0s autopkgtest [02:23:21]: starting date and time: 2024-11-28 02:23:21+0000 0s autopkgtest [02:23:21]: git checkout: 6408f825 Correct logic in old-systemd fallback code 0s autopkgtest [02:23:21]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r2dyhtsy/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.51 lxd-armhf-10.145.243.51:autopkgtest/ubuntu/plucky/armhf 53s autopkgtest [02:24:14]: testbed dpkg architecture: armhf 55s autopkgtest [02:24:16]: testbed apt version: 2.9.14ubuntu1 55s autopkgtest [02:24:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 62s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 62s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [771 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [54.1 kB] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.1 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [69.9 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [928 B] 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [567 kB] 63s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [7448 B] 63s Fetched 1569 kB in 1s (1469 kB/s) 64s Reading package lists... 80s tee: /proc/self/fd/2: Permission denied 104s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 105s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 105s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 106s Reading package lists... 106s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s Calculating upgrade... 109s The following packages were automatically installed and are no longer required: 109s libfwupd2 libgusb2 109s Use 'apt autoremove' to remove them. 109s The following NEW packages will be installed: 109s libdrm-amdgpu1 libfwupd3 109s The following packages will be upgraded: 109s fwupd 109s 1 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 5162 kB of archives. 109s After this operation, 1304 kB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libdrm-amdgpu1 armhf 2.4.123-1 [18.9 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd3 armhf 2.0.2-1 [123 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 2.0.2-1 [5019 kB] 112s Fetched 5162 kB in 2s (2187 kB/s) 112s Selecting previously unselected package libdrm-amdgpu1:armhf. 112s (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 ... 59972 files and directories currently installed.) 112s Preparing to unpack .../libdrm-amdgpu1_2.4.123-1_armhf.deb ... 112s Unpacking libdrm-amdgpu1:armhf (2.4.123-1) ... 112s Selecting previously unselected package libfwupd3:armhf. 112s Preparing to unpack .../libfwupd3_2.0.2-1_armhf.deb ... 112s Unpacking libfwupd3:armhf (2.0.2-1) ... 112s Preparing to unpack .../fwupd_2.0.2-1_armhf.deb ... 113s Unpacking fwupd (2.0.2-1) over (1.9.26-2) ... 113s Setting up libfwupd3:armhf (2.0.2-1) ... 113s Setting up libdrm-amdgpu1:armhf (2.4.123-1) ... 113s Setting up fwupd (2.0.2-1) ... 113s Installing new version of config file /etc/fwupd/remotes.d/lvfs-testing.conf ... 113s Installing new version of config file /etc/fwupd/remotes.d/lvfs.conf ... 113s Installing new version of config file /etc/fwupd/remotes.d/vendor-directory.conf ... 113s Installing new version of config file /etc/grub.d/35_fwupd ... 114s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 114s fwupd.service is a disabled or a static unit not running, not starting it. 114s Processing triggers for man-db (2.13.0-1) ... 115s Processing triggers for dbus (1.14.10-4ubuntu5) ... 115s Processing triggers for libc-bin (2.40-1ubuntu3) ... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 118s The following packages will be REMOVED: 118s libfwupd2* libgusb2* 118s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 118s After this operation, 436 kB disk space will be freed. 118s (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 ... 59983 files and directories currently installed.) 118s Removing libfwupd2:armhf (1.9.26-2) ... 118s Removing libgusb2:armhf (0.4.9-1) ... 118s Processing triggers for libc-bin (2.40-1ubuntu3) ... 121s autopkgtest [02:25:22]: rebooting testbed after setup commands that affected boot 189s autopkgtest [02:26:30]: testbed running kernel: Linux 6.8.0-49-generic #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 6 18:12:14 UTC 2 215s autopkgtest [02:26:56]: @@@@@@@@@@@@@@@@@@@@ apt-source coot 245s Get:1 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (dsc) [2941 B] 245s Get:2 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (tar) [88.5 MB] 245s Get:3 http://ftpmaster.internal/ubuntu plucky/universe coot 1.1.09+dfsg-2build1 (diff) [52.5 kB] 245s gpgv: Signature made Tue Jul 30 06:28:58 2024 UTC 245s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 245s gpgv: Can't check signature: No public key 245s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.09+dfsg-2build1.dsc: no acceptable signature found 248s autopkgtest [02:27:29]: testing package coot version 1.1.09+dfsg-2build1 250s autopkgtest [02:27:31]: build not needed 259s autopkgtest [02:27:40]: test command1: preparing testbed 269s Reading package lists... 269s Building dependency tree... 269s Reading state information... 