0s autopkgtest [19:59:26]: starting date and time: 2025-12-03 19:59:26+0000 0s autopkgtest [19:59:26]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [19:59:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.16s7nu0c/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade coot --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.9-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-4.secgroup --name adt-resolute-amd64-coot-20251203-195926-juju-7f2275-prod-proposed-migration-environment-2-85afc26b-a0e0-4b16-8320-7ded8f97a355 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-coot-20251203-195926-juju-7f2275-prod-proposed-migration-environment-2-85afc26b-a0e0-4b16-8320-7ded8f97a355 from image adt/ubuntu-resolute-amd64-server-20251203.img (UUID c6e78f39-c16c-48bb-9815-0096f6be052e)... 50s autopkgtest [20:00:16]: testbed dpkg architecture: amd64 51s autopkgtest [20:00:17]: testbed apt version: 3.1.12 51s autopkgtest [20:00:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [20:00:17]: testbed release detected to be: None 52s autopkgtest [20:00:18]: updating testbed package index (apt update) 52s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 52s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 52s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 52s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 52s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [157 kB] 52s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [954 kB] 52s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.1 kB] 52s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [220 kB] 52s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [161 kB] 52s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6252 B] 52s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 52s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [349 kB] 52s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [764 kB] 52s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [23.0 kB] 52s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9636 B] 53s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4040 B] 53s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [764 B] 53s Fetched 2796 kB in 1s (3272 kB/s) 54s Reading package lists... 54s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 54s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 55s Reading package lists... 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 55s The following packages will be upgraded: 55s libpython3-stdlib python3 python3-gdbm python3-minimal 55s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 72.9 kB of archives. 55s After this operation, 2048 B of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.9-2 [28.1 kB] 55s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.9-2 [23.0 kB] 55s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.9-2 [10.8 kB] 55s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.13.9-2 [11.0 kB] 56s dpkg-preconfigure: unable to re-open stdin: No such file or directory 56s Fetched 72.9 kB in 0s (0 B/s) 56s (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 ... 83538 files and directories currently installed.) 56s Preparing to unpack .../python3-minimal_3.13.9-2_amd64.deb ... 56s Unpacking python3-minimal (3.13.9-2) over (3.13.7-1) ... 56s Setting up python3-minimal (3.13.9-2) ... 56s (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 ... 83538 files and directories currently installed.) 56s Preparing to unpack .../python3_3.13.9-2_amd64.deb ... 56s running python pre-rtupdate hooks for python3.13... 56s Unpacking python3 (3.13.9-2) over (3.13.7-1) ... 56s Preparing to unpack .../libpython3-stdlib_3.13.9-2_amd64.deb ... 56s Unpacking libpython3-stdlib:amd64 (3.13.9-2) over (3.13.7-1) ... 56s Preparing to unpack .../python3-gdbm_3.13.9-2_amd64.deb ... 56s Unpacking python3-gdbm (3.13.9-2) over (3.13.9-1) ... 56s Setting up python3-gdbm (3.13.9-2) ... 56s Setting up libpython3-stdlib:amd64 (3.13.9-2) ... 56s Setting up python3 (3.13.9-2) ... 56s running python rtupdate hooks for python3.13... 56s running python post-rtupdate hooks for python3.13... 56s Processing triggers for man-db (2.13.1-1) ... 57s autopkgtest [20:00:22]: upgrading testbed (apt dist-upgrade and autopurge) 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Calculating upgrade... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Solving dependencies... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s autopkgtest [20:00:26]: testbed running kernel: Linux 6.17.0-6-generic #6-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 7 13:34:17 UTC 2025 60s autopkgtest [20:00:26]: @@@@@@@@@@@@@@@@@@@@ apt-source coot 70s Get:1 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.18+dfsg-2build1 (dsc) [2996 B] 70s Get:2 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.18+dfsg-2build1 (tar) [97.7 MB] 70s Get:3 http://ftpmaster.internal/ubuntu resolute/universe coot 1.1.18+dfsg-2build1 (diff) [54.5 kB] 70s gpgv: Signature made Thu Nov 27 07:12:11 2025 UTC 70s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 70s gpgv: Can't check signature: No public key 70s dpkg-source: warning: cannot verify inline signature for ./coot_1.1.18+dfsg-2build1.dsc: no acceptable signature found 71s autopkgtest [20:00:37]: testing package coot version 1.1.18+dfsg-2build1 72s autopkgtest [20:00:38]: build not needed 84s autopkgtest [20:00:50]: test command1: preparing testbed 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 84s The following NEW packages will be installed: 84s adwaita-icon-theme coot coot-data coot-doc dconf-gsettings-backend 84s dconf-service fontconfig fontconfig-config fonts-freefont-ttf 84s fonts-noto-core fonts-noto-mono gir1.2-freedesktop gir1.2-gdkpixbuf-2.0 84s gir1.2-graphene-1.0 gir1.2-gtk-4.0 gir1.2-harfbuzz-0.0 gir1.2-pango-1.0 84s gtk-update-icon-cache hicolor-icon-theme libamd-comgr3 libamdhip64-6 84s libasound2-data libasound2t64 libblas3 libboost-iostreams1.88.0 84s libboost-numpy1.88.0 libboost-python1.88.0 libboost-serialization1.88.0 84s libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libccp4-data 84s libccp4c0t64 libclipper2 libcoordgen3 libcootapi-dev libcootapi1.1 84s libcpdb-frontend2t64 libcpdb2t64 libdatrie1 libdconf1 libdeflate0 84s libdrm-intel1 libegl-mesa0 libegl1 libepoxy0 libevent-pthreads-2.1-7t64 84s libfabric1 libfontconfig1 libgbm1 libgdk-pixbuf-2.0-0 84s libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libgles2 84s libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphene-1.0-0 libgraphite2-3 84s libgsl28 libgslcblas0 libgstreamer-gl1.0-0 libgstreamer-plugins-base1.0-0 84s libgstreamer1.0-0 libgtk-4-1 libgtk-4-common libharfbuzz-gobject0 84s libharfbuzz-subset0 libharfbuzz0b libhsa-runtime64-1 libhsakmt1 84s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libinchi1.07 libjbig0 84s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libllvm21 libmaeparser1 84s libmmdb2-0 libogg0 libopenmpi40 liborc-0.4-0t64 libpango-1.0-0 84s libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpciaccess0 84s libpixman-1-0 libpsm2-2 librdkit1t64 librdmacm1t64 librsvg2-2 libsharpyuv0 84s libssm2 libthai-data libthai0 libtiff6 libucx0 libvorbis0a libvorbisfile3 84s libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwebp7 84s libx11-xcb1 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 84s libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcursor1 84s libxdamage1 libxfixes3 libxft2 libxi6 libxinerama1 libxnvctrl0 libxrandr2 84s libxrender1 libxshmfence1 libxxf86vm1 libze1 mesa-libgallium 84s ocl-icd-libopencl1 python3-numpy python3-numpy-dev python3-rdkit rdkit-data 84s refmac-dictionary sfftw2 ttf-bitstream-vera 84s 0 upgraded, 143 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 197 MB of archives. 84s After this operation, 934 MB of additional disk space will be used. 84s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 84s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7 [259 kB] 85s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-9ubuntu1 [939 kB] 85s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7 [2739 kB] 85s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 85s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdk-pixbuf2.0-common all 2.44.4+dfsg-1 [8584 B] 85s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 85s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 85s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 85s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 85s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 85s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 85s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 85s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdk-pixbuf-2.0-0 amd64 2.44.4+dfsg-1 [153 kB] 85s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 gtk-update-icon-cache amd64 4.20.3+ds-2 [55.0 kB] 85s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 hicolor-icon-theme all 0.18-2 [13.3 kB] 85s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 adwaita-icon-theme all 49.0-1 [581 kB] 85s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-noto-mono all 20201225-2 [435 kB] 85s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-noto-core all 20201225-2 [13.3 MB] 85s Get:21 http://ftpmaster.internal/ubuntu resolute/universe amd64 ttf-bitstream-vera all 1.10-11 [242 kB] 85s Get:22 http://ftpmaster.internal/ubuntu resolute/universe amd64 coot-data all 1.1.18+dfsg-2build1 [14.5 MB] 86s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-freefont-ttf all 20211204+svn4273-4 [5649 kB] 86s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 86s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 86s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 86s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 86s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 86s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 86s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 86s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo-gobject2 amd64 1.18.4-1build1 [128 kB] 86s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-freedesktop amd64 1.86.0-6 [65.9 kB] 86s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-gdkpixbuf-2.0 amd64 2.44.4+dfsg-1 [9302 B] 86s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphene-1.0-0 amd64 1.10.8-5 [46.0 kB] 86s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-graphene-1.0 amd64 1.10.8-5 [11.1 kB] 86s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 86s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.1.0-1 [535 kB] 86s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz-gobject0 amd64 12.1.0-1 [33.4 kB] 86s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-harfbuzz-0.0 amd64 12.1.0-1 [44.6 kB] 86s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.3ubuntu1 [180 kB] 86s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.29-2build2 [153 kB] 86s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 86s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.29-2build2 [19.2 kB] 86s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.56.3-2 [239 kB] 86s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.56.3-2 [52.5 kB] 86s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.56.3-2 [29.0 kB] 86s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 86s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoxft-1.0-0 amd64 1.56.3-2 [20.6 kB] 86s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-pango-1.0 amd64 1.56.3-2 [34.7 kB] 86s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo-script-interpreter2 amd64 1.18.4-1build1 [65.0 kB] 86s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libcpdb2t64 amd64 2.0~b7-0ubuntu3 [31.8 kB] 86s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libcpdb-frontend2t64 amd64 2.0~b7-0ubuntu3 [21.5 kB] 86s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libepoxy0 amd64 1.5.10-2 [218 kB] 86s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libglvnd0 amd64 1.7.0-1build2 [65.1 kB] 86s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpciaccess0 