [52.0 kB] 68s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 14.2.0-9ubuntu1 [788 kB] 68s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 14.2.0-9ubuntu1 [78.4 kB] 69s Fetched 928 kB in 1s (1684 kB/s) 69s (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 ... 75952 files and directories currently installed.) 69s Preparing to unpack .../libatomic1_14.2.0-9ubuntu1_amd64.deb ... 69s Unpacking libatomic1:amd64 (14.2.0-9ubuntu1) over (14.2.0-8ubuntu1) ... 69s Preparing to unpack .../gcc-14-base_14.2.0-9ubuntu1_amd64.deb ... 69s Unpacking gcc-14-base:amd64 (14.2.0-9ubuntu1) over (14.2.0-8ubuntu1) ... 69s Setting up gcc-14-base:amd64 (14.2.0-9ubuntu1) ... 69s (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 ... 75952 files and directories currently installed.) 69s Preparing to unpack .../libstdc++6_14.2.0-9ubuntu1_amd64.deb ... 69s Unpacking libstdc++6:amd64 (14.2.0-9ubuntu1) over (14.2.0-8ubuntu1) ... 69s Setting up libstdc++6:amd64 (14.2.0-9ubuntu1) ... 69s (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 ... 75952 files and directories currently installed.) 69s Preparing to unpack .../libgcc-s1_14.2.0-9ubuntu1_amd64.deb ... 69s Unpacking libgcc-s1:amd64 (14.2.0-9ubuntu1) over (14.2.0-8ubuntu1) ... 69s Setting up libgcc-s1:amd64 (14.2.0-9ubuntu1) ... 69s Setting up libatomic1:amd64 (14.2.0-9ubuntu1) ... 69s Processing triggers for libc-bin (2.40-1ubuntu3) ... 69s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s autopkgtest [09:35:50]: upgrading testbed (apt dist-upgrade and autopurge) 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 71s Starting 2 pkgProblemResolver with broken count: 0 71s Done 71s Entering ResolveByKeep 71s 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Starting pkgProblemResolver with broken count: 0 72s Starting 2 pkgProblemResolver with broken count: 0 72s Done 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s autopkgtest [09:35:55]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 75s autopkgtest [09:35:55]: @@@@@@@@@@@@@@@@@@@@ apt-source coot 83s Get:1 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (dsc) [2941 B] 83s Get:2 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (tar) [88.5 MB] 83s Get:3 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (diff) [52.5 kB] 83s gpgv: Signature made Tue Jul 30 06:28:58 2024 UTC 83s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 83s gpgv: Can't check signature: No public key 83s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.09+dfsg-2build1.dsc: no acceptable signature found 85s autopkgtest [09:36:05]: testing package coot version 1.1.09+dfsg-2build1 86s autopkgtest [09:36:06]: build not needed 106s autopkgtest [09:36:26]: test command1: preparing testbed 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Starting pkgProblemResolver with broken count: 0 108s Starting 2 pkgProblemResolver with broken count: 0 108s Done 108s The following NEW packages will be installed: 108s adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend 108s dconf-service fontconfig fontconfig-config fonts-freefont-ttf 108s fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 108s gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 108s gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme libamd-comgr2 108s libamdhip64-5 libasound2-data libasound2t64 libblas3 108s libboost-iostreams1.83.0 libboost-numpy1.83.0 libboost-python1.83.0 108s libboost-serialization1.83.0 libcairo-gobject2 libcairo-script-interpreter2 108s libcairo2 libccp4-data libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev 108s libcootapi1.1 libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1 108s libdeflate0 libepoxy0 libevent-pthreads-2.1-7t64 libfabric1 libfontconfig1 108s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgles2 libglvnd0 108s libgomp1 libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 libgtk-4-1 108s libgtk-4-common libharfbuzz-gobject0 libharfbuzz-subset0 libharfbuzz0b 108s libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 108s libibumad3 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 108s libllvm17t64 libmaeparser1 libmmdb2-0 libmunge2 libogg0 libopenmpi3t64 108s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 108s libpciaccess0 libpixman-1-0 libpmix2t64 libpsm-infinipath1 libpsm2-2 108s librdkit1t64 librdmacm1t64 libsharpyuv0 libssm2 libthai-data libthai0 108s libtiff6 libucx0 libvorbis0a libvorbisfile3 libvulkan1 libwayland-client0 108s libwayland-egl1 libwebp7 libxcb-render0 libxcb-shm0 libxcursor1 libxdamage1 108s libxfixes3 libxft2 libxi6 libxinerama1 libxnvctrl0 libxrandr2 libxrender1 108s ocl-icd-libopencl1 python3-numpy python3-rdkit rdkit-data refmac-dictionary 108s sfftw2 ttf-bitstream-vera ubuntu-mono 108s 0 upgraded, 122 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 171 MB of archives. 108s After this operation, 865 MB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [7888 B] 108s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 108s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 108s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 108s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 108s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 108s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [147 kB] 108s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 gtk-update-icon-cache amd64 4.16.5+ds-2 [52.5 kB] 108s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 hicolor-icon-theme all 0.18-1 [13.5 kB] 108s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 humanity-icon-theme all 0.6.16 [1282 kB] 108s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-mono all 24.04-0ubuntu1 [151 kB] 108s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 adwaita-icon-theme all 47.0-2 [525 kB] 108s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-noto-mono all 20201225-2 [435 kB] 108s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-noto-core all 20201225-2 [13.3 MB] 109s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 ttf-bitstream-vera all 1.10-8.2 [244 kB] 109s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 coot-data all 1.1.09+dfsg-2build1 [11.8 MB] 109s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB] 110s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 111s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 