270s Starting pkgProblemResolver with broken count: 0 270s Starting 2 pkgProblemResolver with broken count: 0 270s Done 271s The following additional packages will be installed: 271s adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend 271s dconf-service fontconfig fontconfig-config fonts-freefont-ttf 271s fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 271s gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 271s gtk-update-icon-cache hicolor-icon-theme humanity-icon-theme libasound2-data 271s libasound2t64 libblas3 libboost-iostreams1.83.0 libboost-numpy1.83.0 271s libboost-python1.83.0 libboost-serialization1.83.0 libcairo-gobject2 271s libcairo-script-interpreter2 libcairo2 libccp4-data libccp4c0t64 libclipper2 271s libcoordgen3 libcootapi-dev libcootapi1.1 libcpdb-frontend2t64 libcpdb2t64 271s libdatrie1 libdconf1 libdeflate0 libepoxy0 libfontconfig1 libfreetype6 271s libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgles2 libglvnd0 271s libgomp1 libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 libgtk-4-1 271s libgtk-4-common libharfbuzz-gobject0 libharfbuzz-subset0 libharfbuzz0b 271s libhwloc15 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 271s libmaeparser1 libmmdb2-0 libmpich12 libogg0 libpango-1.0-0 271s libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpixman-1-0 271s libpython3.12t64 librdkit1t64 libsharpyuv0 libssm2 libthai-data libthai0 271s libtiff6 libvorbis0a libvorbisfile3 libvulkan1 libwayland-client0 271s libwayland-egl1 libwebp7 libxcb-render0 libxcb-shm0 libxcursor1 libxdamage1 271s libxfixes3 libxft2 libxi6 libxinerama1 libxrandr2 libxrender1 python3-numpy 271s python3-rdkit rdkit-data refmac-dictionary sfftw2 ttf-bitstream-vera 271s ubuntu-mono 271s Suggested packages: 271s adwaita-icon-theme-legacy alsa-utils libasound2-plugins gsl-ref-psdoc 271s | gsl-doc-pdf | gsl-doc-info | gsl-ref-html gvfs gcc gfortran 271s python-numpy-doc python3-dev python3-pytest rdkit-doc mpi-defaults-bin 271s sfftw-dev 271s Recommended packages: 271s librsvg2-common alsa-ucm-conf alsa-topology-conf libgdk-pixbuf2.0-bin 271s cpdb-backend-cups libgtk-4-bin libgtk-4-media-gstreamer libhwloc-plugins 271s mesa-vulkan-drivers | vulkan-icd 271s The following NEW packages will be installed: 271s adwaita-icon-theme autopkgtest-satdep coot coot-data coot-doc 271s dconf-gsettings-backend dconf-service fontconfig fontconfig-config 271s fonts-freefont-ttf fonts-noto-core fonts-noto-mono gir1.2-freedesktop 271s gir1.2-gdkpixbuf-2.0 gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 271s gir1.2-pango-1.0 gtk-update-icon-cache hicolor-icon-theme 271s humanity-icon-theme libasound2-data libasound2t64 libblas3 271s libboost-iostreams1.83.0 libboost-numpy1.83.0 libboost-python1.83.0 271s libboost-serialization1.83.0 libcairo-gobject2 libcairo-script-interpreter2 271s libcairo2 libccp4-data libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev 271s libcootapi1.1 libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1 271s libdeflate0 libepoxy0 libfontconfig1 libfreetype6 libgdk-pixbuf-2.0-0 271s libgdk-pixbuf2.0-common libgfortran5 libgles2 libglvnd0 libgomp1 271s libgraphene-1.0-0 libgraphite2-3 libgsl28 libgslcblas0 libgtk-4-1 271s libgtk-4-common libharfbuzz-gobject0 libharfbuzz-subset0 libharfbuzz0b 271s libhwloc15 libinchi1.07 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 271s libmaeparser1 libmmdb2-0 libmpich12 libogg0 libpango-1.0-0 271s libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpixman-1-0 271s libpython3.12t64 librdkit1t64 libsharpyuv0 libssm2 libthai-data libthai0 271s libtiff6 libvorbis0a libvorbisfile3 libvulkan1 libwayland-client0 271s libwayland-egl1 libwebp7 libxcb-render0 libxcb-shm0 libxcursor1 libxdamage1 271s libxfixes3 libxft2 libxi6 libxinerama1 libxrandr2 libxrender1 python3-numpy 271s python3-rdkit rdkit-data refmac-dictionary sfftw2 ttf-bitstream-vera 271s ubuntu-mono 272s 0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded. 272s Need to get 111 MB/111 MB of archives. 272s After this operation, 579 MB of additional disk space will be used. 272s Get:1 /tmp/autopkgtest.G8cenB/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [724 B] 272s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [7888 B] 272s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 272s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 272s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.22-1 [38.9 kB] 272s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 272s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 272s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.4.0-0.1 [16.3 kB] 272s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.4.0-0.1 [184 kB] 272s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 272s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libgdk-pixbuf-2.0-0 armhf 2.42.12+dfsg-1 [135 kB] 272s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf gtk-update-icon-cache armhf 4.16.5+ds-2 [50.7 kB] 272s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf hicolor-icon-theme all 0.18-1 [13.5 kB] 272s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf humanity-icon-theme all 0.6.16 [1282 kB] 272s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf ubuntu-mono all 24.04-0ubuntu1 [151 kB] 272s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf adwaita-icon-theme all 47.0-2 [525 kB] 272s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-noto-mono all 20201225-2 [435 kB] 272s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-noto-core all 20201225-2 [13.3 MB] 273s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf ttf-bitstream-vera all 1.10-8.2 [244 kB] 273s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf coot-data all 1.1.09+dfsg-2build1 [11.8 MB] 273s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 273s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-freefont-ttf all 20211204+svn4273-2 [5641 kB] 273s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-1.1ubuntu2 [37.4 kB] 273s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-1.1ubuntu2 [113 kB] 273s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 273s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 273s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 273s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 273s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 273s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo-gobject2 armhf 1.18.2-2 [126 kB] 273s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-freedesktop armhf 1.82.0-2 [64.3 kB] 273s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-gdkpixbuf-2.0 armhf 2.42.12+dfsg-1 [9434 B] 273s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphene-1.0-0 armhf 1.10.8-4 [46.6 kB] 273s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-graphene-1.0 armhf 1.10.8-4 [11.1 kB] 