amd64 0.18.1-1ubuntu2 [19.0 kB] 86s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-intel1 amd64 2.4.127-1ubuntu1 [69.2 kB] 86s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libx11-xcb1 amd64 2:1.8.12-1build1 [8044 B] 86s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-dri3-0 amd64 1.17.0-2build1 [8036 B] 86s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-present0 amd64 1.17.0-2build1 [6446 B] 86s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-randr0 amd64 1.17.0-2build1 [19.7 kB] 86s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-sync1 amd64 1.17.0-2build1 [10.1 kB] 86s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-xfixes0 amd64 1.17.0-2build1 [11.1 kB] 86s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libxshmfence1 amd64 1.3.3-1 [5262 B] 86s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 mesa-libgallium amd64 25.2.7-1ubuntu1 [11.1 MB] 86s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libgbm1 amd64 25.2.7-1ubuntu1 [34.0 kB] 86s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-client0 amd64 1.24.0-2 [28.5 kB] 86s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libegl-mesa0 amd64 25.2.7-1ubuntu1 [117 kB] 86s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libegl1 amd64 1.7.0-1build2 [31.2 kB] 86s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-glx0 amd64 1.17.0-2build1 [27.6 kB] 86s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libxxf86vm1 amd64 1:1.1.4-2 [10.6 kB] 86s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libvulkan1 amd64 1.4.328.1-1 [156 kB] 86s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1-mesa-dri amd64 25.2.7-1ubuntu1 [36.9 kB] 86s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx-mesa0 amd64 25.2.7-1ubuntu1 [110 kB] 86s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libglx0 amd64 1.7.0-1build2 [40.3 kB] 86s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgl1 amd64 1.7.0-1build2 [101 kB] 86s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libgstreamer1.0-0 amd64 1.27.2-2 [1207 kB] 86s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 liborc-0.4-0t64 amd64 1:0.4.41-1 [252 kB] 86s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libgstreamer-plugins-base1.0-0 amd64 1.27.2-3build1 [910 kB] 86s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-cursor0 amd64 1.24.0-2 [10.8 kB] 86s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libwayland-egl1 amd64 1.24.0-2 [6248 B] 86s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libgstreamer-gl1.0-0 amd64 1.27.2-3build1 [227 kB] 86s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz-subset0 amd64 12.1.0-1 [518 kB] 86s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 librsvg2-2 amd64 2.61.3+dfsg-2 [1865 kB] 86s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB] 86s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcursor1 amd64 1:1.2.3-1 [23.1 kB] 86s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B] 86s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB] 86s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B] 86s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB] 86s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 libgles2 amd64 1.7.0-1build2 [17.5 kB] 86s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libdconf1 amd64 0.49.0-2 [40.3 kB] 86s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 dconf-service amd64 0.49.0-2 [27.7 kB] 86s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 dconf-gsettings-backend amd64 0.49.0-2 [22.2 kB] 86s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libgtk-4-common all 4.20.3+ds-2 [1545 kB] 86s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 libgtk-4-1 amd64 4.20.3+ds-2 [3417 kB] 86s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-gtk-4.0 amd64 4.20.3+ds-2 [220 kB] 86s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 rdkit-data all 202503.6-3ubuntu2 [12.6 MB] 87s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-python1.88.0 amd64 1.88.0-1.4ubuntu2 [360 kB] 87s Get:99 http://ftpmaster.internal/ubuntu resolute/universe amd64 libboost-numpy1.88.0 amd64 1.88.0-1.4ubuntu2 [249 kB] 87s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 libboost-serialization1.88.0 amd64 1.88.0-1.4ubuntu2 [347 kB] 87s Get:101 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcoordgen3 amd64 3.0.2-1 [215 kB] 87s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-iostreams1.88.0 amd64 1.88.0-1.4ubuntu2 [262 kB] 87s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 libinchi1.07 amd64 1.07.3+dfsg-1 [702 kB] 87s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmaeparser1 amd64 1.3.3-3 [93.8 kB] 87s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 librdkit1t64 amd64 202503.6-3ubuntu2 [6279 kB] 87s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rdkit amd64 202503.6-3ubuntu2 [4929 kB] 87s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 refmac-dictionary all 5.41-3 [16.7 MB] 88s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 libasound2-data all 1.2.14-2ubuntu1 [21.3 kB] 88s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 libasound2t64 amd64 1.2.14-2ubuntu1 [409 kB] 88s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 libccp4-data all 8.0.0-5 [65.2 kB] 88s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 libccp4c0t64 amd64 8.0.0-5 [100 kB] 88s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmmdb2-0 amd64 2.0.22-1 [363 kB] 88s Get:113 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10build1 [8360 B] 88s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 88s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 librdmacm1t64 amd64 56.1-1ubuntu1 [71.4 kB] 88s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 libfabric1 amd64 2.1.0-1.1 [697 kB] 88s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc15 amd64 2.12.2-1 [181 kB] 88s Get:118 http://ftpmaster.internal/ubuntu resolute/main amd64 libllvm21 amd64 1:21.1.2-2ubuntu6 [30.7 MB] 88s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd-comgr3 amd64 7.0.2+dfsg-2 [15.2 MB] 