111s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 111s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 111s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 111s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 111s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 111s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-gobject2 amd64 1.18.2-2 [127 kB] 111s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-freedesktop amd64 1.82.0-2 [64.3 kB] 111s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-gdkpixbuf-2.0 amd64 2.42.12+dfsg-1 [9438 B] 111s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphene-1.0-0 amd64 1.10.8-4 [46.0 kB] 111s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-graphene-1.0 amd64 1.10.8-4 [11.1 kB] 111s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 111s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 111s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz-gobject0 amd64 10.0.1-1 [34.6 kB] 111s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-harfbuzz-0.0 amd64 10.0.1-1 [45.3 kB] 111s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 111s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 111s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 111s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 111s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [252 kB] 111s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [51.6 kB] 111s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [29.1 kB] 111s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 111s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoxft-1.0-0 amd64 1.54.0+ds-3 [21.1 kB] 111s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-pango-1.0 amd64 1.54.0+ds-3 [34.5 kB] 111s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo-script-interpreter2 amd64 1.18.2-2 [60.4 kB] 111s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libcpdb2t64 amd64 2.0~b5-1.2build1 [25.8 kB] 111s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libcpdb-frontend2t64 amd64 2.0~b5-1.2build1 [19.8 kB] 111s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 111s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz-subset0 amd64 10.0.1-1 [548 kB] 111s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libvulkan1 amd64 1.3.296.0-1 [143 kB] 111s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-client0 amd64 1.23.0-1 [27.1 kB] 111s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libwayland-egl1 amd64 1.23.0-1 [5662 B] 111s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 111s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcursor1 amd64 1:1.2.2-1 [20.9 kB] 111s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 111s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 111s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 111s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 111s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB] 111s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libgles2 amd64 1.7.0-1build1 [17.1 kB] 111s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libdconf1 amd64 0.40.0-4build2 [39.4 kB] 111s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-service amd64 0.40.0-4build2 [27.5 kB] 111s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 dconf-gsettings-backend amd64 0.40.0-4build2 [22.1 kB] 111s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-4-common all 4.16.5+ds-2 [1244 kB] 111s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libgtk-4-1 amd64 4.16.5+ds-2 [3635 kB] 111s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-gtk-4.0 amd64 4.16.5+ds-2 [214 kB] 111s Get:69 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 rdkit-data all 202409.2-2 [12.6 MB] 111s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 111s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-9ubuntu1 [909 kB] 111s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 111s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 111s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-python1.83.0 amd64 1.83.0-3.2ubuntu2 [312 kB] 111s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-numpy1.83.0 amd64 1.83.0-3.2ubuntu2 [242 kB] 112s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 libboost-serialization1.83.0 amd64 1.83.0-3.2ubuntu2 [343 kB] 112s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcoordgen3 amd64 3.0.2-1 [215 kB] 112s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-3.2ubuntu2 [260 kB] 112s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 libinchi1.07 amd64 1.07.1+dfsg-5 [701 kB] 112s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmaeparser1 amd64 1.3.1-1build1 [90.2 kB] 112s Get:81 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 librdkit1t64 amd64 202409.2-2 [6017 kB] 112s Get:82 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-rdkit amd64 202409.2-2 [4825 kB] 112s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 refmac-dictionary all 5.41-3 [16.7 MB] 114s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2-data all 1.2.12-1 [21.0 kB] 114s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libasound2t64 amd64 1.2.12-1 [394 kB] 114s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4-data all 8.0.0-4 [65.2 kB] 114s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 libccp4c0t64 amd64 8.0.0-4 [104 kB] 114s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmmdb2-0 amd64 2.0.22-1 [363 kB] 114s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 114s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 114s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 114s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 52.0-2ubuntu1 [70.8 kB] 114s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3ubuntu1 [658 kB] 114s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.11.2-1 [193 kB] 114s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.15-4build1 [14.7 kB] 114s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 114s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 114s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 114s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.11.2-1 [16.0 kB] 114s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.4-1 [723 kB] 114s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-18 [26.0 MB] 