273s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 273s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.0.1-1 [463 kB] 273s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz-gobject0 armhf 10.0.1-1 [30.6 kB] 273s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-harfbuzz-0.0 armhf 10.0.1-1 [45.2 kB] 273s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-1.1ubuntu2 [189 kB] 273s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 273s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 273s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 273s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.54.0+ds-3 [212 kB] 273s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.54.0+ds-3 [42.9 kB] 273s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.54.0+ds-3 [24.8 kB] 273s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 273s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoxft-1.0-0 armhf 1.54.0+ds-3 [18.5 kB] 273s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-pango-1.0 armhf 1.54.0+ds-3 [34.5 kB] 273s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo-script-interpreter2 armhf 1.18.2-2 [50.9 kB] 273s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf libcpdb2t64 armhf 2.0~b5-1.2build1 [21.7 kB] 273s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libcpdb-frontend2t64 armhf 2.0~b5-1.2build1 [17.3 kB] 273s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libepoxy0 armhf 1.5.10-2 [192 kB] 273s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz-subset0 armhf 10.0.1-1 [535 kB] 273s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libvulkan1 armhf 1.3.296.0-1 [114 kB] 273s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libwayland-client0 armhf 1.23.0-1 [22.7 kB] 273s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libwayland-egl1 armhf 1.23.0-1 [5352 B] 273s Get:57 http://ftpmaster.internal/ubuntu plucky/main armhf libxfixes3 armhf 1:6.0.0-2build1 [9038 B] 273s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf libxcursor1 armhf 1:1.2.2-1 [17.6 kB] 273s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf libxdamage1 armhf 1:1.1.6-1build1 [5462 B] 273s Get:60 http://ftpmaster.internal/ubuntu plucky/main armhf libxi6 armhf 2:1.8.2-1 [26.5 kB] 273s Get:61 http://ftpmaster.internal/ubuntu plucky/main armhf libxinerama1 armhf 2:1.1.4-3build1 [5866 B] 274s Get:62 http://ftpmaster.internal/ubuntu plucky/main armhf libxrandr2 armhf 2:1.5.4-1 [15.8 kB] 274s Get:63 http://ftpmaster.internal/ubuntu plucky/main armhf libglvnd0 armhf 1.7.0-1build1 [83.7 kB] 274s Get:64 http://ftpmaster.internal/ubuntu plucky/main armhf libgles2 armhf 1.7.0-1build1 [18.0 kB] 274s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf libdconf1 armhf 0.40.0-4build2 [38.4 kB] 274s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf dconf-service armhf 0.40.0-4build2 [27.4 kB] 274s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf dconf-gsettings-backend armhf 0.40.0-4build2 [23.6 kB] 274s Get:68 http://ftpmaster.internal/ubuntu plucky/main armhf libgtk-4-common all 4.16.5+ds-2 [1244 kB] 274s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf libgtk-4-1 armhf 4.16.5+ds-2 [2979 kB] 274s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf gir1.2-gtk-4.0 armhf 4.16.5+ds-2 [214 kB] 274s Get:71 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf rdkit-data all 202409.2-2 [12.6 MB] 274s Get:72 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-4 [126 kB] 274s Get:73 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 274s Get:74 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-4 [2086 kB] 274s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 274s Get:76 http://ftpmaster.internal/ubuntu plucky/main armhf libboost-python1.83.0 armhf 1.83.0-3.2ubuntu2 [307 kB] 274s Get:77 http://ftpmaster.internal/ubuntu plucky/universe armhf libboost-numpy1.83.0 armhf 1.83.0-3.2ubuntu2 [241 kB] 274s Get:78 http://ftpmaster.internal/ubuntu plucky/universe armhf libboost-serialization1.83.0 armhf 1.83.0-3.2ubuntu2 [333 kB] 274s Get:79 http://ftpmaster.internal/ubuntu plucky/universe armhf libcoordgen3 armhf 3.0.2-1 [190 kB] 274s Get:80 http://ftpmaster.internal/ubuntu plucky/main armhf libboost-iostreams1.83.0 armhf 1.83.0-3.2ubuntu2 [257 kB] 274s Get:81 http://ftpmaster.internal/ubuntu plucky/universe armhf libinchi1.07 armhf 1.07.1+dfsg-5 [492 kB] 274s Get:82 http://ftpmaster.internal/ubuntu plucky/universe armhf libmaeparser1 armhf 1.3.1-1build1 [89.3 kB] 274s Get:83 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf librdkit1t64 armhf 202409.2-2 [4920 kB] 274s Get:84 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-rdkit armhf 202409.2-2 [4257 kB] 274s Get:85 http://ftpmaster.internal/ubuntu plucky/universe armhf refmac-dictionary all 5.41-3 [16.7 MB] 275s Get:86 http://ftpmaster.internal/ubuntu plucky/main armhf libasound2-data all 1.2.12-1 [21.0 kB] 275s Get:87 http://ftpmaster.internal/ubuntu plucky/main armhf libasound2t64 armhf 1.2.12-1 [344 kB] 275s Get:88 http://ftpmaster.internal/ubuntu plucky/universe armhf libccp4-data all 8.0.0-4 [65.2 kB] 275s Get:89 http://ftpmaster.internal/ubuntu plucky/universe armhf libccp4c0t64 armhf 8.0.0-4 [82.3 kB] 275s Get:90 http://ftpmaster.internal/ubuntu plucky/universe armhf libmmdb2-0 armhf 2.0.22-1 [305 kB] 275s Get:91 http://ftpmaster.internal/ubuntu plucky/universe armhf libhwloc15 armhf 2.11.2-1 [147 kB] 275s Get:92 http://ftpmaster.internal/ubuntu plucky/universe armhf libmpich12 armhf 4.2.0-14 [1677 kB] 275s Get:93 http://ftpmaster.internal/ubuntu plucky/universe armhf sfftw2 armhf 2.1.5-7 [163 kB] 275s Get:94 http://ftpmaster.internal/ubuntu plucky/universe armhf libclipper2 armhf 2.1.20201109-2build1 [1178 kB] 275s Get:95 http://ftpmaster.internal/ubuntu plucky/universe armhf libgslcblas0 armhf 2.8+dfsg-5 [84.1 kB] 275s Get:96 http://ftpmaster.internal/ubuntu plucky/universe armhf libgsl28 armhf 2.8+dfsg-5 [876 kB] 275s Get:97 http://ftpmaster.internal/ubuntu plucky/universe armhf