89s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsakmt1 amd64 6.4.3+dfsg-3 [67.5 kB] 89s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-3 [630 kB] 89s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamdhip64-6 amd64 6.4.3-4 [10.3 MB] 89s Get:123 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-9ubuntu1 [151 kB] 89s Get:124 http://ftpmaster.internal/ubuntu resolute/main amd64 libibumad3 amd64 56.1-1ubuntu1 [31.3 kB] 89s Get:125 http://ftpmaster.internal/ubuntu resolute/main amd64 libibmad5 amd64 56.1-1ubuntu1 [44.0 kB] 89s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 libucx0 amd64 1.19.0+ds-1build1 [1266 kB] 89s Get:127 http://ftpmaster.internal/ubuntu resolute/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 89s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 libze1 amd64 1.24.1-2 [599 kB] 89s Get:129 http://ftpmaster.internal/ubuntu resolute/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1 [40.9 kB] 89s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhwloc-plugins amd64 2.12.2-1 [22.2 kB] 89s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenmpi40 amd64 5.0.8-8ubuntu1 [3384 kB] 89s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 sfftw2 amd64 2.1.5-7build1 [224 kB] 89s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 libclipper2 amd64 2.1.20201109-2build1 [1188 kB] 89s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgslcblas0 amd64 2.8+dfsg-5.1ubuntu1 [133 kB] 89s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 libgsl28 amd64 2.8+dfsg-5.1ubuntu1 [1104 kB] 89s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 libssm2 amd64 1.4.0-2build1 [87.7 kB] 89s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcootapi1.1 amd64 1.1.18+dfsg-2build1 [4206 kB] 89s Get:138 http://ftpmaster.internal/ubuntu resolute/main amd64 libogg0 amd64 1.3.6-2 [23.4 kB] 89s Get:139 http://ftpmaster.internal/ubuntu resolute/main amd64 libvorbis0a amd64 1.3.7-3build1 [103 kB] 89s Get:140 http://ftpmaster.internal/ubuntu resolute/main amd64 libvorbisfile3 amd64 1.3.7-3build1 [18.0 kB] 89s Get:141 http://ftpmaster.internal/ubuntu resolute/universe amd64 coot amd64 1.1.18+dfsg-2build1 [9020 kB] 90s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 coot-doc all 1.1.18+dfsg-2build1 [2048 kB] 90s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 libcootapi-dev amd64 1.1.18+dfsg-2build1 [24.0 kB] 90s Fetched 197 MB in 5s (37.3 MB/s) 90s Selecting previously unselected package python3-numpy-dev:amd64. 90s (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 ... 83538 files and directories currently installed.) 90s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 90s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 90s Selecting previously unselected package libblas3:amd64. 90s Preparing to unpack .../001-libblas3_3.12.1-7_amd64.deb ... 90s Unpacking libblas3:amd64 (3.12.1-7) ... 90s Selecting previously unselected package libgfortran5:amd64. 90s Preparing to unpack .../002-libgfortran5_15.2.0-9ubuntu1_amd64.deb ... 90s Unpacking libgfortran5:amd64 (15.2.0-9ubuntu1) ... 90s Selecting previously unselected package liblapack3:amd64. 90s Preparing to unpack .../003-liblapack3_3.12.1-7_amd64.deb ... 90s Unpacking liblapack3:amd64 (3.12.1-7) ... 90s Selecting previously unselected package python3-numpy. 90s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 90s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 90s Selecting previously unselected package libgdk-pixbuf2.0-common. 90s Preparing to unpack .../005-libgdk-pixbuf2.0-common_2.44.4+dfsg-1_all.deb ... 90s Unpacking libgdk-pixbuf2.0-common (2.44.4+dfsg-1) ... 90s Selecting previously unselected package libjpeg-turbo8:amd64. 90s Preparing to unpack .../006-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 90s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 90s Selecting previously unselected package libjpeg8:amd64. 90s Preparing to unpack .../007-libjpeg8_8c-2ubuntu11_amd64.deb ... 90s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 90s Selecting previously unselected package libdeflate0:amd64. 90s Preparing to unpack .../008-libdeflate0_1.23-2_amd64.deb ... 90s Unpacking libdeflate0:amd64 (1.23-2) ... 90s Selecting previously unselected package libjbig0:amd64. 90s Preparing to unpack .../009-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 90s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 90s Selecting previously unselected package liblerc4:amd64. 90s Preparing to unpack .../010-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 90s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 90s Selecting previously unselected package libsharpyuv0:amd64. 90s Preparing to unpack .../011-libsharpyuv0_1.5.0-0.1_amd64.deb ... 90s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 90s Selecting previously unselected package libwebp7:amd64. 90s Preparing to unpack .../012-libwebp7_1.5.0-0.1_amd64.deb ... 90s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 90s Selecting previously unselected package libtiff6:amd64. 90s Preparing to unpack .../013-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 90s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 90s Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. 90s Preparing to unpack .../014-libgdk-pixbuf-2.0-0_2.44.4+dfsg-1_amd64.deb ... 90s Unpacking libgdk-pixbuf-2.0-0:amd64 (2.44.4+dfsg-1) ... 90s Selecting previously unselected package gtk-update-icon-cache. 90s Preparing to unpack .../015-gtk-update-icon-cache_4.20.3+ds-2_amd64.deb ... 90s No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed. 90s 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. 90s Unpacking gtk-update-icon-cache (4.20.3+ds-2) ... 90s Selecting previously unselected package hicolor-icon-theme. 90s Preparing to unpack .../016-hicolor-icon-theme_0.18-2_all.deb ... 90s Unpacking hicolor-icon-theme (0.18-2) ... 90s Selecting previously unselected package adwaita-icon-theme. 90s Preparing to unpack .../017-adwaita-icon-theme_49.0-1_all.deb ... 90s Unpacking adwaita-icon-theme (49.0-1) ... 