115s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 116s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 116s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 116s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 116s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-9ubuntu1 [148 kB] 116s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 52.0-2ubuntu1 [29.0 kB] 116s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 52.0-2ubuntu1 [42.6 kB] 116s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.17.0+ds-3build1 [1162 kB] 116s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmpi3t64 amd64 4.1.6-13.3ubuntu2 [2575 kB] 116s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 sfftw2 amd64 2.1.5-7 [224 kB] 116s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 libclipper2 amd64 2.1.20201109-2build1 [1188 kB] 116s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgslcblas0 amd64 2.8+dfsg-5 [290 kB] 116s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgsl28 amd64 2.8+dfsg-5 [1285 kB] 116s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssm2 amd64 1.4.0-2build1 [87.7 kB] 116s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcootapi1.1 amd64 1.1.09+dfsg-2build1 [3416 kB] 117s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libogg0 amd64 1.3.5-3build1 [22.7 kB] 117s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libvorbis0a amd64 1.3.7-2 [98.4 kB] 117s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libvorbisfile3 amd64 1.3.7-2 [17.1 kB] 117s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 coot amd64 1.1.09+dfsg-2build1 [8370 kB] 117s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 coot-doc all 1.1.09+dfsg-2build1 [2048 kB] 117s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcootapi-dev amd64 1.1.09+dfsg-2build1 [23.8 kB] 117s Fetched 171 MB in 9s (18.5 MB/s) 117s Selecting previously unselected package libgdk-pixbuf2.0-common. 117s (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 ... 75952 files and directories currently installed.) 117s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ... 117s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... 117s Selecting previously unselected package libjpeg-turbo8:amd64. 117s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 117s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 117s Selecting previously unselected package libjpeg8:amd64. 117s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_amd64.deb ... 117s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 117s Selecting previously unselected package libdeflate0:amd64. 117s Preparing to unpack .../003-libdeflate0_1.22-1_amd64.deb ... 117s Unpacking libdeflate0:amd64 (1.22-1) ... 117s Selecting previously unselected package libjbig0:amd64. 117s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 117s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 117s Selecting previously unselected package liblerc4:amd64. 117s Preparing to unpack .../005-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 117s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 117s Selecting previously unselected package libsharpyuv0:amd64. 117s Preparing to unpack .../006-libsharpyuv0_1.4.0-0.1_amd64.deb ... 117s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 117s Selecting previously unselected package libwebp7:amd64. 117s Preparing to unpack .../007-libwebp7_1.4.0-0.1_amd64.deb ... 117s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 118s Selecting previously unselected package libtiff6:amd64. 118s Preparing to unpack .../008-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 118s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 118s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 118s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_amd64.deb ... 118s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... 118s Selecting previously unselected package gtk-update-icon-cache. 118s Preparing to unpack .../010-gtk-update-icon-cache_4.16.5+ds-2_amd64.deb ... 118s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 118s No diversion 'diversion of /usr/share/man/man8/update-icon-caches.8.gz to /usr/share/man/man8/update-icon-caches.gtk2.8.gz by libgtk-3-bin', none removed. 118s Unpacking gtk-update-icon-cache (4.16.5+ds-2) ... 118s Selecting previously unselected package hicolor-icon-theme. 118s Preparing to unpack .../011-hicolor-icon-theme_0.18-1_all.deb ... 118s Unpacking hicolor-icon-theme (0.18-1) ... 118s Selecting previously unselected package humanity-icon-theme. 118s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ... 118s Unpacking humanity-icon-theme (0.6.16) ... 119s Selecting previously unselected package ubuntu-mono. 119s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ... 119s Unpacking ubuntu-mono (24.04-0ubuntu1) ... 119s Selecting previously unselected package adwaita-icon-theme. 119s Preparing to unpack .../014-adwaita-icon-theme_47.0-2_all.deb ... 119s Unpacking adwaita-icon-theme (47.0-2) ... 119s Selecting previously unselected package fonts-noto-mono. 119s Preparing to unpack .../015-fonts-noto-mono_20201225-2_all.deb ... 119s Unpacking fonts-noto-mono (20201225-2) ... 119s Selecting previously unselected package fonts-noto-core. 119s Preparing to unpack .../016-fonts-noto-core_20201225-2_all.deb ... 119s Unpacking fonts-noto-core (20201225-2) ... 119s Selecting previously unselected package ttf-bitstream-vera. 119s Preparing to unpack .../017-ttf-bitstream-vera_1.10-8.2_all.deb ... 119s Unpacking ttf-bitstream-vera (1.10-8.2) ... 119s Selecting previously unselected package coot-data. 119s Preparing to unpack .../018-coot-data_1.1.09+dfsg-2build1_all.deb ... 119s Unpacking coot-data (1.1.09+dfsg-2build1) ... 120s Selecting previously unselected package fonts-freefont-ttf. 120s Preparing to unpack .../019-fonts-freefont-ttf_20211204+svn4273-2_all.deb ... 120s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ... 120s Selecting previously unselected package fontconfig-config. 120s Preparing to unpack .../020-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 120s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 120s Selecting previously unselected package libfontconfig1:amd64. 120s Preparing to unpack .../021-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 120s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 120s Selecting previously unselected package libpixman-1-0:amd64. 