libssm2 armhf 1.4.0-2build1 [72.4 kB] 275s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf libcootapi1.1 armhf 1.1.09+dfsg-2build1 [3538 kB] 275s Get:99 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 14.2.0-8ubuntu1 [125 kB] 275s Get:100 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.12t64 armhf 3.12.7-3 [2075 kB] 275s Get:101 http://ftpmaster.internal/ubuntu plucky/main armhf libogg0 armhf 1.3.5-3build1 [20.5 kB] 275s Get:102 http://ftpmaster.internal/ubuntu plucky/main armhf libvorbis0a armhf 1.3.7-2 [86.7 kB] 275s Get:103 http://ftpmaster.internal/ubuntu plucky/main armhf libvorbisfile3 armhf 1.3.7-2 [16.2 kB] 275s Get:104 http://ftpmaster.internal/ubuntu plucky/universe armhf coot armhf 1.1.09+dfsg-2build1 [8377 kB] 276s Get:105 http://ftpmaster.internal/ubuntu plucky/universe armhf coot-doc all 1.1.09+dfsg-2build1 [2048 kB] 276s Get:106 http://ftpmaster.internal/ubuntu plucky/universe armhf libcootapi-dev armhf 1.1.09+dfsg-2build1 [23.8 kB] 277s Fetched 111 MB in 5s (24.5 MB/s) 277s Selecting previously unselected package libgdk-pixbuf2.0-common. 277s (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 ... 59970 files and directories currently installed.) 277s Preparing to unpack .../000-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ... 277s Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... 277s Selecting previously unselected package libjpeg-turbo8:armhf. 277s Preparing to unpack .../001-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 277s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 277s Selecting previously unselected package libjpeg8:armhf. 277s Preparing to unpack .../002-libjpeg8_8c-2ubuntu11_armhf.deb ... 277s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 277s Selecting previously unselected package libdeflate0:armhf. 277s Preparing to unpack .../003-libdeflate0_1.22-1_armhf.deb ... 277s Unpacking libdeflate0:armhf (1.22-1) ... 277s Selecting previously unselected package libjbig0:armhf. 277s Preparing to unpack .../004-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 277s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 277s Selecting previously unselected package liblerc4:armhf. 277s Preparing to unpack .../005-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 277s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 277s Selecting previously unselected package libsharpyuv0:armhf. 277s Preparing to unpack .../006-libsharpyuv0_1.4.0-0.1_armhf.deb ... 277s Unpacking libsharpyuv0:armhf (1.4.0-0.1) ... 277s Selecting previously unselected package libwebp7:armhf. 277s Preparing to unpack .../007-libwebp7_1.4.0-0.1_armhf.deb ... 277s Unpacking libwebp7:armhf (1.4.0-0.1) ... 277s Selecting previously unselected package libtiff6:armhf. 278s Preparing to unpack .../008-libtiff6_4.5.1+git230720-4ubuntu4_armhf.deb ... 278s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 278s Selecting previously unselected package libgdk-pixbuf-2.0-0:armhf. 278s Preparing to unpack .../009-libgdk-pixbuf-2.0-0_2.42.12+dfsg-1_armhf.deb ... 278s Unpacking libgdk-pixbuf-2.0-0:armhf (2.42.12+dfsg-1) ... 278s Selecting previously unselected package gtk-update-icon-cache. 278s Preparing to unpack .../010-gtk-update-icon-cache_4.16.5+ds-2_armhf.deb ... 278s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 278s 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. 278s Unpacking gtk-update-icon-cache (4.16.5+ds-2) ... 278s Selecting previously unselected package hicolor-icon-theme. 278s Preparing to unpack .../011-hicolor-icon-theme_0.18-1_all.deb ... 278s Unpacking hicolor-icon-theme (0.18-1) ... 278s Selecting previously unselected package humanity-icon-theme. 278s Preparing to unpack .../012-humanity-icon-theme_0.6.16_all.deb ... 278s Unpacking humanity-icon-theme (0.6.16) ... 279s Selecting previously unselected package ubuntu-mono. 279s Preparing to unpack .../013-ubuntu-mono_24.04-0ubuntu1_all.deb ... 279s Unpacking ubuntu-mono (24.04-0ubuntu1) ... 280s Selecting previously unselected package adwaita-icon-theme. 280s Preparing to unpack .../014-adwaita-icon-theme_47.0-2_all.deb ... 280s Unpacking adwaita-icon-theme (47.0-2) ... 280s Selecting previously unselected package fonts-noto-mono. 280s Preparing to unpack .../015-fonts-noto-mono_20201225-2_all.deb ... 280s Unpacking fonts-noto-mono (20201225-2) ... 280s Selecting previously unselected package fonts-noto-core. 280s Preparing to unpack .../016-fonts-noto-core_20201225-2_all.deb ... 280s Unpacking fonts-noto-core (20201225-2) ... 281s Selecting previously unselected package ttf-bitstream-vera. 281s Preparing to unpack .../017-ttf-bitstream-vera_1.10-8.2_all.deb ... 281s Unpacking ttf-bitstream-vera (1.10-8.2) ... 281s Selecting previously unselected package coot-data. 281s Preparing to unpack .../018-coot-data_1.1.09+dfsg-2build1_all.deb ... 281s Unpacking coot-data (1.1.09+dfsg-2build1) ... 282s Selecting previously unselected package libfreetype6:armhf. 282s Preparing to unpack .../019-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 282s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 282s Selecting previously unselected package fonts-freefont-ttf. 282s Preparing to unpack .../020-fonts-freefont-ttf_20211204+svn4273-2_all.deb ... 282s Unpacking fonts-freefont-ttf (20211204+svn4273-2) ... 282s Selecting previously unselected package fontconfig-config. 282s Preparing to unpack .../021-fontconfig-config_2.15.0-1.1ubuntu2_armhf.deb ... 282s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 282s Selecting previously unselected package libfontconfig1:armhf. 282s Preparing to unpack .../022-libfontconfig1_2.15.0-1.1ubuntu2_armhf.deb ... 282s Unpacking libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 282s Selecting previously unselected package libpixman-1-0:armhf. 282s Preparing to unpack .../023-libpixman-1-0_0.44.0-3_armhf.deb ... 282s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 282s Selecting previously unselected package libxcb-render0:armhf. 