90s Selecting previously unselected package fonts-noto-mono. 90s Preparing to unpack .../018-fonts-noto-mono_20201225-2_all.deb ... 90s Unpacking fonts-noto-mono (20201225-2) ... 90s Selecting previously unselected package fonts-noto-core. 90s Preparing to unpack .../019-fonts-noto-core_20201225-2_all.deb ... 90s Unpacking fonts-noto-core (20201225-2) ... 91s Selecting previously unselected package ttf-bitstream-vera. 91s Preparing to unpack .../020-ttf-bitstream-vera_1.10-11_all.deb ... 91s Unpacking ttf-bitstream-vera (1.10-11) ... 91s Selecting previously unselected package coot-data. 91s Preparing to unpack .../021-coot-data_1.1.18+dfsg-2build1_all.deb ... 91s Unpacking coot-data (1.1.18+dfsg-2build1) ... 91s Selecting previously unselected package fonts-freefont-ttf. 91s Preparing to unpack .../022-fonts-freefont-ttf_20211204+svn4273-4_all.deb ... 91s Unpacking fonts-freefont-ttf (20211204+svn4273-4) ... 91s Selecting previously unselected package fontconfig-config. 91s Preparing to unpack .../023-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 91s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 91s Selecting previously unselected package libfontconfig1:amd64. 91s Preparing to unpack .../024-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 91s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 91s Selecting previously unselected package libpixman-1-0:amd64. 91s Preparing to unpack .../025-libpixman-1-0_0.46.4-1_amd64.deb ... 91s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 91s Selecting previously unselected package libxcb-render0:amd64. 91s Preparing to unpack .../026-libxcb-render0_1.17.0-2build1_amd64.deb ... 91s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 91s Selecting previously unselected package libxcb-shm0:amd64. 91s Preparing to unpack .../027-libxcb-shm0_1.17.0-2build1_amd64.deb ... 91s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 91s Selecting previously unselected package libxrender1:amd64. 91s Preparing to unpack .../028-libxrender1_1%3a0.9.12-1_amd64.deb ... 91s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 91s Selecting previously unselected package libcairo2:amd64. 91s Preparing to unpack .../029-libcairo2_1.18.4-1build1_amd64.deb ... 91s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 91s Selecting previously unselected package libcairo-gobject2:amd64. 91s Preparing to unpack .../030-libcairo-gobject2_1.18.4-1build1_amd64.deb ... 91s Unpacking libcairo-gobject2:amd64 (1.18.4-1build1) ... 91s Selecting previously unselected package gir1.2-freedesktop:amd64. 91s Preparing to unpack .../031-gir1.2-freedesktop_1.86.0-6_amd64.deb ... 91s Unpacking gir1.2-freedesktop:amd64 (1.86.0-6) ... 91s Selecting previously unselected package gir1.2-gdkpixbuf-2.0:amd64. 91s Preparing to unpack .../032-gir1.2-gdkpixbuf-2.0_2.44.4+dfsg-1_amd64.deb ... 91s Unpacking gir1.2-gdkpixbuf-2.0:amd64 (2.44.4+dfsg-1) ... 91s Selecting previously unselected package libgraphene-1.0-0:amd64. 91s Preparing to unpack .../033-libgraphene-1.0-0_1.10.8-5_amd64.deb ... 91s Unpacking libgraphene-1.0-0:amd64 (1.10.8-5) ... 91s Selecting previously unselected package gir1.2-graphene-1.0:amd64. 91s Preparing to unpack .../034-gir1.2-graphene-1.0_1.10.8-5_amd64.deb ... 91s Unpacking gir1.2-graphene-1.0:amd64 (1.10.8-5) ... 91s Selecting previously unselected package libgraphite2-3:amd64. 91s Preparing to unpack .../035-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 91s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 91s Selecting previously unselected package libharfbuzz0b:amd64. 91s Preparing to unpack .../036-libharfbuzz0b_12.1.0-1_amd64.deb ... 91s Unpacking libharfbuzz0b:amd64 (12.1.0-1) ... 91s Selecting previously unselected package libharfbuzz-gobject0:amd64. 91s Preparing to unpack .../037-libharfbuzz-gobject0_12.1.0-1_amd64.deb ... 91s Unpacking libharfbuzz-gobject0:amd64 (12.1.0-1) ... 91s Selecting previously unselected package gir1.2-harfbuzz-0.0:amd64. 91s Preparing to unpack .../038-gir1.2-harfbuzz-0.0_12.1.0-1_amd64.deb ... 91s Unpacking gir1.2-harfbuzz-0.0:amd64 (12.1.0-1) ... 91s Selecting previously unselected package fontconfig. 91s Preparing to unpack .../039-fontconfig_2.15.0-2.3ubuntu1_amd64.deb ... 91s Unpacking fontconfig (2.15.0-2.3ubuntu1) ... 91s Selecting previously unselected package libthai-data. 91s Preparing to unpack .../040-libthai-data_0.1.29-2build2_all.deb ... 91s Unpacking libthai-data (0.1.29-2build2) ... 91s Selecting previously unselected package libdatrie1:amd64. 91s Preparing to unpack .../041-libdatrie1_0.2.14-1_amd64.deb ... 91s Unpacking libdatrie1:amd64 (0.2.14-1) ... 91s Selecting previously unselected package libthai0:amd64. 91s Preparing to unpack .../042-libthai0_0.1.29-2build2_amd64.deb ... 91s Unpacking libthai0:amd64 (0.1.29-2build2) ... 91s Selecting previously unselected package libpango-1.0-0:amd64. 91s Preparing to unpack .../043-libpango-1.0-0_1.56.3-2_amd64.deb ... 91s Unpacking libpango-1.0-0:amd64 (1.56.3-2) ... 91s Selecting previously unselected package libpangoft2-1.0-0:amd64. 91s Preparing to unpack .../044-libpangoft2-1.0-0_1.56.3-2_amd64.deb ... 91s Unpacking libpangoft2-1.0-0:amd64 (1.56.3-2) ... 91s Selecting previously unselected package libpangocairo-1.0-0:amd64. 91s Preparing to unpack .../045-libpangocairo-1.0-0_1.56.3-2_amd64.deb ... 91s Unpacking libpangocairo-1.0-0:amd64 (1.56.3-2) ... 91s Selecting previously unselected package libxft2:amd64. 91s Preparing to unpack .../046-libxft2_2.3.6-1build1_amd64.deb ... 91s Unpacking libxft2:amd64 (2.3.6-1build1) ... 91s Selecting previously unselected package libpangoxft-1.0-0:amd64. 91s Preparing to unpack .../047-libpangoxft-1.0-0_1.56.3-2_amd64.deb ... 91s Unpacking libpangoxft-1.0-0:amd64 (1.56.3-2) ... 91s Selecting previously unselected package gir1.2-pango-1.0:amd64. 91s Preparing to unpack .../048-gir1.2-pango-1.0_1.56.3-2_amd64.deb ... 91s Unpacking gir1.2-pango-1.0:amd64 (1.56.3-2) ... 91s Selecting previously unselected package libcairo-script-interpreter2:amd64. 