120s Preparing to unpack .../022-libpixman-1-0_0.44.0-3_amd64.deb ... 120s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 120s Selecting previously unselected package libxcb-render0:amd64. 120s Preparing to unpack .../023-libxcb-render0_1.17.0-2_amd64.deb ... 120s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 120s Selecting previously unselected package libxcb-shm0:amd64. 120s Preparing to unpack .../024-libxcb-shm0_1.17.0-2_amd64.deb ... 120s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 120s Selecting previously unselected package libxrender1:amd64. 120s Preparing to unpack .../025-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 120s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 120s Selecting previously unselected package libcairo2:amd64. 120s Preparing to unpack .../026-libcairo2_1.18.2-2_amd64.deb ... 120s Unpacking libcairo2:amd64 (1.18.2-2) ... 120s Selecting previously unselected package libcairo-gobject2:amd64. 120s Preparing to unpack .../027-libcairo-gobject2_1.18.2-2_amd64.deb ... 120s Unpacking libcairo-gobject2:amd64 (1.18.2-2) ... 120s Selecting previously unselected package gir1.2-freedesktop:amd64. 120s Preparing to unpack .../028-gir1.2-freedesktop_1.82.0-2_amd64.deb ... 120s Unpacking gir1.2-freedesktop:amd64 (1.82.0-2) ... 120s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:amd64. 120s Preparing to unpack .../029-gir1.2-gdkpixbuf-2.0_2.42.12+dfsg-1_amd64.deb ... 120s Unpacking gir1.2-gdkpixbuf-2.0:amd64 (2.42.12+dfsg-1) ... 120s Selecting previously unselected package libgraphene-1.0-0:amd64. 120s Preparing to unpack .../030-libgraphene-1.0-0_1.10.8-4_amd64.deb ... 120s Unpacking libgraphene-1.0-0:amd64 (1.10.8-4) ... 120s Selecting previously unselected package gir1.2-graphene-1.0:amd64. 120s Preparing to unpack .../031-gir1.2-graphene-1.0_1.10.8-4_amd64.deb ... 120s Unpacking gir1.2-graphene-1.0:amd64 (1.10.8-4) ... 120s Selecting previously unselected package libgraphite2-3:amd64. 120s Preparing to unpack .../032-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 120s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 120s Selecting previously unselected package libharfbuzz0b:amd64. 120s Preparing to unpack .../033-libharfbuzz0b_10.0.1-1_amd64.deb ... 120s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 120s Selecting previously unselected package libharfbuzz-gobject0:amd64. 120s Preparing to unpack .../034-libharfbuzz-gobject0_10.0.1-1_amd64.deb ... 120s Unpacking libharfbuzz-gobject0:amd64 (10.0.1-1) ... 120s Selecting previously unselected package gir1.2-harfbuzz-0.0:amd64. 120s Preparing to unpack .../035-gir1.2-harfbuzz-0.0_10.0.1-1_amd64.deb ... 120s Unpacking gir1.2-harfbuzz-0.0:amd64 (10.0.1-1) ... 120s Selecting previously unselected package fontconfig. 121s Preparing to unpack .../036-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ... 121s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 121s Selecting previously unselected package libthai-data. 121s Preparing to unpack .../037-libthai-data_0.1.29-2build1_all.deb ... 121s Unpacking libthai-data (0.1.29-2build1) ... 121s Selecting previously unselected package libdatrie1:amd64. 121s Preparing to unpack .../038-libdatrie1_0.2.13-3build1_amd64.deb ... 121s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 121s Selecting previously unselected package libthai0:amd64. 121s Preparing to unpack .../039-libthai0_0.1.29-2build1_amd64.deb ... 121s Unpacking libthai0:amd64 (0.1.29-2build1) ... 121s Selecting previously unselected package libpango-1.0-0:amd64. 121s Preparing to unpack .../040-libpango-1.0-0_1.54.0+ds-3_amd64.deb ... 121s Unpacking libpango-1.0-0:amd64 (1.54.0+ds-3) ... 121s Selecting previously unselected package libpangoft2-1.0-0:amd64. 121s Preparing to unpack .../041-libpangoft2-1.0-0_1.54.0+ds-3_amd64.deb ... 121s Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... 121s Selecting previously unselected package libpangocairo-1.0-0:amd64. 121s Preparing to unpack .../042-libpangocairo-1.0-0_1.54.0+ds-3_amd64.deb ... 121s Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... 121s Selecting previously unselected package libxft2:amd64. 121s Preparing to unpack .../043-libxft2_2.3.6-1build1_amd64.deb ... 121s Unpacking libxft2:amd64 (2.3.6-1build1) ... 121s Selecting previously unselected package libpangoxft-1.0-0:amd64. 121s Preparing to unpack .../044-libpangoxft-1.0-0_1.54.0+ds-3_amd64.deb ... 121s Unpacking libpangoxft-1.0-0:amd64 (1.54.0+ds-3) ... 121s Selecting previously unselected package gir1.2-pango-1.0:amd64. 121s Preparing to unpack .../045-gir1.2-pango-1.0_1.54.0+ds-3_amd64.deb ... 121s Unpacking gir1.2-pango-1.0:amd64 (1.54.0+ds-3) ... 121s Selecting previously unselected package libcairo-script-interpreter2:amd64. 121s Preparing to unpack .../046-libcairo-script-interpreter2_1.18.2-2_amd64.deb ... 121s Unpacking libcairo-script-interpreter2:amd64 (1.18.2-2) ... 121s Selecting previously unselected package libcpdb2t64:amd64. 121s Preparing to unpack .../047-libcpdb2t64_2.0~b5-1.2build1_amd64.deb ... 121s Unpacking libcpdb2t64:amd64 (2.0~b5-1.2build1) ... 121s Selecting previously unselected package libcpdb-frontend2t64:amd64. 121s Preparing to unpack .../048-libcpdb-frontend2t64_2.0~b5-1.2build1_amd64.deb ... 121s Unpacking libcpdb-frontend2t64:amd64 (2.0~b5-1.2build1) ... 121s Selecting previously unselected package libepoxy0:amd64. 121s Preparing to unpack .../049-libepoxy0_1.5.10-2_amd64.deb ... 121s Unpacking libepoxy0:amd64 (1.5.10-2) ... 121s Selecting previously unselected package libharfbuzz-subset0:amd64. 121s Preparing to unpack .../050-libharfbuzz-subset0_10.0.1-1_amd64.deb ... 121s Unpacking libharfbuzz-subset0:amd64 (10.0.1-1) ... 121s Selecting previously unselected package libvulkan1:amd64. 121s Preparing to unpack .../051-libvulkan1_1.3.296.0-1_amd64.deb ... 121s Unpacking libvulkan1:amd64 (1.3.296.0-1) ... 121s Selecting previously unselected package libwayland-client0:amd64. 121s Preparing to unpack .../052-libwayland-client0_1.23.0-1_amd64.deb ... 121s Unpacking libwayland-client0:amd64 (1.23.0-1) ... 121s Selecting previously unselected package libwayland-egl1:amd64. 121s Preparing to unpack .../053-libwayland-egl1_1.23.0-1_amd64.deb ... 121s Unpacking libwayland-egl1:amd64 (1.23.0-1) ... 