282s Preparing to unpack .../024-libxcb-render0_1.17.0-2_armhf.deb ... 282s Unpacking libxcb-render0:armhf (1.17.0-2) ... 283s Selecting previously unselected package libxcb-shm0:armhf. 283s Preparing to unpack .../025-libxcb-shm0_1.17.0-2_armhf.deb ... 283s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 283s Selecting previously unselected package libxrender1:armhf. 283s Preparing to unpack .../026-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 283s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 283s Selecting previously unselected package libcairo2:armhf. 283s Preparing to unpack .../027-libcairo2_1.18.2-2_armhf.deb ... 283s Unpacking libcairo2:armhf (1.18.2-2) ... 283s Selecting previously unselected package libcairo-gobject2:armhf. 283s Preparing to unpack .../028-libcairo-gobject2_1.18.2-2_armhf.deb ... 283s Unpacking libcairo-gobject2:armhf (1.18.2-2) ... 283s Selecting previously unselected package gir1.2-freedesktop:armhf. 283s Preparing to unpack .../029-gir1.2-freedesktop_1.82.0-2_armhf.deb ... 283s Unpacking gir1.2-freedesktop:armhf (1.82.0-2) ... 283s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:armhf. 283s Preparing to unpack .../030-gir1.2-gdkpixbuf-2.0_2.42.12+dfsg-1_armhf.deb ... 283s Unpacking gir1.2-gdkpixbuf-2.0:armhf (2.42.12+dfsg-1) ... 283s Selecting previously unselected package libgraphene-1.0-0:armhf. 283s Preparing to unpack .../031-libgraphene-1.0-0_1.10.8-4_armhf.deb ... 283s Unpacking libgraphene-1.0-0:armhf (1.10.8-4) ... 283s Selecting previously unselected package gir1.2-graphene-1.0:armhf. 283s Preparing to unpack .../032-gir1.2-graphene-1.0_1.10.8-4_armhf.deb ... 283s Unpacking gir1.2-graphene-1.0:armhf (1.10.8-4) ... 283s Selecting previously unselected package libgraphite2-3:armhf. 283s Preparing to unpack .../033-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 283s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 283s Selecting previously unselected package libharfbuzz0b:armhf. 283s Preparing to unpack .../034-libharfbuzz0b_10.0.1-1_armhf.deb ... 283s Unpacking libharfbuzz0b:armhf (10.0.1-1) ... 283s Selecting previously unselected package libharfbuzz-gobject0:armhf. 283s Preparing to unpack .../035-libharfbuzz-gobject0_10.0.1-1_armhf.deb ... 283s Unpacking libharfbuzz-gobject0:armhf (10.0.1-1) ... 283s Selecting previously unselected package gir1.2-harfbuzz-0.0:armhf. 283s Preparing to unpack .../036-gir1.2-harfbuzz-0.0_10.0.1-1_armhf.deb ... 283s Unpacking gir1.2-harfbuzz-0.0:armhf (10.0.1-1) ... 283s Selecting previously unselected package fontconfig. 283s Preparing to unpack .../037-fontconfig_2.15.0-1.1ubuntu2_armhf.deb ... 283s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 283s Selecting previously unselected package libthai-data. 283s Preparing to unpack .../038-libthai-data_0.1.29-2build1_all.deb ... 283s Unpacking libthai-data (0.1.29-2build1) ... 283s Selecting previously unselected package libdatrie1:armhf. 283s Preparing to unpack .../039-libdatrie1_0.2.13-3build1_armhf.deb ... 283s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 283s Selecting previously unselected package libthai0:armhf. 283s Preparing to unpack .../040-libthai0_0.1.29-2build1_armhf.deb ... 283s Unpacking libthai0:armhf (0.1.29-2build1) ... 283s Selecting previously unselected package libpango-1.0-0:armhf. 283s Preparing to unpack .../041-libpango-1.0-0_1.54.0+ds-3_armhf.deb ... 283s Unpacking libpango-1.0-0:armhf (1.54.0+ds-3) ... 284s Selecting previously unselected package libpangoft2-1.0-0:armhf. 284s Preparing to unpack .../042-libpangoft2-1.0-0_1.54.0+ds-3_armhf.deb ... 284s Unpacking libpangoft2-1.0-0:armhf (1.54.0+ds-3) ... 284s Selecting previously unselected package libpangocairo-1.0-0:armhf. 284s Preparing to unpack .../043-libpangocairo-1.0-0_1.54.0+ds-3_armhf.deb ... 284s Unpacking libpangocairo-1.0-0:armhf (1.54.0+ds-3) ... 284s Selecting previously unselected package libxft2:armhf. 284s Preparing to unpack .../044-libxft2_2.3.6-1build1_armhf.deb ... 284s Unpacking libxft2:armhf (2.3.6-1build1) ... 284s Selecting previously unselected package libpangoxft-1.0-0:armhf. 284s Preparing to unpack .../045-libpangoxft-1.0-0_1.54.0+ds-3_armhf.deb ... 284s Unpacking libpangoxft-1.0-0:armhf (1.54.0+ds-3) ... 284s Selecting previously unselected package gir1.2-pango-1.0:armhf. 284s Preparing to unpack .../046-gir1.2-pango-1.0_1.54.0+ds-3_armhf.deb ... 284s Unpacking gir1.2-pango-1.0:armhf (1.54.0+ds-3) ... 284s Selecting previously unselected package libcairo-script-interpreter2:armhf. 284s Preparing to unpack .../047-libcairo-script-interpreter2_1.18.2-2_armhf.deb ... 284s Unpacking libcairo-script-interpreter2:armhf (1.18.2-2) ... 284s Selecting previously unselected package libcpdb2t64:armhf. 284s Preparing to unpack .../048-libcpdb2t64_2.0~b5-1.2build1_armhf.deb ... 284s Unpacking libcpdb2t64:armhf (2.0~b5-1.2build1) ... 284s Selecting previously unselected package libcpdb-frontend2t64:armhf. 284s Preparing to unpack .../049-libcpdb-frontend2t64_2.0~b5-1.2build1_armhf.deb ... 284s Unpacking libcpdb-frontend2t64:armhf (2.0~b5-1.2build1) ... 284s Selecting previously unselected package libepoxy0:armhf. 284s Preparing to unpack .../050-libepoxy0_1.5.10-2_armhf.deb ... 284s Unpacking libepoxy0:armhf (1.5.10-2) ... 284s Selecting previously unselected package libharfbuzz-subset0:armhf. 284s Preparing to unpack .../051-libharfbuzz-subset0_10.0.1-1_armhf.deb ... 284s Unpacking libharfbuzz-subset0:armhf (10.0.1-1) ... 284s Selecting previously unselected package libvulkan1:armhf. 284s Preparing to unpack .../052-libvulkan1_1.3.296.0-1_armhf.deb ... 284s Unpacking libvulkan1:armhf (1.3.296.0-1) ... 284s Selecting previously unselected package libwayland-client0:armhf. 284s Preparing to unpack .../053-libwayland-client0_1.23.0-1_armhf.deb ... 284s Unpacking libwayland-client0:armhf (1.23.0-1) ... 284s Selecting previously unselected package libwayland-egl1:armhf. 