91s Preparing to unpack .../049-libcairo-script-interpreter2_1.18.4-1build1_amd64.deb ... 91s Unpacking libcairo-script-interpreter2:amd64 (1.18.4-1build1) ... 91s Selecting previously unselected package libcpdb2t64:amd64. 91s Preparing to unpack .../050-libcpdb2t64_2.0~b7-0ubuntu3_amd64.deb ... 91s Unpacking libcpdb2t64:amd64 (2.0~b7-0ubuntu3) ... 91s Selecting previously unselected package libcpdb-frontend2t64:amd64. 91s Preparing to unpack .../051-libcpdb-frontend2t64_2.0~b7-0ubuntu3_amd64.deb ... 91s Unpacking libcpdb-frontend2t64:amd64 (2.0~b7-0ubuntu3) ... 91s Selecting previously unselected package libepoxy0:amd64. 91s Preparing to unpack .../052-libepoxy0_1.5.10-2_amd64.deb ... 91s Unpacking libepoxy0:amd64 (1.5.10-2) ... 91s Selecting previously unselected package libglvnd0:amd64. 91s Preparing to unpack .../053-libglvnd0_1.7.0-1build2_amd64.deb ... 91s Unpacking libglvnd0:amd64 (1.7.0-1build2) ... 91s Selecting previously unselected package libpciaccess0:amd64. 91s Preparing to unpack .../054-libpciaccess0_0.18.1-1ubuntu2_amd64.deb ... 91s Unpacking libpciaccess0:amd64 (0.18.1-1ubuntu2) ... 91s Selecting previously unselected package libdrm-intel1:amd64. 91s Preparing to unpack .../055-libdrm-intel1_2.4.127-1ubuntu1_amd64.deb ... 91s Unpacking libdrm-intel1:amd64 (2.4.127-1ubuntu1) ... 91s Selecting previously unselected package libx11-xcb1:amd64. 91s Preparing to unpack .../056-libx11-xcb1_2%3a1.8.12-1build1_amd64.deb ... 91s Unpacking libx11-xcb1:amd64 (2:1.8.12-1build1) ... 91s Selecting previously unselected package libxcb-dri3-0:amd64. 91s Preparing to unpack .../057-libxcb-dri3-0_1.17.0-2build1_amd64.deb ... 91s Unpacking libxcb-dri3-0:amd64 (1.17.0-2build1) ... 91s Selecting previously unselected package libxcb-present0:amd64. 91s Preparing to unpack .../058-libxcb-present0_1.17.0-2build1_amd64.deb ... 91s Unpacking libxcb-present0:amd64 (1.17.0-2build1) ... 91s Selecting previously unselected package libxcb-randr0:amd64. 91s Preparing to unpack .../059-libxcb-randr0_1.17.0-2build1_amd64.deb ... 91s Unpacking libxcb-randr0:amd64 (1.17.0-2build1) ... 92s Selecting previously unselected package libxcb-sync1:amd64. 92s Preparing to unpack .../060-libxcb-sync1_1.17.0-2build1_amd64.deb ... 92s Unpacking libxcb-sync1:amd64 (1.17.0-2build1) ... 92s Selecting previously unselected package libxcb-xfixes0:amd64. 92s Preparing to unpack .../061-libxcb-xfixes0_1.17.0-2build1_amd64.deb ... 92s Unpacking libxcb-xfixes0:amd64 (1.17.0-2build1) ... 92s Selecting previously unselected package libxshmfence1:amd64. 92s Preparing to unpack .../062-libxshmfence1_1.3.3-1_amd64.deb ... 92s Unpacking libxshmfence1:amd64 (1.3.3-1) ... 92s Selecting previously unselected package mesa-libgallium:amd64. 92s Preparing to unpack .../063-mesa-libgallium_25.2.7-1ubuntu1_amd64.deb ... 92s Unpacking mesa-libgallium:amd64 (25.2.7-1ubuntu1) ... 92s Selecting previously unselected package libgbm1:amd64. 92s Preparing to unpack .../064-libgbm1_25.2.7-1ubuntu1_amd64.deb ... 92s Unpacking libgbm1:amd64 (25.2.7-1ubuntu1) ... 92s Selecting previously unselected package libwayland-client0:amd64. 92s Preparing to unpack .../065-libwayland-client0_1.24.0-2_amd64.deb ... 92s Unpacking libwayland-client0:amd64 (1.24.0-2) ... 92s Selecting previously unselected package libegl-mesa0:amd64. 92s Preparing to unpack .../066-libegl-mesa0_25.2.7-1ubuntu1_amd64.deb ... 92s Unpacking libegl-mesa0:amd64 (25.2.7-1ubuntu1) ... 92s Selecting previously unselected package libegl1:amd64. 92s Preparing to unpack .../067-libegl1_1.7.0-1build2_amd64.deb ... 92s Unpacking libegl1:amd64 (1.7.0-1build2) ... 92s Selecting previously unselected package libxcb-glx0:amd64. 92s Preparing to unpack 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libglx0:amd64 (1.7.0-1build2) ... 92s Selecting previously unselected package libgl1:amd64. 92s Preparing to unpack .../074-libgl1_1.7.0-1build2_amd64.deb ... 92s Unpacking libgl1:amd64 (1.7.0-1build2) ... 92s Selecting previously unselected package libgstreamer1.0-0:amd64. 92s Preparing to unpack .../075-libgstreamer1.0-0_1.27.2-2_amd64.deb ... 92s Unpacking libgstreamer1.0-0:amd64 (1.27.2-2) ... 92s Selecting previously unselected package liborc-0.4-0t64:amd64. 92s Preparing to unpack .../076-liborc-0.4-0t64_1%3a0.4.41-1_amd64.deb ... 92s Unpacking liborc-0.4-0t64:amd64 (1:0.4.41-1) ... 92s Selecting previously unselected package libgstreamer-plugins-base1.0-0:amd64. 92s Preparing to unpack .../077-libgstreamer-plugins-base1.0-0_1.27.2-3build1_amd64.deb ... 92s Unpacking libgstreamer-plugins-base1.0-0:amd64 (1.27.2-3build1) ... 92s Selecting previously unselected package libwayland-cursor0:amd64. 92s Preparing to unpack .../078-libwayland-cursor0_1.24.0-2_amd64.deb ... 92s Unpacking libwayland-cursor0:amd64 (1.24.0-2) ... 92s Selecting previously unselected package libwayland-egl1:amd64. 92s Preparing to unpack .../079-libwayland-egl1_1.24.0-2_amd64.deb ... 92s Unpacking libwayland-egl1:amd64 (1.24.0-2) ... 92s Selecting previously unselected package libgstreamer-gl1.0-0:amd64. 92s Preparing to unpack .../080-libgstreamer-gl1.0-0_1.27.2-3build1_amd64.deb ... 92s Unpacking libgstreamer-gl1.0-0:amd64 (1.27.2-3build1) ... 92s Selecting previously unselected package libharfbuzz-subset0:amd64. 92s Preparing to unpack .../081-libharfbuzz-subset0_12.1.0-1_amd64.deb ... 92s Unpacking libharfbuzz-subset0:amd64 (12.1.0-1) ... 92s Selecting previously unselected package librsvg2-2:amd64. 92s Preparing to unpack .../082-librsvg2-2_2.61.3+dfsg-2_amd64.deb ... 92s Unpacking librsvg2-2:amd64 (2.61.3+dfsg-2) ... 92s Selecting previously unselected package libxfixes3:amd64. 92s Preparing to unpack .../083-libxfixes3_1%3a6.0.0-2build1_amd64.deb ... 92s Unpacking libxfixes3:amd64 (1:6.0.0-2build1) ... 92s Selecting previously unselected package libxcursor1:amd64. 92s Preparing to unpack .../084-libxcursor1_1%3a1.2.3-1_amd64.deb ... 92s Unpacking libxcursor1:amd64 (1:1.2.3-1) ... 92s Selecting previously unselected package libxdamage1:amd64. 92s Preparing to unpack .../085-libxdamage1_1%3a1.1.6-1build1_amd64.deb ... 