121s Selecting previously unselected package libxfixes3:amd64. 121s Preparing to unpack .../054-libxfixes3_1%3a6.0.0-2build1_amd64.deb ... 121s Unpacking libxfixes3:amd64 (1:6.0.0-2build1) ... 121s Selecting previously unselected package libxcursor1:amd64. 121s Preparing to unpack .../055-libxcursor1_1%3a1.2.2-1_amd64.deb ... 121s Unpacking libxcursor1:amd64 (1:1.2.2-1) ... 121s Selecting previously unselected package libxdamage1:amd64. 121s Preparing to unpack .../056-libxdamage1_1%3a1.1.6-1build1_amd64.deb ... 121s Unpacking libxdamage1:amd64 (1:1.1.6-1build1) ... 121s Selecting previously unselected package libxi6:amd64. 121s Preparing to unpack .../057-libxi6_2%3a1.8.2-1_amd64.deb ... 121s Unpacking libxi6:amd64 (2:1.8.2-1) ... 121s Selecting previously unselected package libxinerama1:amd64. 121s Preparing to unpack .../058-libxinerama1_2%3a1.1.4-3build1_amd64.deb ... 121s Unpacking libxinerama1:amd64 (2:1.1.4-3build1) ... 121s Selecting previously unselected package libxrandr2:amd64. 121s Preparing to unpack .../059-libxrandr2_2%3a1.5.4-1_amd64.deb ... 121s Unpacking libxrandr2:amd64 (2:1.5.4-1) ... 121s Selecting previously unselected package libglvnd0:amd64. 121s Preparing to unpack .../060-libglvnd0_1.7.0-1build1_amd64.deb ... 121s Unpacking libglvnd0:amd64 (1.7.0-1build1) ... 121s Selecting previously unselected package libgles2:amd64. 121s Preparing to unpack .../061-libgles2_1.7.0-1build1_amd64.deb ... 121s Unpacking libgles2:amd64 (1.7.0-1build1) ... 121s Selecting previously unselected package libdconf1:amd64. 121s Preparing to unpack .../062-libdconf1_0.40.0-4build2_amd64.deb ... 121s Unpacking libdconf1:amd64 (0.40.0-4build2) ... 121s Selecting previously unselected package dconf-service. 121s Preparing to unpack .../063-dconf-service_0.40.0-4build2_amd64.deb ... 121s Unpacking dconf-service (0.40.0-4build2) ... 122s Selecting previously unselected package dconf-gsettings-backend:amd64. 122s Preparing to unpack .../064-dconf-gsettings-backend_0.40.0-4build2_amd64.deb ... 122s Unpacking dconf-gsettings-backend:amd64 (0.40.0-4build2) ... 122s Selecting previously unselected package libgtk-4-common. 122s Preparing to unpack .../065-libgtk-4-common_4.16.5+ds-2_all.deb ... 122s Unpacking libgtk-4-common (4.16.5+ds-2) ... 122s Selecting previously unselected package libgtk-4-1:amd64. 122s Preparing to unpack .../066-libgtk-4-1_4.16.5+ds-2_amd64.deb ... 122s Unpacking libgtk-4-1:amd64 (4.16.5+ds-2) ... 122s Selecting previously unselected package gir1.2-gtk-4.0:amd64. 122s Preparing to unpack .../067-gir1.2-gtk-4.0_4.16.5+ds-2_amd64.deb ... 122s Unpacking gir1.2-gtk-4.0:amd64 (4.16.5+ds-2) ... 122s Selecting previously unselected package rdkit-data. 122s Preparing to unpack .../068-rdkit-data_202409.2-2_all.deb ... 122s Unpacking rdkit-data (202409.2-2) ... 122s Selecting previously unselected package libblas3:amd64. 122s Preparing to unpack .../069-libblas3_3.12.0-4_amd64.deb ... 122s Unpacking libblas3:amd64 (3.12.0-4) ... 122s Selecting previously unselected package libgfortran5:amd64. 122s Preparing to unpack .../070-libgfortran5_14.2.0-9ubuntu1_amd64.deb ... 122s Unpacking libgfortran5:amd64 (14.2.0-9ubuntu1) ... 122s Selecting previously unselected package liblapack3:amd64. 122s Preparing to unpack .../071-liblapack3_3.12.0-4_amd64.deb ... 122s Unpacking liblapack3:amd64 (3.12.0-4) ... 122s Selecting previously unselected package python3-numpy. 122s Preparing to unpack .../072-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 122s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 122s Selecting previously unselected package libboost-python1.83.0. 122s Preparing to unpack .../073-libboost-python1.83.0_1.83.0-3.2ubuntu2_amd64.deb ... 122s Unpacking libboost-python1.83.0 (1.83.0-3.2ubuntu2) ... 122s Selecting previously unselected package libboost-numpy1.83.0. 122s Preparing to unpack .../074-libboost-numpy1.83.0_1.83.0-3.2ubuntu2_amd64.deb ... 122s Unpacking libboost-numpy1.83.0 (1.83.0-3.2ubuntu2) ... 122s Selecting previously unselected package libboost-serialization1.83.0:amd64. 122s Preparing to unpack .../075-libboost-serialization1.83.0_1.83.0-3.2ubuntu2_amd64.deb ... 122s Unpacking libboost-serialization1.83.0:amd64 (1.83.0-3.2ubuntu2) ... 122s Selecting previously unselected package libcoordgen3:amd64. 122s Preparing to unpack .../076-libcoordgen3_3.0.2-1_amd64.deb ... 122s Unpacking libcoordgen3:amd64 (3.0.2-1) ... 122s Selecting previously unselected package libboost-iostreams1.83.0:amd64. 122s Preparing to unpack .../077-libboost-iostreams1.83.0_1.83.0-3.2ubuntu2_amd64.deb ... 122s Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-3.2ubuntu2) ... 122s Selecting previously unselected package libinchi1.07. 122s Preparing to unpack .../078-libinchi1.07_1.07.1+dfsg-5_amd64.deb ... 122s Unpacking libinchi1.07 (1.07.1+dfsg-5) ... 122s Selecting previously unselected package libmaeparser1:amd64. 122s Preparing to unpack .../079-libmaeparser1_1.3.1-1build1_amd64.deb ... 122s Unpacking libmaeparser1:amd64 (1.3.1-1build1) ... 122s Selecting previously unselected package librdkit1t64. 122s Preparing to unpack .../080-librdkit1t64_202409.2-2_amd64.deb ... 122s Unpacking librdkit1t64 (202409.2-2) ... 123s Selecting previously unselected package python3-rdkit. 123s Preparing to unpack .../081-python3-rdkit_202409.2-2_amd64.deb ... 123s Unpacking python3-rdkit (202409.2-2) ... 123s Selecting previously unselected package refmac-dictionary. 123s Preparing to unpack .../082-refmac-dictionary_5.41-3_all.deb ... 123s Unpacking refmac-dictionary (5.41-3) ... 125s Selecting previously unselected package libasound2-data. 125s Preparing to unpack .../083-libasound2-data_1.2.12-1_all.deb ... 125s Unpacking libasound2-data (1.2.12-1) ... 125s Selecting previously unselected package libasound2t64:amd64. 125s Preparing to unpack .../084-libasound2t64_1.2.12-1_amd64.deb ... 125s Unpacking libasound2t64:amd64 (1.2.12-1) ... 125s Selecting previously unselected package libccp4-data. 125s Preparing to unpack .../085-libccp4-data_8.0.0-4_all.deb ... 125s Unpacking libccp4-data (8.0.0-4) ... 125s Selecting previously unselected package libccp4c0t64:amd64. 125s Preparing to unpack .../086-libccp4c0t64_8.0.0-4_amd64.deb ... 125s Unpacking libccp4c0t64:amd64 (8.0.0-4) ... 