284s Preparing to unpack .../054-libwayland-egl1_1.23.0-1_armhf.deb ... 284s Unpacking libwayland-egl1:armhf (1.23.0-1) ... 284s Selecting previously unselected package libxfixes3:armhf. 284s Preparing to unpack .../055-libxfixes3_1%3a6.0.0-2build1_armhf.deb ... 284s Unpacking libxfixes3:armhf (1:6.0.0-2build1) ... 284s Selecting previously unselected package libxcursor1:armhf. 284s Preparing to unpack .../056-libxcursor1_1%3a1.2.2-1_armhf.deb ... 284s Unpacking libxcursor1:armhf (1:1.2.2-1) ... 284s Selecting previously unselected package libxdamage1:armhf. 284s Preparing to unpack .../057-libxdamage1_1%3a1.1.6-1build1_armhf.deb ... 284s Unpacking libxdamage1:armhf (1:1.1.6-1build1) ... 284s Selecting previously unselected package libxi6:armhf. 284s Preparing to unpack .../058-libxi6_2%3a1.8.2-1_armhf.deb ... 284s Unpacking libxi6:armhf (2:1.8.2-1) ... 284s Selecting previously unselected package libxinerama1:armhf. 284s Preparing to unpack .../059-libxinerama1_2%3a1.1.4-3build1_armhf.deb ... 284s Unpacking libxinerama1:armhf (2:1.1.4-3build1) ... 284s Selecting previously unselected package libxrandr2:armhf. 285s Preparing to unpack .../060-libxrandr2_2%3a1.5.4-1_armhf.deb ... 285s Unpacking libxrandr2:armhf (2:1.5.4-1) ... 285s Selecting previously unselected package libglvnd0:armhf. 285s Preparing to unpack .../061-libglvnd0_1.7.0-1build1_armhf.deb ... 285s Unpacking libglvnd0:armhf (1.7.0-1build1) ... 285s Selecting previously unselected package libgles2:armhf. 285s Preparing to unpack .../062-libgles2_1.7.0-1build1_armhf.deb ... 285s Unpacking libgles2:armhf (1.7.0-1build1) ... 285s Selecting previously unselected package libdconf1:armhf. 285s Preparing to unpack .../063-libdconf1_0.40.0-4build2_armhf.deb ... 285s Unpacking libdconf1:armhf (0.40.0-4build2) ... 285s Selecting previously unselected package dconf-service. 285s Preparing to unpack .../064-dconf-service_0.40.0-4build2_armhf.deb ... 285s Unpacking dconf-service (0.40.0-4build2) ... 285s Selecting previously unselected package dconf-gsettings-backend:armhf. 285s Preparing to unpack .../065-dconf-gsettings-backend_0.40.0-4build2_armhf.deb ... 285s Unpacking dconf-gsettings-backend:armhf (0.40.0-4build2) ... 285s Selecting previously unselected package libgtk-4-common. 285s Preparing to unpack .../066-libgtk-4-common_4.16.5+ds-2_all.deb ... 285s Unpacking libgtk-4-common (4.16.5+ds-2) ... 285s Selecting previously unselected package libgtk-4-1:armhf. 285s Preparing to unpack .../067-libgtk-4-1_4.16.5+ds-2_armhf.deb ... 285s Unpacking libgtk-4-1:armhf (4.16.5+ds-2) ... 285s Selecting previously unselected package gir1.2-gtk-4.0:armhf. 285s Preparing to unpack .../068-gir1.2-gtk-4.0_4.16.5+ds-2_armhf.deb ... 285s Unpacking gir1.2-gtk-4.0:armhf (4.16.5+ds-2) ... 285s Selecting previously unselected package rdkit-data. 285s Preparing to unpack .../069-rdkit-data_202409.2-2_all.deb ... 285s Unpacking rdkit-data (202409.2-2) ... 286s Selecting previously unselected package libblas3:armhf. 286s Preparing to unpack .../070-libblas3_3.12.0-4_armhf.deb ... 286s Unpacking libblas3:armhf (3.12.0-4) ... 286s Selecting previously unselected package libgfortran5:armhf. 286s Preparing to unpack .../071-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 286s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 286s Selecting previously unselected package liblapack3:armhf. 286s Preparing to unpack .../072-liblapack3_3.12.0-4_armhf.deb ... 286s Unpacking liblapack3:armhf (3.12.0-4) ... 286s Selecting previously unselected package python3-numpy. 286s Preparing to unpack .../073-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 286s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 286s Selecting previously unselected package libboost-python1.83.0. 286s Preparing to unpack .../074-libboost-python1.83.0_1.83.0-3.2ubuntu2_armhf.deb ... 286s Unpacking libboost-python1.83.0 (1.83.0-3.2ubuntu2) ... 286s Selecting previously unselected package libboost-numpy1.83.0. 286s Preparing to unpack .../075-libboost-numpy1.83.0_1.83.0-3.2ubuntu2_armhf.deb ... 286s Unpacking libboost-numpy1.83.0 (1.83.0-3.2ubuntu2) ... 286s Selecting previously unselected package libboost-serialization1.83.0:armhf. 286s Preparing to unpack .../076-libboost-serialization1.83.0_1.83.0-3.2ubuntu2_armhf.deb ... 286s Unpacking libboost-serialization1.83.0:armhf (1.83.0-3.2ubuntu2) ... 286s Selecting previously unselected package libcoordgen3:armhf. 286s Preparing to unpack .../077-libcoordgen3_3.0.2-1_armhf.deb ... 286s Unpacking libcoordgen3:armhf (3.0.2-1) ... 286s Selecting previously unselected package libboost-iostreams1.83.0:armhf. 287s Preparing to unpack .../078-libboost-iostreams1.83.0_1.83.0-3.2ubuntu2_armhf.deb ... 287s Unpacking libboost-iostreams1.83.0:armhf (1.83.0-3.2ubuntu2) ... 287s Selecting previously unselected package libinchi1.07. 287s Preparing to unpack .../079-libinchi1.07_1.07.1+dfsg-5_armhf.deb ... 287s Unpacking libinchi1.07 (1.07.1+dfsg-5) ... 287s Selecting previously unselected package libmaeparser1:armhf. 287s Preparing to unpack .../080-libmaeparser1_1.3.1-1build1_armhf.deb ... 287s Unpacking libmaeparser1:armhf (1.3.1-1build1) ... 287s Selecting previously unselected package librdkit1t64. 287s Preparing to unpack .../081-librdkit1t64_202409.2-2_armhf.deb ... 287s Unpacking librdkit1t64 (202409.2-2) ... 287s Selecting previously unselected package python3-rdkit. 287s Preparing to unpack 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previously unselected package libmmdb2-0:armhf. 291s Preparing to unpack .../088-libmmdb2-0_2.0.22-1_armhf.deb ... 291s Unpacking libmmdb2-0:armhf (2.0.22-1) ... 291s Selecting previously unselected package libhwloc15:armhf. 291s Preparing to unpack .../089-libhwloc15_2.11.2-1_armhf.deb ... 291s Unpacking libhwloc15:armhf (2.11.2-1) ... 291s Selecting previously unselected package libmpich12:armhf. 291s Preparing to unpack .../090-libmpich12_4.2.0-14_armhf.deb ... 291s Unpacking libmpich12:armhf (4.2.0-14) ... 