92s Unpacking libxdamage1:amd64 (1:1.1.6-1build1) ... 92s Selecting previously unselected package libxi6:amd64. 92s Preparing to unpack .../086-libxi6_2%3a1.8.2-1_amd64.deb ... 92s Unpacking libxi6:amd64 (2:1.8.2-1) ... 92s Selecting previously unselected package libxinerama1:amd64. 92s Preparing to unpack .../087-libxinerama1_2%3a1.1.4-3build1_amd64.deb ... 92s Unpacking libxinerama1:amd64 (2:1.1.4-3build1) ... 92s Selecting previously unselected package libxrandr2:amd64. 92s Preparing to unpack .../088-libxrandr2_2%3a1.5.4-1_amd64.deb ... 92s Unpacking libxrandr2:amd64 (2:1.5.4-1) ... 92s Selecting previously unselected package libgles2:amd64. 92s Preparing to unpack .../089-libgles2_1.7.0-1build2_amd64.deb ... 92s Unpacking libgles2:amd64 (1.7.0-1build2) ... 92s Selecting previously unselected package libdconf1:amd64. 92s Preparing to unpack .../090-libdconf1_0.49.0-2_amd64.deb ... 92s Unpacking libdconf1:amd64 (0.49.0-2) ... 92s Selecting previously unselected package dconf-service. 92s Preparing to unpack .../091-dconf-service_0.49.0-2_amd64.deb ... 92s Unpacking dconf-service (0.49.0-2) ... 92s Selecting previously unselected package dconf-gsettings-backend:amd64. 92s Preparing to unpack .../092-dconf-gsettings-backend_0.49.0-2_amd64.deb ... 92s Unpacking dconf-gsettings-backend:amd64 (0.49.0-2) ... 92s Selecting previously unselected package libgtk-4-common. 92s Preparing to unpack .../093-libgtk-4-common_4.20.3+ds-2_all.deb ... 92s Unpacking libgtk-4-common (4.20.3+ds-2) ... 92s Selecting previously unselected package libgtk-4-1:amd64. 92s Preparing to unpack .../094-libgtk-4-1_4.20.3+ds-2_amd64.deb ... 92s Unpacking libgtk-4-1:amd64 (4.20.3+ds-2) ... 92s Selecting previously unselected package gir1.2-gtk-4.0:amd64. 92s Preparing to unpack .../095-gir1.2-gtk-4.0_4.20.3+ds-2_amd64.deb ... 92s Unpacking gir1.2-gtk-4.0:amd64 (4.20.3+ds-2) ... 92s Selecting previously unselected package rdkit-data. 92s Preparing to unpack .../096-rdkit-data_202503.6-3ubuntu2_all.deb ... 92s Unpacking rdkit-data (202503.6-3ubuntu2) ... 92s Selecting previously unselected package libboost-python1.88.0. 92s Preparing to unpack .../097-libboost-python1.88.0_1.88.0-1.4ubuntu2_amd64.deb ... 92s Unpacking libboost-python1.88.0 (1.88.0-1.4ubuntu2) ... 92s Selecting previously unselected package libboost-numpy1.88.0. 92s Preparing to unpack .../098-libboost-numpy1.88.0_1.88.0-1.4ubuntu2_amd64.deb ... 92s Unpacking libboost-numpy1.88.0 (1.88.0-1.4ubuntu2) ... 92s Selecting previously unselected package libboost-serialization1.88.0:amd64. 92s Preparing to unpack .../099-libboost-serialization1.88.0_1.88.0-1.4ubuntu2_amd64.deb ... 92s Unpacking libboost-serialization1.88.0:amd64 (1.88.0-1.4ubuntu2) ... 92s Selecting previously unselected package libcoordgen3:amd64. 92s Preparing to unpack .../100-libcoordgen3_3.0.2-1_amd64.deb ... 92s Unpacking libcoordgen3:amd64 (3.0.2-1) ... 92s Selecting previously unselected package libboost-iostreams1.88.0:amd64. 92s Preparing to unpack .../101-libboost-iostreams1.88.0_1.88.0-1.4ubuntu2_amd64.deb ... 92s Unpacking libboost-iostreams1.88.0:amd64 (1.88.0-1.4ubuntu2) ... 92s Selecting previously unselected package libinchi1.07. 92s Preparing to unpack .../102-libinchi1.07_1.07.3+dfsg-1_amd64.deb ... 92s Unpacking libinchi1.07 (1.07.3+dfsg-1) ... 92s Selecting previously unselected package libmaeparser1:amd64. 92s Preparing to unpack .../103-libmaeparser1_1.3.3-3_amd64.deb ... 92s Unpacking libmaeparser1:amd64 (1.3.3-3) ... 92s Selecting previously unselected package librdkit1t64. 92s Preparing to unpack .../104-librdkit1t64_202503.6-3ubuntu2_amd64.deb ... 92s Unpacking librdkit1t64 (202503.6-3ubuntu2) ... 92s Selecting previously unselected package python3-rdkit. 92s Preparing to unpack .../105-python3-rdkit_202503.6-3ubuntu2_amd64.deb ... 92s Unpacking python3-rdkit (202503.6-3ubuntu2) ... 93s Selecting previously unselected package refmac-dictionary. 93s Preparing to unpack .../106-refmac-dictionary_5.41-3_all.deb ... 93s Unpacking refmac-dictionary (5.41-3) ... 93s Selecting previously unselected package libasound2-data. 93s Preparing to unpack .../107-libasound2-data_1.2.14-2ubuntu1_all.deb ... 93s Unpacking libasound2-data (1.2.14-2ubuntu1) ... 93s Selecting previously unselected package libasound2t64:amd64. 93s Preparing to unpack .../108-libasound2t64_1.2.14-2ubuntu1_amd64.deb ... 93s Unpacking libasound2t64:amd64 (1.2.14-2ubuntu1) ... 93s Selecting previously unselected package libccp4-data. 93s Preparing to unpack .../109-libccp4-data_8.0.0-5_all.deb ... 93s Unpacking libccp4-data (8.0.0-5) ... 93s Selecting previously unselected package 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unpack .../115-libfabric1_2.1.0-1.1_amd64.deb ... 94s Unpacking libfabric1:amd64 (2.1.0-1.1) ... 94s Selecting previously unselected package libhwloc15:amd64. 94s Preparing to unpack .../116-libhwloc15_2.12.2-1_amd64.deb ... 94s Unpacking libhwloc15:amd64 (2.12.2-1) ... 94s Selecting previously unselected package libllvm21:amd64. 94s Preparing to unpack .../117-libllvm21_1%3a21.1.2-2ubuntu6_amd64.deb ... 94s Unpacking libllvm21:amd64 (1:21.1.2-2ubuntu6) ... 94s Selecting previously unselected package libamd-comgr3:amd64. 94s Preparing to unpack .../118-libamd-comgr3_7.0.2+dfsg-2_amd64.deb ... 94s Unpacking libamd-comgr3:amd64 (7.0.2+dfsg-2) ... 94s Selecting previously unselected package libhsakmt1:amd64. 94s Preparing to unpack .../119-libhsakmt1_6.4.3+dfsg-3_amd64.deb ... 94s Unpacking libhsakmt1:amd64 (6.4.3+dfsg-3) ... 94s Selecting previously unselected package libhsa-runtime64-1:amd64. 94s Preparing to unpack .../120-libhsa-runtime64-1_6.4.3+dfsg-3_amd64.deb ... 94s Unpacking 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libopenmpi40:amd64 (5.0.8-8ubuntu1) ... 99s Setting up sfftw2 (2.1.5-7build1) ... 99s Setting up libclipper2:amd64 (2.1.20201109-2build1) ... 99s Setting up libcootapi1.1 (1.1.18+dfsg-2build1) ... 99s Setting up libcootapi-dev (1.1.18+dfsg-2build1) ... 