125s Selecting previously unselected package libmmdb2-0:amd64. 125s Preparing to unpack .../087-libmmdb2-0_2.0.22-1_amd64.deb ... 125s Unpacking libmmdb2-0:amd64 (2.0.22-1) ... 125s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 125s Preparing to unpack .../088-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 125s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 125s Selecting previously unselected package libpsm-infinipath1. 125s Preparing to unpack .../089-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 125s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 125s Selecting previously unselected package libpsm2-2. 125s Preparing to unpack .../090-libpsm2-2_11.2.185-2.1_amd64.deb ... 125s Unpacking libpsm2-2 (11.2.185-2.1) ... 125s Selecting previously unselected package librdmacm1t64:amd64. 125s Preparing to unpack .../091-librdmacm1t64_52.0-2ubuntu1_amd64.deb ... 125s Unpacking librdmacm1t64:amd64 (52.0-2ubuntu1) ... 125s Selecting previously unselected package libfabric1:amd64. 125s Preparing to unpack .../092-libfabric1_1.17.0-3ubuntu1_amd64.deb ... 125s Unpacking libfabric1:amd64 (1.17.0-3ubuntu1) ... 125s Selecting previously unselected package libhwloc15:amd64. 125s Preparing to unpack .../093-libhwloc15_2.11.2-1_amd64.deb ... 125s Unpacking libhwloc15:amd64 (2.11.2-1) ... 125s Selecting previously unselected package libmunge2:amd64. 125s Preparing to unpack .../094-libmunge2_0.5.15-4build1_amd64.deb ... 125s Unpacking libmunge2:amd64 (0.5.15-4build1) ... 125s Selecting previously unselected package libpciaccess0:amd64. 125s Preparing to unpack .../095-libpciaccess0_0.17-3build1_amd64.deb ... 125s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 125s Selecting previously unselected package libxnvctrl0:amd64. 125s Preparing to unpack .../096-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 125s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 125s Selecting previously unselected package ocl-icd-libopencl1:amd64. 125s Preparing to unpack .../097-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 125s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 125s Selecting previously unselected package libhwloc-plugins:amd64. 125s Preparing to unpack .../098-libhwloc-plugins_2.11.2-1_amd64.deb ... 125s Unpacking libhwloc-plugins:amd64 (2.11.2-1) ... 125s Selecting previously unselected package libpmix2t64:amd64. 125s Preparing to unpack .../099-libpmix2t64_5.0.4-1_amd64.deb ... 125s Unpacking libpmix2t64:amd64 (5.0.4-1) ... 125s Selecting previously unselected package libllvm17t64:amd64. 125s Preparing to unpack .../100-libllvm17t64_1%3a17.0.6-18_amd64.deb ... 125s Unpacking libllvm17t64:amd64 (1:17.0.6-18) ... 126s Selecting previously unselected package libamd-comgr2:amd64. 126s Preparing to unpack .../101-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 126s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 126s Selecting previously unselected package libhsakmt1:amd64. 126s Preparing to unpack .../102-libhsakmt1_5.7.0-1build1_amd64.deb ... 126s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 126s Selecting previously unselected package libhsa-runtime64-1. 126s Preparing to unpack .../103-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 126s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 126s Selecting previously unselected package libamdhip64-5. 126s Preparing to unpack .../104-libamdhip64-5_5.7.1-5_amd64.deb ... 126s Unpacking libamdhip64-5 (5.7.1-5) ... 126s Selecting previously unselected package libgomp1:amd64. 126s Preparing to unpack .../105-libgomp1_14.2.0-9ubuntu1_amd64.deb ... 126s Unpacking libgomp1:amd64 (14.2.0-9ubuntu1) ... 126s Selecting previously unselected package libibumad3:amd64. 126s Preparing to unpack .../106-libibumad3_52.0-2ubuntu1_amd64.deb ... 126s Unpacking libibumad3:amd64 (52.0-2ubuntu1) ... 126s Selecting previously unselected package libibmad5:amd64. 126s Preparing to unpack .../107-libibmad5_52.0-2ubuntu1_amd64.deb ... 126s Unpacking libibmad5:amd64 (52.0-2ubuntu1) ... 126s Selecting previously unselected package libucx0:amd64. 126s Preparing to unpack .../108-libucx0_1.17.0+ds-3build1_amd64.deb ... 126s Unpacking libucx0:amd64 (1.17.0+ds-3build1) ... 126s Selecting previously unselected package libopenmpi3t64:amd64. 127s Preparing to unpack .../109-libopenmpi3t64_4.1.6-13.3ubuntu2_amd64.deb ... 127s Unpacking libopenmpi3t64:amd64 (4.1.6-13.3ubuntu2) ... 127s Selecting previously unselected package sfftw2. 127s Preparing to unpack .../110-sfftw2_2.1.5-7_amd64.deb ... 127s Unpacking sfftw2 (2.1.5-7) ... 127s Selecting previously unselected package libclipper2:amd64. 127s Preparing to unpack .../111-libclipper2_2.1.20201109-2build1_amd64.deb ... 127s Unpacking libclipper2:amd64 (2.1.20201109-2build1) ... 127s Selecting previously unselected package libgslcblas0:amd64. 127s Preparing to unpack .../112-libgslcblas0_2.8+dfsg-5_amd64.deb ... 127s Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... 127s Selecting previously unselected package libgsl28:amd64. 127s Preparing to unpack .../113-libgsl28_2.8+dfsg-5_amd64.deb ... 127s Unpacking libgsl28:amd64 (2.8+dfsg-5) ... 127s Selecting previously unselected package libssm2:amd64. 127s Preparing to unpack .../114-libssm2_1.4.0-2build1_amd64.deb ... 127s Unpacking libssm2:amd64 (1.4.0-2build1) ... 127s Selecting previously unselected package libcootapi1.1. 127s Preparing to unpack .../115-libcootapi1.1_1.1.09+dfsg-2build1_amd64.deb ... 127s Unpacking libcootapi1.1 (1.1.09+dfsg-2build1) ... 127s Selecting previously unselected package libogg0:amd64. 127s Preparing to unpack .../116-libogg0_1.3.5-3build1_amd64.deb ... 127s Unpacking libogg0:amd64 (1.3.5-3build1) ... 127s Selecting previously unselected package libvorbis0a:amd64. 127s Preparing to unpack .../117-libvorbis0a_1.3.7-2_amd64.deb ... 127s Unpacking libvorbis0a:amd64 (1.3.7-2) ... 127s Selecting previously unselected package libvorbisfile3:amd64. 127s Preparing to unpack .../118-libvorbisfile3_1.3.7-2_amd64.deb ... 127s Unpacking libvorbisfile3:amd64 (1.3.7-2) ... 127s Selecting previously unselected package coot. 127s Preparing to unpack .../119-coot_1.1.09+dfsg-2build1_amd64.deb ... 127s Unpacking coot (1.1.09+dfsg-2build1) ... 127s Selecting previously unselected package coot-doc. 127s Preparing to unpack .../120-coot-doc_1.1.09+dfsg-2build1_all.deb ... 