291s Selecting previously unselected package sfftw2. 291s Preparing to unpack .../091-sfftw2_2.1.5-7_armhf.deb ... 291s Unpacking sfftw2 (2.1.5-7) ... 291s Selecting previously unselected package libclipper2:armhf. 291s Preparing to unpack .../092-libclipper2_2.1.20201109-2build1_armhf.deb ... 291s Unpacking libclipper2:armhf (2.1.20201109-2build1) ... 291s Selecting previously unselected package libgslcblas0:armhf. 291s Preparing to unpack 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libpython3.12t64:armhf (3.12.7-3) ... 292s Selecting previously unselected package libogg0:armhf. 292s Preparing to unpack .../099-libogg0_1.3.5-3build1_armhf.deb ... 292s Unpacking libogg0:armhf (1.3.5-3build1) ... 292s Selecting previously unselected package libvorbis0a:armhf. 292s Preparing to unpack .../100-libvorbis0a_1.3.7-2_armhf.deb ... 292s Unpacking libvorbis0a:armhf (1.3.7-2) ... 292s Selecting previously unselected package libvorbisfile3:armhf. 292s Preparing to unpack .../101-libvorbisfile3_1.3.7-2_armhf.deb ... 292s Unpacking libvorbisfile3:armhf (1.3.7-2) ... 292s Selecting previously unselected package coot. 292s Preparing to unpack .../102-coot_1.1.09+dfsg-2build1_armhf.deb ... 292s Unpacking coot (1.1.09+dfsg-2build1) ... 293s Selecting previously unselected package coot-doc. 293s Preparing to unpack .../103-coot-doc_1.1.09+dfsg-2build1_all.deb ... 293s Unpacking coot-doc (1.1.09+dfsg-2build1) ... 293s Selecting previously unselected package libcootapi-dev. 293s Preparing to unpack .../104-libcootapi-dev_1.1.09+dfsg-2build1_armhf.deb ... 293s Unpacking libcootapi-dev (1.1.09+dfsg-2build1) ... 293s Selecting previously unselected package autopkgtest-satdep. 293s Preparing to unpack .../105-1-autopkgtest-satdep.deb ... 293s Unpacking autopkgtest-satdep (0) ... 293s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 293s Setting up libboost-python1.83.0 (1.83.0-3.2ubuntu2) ... 293s Setting up libpixman-1-0:armhf (0.44.0-3) ... 293s Setting up coot-doc (1.1.09+dfsg-2build1) ... 293s Setting up libsharpyuv0:armhf (1.4.0-0.1) ... 293s Setting up ttf-bitstream-vera (1.10-8.2) ... 293s Setting up libxdamage1:armhf (1:1.1.6-1build1) ... 293s Setting up libogg0:armhf (1.3.5-3build1) ... 293s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 293s Setting up fonts-noto-mono (20201225-2) ... 293s Setting up hicolor-icon-theme (0.18-1) ... 293s Setting up libxi6:armhf (2:1.8.2-1) ... 293s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 293s Setting up libdatrie1:armhf (0.2.13-3build1) ... 293s Setting up libgslcblas0:armhf (2.8+dfsg-5) ... 293s Setting up libmmdb2-0:armhf (2.0.22-1) ... 293s Setting up libxcb-render0:armhf (1.17.0-2) ... 293s Setting up libglvnd0:armhf (1.7.0-1build1) ... 293s Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... 293s Setting up libdeflate0:armhf (1.22-1) ... 293s Setting up fonts-freefont-ttf (20211204+svn4273-2) ... 293s Setting up libcpdb2t64:armhf (2.0~b5-1.2build1) ... 293s Setting up libxcb-shm0:armhf (1.17.0-2) ... 293s Setting up libcpdb-frontend2t64:armhf (2.0~b5-1.2build1) ... 293s Setting up libccp4-data (8.0.0-4) ... 293s Setting up libgomp1:armhf (14.2.0-8ubuntu1) ... 293s Setting up rdkit-data (202409.2-2) ... 293s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 293s Setting up refmac-dictionary (5.41-3) ... 293s Setting up libdconf1:armhf (0.40.0-4build2) ... 293s Setting up libpython3.12t64:armhf (3.12.7-3) ... 293s Setting up libasound2-data (1.2.12-1) ... 293s Setting up 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Setting up libvulkan1:armhf (1.3.296.0-1) ... 293s Setting up libwebp7:armhf (1.4.0-0.1) ... 293s Setting up libmpich12:armhf (4.2.0-14) ... 293s Setting up libccp4c0t64:armhf (8.0.0-4) ... 293s Setting up libharfbuzz0b:armhf (10.0.1-1) ... 293s Setting up libthai-data (0.1.29-2build1) ... 293s Setting up libwayland-egl1:armhf (1.23.0-1) ... 293s Setting up libcoordgen3:armhf (3.0.2-1) ... 293s Setting up libgsl28:armhf (2.8+dfsg-5) ... 293s Setting up libinchi1.07 (1.07.1+dfsg-5) ... 293s Setting up fonts-noto-core (20201225-2) ... 293s Setting up libgraphene-1.0-0:armhf (1.10.8-4) ... 293s Setting up libwayland-client0:armhf (1.23.0-1) ... 293s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 293s Setting up gir1.2-graphene-1.0:armhf (1.10.8-4) ... 293s Setting up liblapack3:armhf (3.12.0-4) ... 293s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 293s Setting up libssm2:armhf (1.4.0-2build1) ... 293s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 293s Setting up libxcursor1:armhf (1:1.2.2-1) ... 293s Setting up sfftw2 (2.1.5-7) ... 293s Setting up dconf-service (0.40.0-4build2) ... 293s Setting up libharfbuzz-gobject0:armhf (10.0.1-1) ... 293s Setting up libmaeparser1:armhf (1.3.1-1build1) ... 293s Setting up libthai0:armhf (0.1.29-2build1) ... 293s Setting up libvorbisfile3:armhf (1.3.7-2) ... 293s Setting up libclipper2:armhf (2.1.20201109-2build1) ... 293s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 296s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 296s Setting up libharfbuzz-subset0:armhf (10.0.1-1) ... 296s Setting up libgdk-pixbuf-2.0-0:armhf (2.42.12+dfsg-1) ... 296s Setting up coot-data (1.1.09+dfsg-2build1) ... 296s Setting up gtk-update-icon-cache (4.16.5+ds-2) ... 296s Setting up dconf-gsettings-backend:armhf (0.40.0-4build2) ... 296s Setting up gir1.2-gdkpixbuf-2.0:armhf (2.42.12+dfsg-1) ... 296s Setting up libcootapi1.1 (1.1.09+dfsg-2build1) ... 296s Setting up libcootapi-dev (1.1.09+dfsg-2build1) ... 296s Setting up libgtk-4-common (4.16.5+ds-2) ... 296s Setting up adwaita-icon-theme (47.0-2) ... 297s update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode 297s Setting up humanity-icon-theme (0.6.16) ... 297s Setting up ubuntu-mono (24.04-0ubuntu1) ... 297s Processing triggers for man-db (2.13.0-1) ... 298s Processing triggers for libglib2.0-0t64:armhf (2.82.2-3) ... 298s Processing triggers for sgml-base (1.31) ... 