99s Processing triggers for libc-bin (2.42-2ubuntu2) ... 99s Processing triggers for man-db (2.13.1-1) ... 99s Processing triggers for libglib2.0-0t64:amd64 (2.86.2-1) ... 99s Setting up libgtk-4-1:amd64 (4.20.3+ds-2) ... 99s Setting up gir1.2-gtk-4.0:amd64 (4.20.3+ds-2) ... 99s Setting up coot (1.1.18+dfsg-2build1) ... 99s Processing triggers for libc-bin (2.42-2ubuntu2) ... 101s autopkgtest [20:01:07]: test command1: coot --self-test 101s autopkgtest [20:01:07]: test command1: [----------------------- 101s INFO:: Running internal self tests 104s INFO:: Test Clipper core : OK 104s INFO:: Test Clipper contrib: OK 104s run_internal_tests() --------- we have 8 internal test functionns 104s Entering test: kevin's torsion test 104s PASS: kevin's torsion test 104s Entering test: test_alt_conf_rotamers 104s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 104s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 104s chis.size() 2 (should be 2) 104s DEBUG:: i_rot 0 chi: alt-conf: A chi-1: 65.911 104s DEBUG:: i_rot 1 chi: alt-conf: B chi-1: -144.68 104s For residue 80 chis size 1 104s residue 80 chis: -56.8781 -80.8484 104s PASS: test_alt_conf_rotamers 104s Entering test: test_fragmemt_atom_selection 104s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 104s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 104s ----------------- create_mmdbmanager_from_inverted_atom_selection() 104s n_initial: 1465 n_1: 1401 n_2: 64 104s PASS: test_fragmemt_atom_selection 104s Entering test: test_add_atom 104s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 104s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 104s PASS: test_add_atom 104s Entering test: test segid exchange 104s INFO:: Reading coordinate file: /usr/share/coot/data/tutorial-modern.pdb 104s INFO:: file /usr/share/coot/data/tutorial-modern.pdb has been read. 104s Test with a rogue segid 104s INFO:: No consistent segids for residue 1 104s PASS: test segid exchange 104s Entering test: test peak search non-close 104s mtz_file_name /usr/share/coot/data/rnasa-1.8-all_refmac1.mtz 104s INFO:: FFT Resolution: 0.444444 104s INFO:: Map Sampling Rate: 1.500000 104s INFO:: Grid: Nuvw = ( 132, 160, 80) 104s INFO:: Cell: Cell (64.897,78.323,38.792, 90, 90, 90) 104s INFO:: Spacegroup: P 21 21 21 104s There are 2260 peaks and 0 problem peaks 104s PASS: test peak search non-close 104s Entering test: test symop card 104s 1 0 0 104s 0 1 0 104s 0 0 1 104s translations: -1 0 0 104s PASS: test symop card 104s Entering test: SSM sequence alignment output 104s 104s -- 104s Moving: DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNR--ESVLPTQSYGYYHEYTVITP--GARTRG 104s Target: ---SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 104s 104s Moving: TRRI.ICGEATQEDY..YTGDHYATFSLIDQTC 104s 104s -- 104s Moving: D 104s Target: --SGTVCLSALPPEATDTLNLIASDGPFPYSQDG 104s 104s -- 104s Moving: DVSGTVCLSALPPEATDTLNIASDGPFPYSQDGVVFQNR--ESVLPQSYG 104s Target: --SGTVCLSALPPEATDTLNIASDGPFPYSQDXXxxxxxxxxxxxxxxxG 104s 104s -- 104s PASS: SSM sequence alignment output 105s autopkgtest [20:01:11]: test command1: -----------------------] 105s autopkgtest [20:01:11]: test command1: - - - - - - - - - - results - - - - - - - - - - 105s command1 PASS 105s autopkgtest [20:01:11]: test command2: preparing testbed 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Solving dependencies... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s autopkgtest [20:01:15]: test command2: pyrogen --help 109s autopkgtest [20:01:15]: test command2: [----------------------- 109s Usage: pyrogen [options] file-or-SMILES 109s if file-or-SMILES has extension ".smi" or ".smiles" then it is treated as a file 109s 109s Options: 109s -h, --help show this help message and exit 109s -c FILE, --mmcif=FILE 109s Make restraints from input mmcif FILE 109s -m FILE, --mol=FILE Make restraints from input sdf/mol FILE 109s -r COMP_ID, --residue-type=COMP_ID 109s Create restraints for this type. Default is LIG 109s -4, --quartet-planes Use 4-atom plane restraints, 109s forces --quartet-hydrogens 109s -H, --quartet-hydrogens 109s Use 4-atom hydrogen plane restraints 109s -b, --no-shift-hydrogen-atoms 109s Stop addition or deletion of Hydrogen atoms for 109s formally-charged atoms 109s -n, --no-mogul Don't run CSD Mogul to update bond and angle 109s restraints 109s -N COMPOUND_NAME, --name=COMPOUND_NAME 109s Compound name 109s -S, --smiles Write the SMILES for the input molecule 109s -t, --tautomers Show SMILES for tautomers, don't generate restraints 109s -T MOGUL_DIR, --tmp-directory=MOGUL_DIR 109s Directory into which the tmp files (e.g. for mogul) 109s are written 109s -d OUTPUT_DIR, --directory=OUTPUT_DIR 109s Directory into which the output files (e.g. mmCIF and 109s PDB) are written 109s -o OUTPUT_POSTFIX, --output-postfix=OUTPUT_POSTFIX 109s string to add to output file names, default is 109s "pyrogen" 109s -p, --picture Additionally output a chemical diagram PNG 109s -P, --preserve-input-coordinates 109s Preserve the inputput coordinates (if possible) 109s -v, --version Print version information 109s -a, --no-match-vs-reference-dictionaries 109s Don't match atom names vs. dictionary molecules 109s (default False) 109s -R DICT_FILES_FOR_NAMES_MATCH, --reference-dictionary-files=DICT_FILES_FOR_NAMES_MATCH 109s Try to match the atom names of the output molecule to 109s this dictionary in these files (comma-separated list) 109s -C COMP_ID_LIST_FOR_NAMES_MATCH, --reference-dictionary-comp-ids=COMP_ID_LIST_FOR_NAMES_MATCH 109s Try to match the atom names of the output molecule to 109s these comp-ids (comma-separated list) 109s -w, --wwPDB Fetch the wwPDB ligand definition and use that 109s -f FETCH (Just) fetch from the PDBe the CCD entry for the given 109s compound-id 109s -q, --quiet print less messages 109s autopkgtest [20:01:15]: test command2: -----------------------] 110s command2 PASS 110s autopkgtest [20:01:16]: test command2: - - - - - - - - - - results - - - - - - - - - - 110s autopkgtest [20:01:16]: @@@@@@@@@@@@@@@@@@@@ summary 110s command1 PASS 110s command2 PASS