127s Unpacking coot-doc (1.1.09+dfsg-2build1) ... 127s Selecting previously unselected package libcootapi-dev. 127s Preparing to unpack .../121-libcootapi-dev_1.1.09+dfsg-2build1_amd64.deb ... 127s Unpacking libcootapi-dev (1.1.09+dfsg-2build1) ... 127s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 127s Setting up libboost-python1.83.0 (1.83.0-3.2ubuntu2) ... 127s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 127s Setting up coot-doc (1.1.09+dfsg-2build1) ... 127s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 127s Setting up libpciaccess0:amd64 (0.17-3build1) ... 127s Setting up ttf-bitstream-vera (1.10-8.2) ... 127s Setting up libxdamage1:amd64 (1:1.1.6-1build1) ... 127s Setting up libogg0:amd64 (1.3.5-3build1) ... 127s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 127s Setting up fonts-noto-mono (20201225-2) ... 127s Setting up hicolor-icon-theme (0.18-1) ... 127s Setting up libxi6:amd64 (2:1.8.2-1) ... 127s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 127s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 127s Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... 127s Setting up libmmdb2-0:amd64 (2.0.22-1) ... 127s Setting up libxcb-render0:amd64 (1.17.0-2) ... 127s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 127s Setting up libglvnd0:amd64 (1.7.0-1build1) ... 127s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... 127s Setting up libibumad3:amd64 (52.0-2ubuntu1) ... 127s Setting up libdeflate0:amd64 (1.22-1) ... 127s Setting up fonts-freefont-ttf (20211204+svn4273-2) ... 127s Setting up libcpdb2t64:amd64 (2.0~b5-1.2build1) ... 127s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 127s Setting up libibmad5:amd64 (52.0-2ubuntu1) ... 127s Setting up libcpdb-frontend2t64:amd64 (2.0~b5-1.2build1) ... 127s Setting up libccp4-data (8.0.0-4) ... 127s Setting up libgomp1:amd64 (14.2.0-9ubuntu1) ... 127s Setting up rdkit-data (202409.2-2) ... 127s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 127s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 127s Setting up refmac-dictionary (5.41-3) ... 127s Setting up libdconf1:amd64 (0.40.0-4build2) ... 127s Setting up libasound2-data (1.2.12-1) ... 127s Setting up libboost-serialization1.83.0:amd64 (1.83.0-3.2ubuntu2) ... 127s Setting up libboost-numpy1.83.0 (1.83.0-3.2ubuntu2) ... 127s Setting up libblas3:amd64 (3.12.0-4) ... 127s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 127s Setting up libgles2:amd64 (1.7.0-1build1) ... 127s Setting up libasound2t64:amd64 (1.2.12-1) ... 127s Setting up libmunge2:amd64 (0.5.15-4build1) ... 127s Setting up libllvm17t64:amd64 (1:17.0.6-18) ... 127s Setting up libepoxy0:amd64 (1.5.10-2) ... 127s Setting up libxfixes3:amd64 (1:6.0.0-2build1) ... 127s Setting up libboost-iostreams1.83.0:amd64 (1.83.0-3.2ubuntu2) ... 127s Setting up libxinerama1:amd64 (2:1.1.4-3build1) ... 127s Setting up libhwloc15:amd64 (2.11.2-1) ... 127s Setting up libvorbis0a:amd64 (1.3.7-2) ... 127s Setting up libxrandr2:amd64 (2:1.5.4-1) ... 127s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 127s Setting up libgfortran5:amd64 (14.2.0-9ubuntu1) ... 127s Setting up libvulkan1:amd64 (1.3.296.0-1) ... 127s Setting up libwebp7:amd64 (1.4.0-0.1) ... 127s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 127s Setting up libccp4c0t64:amd64 (8.0.0-4) ... 127s Setting up libpsm2-2 (11.2.185-2.1) ... 127s Setting up librdmacm1t64:amd64 (52.0-2ubuntu1) ... 127s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 127s Setting up libthai-data (0.1.29-2build1) ... 127s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 127s Setting up libwayland-egl1:amd64 (1.23.0-1) ... 127s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 127s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 127s Setting up libcoordgen3:amd64 (3.0.2-1) ... 127s Setting up libgsl28:amd64 (2.8+dfsg-5) ... 127s Setting up libinchi1.07 (1.07.1+dfsg-5) ... 127s Setting up fonts-noto-core (20201225-2) ... 127s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 127s Setting up libgraphene-1.0-0:amd64 (1.10.8-4) ... 127s Setting up libwayland-client0:amd64 (1.23.0-1) ... 127s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 127s Setting up gir1.2-graphene-1.0:amd64 (1.10.8-4) ... 127s Setting up libfabric1:amd64 (1.17.0-3ubuntu1) ... 127s Setting up liblapack3:amd64 (3.12.0-4) ... 127s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 127s Setting up libssm2:amd64 (1.4.0-2build1) ... 127s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 127s Setting up libxcursor1:amd64 (1:1.2.2-1) ... 127s Setting up dconf-service (0.40.0-4build2) ... 127s Setting up libharfbuzz-gobject0:amd64 (10.0.1-1) ... 127s Setting up libhwloc-plugins:amd64 (2.11.2-1) ... 127s Setting up libmaeparser1:amd64 (1.3.1-1build1) ... 127s Setting up libthai0:amd64 (0.1.29-2build1) ... 127s Setting up libvorbisfile3:amd64 (1.3.7-2) ... 127s Setting up libpmix2t64:amd64 (5.0.4-1) ... 127s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 129s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 129s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 129s Setting up libharfbuzz-subset0:amd64 (10.0.1-1) ... 129s Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... 129s Setting up coot-data (1.1.09+dfsg-2build1) ... 129s Setting up gtk-update-icon-cache (4.16.5+ds-2) ... 129s Setting up dconf-gsettings-backend:amd64 (0.40.0-4build2) ... 129s Setting up gir1.2-gdkpixbuf-2.0:amd64 (2.42.12+dfsg-1) ... 129s Setting up libamdhip64-5 (5.7.1-5) ... 129s Setting up libgtk-4-common (4.16.5+ds-2) ... 129s Setting up libucx0:amd64 (1.17.0+ds-3build1) ... 129s Setting up libopenmpi3t64:amd64 (4.1.6-13.3ubuntu2) ... 129s Setting up sfftw2 (2.1.5-7) ... 129s Setting up libclipper2:amd64 (2.1.20201109-2build1) ... 129s Setting up libcootapi1.1 (1.1.09+dfsg-2build1) ... 129s Setting up libcootapi-dev (1.1.09+dfsg-2build1) ... 129s Setting up adwaita-icon-theme (47.0-2) ... 129s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 129s Setting up humanity-icon-theme (0.6.16) ... 129s Setting up ubuntu-mono (24.04-0ubuntu1) ... 129s Processing triggers for man-db (2.13.0-1) ... 130s Processing triggers for libglib2.0-0t64:amd64 (2.82.2-3) ... 130s Processing triggers for sgml-base (1.31) ... 