298s Setting up libfontconfig1:armhf (2.15.0-1.1ubuntu2) ... 298s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 300s Regenerating fonts cache... done. 300s Setting up libxft2:armhf (2.3.6-1build1) ... 300s Processing triggers for libc-bin (2.40-1ubuntu3) ... 300s Setting up libpango-1.0-0:armhf (1.54.0+ds-3) ... 300s Setting up libcairo2:armhf (1.18.2-2) ... 300s Setting up libcairo-gobject2:armhf (1.18.2-2) ... 300s Setting up libpangoft2-1.0-0:armhf (1.54.0+ds-3) ... 300s Setting up libpangocairo-1.0-0:armhf (1.54.0+ds-3) ... 300s Setting up libcairo-script-interpreter2:armhf (1.18.2-2) ... 300s Setting up gir1.2-freedesktop:armhf (1.82.0-2) ... 300s Setting up libpangoxft-1.0-0:armhf (1.54.0+ds-3) ... 300s Setting up librdkit1t64 (202409.2-2) ... 300s Setting up gir1.2-harfbuzz-0.0:armhf (10.0.1-1) ... 300s Setting up gir1.2-pango-1.0:armhf (1.54.0+ds-3) ... 300s Setting up python3-rdkit (202409.2-2) ... 301s Setting up libgtk-4-1:armhf (4.16.5+ds-2) ... 301s Setting up gir1.2-gtk-4.0:armhf (4.16.5+ds-2) ... 301s Setting up coot (1.1.09+dfsg-2build1) ... 301s /usr/lib/python3/dist-packages/coot/tautomer.py:289: SyntaxWarning: invalid escape sequence '\C' 301s ('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'}), 302s Setting up autopkgtest-satdep (0) ... 302s Processing triggers for libc-bin (2.40-1ubuntu3) ... 335s (Reading database ... 88536 files and directories currently installed.) 335s Removing autopkgtest-satdep (0) ... 341s autopkgtest [02:29:02]: test command1: coot --self-test 341s autopkgtest [02:29:02]: test command1: [----------------------- 343s INFO:: Running internal self tests 349s INFO:: Test Clipper core : OK 349s INFO:: Test Clipper contrib: OK 349s run_internal_tests() --------- we have 8 internal test functionns 349s Entering test: kevin's torsion test 349s PASS: kevin's torsion test 349s Entering test: test_alt_conf_rotamers 349s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 349s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 349s chis.size() 2 (should be 2) 349s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911 349s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68 349s For residue 80 chis size 1 349s residue 80 chis: -56.8781 -80.8484 349s PASS: test_alt_conf_rotamers 349s Entering test: test_fragmemt_atom_selection 349s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 349s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 349s ----------------- create_mmdbmanager_from_inverted_atom_selection() 349s n_initial: 1465 n_1: 1401 n_2: 64 349s PASS: test_fragmemt_atom_selection 349s Entering test: test_add_atom 349s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 349s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 349s PASS: test_add_atom 349s Entering test: test segid exchange 349s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 349s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 349s Test with a rogue segid 349s INFO:: No consistent segids for residue 1 349s PASS: test segid exchange 349s Entering test: test peak search non-close 349s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz 349s FFT Reso...0.444444 349s Sampling rate...1.5 349s Grid...Nuvw = ( 132, 160, 80) 349s Cell... Cell (64.897,78.323,38.792, 90, 90, 90) 349s Spacegroup...P 21 21 21 349s There are 2260 peaks and 0 problem peaks 349s PASS: test peak search non-close 349s Entering test: test symop card 349s 1 0 0 349s 0 1 0 349s 0 0 1 349s translations: -1 0 0 349s PASS: test symop card 349s Entering test: SSM sequence alignment output 349s 349s -- 349s Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG 349s Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 349s 349s Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC 349s 349s -- 349s Moving: D 349s Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 349s 349s -- 349s Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG 349s Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG 349s 349s -- 349s PASS: SSM sequence alignment output 349s autopkgtest [02:29:10]: test command1: -----------------------] 353s autopkgtest [02:29:14]: test command1: - - - - - - - - - - results - - - - - - - - - - 353s command1 PASS 357s autopkgtest [02:29:18]: test command2: preparing testbed 366s Reading package lists... 367s Building dependency tree... 367s Reading state information... 368s Starting pkgProblemResolver with broken count: 0 368s Starting 2 pkgProblemResolver with broken count: 0 368s Done 369s The following NEW packages will be installed: 369s autopkgtest-satdep 369s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 369s Need to get 0 B/724 B of archives. 369s After this operation, 0 B of additional disk space will be used. 369s Get:1 /tmp/autopkgtest.G8cenB/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [724 B] 370s Selecting previously unselected package autopkgtest-satdep. 370s (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 ... 88536 files and directories currently installed.) 370s Preparing to unpack .../2-autopkgtest-satdep.deb ... 370s Unpacking autopkgtest-satdep (0) ... 370s Setting up autopkgtest-satdep (0) ... 387s (Reading database ... 88536 files and directories currently installed.) 387s Removing autopkgtest-satdep (0) ... 393s autopkgtest [02:29:54]: test command2: pyrogen --help 393s autopkgtest [02:29:54]: test command2: [----------------------- 397s /usr/bin/pyrogen: line 33: 2882 Segmentation fault (core dumped) /usr/bin/python3 -m pyrogen "${@}" 398s autopkgtest [02:29:59]: test command2: -----------------------] 402s autopkgtest [02:30:03]: test command2: - - - - - - - - - - results - - - - - - - - - - 402s command2 FAIL non-zero exit status 139 402s autopkgtest [02:30:03]: test command2: - - - - - - - - - - stderr - - - - - - - - - - 402s /usr/bin/pyrogen: line 33: 2882 Segmentation fault (core dumped) /usr/bin/python3 -m pyrogen "${@}" 406s autopkgtest [02:30:07]: @@@@@@@@@@@@@@@@@@@@ summary 406s command1 PASS 406s command2 FAIL non-zero exit status 139