130s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 130s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 133s Regenerating fonts cache... done. 133s Setting up libxft2:amd64 (2.3.6-1build1) ... 133s Processing triggers for libc-bin (2.40-1ubuntu3) ... 133s Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... 133s Setting up libcairo2:amd64 (1.18.2-2) ... 133s Setting up libcairo-gobject2:amd64 (1.18.2-2) ... 133s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... 133s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... 133s Setting up libcairo-script-interpreter2:amd64 (1.18.2-2) ... 133s Setting up gir1.2-freedesktop:amd64 (1.82.0-2) ... 133s Setting up libpangoxft-1.0-0:amd64 (1.54.0+ds-3) ... 133s Setting up librdkit1t64 (202409.2-2) ... 133s Setting up gir1.2-harfbuzz-0.0:amd64 (10.0.1-1) ... 133s Setting up gir1.2-pango-1.0:amd64 (1.54.0+ds-3) ... 133s Setting up python3-rdkit (202409.2-2) ... 133s Setting up libgtk-4-1:amd64 (4.16.5+ds-2) ... 133s Setting up gir1.2-gtk-4.0:amd64 (4.16.5+ds-2) ... 133s Setting up coot (1.1.09+dfsg-2build1) ... 133s /usr/lib/python3/dist-packages/coot/tautomer.py:289: SyntaxWarning: invalid escape sequence '\C' 133s ('Remove stereochemistry from mobile double bonds', 'C/C=C\C(C)=O', {'C=C(O)C=CC', 'C=CCC(=C)O', 'CC=CC(C)=O', 'C=CCC(C)=O', 'C=CC=C(C)O'}), 133s Processing triggers for libc-bin (2.40-1ubuntu3) ... 135s autopkgtest [09:36:55]: test command1: coot --self-test 135s autopkgtest [09:36:55]: test command1: [----------------------- 135s INFO:: Running internal self tests 139s INFO:: Test Clipper core : OK 139s INFO:: Test Clipper contrib: OK 139s run_internal_tests() --------- we have 8 internal test functionns 139s Entering test: kevin's torsion test 139s PASS: kevin's torsion test 139s Entering test: test_alt_conf_rotamers 139s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 139s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 139s chis.size() 2 (should be 2) 139s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911 139s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68 139s For residue 80 chis size 1 139s residue 80 chis: -56.8781 -80.8484 139s PASS: test_alt_conf_rotamers 139s Entering test: test_fragmemt_atom_selection 139s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 139s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 139s ----------------- create_mmdbmanager_from_inverted_atom_selection() 139s n_initial: 1465 n_1: 1401 n_2: 64 139s PASS: test_fragmemt_atom_selection 139s Entering test: test_add_atom 139s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 139s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 139s PASS: test_add_atom 139s Entering test: test segid exchange 139s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 139s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 139s Test with a rogue segid 139s INFO:: No consistent segids for residue 1 139s PASS: test segid exchange 139s Entering test: test peak search non-close 139s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz 139s FFT Reso...0.444444 139s Sampling rate...1.5 139s Grid...Nuvw = ( 132, 160, 80) 139s Cell... Cell (64.897,78.323,38.792, 90, 90, 90) 139s Spacegroup...P 21 21 21 139s There are 2260 peaks and 0 problem peaks 139s PASS: test peak search non-close 139s Entering test: test symop card 139s 1 0 0 139s 0 1 0 139s 0 0 1 139s translations: -1 0 0 139s PASS: test symop card 139s Entering test: SSM sequence alignment output 139s 139s -- 139s Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG 139s Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 139s 139s Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC 139s 139s -- 139s Moving: D 139s Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 139s 139s -- 139s Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG 139s Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG 139s 139s -- 139s PASS: SSM sequence alignment output 140s autopkgtest [09:37:00]: test command1: -----------------------] 140s autopkgtest [09:37:00]: test command1: - - - - - - - - - - results - - - - - - - - - - 140s command1 PASS 140s autopkgtest [09:37:00]: test command2: preparing testbed 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Starting pkgProblemResolver with broken count: 0 141s Starting 2 pkgProblemResolver with broken count: 0 141s Done 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 143s autopkgtest [09:37:03]: test command2: pyrogen --help 143s autopkgtest [09:37:03]: test command2: [----------------------- 143s Traceback (most recent call last): 143s File "", line 198, in _run_module_as_main 143s File "", line 88, in _run_code 143s File "/usr/lib/python3/dist-packages/coot/pyrogen.py", line 38, in 143s import pyrogen_swig as pysw # relies on above rdkit.Chem import AllChem (but ideally should not) 143s ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 143s File "/usr/lib/python3/dist-packages/coot/pyrogen_swig.py", line 12, in 143s import _pyrogen_swig 143s ImportError: /usr/lib/x86_64-linux-gnu/coot/libcoot-lidia-core.so.0: undefined symbol: _ZN5RDKit9ConformerC1ERKS0_ 143s autopkgtest [09:37:03]: test command2: -----------------------] 144s autopkgtest [09:37:04]: test command2: - - - - - - - - - - results - - - - - - - - - - 144s command2 FAIL non-zero exit status 1 144s autopkgtest [09:37:04]: test command2: - - - - - - - - - - stderr - - - - - - - - - - 144s Traceback (most recent call last): 144s File "", line 198, in _run_module_as_main 144s File "", line 88, in _run_code 144s File "/usr/lib/python3/dist-packages/coot/pyrogen.py", line 38, in 144s import pyrogen_swig as pysw # relies on above rdkit.Chem import AllChem (but ideally should not) 144s ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 144s File "/usr/lib/python3/dist-packages/coot/pyrogen_swig.py", line 12, in 144s import _pyrogen_swig 144s ImportError: /usr/lib/x86_64-linux-gnu/coot/libcoot-lidia-core.so.0: undefined symbol: _ZN5RDKit9ConformerC1ERKS0_ 144s autopkgtest [09:37:04]: @@@@@@@@@@@@@@@@@@@@ summary 144s command1 PASS 144s command2 FAIL non-zero exit status 1 170s nova [W] Skipping flock for amd64 170s Creating nova instance adt-plucky-amd64-coot-20241203-093439-juju-7f2275-prod-proposed-migration-environment-15-e7fbebe5-3e2b-472b-8295-c0ea477fc06c from image adt/ubuntu-plucky-amd64-server-20241203.img (UUID 9e8e99d5-3366-42e6-8f42-63b527e5abcc)...